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Vanadium in PDB 3q8y: Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate

Enzymatic activity of Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate

All present enzymatic activity of Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate, PDB code: 3q8y was solved by S.K.Srivastava, K.Rajasree, B.Gopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.67 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 119.910, 71.367, 160.080, 90.00, 108.04, 90.00
R / Rfree (%) 25.1 / 27.1

Other elements in 3q8y:

The structure of Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate (pdb code 3q8y). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 8 binding sites of Vanadium where determined in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate, PDB code: 3q8y:
Jump to Vanadium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Vanadium binding site 1 out of 8 in 3q8y

Go back to Vanadium Binding Sites List in 3q8y
Vanadium binding site 1 out of 8 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate


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 Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V159

b:96.1
occ:1.00
 V A:VO4159 0.0 96.1 1.0
O1 A:VO4159 1.9 94.2 1.0
O4 A:VO4159 1.9 95.5 1.0
O2 A:VO4159 1.9 96.0 1.0
O3 A:VO4159 1.9 97.9 1.0
ND1 A:HIS115 2.4 57.0 1.0
C5' A:ADP158 3.2 0.6 1.0
CE1 A:HIS115 3.3 56.3 1.0
CG A:HIS115 3.3 55.0 1.0
O3B A:ADP158 3.4 0.6 1.0
CB A:HIS115 3.6 53.4 1.0
CA A:HIS115 3.8 53.6 1.0
C4' A:ADP158 3.9 0.3 1.0
O1B A:ADP158 4.1 1.0 1.0
N A:GLY116 4.2 55.4 1.0
O3' A:ADP158 4.3 0.8 1.0
NH2 A:ARG102 4.3 54.6 1.0
O5' A:ADP158 4.3 0.1 1.0
PB A:ADP158 4.4 0.7 1.0
O A:GLY116 4.4 59.3 1.0
NZ A:LYS9 4.4 54.0 1.0
NE2 A:HIS115 4.4 55.5 1.0
CD2 A:HIS115 4.4 54.9 1.0
C A:HIS115 4.5 53.9 1.0
O A:ILE114 4.6 53.7 1.0
CE A:LYS9 4.6 51.6 1.0
C3' A:ADP158 4.7 0.5 1.0
OH A:TYR49 4.7 80.0 1.0
N A:HIS115 4.9 52.3 1.0
O2A A:ADP158 5.0 0.2 1.0

Vanadium binding site 2 out of 8 in 3q8y

Go back to Vanadium Binding Sites List in 3q8y
Vanadium binding site 2 out of 8 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate


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 Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V159

b:68.5
occ:1.00
 V B:VO4159 0.0 68.5 1.0
O2 B:VO4159 1.9 69.8 1.0
O3 B:VO4159 1.9 66.3 1.0
O1 B:VO4159 1.9 68.3 1.0
O4 B:VO4159 1.9 67.0 1.0
ND1 B:HIS115 2.5 45.5 1.0
CE1 B:HIS115 3.3 45.6 1.0
O1B B:ADP158 3.4 0.5 1.0
CG B:HIS115 3.5 44.2 1.0
O3' B:ADP158 3.6 89.0 1.0
CB B:HIS115 3.9 42.4 1.0
CA B:HIS115 4.0 41.6 1.0
O B:GLY116 4.2 48.4 1.0
N B:GLY116 4.2 44.2 1.0
O3B B:ADP158 4.3 0.4 1.0
PB B:ADP158 4.3 0.0 1.0
NH2 B:ARG102 4.4 37.6 1.0
NE2 B:HIS115 4.4 46.2 1.0
C3' B:ADP158 4.5 90.6 1.0
CD2 B:HIS115 4.6 45.2 1.0
C B:HIS115 4.7 43.0 1.0
NZ B:LYS9 4.7 38.9 1.0
O B:ILE114 4.9 39.2 1.0
NH1 B:ARG102 5.0 43.1 1.0

Vanadium binding site 3 out of 8 in 3q8y

Go back to Vanadium Binding Sites List in 3q8y
Vanadium binding site 3 out of 8 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate


