Magnesium in PDB 3q8v: Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Udp

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

The structure of Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Udp, PDB code: 3q8v 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)	32.30 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	186.665, 72.916, 102.144, 90.00, 108.42, 90.00
R / Rfree (%)	23 / 28.3

The binding sites of Magnesium atom in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Udp (pdb code 3q8v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Udp, PDB code: 3q8v:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Udp


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 Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg159 b:48.5 occ:1.00 O3B A:UDP158 2.3 66.0 1.0 NH1 A:ARG102 2.8 21.2 1.0 O2B A:UDP158 3.2 70.4 1.0 OG1 A:THR91 3.3 25.6 1.0 O A:HOH181 3.3 19.4 1.0 PB A:UDP158 3.3 69.2 1.0 N A:THR91 4.1 23.3 1.0 CZ A:ARG102 4.1 20.9 1.0 O A:GLY89 4.2 19.6 1.0 O3A A:UDP158 4.3 70.9 1.0 CA A:THR91 4.4 23.5 1.0 O1B A:UDP158 4.4 70.0 1.0 CB A:THR91 4.4 24.1 1.0 C A:SER90 4.7 22.5 1.0 NH2 A:ARG102 4.7 18.1 1.0 CA A:SER90 5.0 21.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Staphylococcus Aureus Nucleoside Diphosphate Kinase Complexed with Udp


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 Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg159 b:45.4 occ:1.00 O B:HOH179 2.0 29.8 1.0 O B:HOH198 2.2 29.2 1.0 O1A B:UDP158 2.2 32.4 1.0 O3B B:UDP158 2.3 32.4 1.0 PB B:UDP158 3.5 29.0 1.0 PA B:UDP158 3.5 29.8 1.0 OD1 B:ASP118 3.8 33.6 1.0 O3A B:UDP158 3.9 34.0 1.0 O2B B:UDP158 3.9 25.7 1.0 CG B:ASP118 4.3 30.4 1.0 O B:HOH180 4.3 9.0 1.0 CB B:ASP118 4.4 26.6 1.0 O2A B:UDP158 4.4 34.3 1.0 NE2 B:HIS52 4.4 20.9 1.0 CE1 B:HIS115 4.5 20.3 1.0 C5' B:UDP158 4.5 31.2 1.0 O5' B:UDP158 4.5 31.8 1.0 O1B B:UDP158 4.6 31.6 1.0 ND1 B:HIS115 4.7 20.1 1.0 O B:GLY116 4.9 19.0 1.0 CE1 B:HIS52 4.9 26.4 1.0 O B:HOH199 4.9 31.1 1.0 O B:HOH190 5.0 3.4 1.0

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


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 Udp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg159 b:52.1 occ:1.00 O D:HOH208 2.1 52.6 1.0 O D:HOH209 2.5 44.1 1.0 O2B D:UDP158 2.8 56.9 1.0 O1A D:UDP158 2.8 61.6 1.0 O3A D:UDP158 3.1 59.8 1.0 PB D:UDP158 3.5 55.9 1.0 PA D:UDP158 3.6 60.0 1.0 O D:HOH184 3.8 16.1 1.0 O D:HOH183 3.8 28.9 1.0 CE1 D:HIS115 3.9 29.1 1.0 O D:HOH207 3.9 33.2 1.0 OE2 D:GLU51 4.0 59.7 1.0 O1B D:UDP158 4.1 52.8 1.0 ND1 D:HIS115 4.1 28.2 1.0 OD1 D:ASP118 4.1 40.7 1.0 C5' D:UDP158 4.3 60.0 1.0 NE2 D:HIS52 4.4 53.4 1.0 O5' D:UDP158 4.4 60.0 1.0 CG D:ASP118 4.6 37.1 1.0 O D:GLY116 4.6 25.4 1.0 CB D:ASP118 4.7 32.7 1.0 O3B D:UDP158 4.7 54.3 1.0 O2A D:UDP158 4.9 60.0 1.0

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