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Magnesium in PDB 1dek: Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp

Enzymatic activity of Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp

All present enzymatic activity of Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp:
2.7.4.13;

Protein crystallography data

The structure of Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp, PDB code: 1dek was solved by A.Teplyakov, P.Sebastiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 155.200, 58.500, 75.700, 90.00, 108.10, 90.00
R / Rfree (%) 18.7 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp (pdb code 1dek). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp, PDB code: 1dek:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1dek

Go back to Magnesium Binding Sites List in 1dek
Magnesium binding site 1 out of 2 in the Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg300

b:44.1
occ:1.00
OE1 A:GLU108 2.5 44.7 1.0
OH A:TYR42 2.6 35.8 1.0
OE1 A:GLN85 2.7 31.4 1.0
CD A:GLU108 3.4 48.7 1.0
CB A:GLU108 3.5 38.5 1.0
CZ A:TYR42 3.6 29.0 1.0
CB A:CYS88 3.6 26.4 1.0
CE2 A:TYR42 3.7 23.7 1.0
O A:HOH425 3.8 57.1 1.0
CG A:GLU108 3.9 40.4 1.0
CD A:GLN85 3.9 23.4 1.0
OE2 A:GLU108 4.5 60.0 1.0
O A:GLN85 4.5 16.2 1.0
SG A:CYS88 4.6 31.3 1.0
NE2 A:GLN85 4.6 26.6 1.0
CA A:GLU108 4.8 42.7 1.0
CE1 A:TYR42 4.8 25.0 1.0
CG A:GLN85 4.9 21.3 1.0
CA A:GLN85 4.9 21.0 1.0
N A:GLU108 4.9 53.5 1.0
CA A:CYS88 4.9 23.2 1.0
CB A:GLN85 5.0 21.2 1.0
N A:TYR89 5.0 19.9 1.0
C A:CYS88 5.0 21.1 1.0

Magnesium binding site 2 out of 2 in 1dek

Go back to Magnesium Binding Sites List in 1dek
Magnesium binding site 2 out of 2 in the Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg300

b:37.5
occ:0.50
OE2 B:GLU108 2.3 71.4 1.0
OH B:TYR42 2.3 41.0 1.0
OE1 B:GLN85 2.5 40.8 1.0
CE2 B:TYR42 2.9 33.8 1.0
CZ B:TYR42 3.0 38.6 1.0
CD B:GLU108 3.3 79.4 1.0
O B:HOH378 3.5 52.3 1.0
CG B:GLU108 3.5 73.7 1.0
CD B:GLN85 3.6 36.0 1.0
CB B:CYS88 3.7 33.0 1.0
O B:GLN85 3.8 32.5 1.0
CD2 B:TYR42 4.2 30.6 1.0
NE2 B:GLN85 4.3 37.1 1.0
CE1 B:TYR42 4.3 36.0 1.0
OE1 B:GLU108 4.4 79.0 1.0
CA B:GLN85 4.5 26.3 1.0
CB B:GLN85 4.6 28.1 1.0
C B:GLN85 4.6 27.3 1.0
CG B:GLN85 4.7 35.2 1.0
N B:TYR89 4.7 23.0 1.0
SG B:CYS88 4.7 36.6 1.0
C B:CYS88 4.9 29.4 1.0
CA B:CYS88 4.9 27.7 1.0

Reference:

A.Teplyakov, P.Sebastiao, G.Obmolova, A.Perrakis, G.S.Brush, M.J.Bessman, K.S.Wilson. Crystal Structure of Bacteriophage T4 Deoxynucleotide Kinase with Its Substrates Dgmp and Atp. Embo J. V. 15 3487 1996.
ISSN: ISSN 0261-4189
PubMed: 8670851
Page generated: Mon Dec 14 05:50:24 2020

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