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Magnesium in PDB 3q8u: Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp

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

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

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp, PDB code: 3q8u 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) 34.52 / 2.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.270, 103.065, 127.000, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 25.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp (pdb code 3q8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp, PDB code: 3q8u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3q8u

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Magnesium binding site 1 out of 5 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg159

b:48.9
occ:1.00
 O A:HOH161 1.7 23.6 1.0
O A:HOH162 2.0 19.7 1.0
O2A A:ADP158 2.1 25.9 1.0
O1B A:ADP158 2.8 21.1 1.0
O A:HOH166 2.9 26.5 1.0
OD1 A:ASP118 3.1 24.3 1.0
O A:HOH165 3.2 21.9 1.0
PA A:ADP158 3.3 24.6 1.0
OE2 A:GLU51 3.7 32.3 1.0
O3A A:ADP158 3.8 23.1 1.0
CG A:ASP118 3.9 21.7 1.0
PB A:ADP158 3.9 19.9 1.0
O1A A:ADP158 4.0 23.2 1.0
CB A:ASP118 4.0 18.0 1.0
O A:HOH163 4.1 8.4 1.0
NE2 A:HIS52 4.4 26.6 1.0
CD A:GLU51 4.5 34.1 1.0
O5' A:ADP158 4.5 23.8 1.0
CE1 A:HIS52 4.5 26.5 1.0
C5' A:ADP158 4.7 18.9 1.0
O3B A:ADP158 4.7 18.4 1.0
OE1 A:GLU51 4.8 33.7 1.0
O A:HOH253 4.9 21.3 1.0
OD2 A:ASP118 4.9 21.3 1.0

Magnesium binding site 2 out of 5 in 3q8u

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Magnesium binding site 2 out of 5 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg159

b:2.0
occ:1.00
 O2A B:ADP158 2.2 9.9 1.0
O3B B:ADP158 2.3 9.7 1.0
O B:HOH165 2.4 19.6 1.0
O B:HOH160 2.4 10.3 1.0
OD1 B:ASP118 2.5 19.1 1.0
O B:HOH426 2.6 53.0 1.0
PA B:ADP158 3.5 13.8 1.0
CG B:ASP118 3.5 18.0 1.0
PB B:ADP158 3.5 13.1 1.0
O3A B:ADP158 3.7 12.9 1.0
CB B:ASP118 3.9 15.5 1.0
O B:HOH194 4.0 10.4 1.0
O2B B:ADP158 4.2 10.4 1.0
O B:HOH172 4.4 19.3 1.0
O B:HOH161 4.4 11.7 1.0
O1A B:ADP158 4.5 14.2 1.0
NE2 B:HIS52 4.6 23.0 1.0
OD2 B:ASP118 4.6 20.8 1.0
O B:HOH422 4.6 20.6 1.0
OE2 B:GLU51 4.6 25.9 1.0
O5' B:ADP158 4.7 12.1 1.0
O1B B:ADP158 4.7 9.7 1.0
C5' B:ADP158 4.8 14.7 1.0
OE1 B:GLU51 4.8 28.3 1.0
CE1 B:HIS52 4.9 22.8 1.0

Magnesium binding site 3 out of 5 in 3q8u

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Magnesium binding site 3 out of 5 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg159

b:40.7
occ:1.00
 O D:HOH160 1.8 32.1 1.0
O D:HOH161 2.1 24.9 1.0
O2A D:ADP158 2.2 32.1 1.0
O3B D:ADP158 2.7 24.4 1.0
PA D:ADP158 3.3 26.2 1.0
OD1 D:ASP118 3.4 25.0 1.0
PB D:ADP158 3.8 30.2 1.0
O3A D:ADP158 3.8 30.2 1.0
O1A D:ADP158 3.9 26.5 1.0
CB D:ASP118 4.0 18.8 1.0
CG D:ASP118 4.1 21.7 1.0
OE1 D:GLU51 4.2 34.9 1.0
O2B D:ADP158 4.4 23.2 1.0
OE2 D:GLU51 4.4 33.6 1.0
NE2 D:HIS52 4.4 28.9 1.0
O D:HOH256 4.5 19.2 1.0
CD D:GLU51 4.6 32.9 1.0
O5' D:ADP158 4.6 28.3 1.0
O D:HOH174 4.7 23.5 1.0
C5' D:ADP158 4.7 27.8 1.0
CE1 D:HIS52 4.8 28.1 1.0

Magnesium binding site 4 out of 5 in 3q8u

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Magnesium binding site 4 out of 5 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg159

b:24.6
occ:1.00
 O E:HOH169 1.9 21.9 1.0
O2A E:ADP158 2.0 12.7 1.0
O E:HOH165 2.1 16.6 1.0
O E:HOH170 2.4 24.8 1.0
O3B E:ADP158 2.6 12.5 1.0
OD1 E:ASP118 2.7 22.0 1.0
PA E:ADP158 3.2 15.5 1.0
O E:HOH161 3.2 38.1 1.0
O E:HOH160 3.5 23.1 1.0
O3A E:ADP158 3.7 12.8 1.0
CG E:ASP118 3.7 20.2 1.0
PB E:ADP158 3.7 14.0 1.0
CB E:ASP118 4.0 16.7 1.0
O1A E:ADP158 4.0 11.3 1.0
O E:HOH207 4.4 21.8 1.0
OE1 E:GLU51 4.4 35.4 1.0
OE2 E:GLU51 4.4 32.3 1.0
O2B E:ADP158 4.5 10.9 1.0
O5' E:ADP158 4.5 14.6 1.0
O E:HOH164 4.5 9.8 1.0
NE2 E:HIS52 4.6 23.3 1.0
CE1 E:HIS52 4.6 22.6 1.0
CD E:GLU51 4.7 34.0 1.0
C5' E:ADP158 4.8 14.3 1.0
OD2 E:ASP118 4.8 18.9 1.0
O1B E:ADP158 4.9 8.6 1.0

Magnesium binding site 5 out of 5 in 3q8u

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Magnesium binding site 5 out of 5 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg159

b:43.7
occ:1.00
 O2A F:ADP158 2.2 35.6 1.0
O F:HOH428 2.5 35.7 1.0
O F:HOH429 2.7 26.8 1.0
OD1 F:ASP118 2.9 25.1 1.0
OE1 F:GLU51 3.4 35.2 1.0
PA F:ADP158 3.6 35.2 1.0
O3B F:ADP158 3.7 29.4 1.0
CG F:ASP118 3.8 21.8 1.0
OE2 F:GLU51 3.9 35.5 1.0
CD F:GLU51 3.9 34.9 1.0
CB F:ASP118 4.0 19.1 1.0
O3A F:ADP158 4.4 36.1 1.0
O1A F:ADP158 4.4 36.4 1.0
NE2 F:HIS52 4.5 27.1 1.0
CE1 F:HIS52 4.5 27.9 1.0
O5' F:ADP158 4.6 38.1 1.0
PB F:ADP158 4.8 32.6 1.0
O F:HOH169 4.9 15.3 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 V.1814 1349 2011.
ISSN: ISSN 0006-3002
PubMed: 21745603
DOI: 10.1016/J.BBAPAP.2011.06.008
Page generated: Mon Dec 14 08:42:08 2020

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