Atomistry » Magnesium » PDB 2xbp-2xnd » 2xje
Atomistry »
  Magnesium »
    PDB 2xbp-2xnd »
      2xje »

Magnesium in PDB 2xje: Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Uridine 5'-Monophosphate and Adenosine Triphosphate

Enzymatic activity of Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Uridine 5'-Monophosphate and Adenosine Triphosphate

All present enzymatic activity of Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Uridine 5'-Monophosphate and Adenosine Triphosphate:
3.1.3.5;

Protein crystallography data

The structure of Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Uridine 5'-Monophosphate and Adenosine Triphosphate, PDB code: 2xje 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) 49.09 / 2.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 91.650, 127.610, 130.470, 90.00, 90.00, 90.00
R / Rfree (%) 21.471 / 26.905

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 Uridine 5'-Monophosphate and Adenosine Triphosphate (pdb code 2xje). 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 the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Uridine 5'-Monophosphate and Adenosine Triphosphate, PDB code: 2xje:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2xje

Go back to Magnesium Binding Sites List in 2xje
Magnesium binding site 1 out of 2 in the Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Uridine 5'-Monophosphate and Adenosine Triphosphate


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 Uridine 5'-Monophosphate and Adenosine Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1492

b:23.5
occ:0.50
O3G A:ATP1490 2.1 47.1 1.0
O1B A:ATP1490 2.1 46.6 1.0
O A:HOH2175 2.9 31.7 1.0
PB A:ATP1490 3.2 44.5 1.0
PG A:ATP1490 3.4 45.8 1.0
O3B A:ATP1490 3.7 44.4 1.0
O2B A:ATP1490 3.7 46.6 1.0
O1G A:ATP1490 4.3 45.4 1.0
O2G A:ATP1490 4.5 46.0 1.0
NH1 A:ARG456 4.5 31.4 1.0
O3A A:ATP1490 4.6 47.7 1.0
OH A:TYR457 4.6 23.4 1.0
NZ A:LYS362 4.7 40.2 1.0
O A:HOH2177 4.7 51.8 1.0

Magnesium binding site 2 out of 2 in 2xje

Go back to Magnesium Binding Sites List in 2xje
Magnesium binding site 2 out of 2 in the Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Uridine 5'-Monophosphate and Adenosine Triphosphate


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 the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Uridine 5'-Monophosphate and Adenosine Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1493

b:23.7
occ:1.00
O2P A:U5P1489 2.0 34.4 1.0
OD1 A:ASP351 2.1 24.0 1.0
O A:ASP54 2.2 23.7 1.0
OD1 A:ASN52 2.2 28.1 1.0
O A:HOH2140 2.3 20.5 1.0
O A:HOH2138 2.4 23.6 1.0
CG A:ASN52 2.9 25.5 1.0
ND2 A:ASN52 2.9 27.6 1.0
CG A:ASP351 3.1 24.0 1.0
C A:ASP54 3.3 23.2 1.0
OD2 A:ASP351 3.4 22.1 1.0
P A:U5P1489 3.4 36.2 1.0
O A:HOH2174 3.7 35.9 1.0
CA A:ASP54 4.0 24.8 1.0
N A:ASP54 4.0 22.8 1.0
O1P A:U5P1489 4.0 32.8 1.0
CB A:ASP54 4.1 25.3 1.0
OG1 A:THR56 4.2 25.8 1.0
O3P A:U5P1489 4.2 31.2 1.0
O A:HOH2171 4.2 23.0 1.0
OD2 A:ASP356 4.2 28.9 1.0
CB A:ASN52 4.3 23.7 1.0
N A:TYR55 4.4 23.6 1.0
CB A:ASP351 4.5 21.0 1.0
O5' A:U5P1489 4.5 40.8 1.0
C A:MET53 4.6 23.3 1.0
CB A:TYR55 4.8 23.6 1.0
C5' A:U5P1489 4.8 45.7 1.0
N A:ASP351 4.8 21.5 1.0
N A:MET53 4.8 23.1 1.0
N A:THR56 4.9 23.3 1.0
CA A:TYR55 4.9 23.3 1.0
C A:TYR55 4.9 23.7 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: Wed Aug 14 07:11:28 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy