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Magnesium in PDB 2vp0: Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase

Enzymatic activity of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase

All present enzymatic activity of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase:
2.7.1.145;

Protein crystallography data

The structure of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase, PDB code: 2vp0 was solved by N.E.Mikkelsen, B.Munch-Petersen, H.Eklund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.041, 64.978, 69.109, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase (pdb code 2vp0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase, PDB code: 2vp0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2vp0

Go back to Magnesium Binding Sites List in 2vp0
Magnesium binding site 1 out of 2 in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1209

b:29.6
occ:1.00
 O A:HOH2007 2.1 30.9 1.0
O2G A:TTP1210 2.1 23.8 1.0
OG1 A:THR34 2.2 29.4 1.0
O1B A:TTP1210 2.2 23.2 1.0
OE2 A:GLU52 2.4 33.5 1.0
OE2 A:GLU104 2.4 26.8 1.0
PG A:TTP1210 3.3 24.8 1.0
CB A:THR34 3.3 28.4 1.0
CD A:GLU52 3.3 34.9 1.0
CD A:GLU104 3.3 26.2 1.0
PB A:TTP1210 3.3 22.4 1.0
O3B A:TTP1210 3.5 24.2 1.0
OE1 A:GLU104 3.5 24.9 1.0
OE1 A:GLU52 3.7 36.3 1.0
O A:HOH2008 3.7 29.2 1.0
N A:THR34 3.9 26.5 1.0
O3A A:TTP1210 3.9 24.0 1.0
O3G A:TTP1210 4.1 26.1 1.0
NH2 A:ARG169 4.1 23.3 1.0
CA A:THR34 4.2 28.1 1.0
O A:HOH2071 4.2 27.3 1.0
O1G A:TTP1210 4.4 24.1 1.0
CG2 A:THR34 4.4 27.8 1.0
O A:HOH2073 4.5 26.7 1.0
O2B A:TTP1210 4.6 25.0 1.0
CG A:GLU52 4.6 31.1 1.0
CA A:GLU52 4.7 28.5 1.0
CG A:GLU104 4.7 23.9 1.0
CB A:GLU52 4.8 28.8 1.0
NH1 A:ARG167 4.9 26.2 1.0
CB A:LYS33 4.9 24.6 1.0
C A:LYS33 4.9 25.7 1.0

Magnesium binding site 2 out of 2 in 2vp0

Go back to Magnesium Binding Sites List in 2vp0
Magnesium binding site 2 out of 2 in the Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1209

b:47.9
occ:1.00
 O1B B:TTP1210 1.9 32.0 1.0
OE1 B:GLU52 2.1 43.4 1.0
OG1 B:THR34 2.1 44.6 1.0
O3G B:TTP1210 2.2 35.9 1.0
OE2 B:GLU104 2.4 33.6 1.0
PB B:TTP1210 3.0 32.0 1.0
PG B:TTP1210 3.1 33.9 1.0
O3B B:TTP1210 3.2 34.7 1.0
CD B:GLU52 3.3 43.4 1.0
CB B:THR34 3.3 43.5 1.0
CD B:GLU104 3.4 33.8 1.0
O B:HOH2005 3.7 26.3 1.0
O3A B:TTP1210 3.7 32.2 1.0
OE1 B:GLU104 3.7 33.5 1.0
OE2 B:GLU52 3.7 45.2 1.0
O1G B:TTP1210 3.9 34.1 1.0
NH2 B:ARG169 3.9 26.6 1.0
N B:THR34 4.0 42.7 1.0
O B:HOH2049 4.2 32.5 1.0
O2B B:TTP1210 4.2 32.1 1.0
CA B:THR34 4.2 43.8 1.0
CG2 B:THR34 4.3 43.7 1.0
O2G B:TTP1210 4.4 35.2 1.0
O B:HOH2050 4.4 36.7 1.0
NH1 B:ARG167 4.5 32.5 1.0
CG B:GLU52 4.5 40.0 1.0
CG B:GLU104 4.8 33.3 1.0
CA B:GLU52 4.8 37.1 1.0
CB B:LYS33 4.9 40.9 1.0
CB B:GLU52 4.9 37.6 1.0

Reference:

N.E.Mikkelsen, B.Munch-Petersen, H.Eklund. Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase. Febs J. V. 275 2151 2008.
ISSN: ISSN 1742-464X
PubMed: 18384378
DOI: 10.1111/J.1742-4658.2008.06369.X
Page generated: Mon Dec 14 07:42:27 2020

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