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Vanadium in PDB 3gqi: Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates

Enzymatic activity of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates

All present enzymatic activity of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates:
2.7.10.1; 3.1.4.11;

Protein crystallography data

The structure of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates, PDB code: 3gqi was solved by J.H.Bae, E.D.Lew, S.Yuzawa, F.Tome, I.Lax, J.Schlessinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.935, 64.596, 94.209, 90.00, 96.50, 90.00
R / Rfree (%) 24.9 / 28.9

Other elements in 3gqi:

The structure of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates (pdb code 3gqi). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 10 binding sites of Vanadium where determined in the Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates, PDB code: 3gqi:
Jump to Vanadium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Vanadium binding site 1 out of 10 in 3gqi

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Vanadium binding site 1 out of 10 in the Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1

b:83.4
occ:1.00
V10 A:DVT1 0.0 83.4 1.0
O28 A:DVT1 1.6 81.2 1.0
O15 A:DVT1 1.8 82.9 1.0
O27 A:DVT1 1.9 82.3 1.0
O18 A:DVT1 1.9 83.1 1.0
O23 A:DVT1 2.1 83.2 1.0
O2 A:DVT1 2.3 85.0 1.0
V8 A:DVT1 3.1 83.6 1.0
V3 A:DVT1 3.1 83.4 1.0
V1 A:DVT1 3.1 83.9 1.0
V9 A:DVT1 3.2 83.7 1.0
O3 A:DVT1 3.5 83.6 1.0
O17 A:DVT1 3.6 84.5 1.0
O4 A:DVT1 3.6 83.4 1.0
O24 A:DVT1 3.7 83.0 1.0
V2 A:DVT1 4.3 81.5 1.0
O10 A:DVT1 4.4 85.0 1.0
O5 A:DVT1 4.5 83.8 1.0
O26 A:DVT1 4.5 82.4 1.0
O1 A:DVT1 4.5 83.8 1.0
O20 A:DVT1 4.5 83.8 1.0
O9 A:DVT1 4.5 84.5 1.0
O8 A:DVT1 4.7 83.7 1.0
O16 A:DVT1 4.7 84.2 1.0

Vanadium binding site 2 out of 10 in 3gqi

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Vanadium binding site 2 out of 10 in the Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1

b:83.9
occ:1.00
V1 A:DVT1 0.0 83.9 1.0
O5 A:DVT1 1.6 83.8 1.0
O15 A:DVT1 1.9 82.9 1.0
O3 A:DVT1 1.9 83.6 1.0
O4 A:DVT1 2.0 83.4 1.0
O1 A:DVT1 2.0 83.8 1.0
O2 A:DVT1 2.3 85.0 1.0
V2 A:DVT1 3.1 81.5 1.0
V10 A:DVT1 3.1 83.4 1.0
V9 A:DVT1 3.2 83.7 1.0
V3 A:DVT1 3.2 83.4 1.0
O27 A:DVT1 3.6 82.3 1.0
O9 A:DVT1 3.6 84.5 1.0
O8 A:DVT1 3.6 83.7 1.0
O18 A:DVT1 3.6 83.1 1.0
V8 A:DVT1 4.3 83.6 1.0
O26 A:DVT1 4.4 82.4 1.0
O7 A:DVT1 4.4 84.3 1.0
O10 A:DVT1 4.5 85.0 1.0
O28 A:DVT1 4.5 81.2 1.0
O23 A:DVT1 4.6 83.2 1.0
O17 A:DVT1 4.6 84.5 1.0
O24 A:DVT1 4.6 83.0 1.0
O16 A:DVT1 4.7 84.2 1.0

