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Magnesium in PDB 2xjb: Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Deoxyguanosine Monophosphate and Deoxyadenosine Triphosphate

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

All present enzymatic activity of Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Deoxyguanosine Monophosphate and Deoxyadenosine 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 Deoxyguanosine Monophosphate and Deoxyadenosine Triphosphate, PDB code: 2xjb 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 (°) 91.550, 127.430, 130.500, 90.00, 90.00, 90.00
R / Rfree (%) 17.502 / 22.18

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 Deoxyguanosine Monophosphate and Deoxyadenosine Triphosphate (pdb code 2xjb). 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 Deoxyguanosine Monophosphate and Deoxyadenosine Triphosphate, PDB code: 2xjb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2xjb

Go back to Magnesium Binding Sites List in 2xjb
Magnesium binding site 1 out of 2 in the Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Deoxyguanosine Monophosphate and Deoxyadenosine 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 Deoxyguanosine Monophosphate and Deoxyadenosine Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1494

b:31.8
occ:1.00
OP1 A:DG1491 1.9 28.9 1.0
OD1 A:ASN52 2.0 33.3 1.0
OD1 A:ASP351 2.1 27.4 1.0
O A:ASP54 2.2 27.7 1.0
O A:HOH2213 2.2 22.5 1.0
O A:HOH2216 2.3 21.4 1.0
CG A:ASP351 3.1 28.2 1.0
CG A:ASN52 3.1 31.9 1.0
OD2 A:ASP351 3.3 29.1 1.0
C A:ASP54 3.3 27.5 1.0
P A:DG1491 3.5 37.3 1.0
ND2 A:ASN52 3.6 35.9 1.0
O A:HOH2263 3.7 35.6 1.0
CA A:ASP54 4.0 29.1 1.0
CB A:ASP54 4.1 29.5 1.0
N A:ASP54 4.1 28.1 1.0
OG1 A:THR56 4.1 25.6 1.0
OP2 A:DG1491 4.2 32.4 1.0
OD2 A:ASP356 4.2 24.2 1.0
OP3 A:DG1491 4.2 30.1 1.0
O A:HOH2080 4.2 24.8 1.0
CB A:ASN52 4.3 29.0 1.0
O5' A:DG1491 4.4 34.6 1.0
N A:TYR55 4.4 27.2 1.0
CB A:ASP351 4.5 25.8 1.0
CB A:TYR55 4.5 25.1 1.0
N A:ASP351 4.7 25.2 1.0
CA A:TYR55 4.8 26.1 1.0
C A:MET53 4.8 28.2 1.0
N A:THR56 4.8 26.4 1.0
C5' A:DG1491 4.8 34.7 1.0
C A:TYR55 4.8 26.7 1.0
CE2 A:PHE157 4.9 28.6 1.0

Magnesium binding site 2 out of 2 in 2xjb

Go back to Magnesium Binding Sites List in 2xjb
Magnesium binding site 2 out of 2 in the Crystal Structure of the D52N Variant of Cytosolic 5'-Nucleotidase II in Complex with Deoxyguanosine Monophosphate and Deoxyadenosine 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 Deoxyguanosine Monophosphate and Deoxyadenosine Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1495

b:36.0
occ:0.50
O2G A:DTP1490 2.1 49.2 1.0
O1B A:DTP1490 2.3 52.5 1.0
O A:HOH2255 2.4 49.4 1.0
PB A:DTP1490 3.0 46.9 1.0
O2B A:DTP1490 3.3 50.4 1.0
PG A:DTP1490 3.3 48.8 1.0
O3B A:DTP1490 3.4 46.5 1.0
O A:HOH2251 4.2 59.5 1.0
O A:HOH2254 4.3 47.0 0.5
O3G A:DTP1490 4.3 47.7 1.0
O1G A:DTP1490 4.4 49.8 1.0
O3A A:DTP1490 4.4 52.8 1.0
OH A:TYR457 4.4 33.0 1.0
O A:HOH2256 4.5 41.0 1.0
NH1 A:ARG456 4.5 49.8 1.0
NZ A:LYS362 4.7 50.1 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: Wed Aug 14 07:10:32 2024

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