Magnesium in PDB 2yvp: Crystal Structure of NDX2 in Complex with MG2+ and Ampcpr From Thermus Thermophilus HB8

The structure of Crystal Structure of NDX2 in Complex with MG2+ and Ampcpr From Thermus Thermophilus HB8, PDB code: 2yvp was solved by T.Wakamatsu, N.Nakagawa, S.Kuramitsu, S.Yokoyama, R.Masui, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.34 / 1.66
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	40.679, 100.748, 97.369, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 20.4

The binding sites of Magnesium atom in the Crystal Structure of NDX2 in Complex with MG2+ and Ampcpr From Thermus Thermophilus HB8 (pdb code 2yvp). 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 NDX2 in Complex with MG2+ and Ampcpr From Thermus Thermophilus HB8, PDB code: 2yvp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of NDX2 in Complex with MG2+ and Ampcpr From Thermus Thermophilus HB8


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 NDX2 in Complex with MG2+ and Ampcpr From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg183 b:11.6 occ:1.00 OE2 A:GLU139 2.0 12.4 1.0 O A:HOH189 2.0 9.1 1.0 OE2 A:GLU94 2.1 9.7 1.0 O1A A:RBY186 2.1 16.6 1.0 OE2 A:GLU90 2.1 11.6 1.0 O A:HOH203 2.2 14.9 1.0 CD A:GLU139 3.0 14.6 1.0 CD A:GLU94 3.1 9.8 1.0 CD A:GLU90 3.1 11.1 1.0 MG A:MG184 3.2 10.5 1.0 PA A:RBY186 3.4 18.1 1.0 OE1 A:GLU139 3.4 15.4 1.0 CG A:GLU94 3.4 9.3 1.0 OE1 A:GLU90 3.5 12.1 1.0 O A:HOH193 3.6 11.3 1.0 O5' A:RBY186 3.8 20.6 1.0 O A:ALA74 3.8 9.6 1.0 MG A:MG185 3.8 28.4 1.0 C5' A:RBY186 4.0 24.9 1.0 OE2 A:GLU93 4.0 15.3 1.0 O2A A:RBY186 4.2 19.2 1.0 OE1 A:GLU94 4.2 9.7 1.0 CG A:GLU139 4.3 15.5 1.0 CG A:GLU90 4.5 10.0 1.0 OE1 A:GLU136 4.6 29.7 1.0 O A:HOH240 4.6 22.0 1.0 CX A:RBY186 4.7 21.7 1.0 CA A:GLY75 4.7 10.2 1.0 O A:HOH190 4.8 10.1 1.0 C A:ALA74 4.8 8.9 1.0 CB A:GLU90 4.8 10.2 1.0 CB A:GLU94 5.0 10.1 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of NDX2 in Complex with MG2+ and Ampcpr From Thermus Thermophilus HB8


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 NDX2 in Complex with MG2+ and Ampcpr From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg184 b:10.5 occ:1.00 O A:HOH190 1.9 10.1 1.0 O A:ALA74 2.0 9.6 1.0 O A:HOH193 2.0 11.3 1.0 OE2 A:GLU94 2.1 9.7 1.0 O2B A:RBY186 2.2 20.8 1.0 O1A A:RBY186 2.3 16.6 1.0 CD A:GLU94 3.0 9.8 1.0 C A:ALA74 3.2 8.9 1.0 MG A:MG183 3.2 11.6 1.0 OE1 A:GLU94 3.2 9.7 1.0 PB A:RBY186 3.3 23.3 1.0 PA A:RBY186 3.5 18.1 1.0 OE2 A:GLU139 3.6 12.4 1.0 CX A:RBY186 3.7 21.7 1.0 OE2 A:GLU90 3.9 11.6 1.0 O1B A:RBY186 4.0 25.4 1.0 CA A:GLY75 4.0 10.2 1.0 N A:GLY75 4.1 9.2 1.0 N A:ALA74 4.1 9.4 1.0 CA A:ALA74 4.1 8.6 1.0 OE1 A:GLN60 4.2 12.2 1.0 O A:HOH191 4.3 10.0 1.0 NE2 A:GLN60 4.4 7.3 1.0 NH2 A:ARG62 4.4 12.9 1.0 CG A:GLU94 4.4 9.3 1.0 O5' A:RBY186 4.5 20.6 1.0 OR5 A:RBY186 4.6 26.8 1.0 CB A:ALA74 4.6 9.6 1.0 O2A A:RBY186 4.6 19.2 1.0 O A:HOH203 4.7 14.9 1.0 CD A:GLN60 4.8 8.6 1.0 CD A:GLU139 4.8 14.6 1.0 CD A:GLU90 4.8 11.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of NDX2 in Complex with MG2+ and Ampcpr From Thermus Thermophilus HB8


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 NDX2 in Complex with MG2+ and Ampcpr From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg185 b:28.4 occ:1.00 O A:HOH235 2.0 21.8 1.0 O A:HOH203 2.1 14.9 1.0 O A:HOH246 2.1 28.0 1.0 OE1 A:GLU90 2.1 12.1 1.0 O2A A:RBY186 2.5 19.2 1.0 O A:HOH240 2.5 22.0 1.0 CD A:GLU90 3.2 11.1 1.0 PA A:RBY186 3.3 18.1 1.0 OE1 A:GLU136 3.4 29.7 1.0 O5' A:RBY186 3.6 20.6 1.0 O1A A:RBY186 3.7 16.6 1.0 OE2 A:GLU90 3.7 11.6 1.0 C5' A:RBY186 3.7 24.9 1.0 MG A:MG183 3.8 11.6 1.0 NH1 A:ARG89 3.9 13.0 1.0 N A:LYS76 4.1 12.2 1.0 OE2 A:GLU93 4.3 15.3 1.0 O A:LYS76 4.5 14.7 1.0 CA A:GLY75 4.5 10.2 1.0 CG A:GLU90 4.5 10.0 1.0 CD A:GLU136 4.5 29.3 1.0 NH2 A:ARG89 4.6 14.0 1.0 O A:HOH189 4.7 9.1 1.0 CZ A:ARG89 4.7 12.9 1.0 C A:GLY75 4.7 10.9 1.0 CX A:RBY186 4.7 21.7 1.0 CB A:LYS76 4.8 14.9 1.0 CA A:LYS76 4.9 13.5 1.0

T.Wakamatsu, N.Nakagawa, S.Kuramitsu, R.Masui. Structural Basis For Different Substrate Specificities of Two Adp-Ribose Pyrophosphatases From Thermus Thermophilus HB8 J.Bacteriol. V. 190 1108 2008.
ISSN: ISSN 0021-9193
PubMed: 18039767
DOI: 10.1128/JB.01522-07