Vanadium binding site 3 out of 10 in 3gqi

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Vanadium binding site 3 out of 10 in the Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1

b:83.7
occ:1.00
V9 A:DVT1 0.0 83.7 1.0
O26 A:DVT1 1.6 82.4 1.0
O4 A:DVT1 1.8 83.4 1.0
O27 A:DVT1 1.9 82.3 1.0
O8 A:DVT1 2.0 83.7 1.0
O24 A:DVT1 2.0 83.0 1.0
O2 A:DVT1 2.2 85.0 1.0
V2 A:DVT1 3.1 81.5 1.0
V7 A:DVT1 3.1 85.5 1.0
V8 A:DVT1 3.1 83.6 1.0
V1 A:DVT1 3.2 83.9 1.0
V10 A:DVT1 3.2 83.4 1.0
O1 A:DVT1 3.4 83.8 1.0
O25 A:DVT1 3.4 84.1 1.0
O15 A:DVT1 3.4 82.9 1.0
O23 A:DVT1 3.5 83.2 1.0
O16 A:DVT1 3.6 84.2 1.0
ND2 A:ASN506 3.9 77.4 1.0
O21 A:DVT1 4.3 84.0 1.0
O7 A:DVT1 4.4 84.3 1.0
O20 A:DVT1 4.4 83.8 1.0
O5 A:DVT1 4.4 83.8 1.0
O11 A:DVT1 4.4 84.3 1.0
O3 A:DVT1 4.5 83.6 1.0
V3 A:DVT1 4.5 83.4 1.0
O28 A:DVT1 4.5 81.2 1.0
O9 A:DVT1 4.5 84.5 1.0
O18 A:DVT1 4.5 83.1 1.0
O17 A:DVT1 4.6 84.5 1.0

Vanadium binding site 4 out of 10 in 3gqi

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Vanadium binding site 4 out of 10 in the Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 4 of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1

b:85.5
occ:1.00
V7 A:DVT1 0.0 85.5 1.0
O25 A:DVT1 1.6 84.1 1.0
O11 A:DVT1 1.8 84.3 1.0
O21 A:DVT1 1.8 84.0 1.0
O24 A:DVT1 2.1 83.0 1.0
O8 A:DVT1 2.1 83.7 1.0
O16 A:DVT1 2.3 84.2 1.0
V5 A:DVT1 3.0 83.9 1.0
V9 A:DVT1 3.1 83.7 1.0
V2 A:DVT1 3.1 81.5 1.0
V6 A:DVT1 3.1 84.5 1.0
V8 A:DVT1 3.2 83.6 1.0
O6 A:DVT1 3.4 84.3 1.0
O26 A:DVT1 3.4 82.4 1.0
O7 A:DVT1 3.4 84.3 1.0
ND2 A:ASN506 3.5 77.4 1.0
O20 A:DVT1 3.5 83.8 1.0
O2 A:DVT1 3.7 85.0 1.0
CD A:PRO505 4.2 86.1 1.0
O14 A:DVT1 4.3 84.3 1.0
O4 A:DVT1 4.4 83.4 1.0
O22 A:DVT1 4.4 85.0 1.0
O13 A:DVT1 4.4 84.6 1.0
O27 A:DVT1 4.4 82.3 1.0
CG A:ASN506 4.5 79.0 1.0
O1 A:DVT1 4.5 83.8 1.0
O19 A:DVT1 4.5 84.7 1.0
V4 A:DVT1 4.5 82.6 1.0
O23 A:DVT1 4.6 83.2 1.0
CB A:ASN506 4.6 80.2 1.0
O9 A:DVT1 4.6 84.5 1.0
O17 A:DVT1 4.7 84.5 1.0
N A:ASN506 4.7 82.2 1.0
CG A:PRO505 4.9 85.5 1.0
CB A:PRO505 4.9 85.1 1.0
N A:PRO505 5.0 87.0 1.0

Vanadium binding site 5 out of 10 in 3gqi

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Vanadium binding site 5 out of 10 in the Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 5 of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1

