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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: Mon Dec 14 07:46:50 2020

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