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Magnesium in PDB 2xcv: Crystal Structure of the D52N Variant of Cytosolic 5'- Nucleotidase II in Complex with Inosine Monophosphate and 2,3-Bisphosphoglycerate

Enzymatic activity of Crystal Structure of the D52N Variant of Cytosolic 5'- Nucleotidase II in Complex with Inosine Monophosphate and 2,3-Bisphosphoglycerate

All present enzymatic activity of Crystal Structure of the D52N Variant of Cytosolic 5'- Nucleotidase II in Complex with Inosine Monophosphate and 2,3-Bisphosphoglycerate:
3.1.3.5;

Protein crystallography data

The structure of Crystal Structure of the D52N Variant of Cytosolic 5'- Nucleotidase II in Complex with Inosine Monophosphate and 2,3-Bisphosphoglycerate, PDB code: 2xcv was solved by K.Wallden, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.68 / 2.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 91.570, 127.790, 130.610, 90.00, 90.00, 90.00
R / Rfree (%) 17.627 / 22.868

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the D52N Variant of Cytosolic 5'- Nucleotidase II in Complex with Inosine Monophosphate and 2,3-Bisphosphoglycerate (pdb code 2xcv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the D52N Variant of Cytosolic 5'- Nucleotidase II in Complex with Inosine Monophosphate and 2,3-Bisphosphoglycerate, PDB code: 2xcv:

Magnesium binding site 1 out of 1 in 2xcv

Go back to Magnesium Binding Sites List in 2xcv
Magnesium binding site 1 out of 1 in the Crystal Structure of the D52N Variant of Cytosolic 5'- Nucleotidase II in Complex with Inosine Monophosphate and 2,3-Bisphosphoglycerate


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 the D52N Variant of Cytosolic 5'- Nucleotidase II in Complex with Inosine Monophosphate and 2,3-Bisphosphoglycerate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1492

b:22.6
occ:1.00
 O2P A:IMP1491 1.9 27.4 1.0
O A:ASP54 2.1 26.0 1.0
OD1 A:ASP351 2.1 21.4 1.0
ND2 A:ASN52 2.2 28.4 1.0
O A:HOH2215 2.2 22.1 1.0
O A:HOH2218 2.2 14.8 1.0
CG A:ASP351 3.1 24.2 1.0
CG A:ASN52 3.1 28.4 1.0
C A:ASP54 3.3 26.7 1.0
OD2 A:ASP351 3.3 26.2 1.0
P A:IMP1491 3.4 36.3 1.0
OD1 A:ASN52 3.5 34.7 1.0
O A:HOH2257 3.7 41.3 1.0
CA A:ASP54 3.9 26.4 1.0
O1P A:IMP1491 4.0 29.2 1.0
CB A:ASP54 4.0 27.4 1.0
N A:ASP54 4.0 24.2 1.0
O3P A:IMP1491 4.1 30.9 1.0
OD2 A:ASP356 4.1 29.3 1.0
O A:HOH2028 4.3 30.2 1.0
OG1 A:THR56 4.3 28.5 1.0
O5' A:IMP1491 4.4 33.5 1.0
N A:TYR55 4.4 25.9 1.0
CB A:ASN52 4.4 26.6 1.0
CB A:ASP351 4.5 22.7 1.0
CB A:TYR55 4.7 25.5 1.0
C A:MET53 4.7 23.9 1.0
N A:ASP351 4.8 22.4 1.0
CA A:TYR55 4.9 25.7 1.0
N A:THR56 4.9 25.6 1.0
C5' A:IMP1491 4.9 30.7 1.0
N A:MET53 4.9 23.2 1.0
C A:TYR55 5.0 26.1 1.0
CE2 A:PHE157 5.0 23.1 1.0

Reference:

K.Wallden, P.Nordlund. Structural Basis For the Allosteric Regulation and Substrate Recognition of Human Cytosolic 5'-Nucleotidase II J.Mol.Biol. V. 408 684 2011.
ISSN: ISSN 0022-2836
PubMed: 21396942
DOI: 10.1016/J.JMB.2011.02.059
Page generated: Sun Aug 10 16:23:40 2025

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