Atomistry » Magnesium » PDB 3q89-3qpo » 3q8u
Atomistry »
  Magnesium »
    PDB 3q89-3qpo »
      3q8u »

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

Go back to Magnesium Binding Sites List in 3q8u
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

Go back to Magnesium Binding Sites List in 3q8u
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

Go back to Magnesium Binding Sites List in 3q8u
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

Go back to Magnesium Binding Sites List in 3q8u
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

Go back to Magnesium Binding Sites List in 3q8u
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: Thu Aug 15 09:59:53 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy