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Vanadium in PDB 1dkt: CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate

Protein crystallography data

The structure of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate, PDB code: 1dkt was solved by Y.Bourne, A.S.Arvai, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.000, 94.000, 131.600, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 25.8

Vanadium Binding Sites:

The binding sites of Vanadium atom in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate (pdb code 1dkt). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 7 binding sites of Vanadium where determined in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate, PDB code: 1dkt:
Jump to Vanadium binding site number: 1; 2; 3; 4; 5; 6; 7;

Vanadium binding site 1 out of 7 in 1dkt

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Vanadium binding site 1 out of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V100

b:18.1
occ:1.00
 V1 A:V7O100 0.0 18.1 1.0
O3 A:V7O100 1.5 24.9 1.0
O1 A:V7O100 1.6 37.9 1.0
O2 A:V7O100 1.7 18.5 1.0
O4 A:V7O100 1.7 18.1 1.0
V2 A:V7O100 3.0 22.1 1.0
V3 A:V7O100 3.2 17.8 1.0
OG A:SER51 3.3 52.3 1.0
CB A:SER51 3.4 44.9 1.0
NH1 A:ARG71 3.4 24.7 1.0
O A:HOH561 3.8 75.1 1.0
O6 A:V7O100 3.8 25.3 1.0
O7 A:V7O100 3.9 23.4 1.0
O A:HOH559 3.9 15.6 1.0
O A:HOH581 4.1 58.3 1.0
O A:HOH583 4.2 2.4 1.0
O5 A:V7O100 4.3 27.9 1.0
CZ A:ARG71 4.4 30.4 1.0
O8 A:V7O100 4.4 5.3 1.0
O9 A:V7O100 4.5 10.7 1.0
NH2 A:ARG71 4.5 28.3 1.0
CA A:SER51 4.6 40.5 1.0

Vanadium binding site 2 out of 7 in 1dkt

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Vanadium binding site 2 out of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V100

b:22.1
occ:1.00
 V2 A:V7O100 0.0 22.1 1.0
O5 A:V7O100 1.6 27.9 1.0
O6 A:V7O100 1.6 25.3 1.0
O4 A:V7O100 1.9 18.1 1.0
NH2 A:ARG71 3.0 28.3 1.0
O2 A:V7O100 3.0 18.5 1.0
V1 A:V7O100 3.0 18.1 1.0
V3 A:V7O100 3.1 17.8 1.0
O8 A:V7O100 3.3 5.3 1.0
CZ A:ARG71 3.7 30.4 1.0
NH1 A:ARG71 3.7 24.7 1.0
O9 A:V7O100 3.8 10.7 1.0
O A:HOH583 3.8 2.4 1.0
O1 A:V7O100 3.8 37.9 1.0
O A:HOH560 3.9 21.0 1.0
O3 A:V7O100 4.2 24.9 1.0
O7 A:V7O100 4.7 23.4 1.0
O A:HOH559 4.8 15.6 1.0
NE A:ARG71 4.9 29.8 1.0
CE A:LYS11 5.0 18.0 1.0

Vanadium binding site 3 out of 7 in 1dkt

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Vanadium binding site 3 out of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V100

