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Magnesium in PDB 2jao: Crystal Structure of D12N Variant of Mouse Cytosolic 5'(3')- Deoxyribonucleotidase (Cdn) in Complex with Deoxyguanosine 5'- Monophosphate

Protein crystallography data

The structure of Crystal Structure of D12N Variant of Mouse Cytosolic 5'(3')- Deoxyribonucleotidase (Cdn) in Complex with Deoxyguanosine 5'- Monophosphate, PDB code: 2jao was solved by K.Wallden, B.Ruzzenente, V.Bianchi, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.08 / 2.00
Space group P 62
Cell size a, b, c (Å), α, β, γ (°) 76.250, 76.250, 85.760, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of D12N Variant of Mouse Cytosolic 5'(3')- Deoxyribonucleotidase (Cdn) in Complex with Deoxyguanosine 5'- Monophosphate (pdb code 2jao). 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 D12N Variant of Mouse Cytosolic 5'(3')- Deoxyribonucleotidase (Cdn) in Complex with Deoxyguanosine 5'- Monophosphate, PDB code: 2jao:

Magnesium binding site 1 out of 1 in 2jao

Go back to Magnesium Binding Sites List in 2jao
Magnesium binding site 1 out of 1 in the Crystal Structure of D12N Variant of Mouse Cytosolic 5'(3')- Deoxyribonucleotidase (Cdn) in Complex with Deoxyguanosine 5'- Monophosphate


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 D12N Variant of Mouse Cytosolic 5'(3')- Deoxyribonucleotidase (Cdn) in Complex with Deoxyguanosine 5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1202

b:21.5
occ:1.00
OP3 A:DGP1201 1.9 23.5 0.5
O A:HOH2174 2.1 23.8 1.0
OD1 A:ASN12 2.2 18.5 1.0
O A:HOH2175 2.2 20.9 1.0
OP3 A:DGP1201 2.2 21.8 0.5
OD1 A:ASP147 2.2 24.1 1.0
O A:ASP14 2.2 19.6 1.0
CG A:ASN12 3.2 19.9 1.0
CG A:ASP147 3.2 21.9 1.0
P A:DGP1201 3.3 22.4 0.5
C A:ASP14 3.3 19.4 1.0
OD2 A:ASP147 3.6 22.7 1.0
P A:DGP1201 3.6 22.6 0.5
OP2 A:DGP1201 3.7 22.4 0.5
ND2 A:ASN12 3.7 17.2 1.0
OD1 A:ASP146 4.0 19.8 1.0
O A:HOH2173 4.0 14.8 0.5
CA A:ASP14 4.0 20.0 1.0
O A:HOH2172 4.1 13.7 0.5
CB A:ASP14 4.1 20.0 1.0
OP1 A:DGP1201 4.1 20.7 0.5
N A:ASP14 4.1 18.7 1.0
OP2 A:DGP1201 4.2 20.9 0.5
O A:HOH2169 4.3 46.3 1.0
N A:GLY15 4.3 19.4 1.0
O5' A:DGP1201 4.4 22.8 0.5
CB A:ASN12 4.5 17.9 1.0
N A:ASP147 4.5 18.8 1.0
OP1 A:DGP1201 4.5 22.0 0.5
CE1 A:PHE46 4.6 27.0 1.0
CA A:GLY15 4.6 18.2 1.0
CB A:ASP147 4.6 20.1 1.0
O5' A:DGP1201 4.7 24.9 0.5
CZ A:PHE46 4.7 27.9 1.0
C5' A:DGP1201 4.7 29.1 1.0
CG A:ASP146 4.8 21.2 1.0
O A:HOH2121 4.8 31.3 1.0
C A:MET13 4.9 19.8 1.0
N A:LYS148 4.9 23.1 1.0
CA A:ASP147 5.0 20.8 1.0

Reference:

K.Wallden, A.Rinaldo-Matthis, B.Ruzzenente, C.Rampazzo, V.Bianchi, P.Nordlund. Crystal Structures of Human and Murine Deoxyribonucleotidases: Insights Into Recognition of Substrates and Nucleotide Analogues. Biochemistry V. 46 13809 2007.
ISSN: ISSN 0006-2960
PubMed: 17985935
DOI: 10.1021/BI7014794
Page generated: Mon Dec 14 07:29:08 2020

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