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Magnesium in PDB 1del: Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp and Amp

Enzymatic activity of Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp and Amp

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

Protein crystallography data

The structure of Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp and Amp, PDB code: 1del 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 / 2.20
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 (%) 18.6 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp and Amp (pdb code 1del). 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 and Amp, PDB code: 1del:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1del

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


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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg300

b:51.4
occ:1.00
OE1 A:GLN85 2.4 31.0 1.0
OE1 A:GLU108 2.4 60.2 1.0
OH A:TYR42 2.6 46.0 1.0
CD A:GLU108 3.5 50.8 1.0
CB A:GLU108 3.5 41.9 1.0
CD A:GLN85 3.6 29.9 1.0
CB A:CYS88 3.6 21.1 1.0
O A:HOH360 3.6 46.6 1.0
CZ A:TYR42 3.6 36.6 1.0
CE1 A:TYR42 3.8 26.6 1.0
CG A:GLU108 3.9 45.1 1.0
NE2 A:GLN85 4.3 22.7 1.0
O A:HOH401 4.3 33.4 0.5
O A:GLN85 4.5 21.5 1.0
SG A:CYS88 4.5 32.9 1.0
OE2 A:GLU108 4.5 63.7 1.0
CG A:GLN85 4.6 22.1 1.0
CA A:GLU108 4.6 44.5 1.0
N A:GLU108 4.7 55.2 1.0
CB A:GLN85 4.8 27.3 1.0
CA A:GLN85 4.8 22.0 1.0
CE2 A:TYR42 4.9 31.5 1.0
CA A:CYS88 4.9 22.6 1.0

Magnesium binding site 2 out of 2 in 1del

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


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 and Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg300

b:43.5
occ:0.50
OH B:TYR42 2.4 40.1 1.0
OE2 B:GLU108 2.4 73.9 1.0
OE1 B:GLN85 2.5 39.5 1.0
CG B:GLU108 3.1 72.8 1.0
CD B:GLU108 3.1 73.9 1.0
CZ B:TYR42 3.1 35.0 1.0
CE2 B:TYR42 3.1 31.5 1.0
CB B:CYS88 3.6 34.6 1.0
CD B:GLN85 3.6 40.0 1.0
O B:HOH382 3.7 33.9 0.5
O B:GLN85 4.0 35.1 1.0
O B:HOH385 4.2 35.1 0.5
NE2 B:GLN85 4.3 35.2 1.0
OE1 B:GLU108 4.3 76.8 1.0
CE1 B:TYR42 4.5 35.1 1.0
CD2 B:TYR42 4.5 27.3 1.0
CB B:GLU108 4.5 65.5 1.0
SG B:CYS88 4.6 38.4 1.0
N B:TYR89 4.6 25.6 1.0
CG B:GLN85 4.7 38.6 1.0
C B:CYS88 4.7 30.9 1.0
CA B:CYS88 4.7 32.1 1.0
CA B:GLN85 4.8 31.4 1.0
C B:GLN85 4.8 34.8 1.0
CB B:GLN85 4.8 36.3 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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