b:17.8
occ:1.00
 V3 A:V7O100 0.0 17.8 1.0
O8 A:V7O100 1.5 5.3 1.0
O7 A:V7O100 1.7 23.4 1.0
O9 A:V7O100 1.7 10.7 1.0
O4 A:V7O100 1.8 18.1 1.0
O A:HOH559 3.1 15.6 1.0
V2 A:V7O100 3.1 22.1 1.0
V1 A:V7O100 3.2 18.1 1.0
O2 A:V7O100 3.3 18.5 1.0
V4 A:V7O100 3.3 21.2 1.0
NH1 A:ARG71 3.4 24.7 1.0
O3 A:V7O100 3.4 24.9 1.0
O5 A:V7O100 3.5 27.9 1.0
NH2 A:ARG71 3.7 28.3 1.0
CB A:SER51 3.9 44.9 1.0
NE1 A:TRP54 3.9 12.4 1.0
O10 A:V7O100 4.0 27.2 1.0
CZ A:ARG71 4.0 30.4 1.0
NH1 A:ARG20 4.1 28.6 1.0
O11 A:V7O100 4.2 7.1 1.0
O A:HOH551 4.3 47.0 1.0
O6 A:V7O100 4.3 25.3 1.0
CE A:LYS11 4.4 18.0 1.0
O A:HOH560 4.5 21.0 1.0
NZ A:LYS11 4.6 25.3 1.0
OG A:SER51 4.7 52.3 1.0
N A:SER51 4.7 36.1 1.0
O1 A:V7O100 4.7 37.9 1.0
CE2 A:TRP54 4.8 2.0 1.0
CZ2 A:TRP54 4.8 2.9 1.0
CA A:SER51 4.9 40.5 1.0
O12 A:V7O100 4.9 4.7 1.0
CD1 A:TRP54 4.9 9.9 1.0
O A:HOH583 4.9 2.4 1.0

Vanadium binding site 4 out of 7 in 1dkt

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Vanadium binding site 4 out of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 4 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V100

b:21.2
occ:1.00
 V4 A:V7O100 0.0 21.2 1.0
O11 A:V7O100 1.5 7.1 1.0
O10 A:V7O100 1.5 27.2 1.0
O12 A:V7O100 1.8 4.7 1.0
O9 A:V7O100 1.8 10.7 1.0
O A:HOH559 2.9 15.6 1.0
V5 A:V7O100 3.1 21.9 1.0
V3 A:V7O100 3.3 17.8 1.0
O A:HOH551 3.3 47.0 1.0
O8 A:V7O100 3.4 5.3 1.0
O7 A:V7O100 3.6 23.4 1.0
O16 A:V7O100 3.8 20.0 1.0
O A:HOH560 4.1 21.0 1.0
O13 A:V7O100 4.1 2.0 1.0
O A:HOH552 4.2 43.1 1.0
O14 A:V7O100 4.2 17.7 1.0
NZ A:LYS11 4.3 25.3 1.0
O15 A:V7O100 4.5 18.0 1.0
V6 A:V7O100 4.5 16.8 1.0
NH1 A:ARG20 4.5 28.6 1.0
NH2 A:ARG20 4.6 35.0 1.0
O4 A:V7O100 4.6 18.1 1.0
O A:HOH547 4.7 31.9 1.0
NH2 B:ARG20 4.7 41.7 1.0
O A:HOH558 4.9 45.1 1.0
CZ A:ARG20 4.9 28.3 1.0
O5 A:V7O100 5.0 27.9 1.0

Vanadium binding site 5 out of 7 in 1dkt

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Vanadium binding site 5 out of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 5 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V100

b:21.9
occ:1.00
 V5 A:V7O100 0.0 21.9 1.0
O13 A:V7O100 1.5 2.0 1.0
O12 A:V7O100 1.7 4.7 1.0
O14 A:V7O100 1.7 17.7 1.0
V4 A:V7O100 3.1 21.2 1.0
V6 A:V7O100 3.1 16.8 1.0
O15 A:V7O100 3.1 18.0 1.0
V7 A:V7O100 3.2 22.9 1.0
O A:HOH559 3.2 15.6 1.0
O17 A:V7O100 3.3 22.1 1.0
O16 A:V7O100 3.5 20.0 1.0
O11 A:V7O100 3.6 7.1 1.0
NH2 B:ARG20 3.9 41.7 1.0
O19 A:V7O100 4.0 28.5 1.0
O A:HOH560 4.1 21.0 1.0
O18 A:V7O100 4.1 18.6 1.0
O9 A:V7O100 4.2 10.7 1.0
O10 A:V7O100 4.2 27.2 1.0
NZ B:LYS11 4.2 43.4 1.0
NH1 B:ARG71 4.4 24.6 1.0
NH2 B:ARG71 4.4 31.2 1.0
O A:HOH556 4.4 43.2 1.0
NE1 B:TRP54 4.8 16.6 1.0
CE B:LYS11 4.8 37.2 1.0
CZ B:ARG71 4.8 29.8 1.0
O A:HOH583 4.9 2.4 1.0
O A:HOH558 4.9 45.1 1.0

