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Magnesium 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:

Vanadium (V) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp and Vanadate, PDB code: 3q8y:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3q8y

Go back to Magnesium Binding Sites List in 3q8y
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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
B:Mg160

b:53.2
occ:1.00
O1A B:ADP158 2.7 0.4 1.0
O B:HOH181 2.9 23.9 1.0
O2A B:ADP158 3.2 0.8 1.0
PA B:ADP158 3.2 0.4 1.0
O B:HOH182 3.6 24.6 1.0
O5' B:ADP158 3.8 99.2 1.0
O B:HOH180 4.0 26.0 1.0
C5' B:ADP158 4.2 94.7 1.0
O3A B:ADP158 4.8 0.3 1.0

Magnesium binding site 2 out of 4 in 3q8y

Go back to Magnesium Binding Sites List in 3q8y
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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
D:Mg160

b:0.8
occ:1.00
O1A D:ADP158 2.0 0.1 1.0
O D:HOH168 2.2 25.5 1.0
O H:HOH171 2.2 12.6 1.0
OD1 D:ASP118 3.2 69.4 1.0
PA D:ADP158 3.2 0.1 1.0
O3A D:ADP158 3.4 0.3 1.0
OE1 D:GLU51 3.7 94.0 1.0
O5' D:ADP158 3.7 1.0 1.0
OE2 D:GLU51 4.1 90.8 1.0
CD D:GLU51 4.3 92.8 1.0
CG D:ASP118 4.4 66.6 1.0
O D:HOH161 4.5 41.2 1.0
O2A D:ADP158 4.6 0.9 1.0
C5' D:ADP158 4.8 0.2 1.0
PB D:ADP158 4.8 0.1 1.0
O3B D:ADP158 5.0 0.0 1.0

Magnesium binding site 3 out of 4 in 3q8y

Go back to Magnesium Binding Sites List in 3q8y
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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
E:Mg160

b:61.5
occ:1.00
O1A E:ADP158 2.2 0.8 1.0
PA E:ADP158 2.9 0.2 1.0
O2A E:ADP158 3.0 0.7 1.0
O E:HOH162 3.2 22.5 1.0
O3A E:ADP158 3.3 0.8 1.0
O3B E:ADP158 4.4 0.4 1.0
O5' E:ADP158 4.4 0.9 1.0
OD1 E:ASP118 4.5 76.5 1.0
CE1 E:HIS52 4.6 97.0 1.0
PB E:ADP158 4.6 0.7 1.0
OE1 E:GLU51 4.7 98.3 1.0

Magnesium binding site 4 out of 4 in 3q8y

Go back to Magnesium Binding Sites List in 3q8y
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg 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
H:Mg160

b:74.2
occ:1.00
O1A H:ADP158 2.2 0.8 1.0
O H:HOH182 3.0 10.6 1.0
PA H:ADP158 3.3 0.8 1.0
O3A H:ADP158 3.3 0.2 1.0
OD1 H:ASP118 3.7 97.7 1.0
O5' H:ADP158 4.0 0.6 1.0
O2A H:ADP158 4.6 0.7 1.0
CG H:ASP118 4.8 97.2 1.0
PB H:ADP158 4.8 0.2 1.0
O H:HOH162 5.0 11.9 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: Mon Dec 14 08:42:12 2020

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