b:84.5
occ:1.00
V6 A:DVT1 0.0 84.5 1.0
O22 A:DVT1 1.6 85.0 1.0
O6 A:DVT1 1.9 84.3 1.0
O21 A:DVT1 1.9 84.0 1.0
O19 A:DVT1 1.9 84.7 1.0
O20 A:DVT1 2.1 83.8 1.0
O16 A:DVT1 2.3 84.2 1.0
V5 A:DVT1 3.0 83.9 1.0
V8 A:DVT1 3.1 83.6 1.0
V7 A:DVT1 3.1 85.5 1.0
V4 A:DVT1 3.2 82.6 1.0
O24 A:DVT1 3.6 83.0 1.0
O11 A:DVT1 3.6 84.3 1.0
O13 A:DVT1 3.6 84.6 1.0
O17 A:DVT1 3.7 84.5 1.0
CA A:LYS504 3.9 90.8 1.0
N A:ASN506 3.9 82.2 1.0
CD A:LYS504 4.0 92.8 1.0
C A:LYS504 4.1 89.0 1.0
CD A:PRO505 4.2 86.1 1.0
CG A:ARG507 4.2 92.9 1.0
N A:PRO505 4.2 87.0 1.0
CB A:ASN506 4.2 80.2 1.0
V2 A:DVT1 4.3 81.5 1.0
CB A:LYS504 4.4 91.2 1.0
O14 A:DVT1 4.4 84.3 1.0
NE A:ARG507 4.4 0.5 1.0
O25 A:DVT1 4.4 84.1 1.0
CA A:ASN506 4.4 81.7 1.0
N A:ARG507 4.4 82.6 1.0
O7 A:DVT1 4.5 84.3 1.0
O23 A:DVT1 4.5 83.2 1.0
O12 A:DVT1 4.5 84.8 1.0
O9 A:DVT1 4.6 84.5 1.0
O8 A:DVT1 4.6 83.7 1.0
C A:ASN506 4.7 82.0 1.0
O A:ASP503 4.7 95.0 1.0
O2 A:DVT1 4.7 85.0 1.0
CD A:ARG507 4.8 97.0 1.0
O A:LYS504 4.8 89.8 1.0
ND2 A:ASN506 4.8 77.4 1.0
CG A:LYS504 4.9 91.6 1.0
C A:PRO505 5.0 83.4 1.0

Vanadium binding site 6 out of 10 in 3gqi

Go back to Vanadium Binding Sites List in 3gqi
Vanadium binding site 6 out of 10 in the Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 6 of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1

b:83.6
occ:1.00
V8 A:DVT1 0.0 83.6 1.0
O20 A:DVT1 1.7 83.8 1.0
O23 A:DVT1 1.7 83.2 1.0
O24 A:DVT1 1.9 83.0 1.0
O17 A:DVT1 1.9 84.5 1.0
O16 A:DVT1 2.0 84.2 1.0
O2 A:DVT1 2.0 85.0 1.0
V2 A:DVT1 3.0 81.5 1.0
V4 A:DVT1 3.0 82.6 1.0
V9 A:DVT1 3.1 83.7 1.0
V10 A:DVT1 3.1 83.4 1.0
V6 A:DVT1 3.1 84.5 1.0
V3 A:DVT1 3.1 83.4 1.0
O27 A:DVT1 3.1 82.3 1.0
V7 A:DVT1 3.2 85.5 1.0
O19 A:DVT1 3.2 84.7 1.0
O21 A:DVT1 3.2 84.0 1.0
O18 A:DVT1 3.2 83.1 1.0
O9 A:DVT1 3.3 84.5 1.0
O8 A:DVT1 3.4 83.7 1.0
V5 A:DVT1 4.2 83.9 1.0
ND2 A:ASN506 4.2 77.4 1.0
O13 A:DVT1 4.2 84.6 1.0
CB A:ASN506 4.2 80.2 1.0
O7 A:DVT1 4.3 84.3 1.0
O1 A:DVT1 4.3 83.8 1.0
O28 A:DVT1 4.3 81.2 1.0
O4 A:DVT1 4.3 83.4 1.0
O22 A:DVT1 4.3 85.0 1.0
O3 A:DVT1 4.3 83.6 1.0
O15 A:DVT1 4.3 82.9 1.0
O12 A:DVT1 4.3 84.8 1.0
V1 A:DVT1 4.3 83.9 1.0
O10 A:DVT1 4.4 85.0 1.0
O26 A:DVT1 4.4 82.4 1.0
O6 A:DVT1 4.4 84.3 1.0
O25 A:DVT1 4.4 84.1 1.0
O11 A:DVT1 4.5 84.3 1.0
CG A:ASN506 4.8 79.0 1.0

