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

The structure of Crystal Structure of NDX2 in Complex with MG2+ and Amp From Thermus Thermophilus HB8, PDB code: 2yvo 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)	27.26 / 1.67
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	40.699, 100.899, 97.172, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.5

The binding sites of Magnesium atom in the Crystal Structure of NDX2 in Complex with MG2+ and Amp From Thermus Thermophilus HB8 (pdb code 2yvo). 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 Amp From Thermus Thermophilus HB8, PDB code: 2yvo:
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 Amp 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 Amp From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:8.4 occ:1.00 O1P A:AMP2001 2.1 7.9 1.0 O A:HOH2003 2.1 7.4 1.0 OE2 A:GLU90 2.1 6.4 1.0 OE2 A:GLU139 2.1 8.5 1.0 OE1 A:GLU94 2.2 7.0 1.0 O A:HOH2004 2.2 7.5 1.0 CD A:GLU139 3.1 12.8 1.0 CD A:GLU90 3.1 6.5 1.0 CD A:GLU94 3.1 7.2 1.0 MG A:MG1002 3.2 6.6 1.0 P A:AMP2001 3.3 7.7 1.0 OE1 A:GLU90 3.4 7.3 1.0 OE1 A:GLU139 3.5 13.9 1.0 CG A:GLU94 3.5 7.6 1.0 O A:HOH2009 3.6 7.3 1.0 MG A:MG1003 3.6 7.8 1.0 O3P A:AMP2001 3.7 8.0 1.0 O A:ALA74 3.8 7.3 1.0 O5' A:AMP2001 3.9 12.7 1.0 C5' A:AMP2001 4.0 18.0 1.0 OE2 A:GLU93 4.0 11.4 1.0 OE2 A:GLU136 4.0 22.3 1.0 OE2 A:GLU94 4.3 7.9 1.0 O A:HOH2007 4.4 9.3 1.0 CG A:GLU139 4.4 13.3 1.0 CG A:GLU90 4.5 6.5 1.0 O2P A:AMP2001 4.5 9.4 1.0 CA A:GLY75 4.7 7.2 1.0 O A:HOH2002 4.7 6.9 1.0 CD A:GLU136 4.8 23.4 1.0 CB A:GLU90 4.8 6.6 1.0 C A:ALA74 4.8 6.4 1.0 O A:HOH2006 4.9 7.0 1.0 OE1 A:GLU136 4.9 22.9 1.0 O A:HOH2027 5.0 16.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of NDX2 in Complex with MG2+ and Amp 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 Amp From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:6.6 occ:1.00 O A:HOH2002 2.0 6.9 1.0 O A:ALA74 2.0 7.3 1.0 O A:HOH2009 2.1 7.3 1.0 OE1 A:GLU94 2.1 7.0 1.0 O A:HOH2006 2.1 7.0 1.0 O1P A:AMP2001 2.1 7.9 1.0 CD A:GLU94 3.0 7.2 1.0 MG A:MG1001 3.2 8.4 1.0 C A:ALA74 3.2 6.4 1.0 OE2 A:GLU94 3.3 7.9 1.0 P A:AMP2001 3.3 7.7 1.0 O2P A:AMP2001 3.4 9.4 1.0 OE2 A:GLU139 3.6 8.5 1.0 OE2 A:GLU90 4.0 6.4 1.0 CA A:GLY75 4.0 7.2 1.0 N A:GLY75 4.0 6.5 1.0 N A:ALA74 4.1 6.9 1.0 NH2 A:ARG62 4.2 10.1 1.0 CA A:ALA74 4.2 6.2 1.0 OE1 A:GLN60 4.2 8.7 1.0 O5' A:AMP2001 4.3 12.7 1.0 O A:HOH2008 4.4 8.4 1.0 NE2 A:GLN60 4.4 5.5 1.0 CG A:GLU94 4.4 7.6 1.0 O3P A:AMP2001 4.5 8.0 1.0 CB A:ALA74 4.7 7.1 1.0 CD A:GLU90 4.7 6.5 1.0 CD A:GLN60 4.8 5.5 1.0 CD A:GLU139 4.8 12.8 1.0 O A:HOH2034 4.8 15.4 1.0 O A:HOH2004 4.8 7.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of NDX2 in Complex with MG2+ and Amp 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 Amp From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:7.8 occ:1.00 OE1 A:GLU90 2.0 7.3 1.0 O A:HOH2011 2.1 10.5 1.0 O3P A:AMP2001 2.1 8.0 1.0 O A:HOH2004 2.2 7.5 1.0 O A:HOH2027 2.2 16.6 1.0 O A:HOH2007 2.2 9.3 1.0 CD A:GLU90 3.1 6.5 1.0 P A:AMP2001 3.2 7.7 1.0 OE2 A:GLU90 3.5 6.4 1.0 MG A:MG1001 3.6 8.4 1.0 O1P A:AMP2001 3.6 7.9 1.0 C5' A:AMP2001 3.8 18.0 1.0 OE2 A:GLU136 3.8 22.3 1.0 O5' A:AMP2001 3.8 12.7 1.0 OE1 A:GLU136 3.9 22.9 1.0 NH1 A:ARG89 3.9 9.4 1.0 N A:LYS76 4.0 7.4 1.0 OE2 A:GLU93 4.1 11.4 1.0 O A:HOH2088 4.2 39.5 1.0 CD A:GLU136 4.3 23.4 1.0 CG A:GLU90 4.4 6.5 1.0 O A:LYS76 4.4 9.3 1.0 CA A:GLY75 4.4 7.2 1.0 O2P A:AMP2001 4.5 9.4 1.0 O A:HOH2003 4.6 7.4 1.0 C A:GLY75 4.6 6.9 1.0 NH2 A:ARG89 4.7 10.9 1.0 CB A:LYS76 4.7 8.3 1.0 CZ A:ARG89 4.8 10.1 1.0 CA A:LYS76 4.8 7.5 1.0 OE2 A:GLU139 5.0 8.5 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