Vanadium binding site 6 out of 7 in 1dkt

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Vanadium binding site 6 out of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 6 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V100

b:16.8
occ:1.00
 V6 A:V7O100 0.0 16.8 1.0
O15 A:V7O100 1.5 18.0 1.0
O16 A:V7O100 1.5 20.0 1.0
O14 A:V7O100 1.8 17.7 1.0
V7 A:V7O100 2.8 22.9 1.0
O18 A:V7O100 2.9 18.6 1.0
OG B:SER51 3.0 33.0 1.0
O A:HOH560 3.0 21.0 1.0
V5 A:V7O100 3.1 21.9 1.0
CB B:SER51 3.1 39.8 1.0
O12 A:V7O100 3.4 4.7 1.0
N B:SER51 3.6 40.3 1.0
O17 A:V7O100 3.8 22.1 1.0
NE1 B:TRP54 3.9 16.6 1.0
O13 A:V7O100 3.9 2.0 1.0
NH1 B:ARG71 4.0 24.6 1.0
CA B:SER51 4.0 42.3 1.0
O11 A:V7O100 4.1 7.1 1.0
CD1 B:TRP54 4.3 16.3 1.0
O19 A:V7O100 4.3 28.5 1.0
V4 A:V7O100 4.5 21.2 1.0
NH2 B:ARG20 4.7 41.7 1.0
C B:GLN50 4.7 38.1 1.0
O A:HOH582 4.8 51.8 1.0
O A:HOH583 4.9 2.4 1.0

Vanadium binding site 7 out of 7 in 1dkt

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Vanadium binding site 7 out of 7 in the CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 7 of CKSHS1: Human Cyclin Dependent Kinase Subunit, Type 1 Complex with Metavanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V100

b:22.9
occ:1.00
 V7 A:V7O100 0.0 22.9 1.0
O18 A:V7O100 1.5 18.6 1.0
O19 A:V7O100 1.5 28.5 1.0
O17 A:V7O100 1.7 22.1 1.0
O14 A:V7O100 1.7 17.7 1.0
V6 A:V7O100 2.8 16.8 1.0
NH1 B:ARG71 2.9 24.6 1.0
V5 A:V7O100 3.2 21.9 1.0
OG B:SER51 3.4 33.0 1.0
O15 A:V7O100 3.8 18.0 1.0
O A:HOH556 3.8 43.2 1.0
O13 A:V7O100 3.8 2.0 1.0
CZ B:ARG71 3.8 29.8 1.0
NH2 B:ARG71 3.9 31.2 1.0
O B:HOH555 3.9 38.7 1.0
O A:HOH560 3.9 21.0 1.0
CB B:SER51 3.9 39.8 1.0
O A:HOH583 4.0 2.4 1.0
O16 A:V7O100 4.2 20.0 1.0
O A:HOH557 4.3 36.6 1.0
O A:HOH582 4.5 51.8 1.0
O12 A:V7O100 4.6 4.7 1.0
NE1 B:TRP54 4.8 16.6 1.0
O A:HOH581 4.8 58.3 1.0
O A:HOH559 4.9 15.6 1.0

Reference:

A.S.Arvai, Y.Bourne, M.J.Hickey, J.A.Tainer. Crystal Structure of the Human Cell Cycle Protein CKSHS1: Single Domain Fold with Similarity to Kinase N-Lobe Domain. J.Mol.Biol. V. 249 835 1995.
ISSN: ISSN 0022-2836
PubMed: 7791211
DOI: 10.1006/JMBI.1995.0341
Page generated: Fri Oct 11 11:22:30 2024

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