Vanadium binding site 7 out of 10 in 3gqi

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Vanadium binding site 7 out of 10 in the Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 7 of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1

b:83.9
occ:1.00
V5 A:DVT1 0.0 83.9 1.0
O14 A:DVT1 1.6 84.3 1.0
O6 A:DVT1 1.9 84.3 1.0
O13 A:DVT1 1.9 84.6 1.0
O11 A:DVT1 1.9 84.3 1.0
O7 A:DVT1 2.0 84.3 1.0
O16 A:DVT1 2.2 84.2 1.0
V2 A:DVT1 3.0 81.5 1.0
V7 A:DVT1 3.0 85.5 1.0
V6 A:DVT1 3.0 84.5 1.0
V4 A:DVT1 3.1 82.6 1.0
O21 A:DVT1 3.5 84.0 1.0
O19 A:DVT1 3.5 84.7 1.0
O8 A:DVT1 3.5 83.7 1.0
O9 A:DVT1 3.6 84.5 1.0
O A:ASP503 4.0 95.0 1.0
NZ A:LYS504 4.0 94.1 1.0
V8 A:DVT1 4.2 83.6 1.0
O25 A:DVT1 4.3 84.1 1.0
O22 A:DVT1 4.4 85.0 1.0
O20 A:DVT1 4.4 83.8 1.0
O24 A:DVT1 4.4 83.0 1.0
O1 A:DVT1 4.4 83.8 1.0
O12 A:DVT1 4.5 84.8 1.0
CD A:LYS504 4.5 92.8 1.0
O17 A:DVT1 4.6 84.5 1.0
O2 A:DVT1 4.6 85.0 1.0
CE A:LYS504 4.7 93.4 1.0
CD A:PRO505 4.7 86.1 1.0

Vanadium binding site 8 out of 10 in 3gqi

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Vanadium binding site 8 out of 10 in the Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 8 of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1

b:81.5
occ:1.00
V2 A:DVT1 0.0 81.5 1.0
O7 A:DVT1 1.6 84.3 1.0
O1 A:DVT1 1.7 83.8 1.0
O8 A:DVT1 1.9 83.7 1.0
O9 A:DVT1 1.9 84.5 1.0
O16 A:DVT1 2.0 84.2 1.0
O2 A:DVT1 2.1 85.0 1.0
V5 A:DVT1 3.0 83.9 1.0
V8 A:DVT1 3.0 83.6 1.0
V9 A:DVT1 3.1 83.7 1.0
O13 A:DVT1 3.1 84.6 1.0
V4 A:DVT1 3.1 82.6 1.0
V1 A:DVT1 3.1 83.9 1.0
V7 A:DVT1 3.1 85.5 1.0
V3 A:DVT1 3.1 83.4 1.0
O4 A:DVT1 3.2 83.4 1.0
O3 A:DVT1 3.2 83.6 1.0
O11 A:DVT1 3.3 84.3 1.0
O24 A:DVT1 3.4 83.0 1.0
O17 A:DVT1 3.4 84.5 1.0
O14 A:DVT1 4.2 84.3 1.0
O20 A:DVT1 4.3 83.8 1.0
O27 A:DVT1 4.3 82.3 1.0
O23 A:DVT1 4.3 83.2 1.0
V6 A:DVT1 4.3 84.5 1.0
O21 A:DVT1 4.3 84.0 1.0
O26 A:DVT1 4.3 82.4 1.0
O5 A:DVT1 4.3 83.8 1.0
O15 A:DVT1 4.3 82.9 1.0
V10 A:DVT1 4.3 83.4 1.0
O19 A:DVT1 4.4 84.7 1.0
O6 A:DVT1 4.4 84.3 1.0
O12 A:DVT1 4.4 84.8 1.0
O25 A:DVT1 4.4 84.1 1.0
O10 A:DVT1 4.4 85.0 1.0
O18 A:DVT1 4.4 83.1 1.0