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 Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:V158

b:0.7
occ:0.90
 V C:VO4158 0.0 0.7 0.9
O2 C:VO4158 1.9 0.7 0.9
O4 C:VO4158 1.9 0.7 0.9
O3 C:VO4158 1.9 0.1 0.9
O1 C:VO4158 1.9 0.8 0.9
ND1 C:HIS115 3.0 54.6 1.0
CE1 C:HIS115 3.7 54.6 1.0
CG C:HIS115 3.9 52.2 1.0
O C:GLY116 4.2 54.5 1.0
CB C:HIS115 4.3 50.1 1.0
NH2 C:ARG102 4.3 45.5 1.0
CA C:HIS115 4.3 48.6 1.0
N C:GLY116 4.5 50.0 1.0
NZ C:LYS9 4.7 49.2 1.0
NH1 C:ARG102 4.7 50.4 1.0
NE2 C:HIS115 4.8 54.0 1.0
CD2 C:HIS115 4.9 52.8 1.0

Vanadium binding site 4 out of 8 in 3q8y

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Vanadium binding site 4 out of 8 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate


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 Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:V159

b:0.2
occ:0.80
 V D:VO4159 0.0 0.2 0.8
O4 D:VO4159 1.9 0.0 0.8
O3 D:VO4159 1.9 0.7 0.8
O1 D:VO4159 1.9 0.3 0.8
O2 D:VO4159 1.9 0.8 0.8
O3' D:ADP158 2.6 0.9 1.0
ND1 D:HIS115 2.7 53.5 1.0
O1B D:ADP158 3.1 0.7 1.0
OH D:TYR49 3.5 80.0 1.0
CG D:HIS115 3.6 52.0 1.0
CE1 D:HIS115 3.7 53.4 1.0
CB D:HIS115 3.8 50.4 1.0
O2' D:ADP158 3.8 0.1 1.0
NZ D:LYS9 3.8 50.0 1.0
O2B D:ADP158 3.8 0.1 1.0
C3' D:ADP158 4.0 0.8 1.0
CE1 D:TYR49 4.0 82.2 1.0
PB D:ADP158 4.0 0.1 1.0
CE D:LYS9 4.0 48.3 1.0
CZ D:TYR49 4.2 81.6 1.0
CA D:HIS115 4.3 49.0 1.0
C2' D:ADP158 4.5 0.3 1.0
O2A D:ADP158 4.5 0.9 1.0
C4' D:ADP158 4.5 0.1 1.0
NE2 D:HIS115 4.8 53.0 1.0
CD2 D:HIS115 4.8 52.4 1.0

Vanadium binding site 5 out of 8 in 3q8y

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Vanadium binding site 5 out of 8 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate


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 Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:V159

b:83.2
occ:1.00
 V E:VO4159 0.0 83.2 1.0
O3 E:VO4159 1.9 83.2 1.0
O4 E:VO4159 1.9 83.4 1.0
O2 E:VO4159 1.9 84.3 1.0
O1 E:VO4159 1.9 82.7 1.0
ND1 E:HIS115 2.4 57.7 1.0
O2B E:ADP158 2.5 0.8 1.0
CE1 E:HIS115 3.3 58.2 1.0
CG E:HIS115 3.4 55.9 1.0
O3' E:ADP158 3.5 1.0 1.0
PB E:ADP158 3.6 0.7 1.0
CB E:HIS115 3.6 53.4 1.0
CA E:HIS115 3.9 52.2 1.0
O3B E:ADP158 3.9 0.4 1.0
O1B E:ADP158 4.0 0.4 1.0
C3' E:ADP158 4.3 0.9 1.0
NZ E:LYS9 4.4 49.2 1.0
N E:GLY116 4.4 54.6 1.0
NE2 E:HIS115 4.4 58.3 1.0
CD2 E:HIS115 4.4 57.2 1.0
O E:GLY116 4.5 59.3 1.0
NH2 E:ARG102 4.5 47.4 1.0
OH E:TYR49 4.5 79.9 1.0
CE E:LYS9 4.6 48.0 1.0
C E:HIS115 4.7 53.1 1.0
O E:ILE114 4.8 48.4 1.0
C4' E:ADP158 4.9 1.0 1.0
O3A E:ADP158 4.9 0.8 1.0
O5' E:ADP158 5.0 0.9 1.0

Vanadium binding site 6 out of 8 in 3q8y

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Vanadium binding site 6 out of 8 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate


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 Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:V158

b:0.9
occ:1.00
 V F:VO4158 0.0 0.9 1.0
O1 F:VO4158 1.9 0.0 1.0
O2 F:VO4158 1.9 0.9 1.0
O4 F:VO4158 1.9 0.5 1.0
O3 F:VO4158 1.9 0.8 1.0
ND1 F:HIS115 2.8 57.3 1.0
NZ F:LYS9 3.7 52.4 1.0
CG F:HIS115 3.7 54.5 1.0
OH F:TYR49 3.7 82.9 1.0
CE1 F:HIS115 3.8 56.9 1.0
CB F:HIS115 3.9 52.5 1.0
CE F:LYS9 4.1 50.2 1.0
CE1 F:TYR49 4.2 86.5 1.0
O F:HOH168 4.3 38.8 1.0
CA F:HIS115 4.4 50.9 1.0
CZ F:TYR49 4.4 85.2 1.0
NE2 F:HIS115 4.9 56.2 1.0
CD2 F:HIS115 4.9 55.0 1.0

Vanadium binding site 7 out of 8 in 3q8y

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Vanadium binding site 7 out of 8 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate


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 Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:V159

b:88.1
occ:0.80
 V G:VO4159 0.0 88.1 0.8
O4 G:VO4159 1.9 86.8 0.8
O3 G:VO4159 1.9 86.7 0.8
O1 G:VO4159 1.9 87.2 0.8
O2 G:VO4159 1.9 87.8 0.8
ND1 G:HIS115 2.2 53.8 1.0
CG G:HIS115 3.2 51.8 1.0
CE1 G:HIS115 3.2 53.4 1.0
CB G:HIS115 3.4 50.0 1.0
O2B G:ADP158 3.4 0.7 0.8
O3A G:ADP158 3.5 0.0 0.8
CA G:HIS115 3.7 49.3 1.0
NZ G:LYS9 4.2 49.2 1.0
PB G:ADP158 4.2 0.6 0.8
OH G:TYR49 4.3 77.8 1.0
CD2 G:HIS115 4.3 52.0 1.0
NE2 G:HIS115 4.3 53.0 1.0
CE G:LYS9 4.3 47.5 1.0
N G:GLY116 4.3 51.1 1.0
O G:GLY116 4.6 55.6 1.0
C G:HIS115 4.6 49.9 1.0
NH2 G:ARG102 4.6 47.3 1.0
O G:ILE114 4.6 47.5 1.0
PA G:ADP158 4.7 0.5 0.8
O2A G:ADP158 4.7 0.1 0.8
C5' G:ADP158 4.8 0.8 0.8
CE1 G:TYR49 4.8 80.3 1.0
N G:HIS115 4.9 47.5 1.0

Vanadium binding site 8 out of 8 in 3q8y

Go back to Vanadium Binding Sites List in 3q8y
Vanadium binding site 8 out of 8 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate


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 Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:V159

b:0.2
occ:0.80
 V H:VO4159 0.0 0.2 0.8
O2 H:VO4159 1.9 0.8 0.8
O1 H:VO4159 1.9 0.4 0.8
O3 H:VO4159 1.9 0.3 0.8
O4 H:VO4159 1.9 0.4 0.8
ND1 H:HIS115 2.3 79.4 1.0
O3B H:ADP158 2.6 0.0 1.0
O2B H:ADP158 2.6 0.8 1.0
PB H:ADP158 3.0 0.2 1.0
CG H:HIS115 3.2 78.5 1.0
CE1 H:HIS115 3.3 80.1 1.0
CB H:HIS115 3.5 75.8 1.0
CA H:HIS115 3.8 75.3 1.0
O1B H:ADP158 4.0 0.9 1.0
O H:HOH172 4.1 47.1 1.0
NZ H:LYS9 4.1 67.9 1.0
O3A H:ADP158 4.3 0.2 1.0
CE H:LYS9 4.4 67.5 1.0
O2A H:ADP158 4.4 0.7 1.0
N H:GLY116 4.4 79.4 1.0
CD2 H:HIS115 4.4 80.6 1.0
OH H:TYR49 4.4 97.4 1.0
NE2 H:HIS115 4.4 81.3 1.0
O3' H:ADP158 4.5 0.7 1.0
NH2 H:ARG102 4.6 68.7 1.0
C H:HIS115 4.6 77.8 1.0
O H:ILE114 4.6 70.5 1.0
O H:GLY116 4.6 83.9 1.0
N H:HIS115 4.9 72.9 1.0
CE1 H:TYR49 4.9 99.2 1.0

Reference:

S.K.Srivastava, K.Rajasree, B.Gopal. Conformational Basis For Substrate Recognition and Regulation of Catalytic Activity in Staphylococcus Aureus Nucleoside Di-Phosphate Kinase. Biochim.Biophys.Acta 2011.
ISSN: ISSN 0006-3002
PubMed: 21745603
DOI: 10.1016/J.BBAPAP.2011.06.008
Page generated: Fri Oct 11 19:26:34 2024

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