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

The structure of Crystal Structure of NDX2 in Complex with MG2+ From Thermus Thermophilus HB8, PDB code: 2yvm 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)	25.99 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	40.763, 101.176, 97.492, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of NDX2 in Complex with MG2+ From Thermus Thermophilus HB8 (pdb code 2yvm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of NDX2 in Complex with MG2+ From Thermus Thermophilus HB8, PDB code: 2yvm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of NDX2 in Complex with MG2+ 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+ From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:19.1 occ:1.00 O A:HOH1007 1.9 15.6 1.0 O A:HOH1015 1.9 12.5 1.0 OE2 A:GLU139 2.1 20.3 1.0 OE1 A:GLU94 2.2 11.2 1.0 O A:HOH1036 2.2 21.4 1.0 OE1 A:GLU90 2.2 15.3 1.0 CD A:GLU90 3.1 14.9 1.0 MG A:MG1002 3.1 18.5 1.0 CD A:GLU139 3.1 22.5 1.0 CD A:GLU94 3.2 13.0 1.0 OE2 A:GLU90 3.4 15.7 1.0 O A:HOH1119 3.5 16.0 1.0 OE1 A:GLU139 3.5 22.5 1.0 CG A:GLU94 3.5 11.4 1.0 O A:HOH1037 3.6 23.1 1.0 O A:ALA74 3.8 9.9 1.0 OE2 A:GLU93 4.1 18.3 1.0 OE2 A:GLU94 4.3 12.7 1.0 CG A:GLU139 4.4 22.1 1.0 CG A:GLU90 4.5 13.6 1.0 OE2 A:GLU136 4.5 38.3 1.0 O A:HOH1004 4.7 10.9 1.0 O A:HOH1069 4.7 27.5 1.0 CB A:GLU90 4.8 12.3 1.0 O A:HOH1013 4.8 14.7 1.0 CA A:GLY75 4.8 11.9 1.0 C A:ALA74 4.9 9.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of NDX2 in Complex with MG2+ 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+ From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:18.5 occ:1.00 O A:HOH1004 2.0 10.9 1.0 O A:ALA74 2.0 9.9 1.0 OE1 A:GLU94 2.1 11.2 1.0 O A:HOH1015 2.1 12.5 1.0 O A:HOH1037 2.2 23.1 1.0 O A:HOH1013 2.2 14.7 1.0 CD A:GLU94 3.0 13.0 1.0 MG A:MG1001 3.1 19.1 1.0 C A:ALA74 3.2 9.7 1.0 OE2 A:GLU94 3.3 12.7 1.0 O A:HOH1119 3.4 16.0 1.0 OE2 A:GLU139 3.6 20.3 1.0 OE1 A:GLU90 3.9 15.3 1.0 N A:ALA74 4.0 9.5 1.0 CA A:GLY75 4.1 11.9 1.0 N A:GLY75 4.1 9.6 1.0 CA A:ALA74 4.2 9.0 1.0 OE1 A:GLN60 4.2 12.9 1.0 NH2 A:ARG62 4.3 14.0 1.0 CG A:GLU94 4.4 11.4 1.0 O A:HOH1008 4.4 13.2 1.0 NE2 A:GLN60 4.4 10.7 1.0 O A:HOH1088 4.5 38.9 1.0 CD A:GLU90 4.6 14.9 1.0 O A:HOH1036 4.7 21.4 1.0 CD A:GLU139 4.7 22.5 1.0 CB A:ALA74 4.7 11.4 1.0 O A:HOH1007 4.8 15.6 1.0 CD A:GLN60 4.8 10.4 1.0 O A:HOH1069 5.0 27.5 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