Vanadium binding site 9 out of 10 in 3gqi

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Vanadium binding site 9 out of 10 in the Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 9 of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1

b:82.6
occ:1.00
V4 A:DVT1 0.0 82.6 1.0
O12 A:DVT1 1.6 84.8 1.0
O13 A:DVT1 1.8 84.6 1.0
O19 A:DVT1 1.9 84.7 1.0
O17 A:DVT1 2.0 84.5 1.0
O9 A:DVT1 2.0 84.5 1.0
O16 A:DVT1 2.2 84.2 1.0
V3 A:DVT1 3.0 83.4 1.0
V8 A:DVT1 3.0 83.6 1.0
V2 A:DVT1 3.1 81.5 1.0
V5 A:DVT1 3.1 83.9 1.0
V6 A:DVT1 3.2 84.5 1.0
O10 A:DVT1 3.3 85.0 1.0
O20 A:DVT1 3.4 83.8 1.0
O7 A:DVT1 3.4 84.3 1.0
O6 A:DVT1 3.5 84.3 1.0
O2 A:DVT1 3.6 85.0 1.0
NH2 A:ARG507 4.1 0.9 1.0
O3 A:DVT1 4.3 83.6 1.0
O18 A:DVT1 4.3 83.1 1.0
O23 A:DVT1 4.4 83.2 1.0
O14 A:DVT1 4.4 84.3 1.0
O1 A:DVT1 4.4 83.8 1.0
O22 A:DVT1 4.5 85.0 1.0
V7 A:DVT1 4.5 85.5 1.0
O21 A:DVT1 4.5 84.0 1.0
NE A:ARG507 4.5 0.5 1.0
O24 A:DVT1 4.5 83.0 1.0
NZ A:LYS504 4.6 94.1 1.0
O8 A:DVT1 4.6 83.7 1.0
O11 A:DVT1 4.6 84.3 1.0
CZ A:ARG507 4.7 0.6 1.0

Vanadium binding site 10 out of 10 in 3gqi

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Vanadium binding site 10 out of 10 in the Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 10 of Crystal Structure of Activated Receptor Tyrosine Kinase in Complex with Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1

b:83.4
occ:1.00
V3 A:DVT1 0.0 83.4 1.0
O10 A:DVT1 1.6 85.0 1.0
O3 A:DVT1 1.8 83.6 1.0
O18 A:DVT1 1.9 83.1 1.0
O17 A:DVT1 2.0 84.5 1.0
O9 A:DVT1 2.0 84.5 1.0
O2 A:DVT1 2.3 85.0 1.0
V4 A:DVT1 3.0 82.6 1.0
V8 A:DVT1 3.1 83.6 1.0
V10 A:DVT1 3.1 83.4 1.0
V2 A:DVT1 3.1 81.5 1.0
V1 A:DVT1 3.2 83.9 1.0
O12 A:DVT1 3.3 84.8 1.0
O15 A:DVT1 3.4 82.9 1.0
O23 A:DVT1 3.4 83.2 1.0
O1 A:DVT1 3.5 83.8 1.0
O16 A:DVT1 3.7 84.2 1.0
O13 A:DVT1 4.3 84.6 1.0
O28 A:DVT1 4.4 81.2 1.0
O27 A:DVT1 4.4 82.3 1.0
O7 A:DVT1 4.4 84.3 1.0
O19 A:DVT1 4.4 84.7 1.0
O5 A:DVT1 4.4 83.8 1.0
O20 A:DVT1 4.5 83.8 1.0
V9 A:DVT1 4.5 83.7 1.0
O4 A:DVT1 4.5 83.4 1.0
O24 A:DVT1 4.6 83.0 1.0
O8 A:DVT1 4.6 83.7 1.0
NH2 A:ARG507 4.9 0.9 1.0

Reference:

J.H.Bae, E.D.Lew, S.Yuzawa, F.Tome, I.Lax, J.Schlessinger. The Selectivity of Receptor Tyrosine Kinase Signaling Is Controlled By A Secondary SH2 Domain Binding Site. Cell(Cambridge,Mass.) V. 138 514 2009.
ISSN: ISSN 0092-8674
PubMed: 19665973
DOI: 10.1016/J.CELL.2009.05.028
Page generated: Thu Oct 29 07:05:01 2020

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