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Magnesium in PDB 3v4k: First-in-Class Small Molecule Inhibitors of the Single-Strand Dna Cytosine Deaminase APOBEC3G

Protein crystallography data

The structure of First-in-Class Small Molecule Inhibitors of the Single-Strand Dna Cytosine Deaminase APOBEC3G, PDB code: 3v4k was solved by S.M.D.Shandilya, A.Ali, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.75 / 1.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.190, 72.170, 96.810, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.5

Other elements in 3v4k:

The structure of First-in-Class Small Molecule Inhibitors of the Single-Strand Dna Cytosine Deaminase APOBEC3G also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the First-in-Class Small Molecule Inhibitors of the Single-Strand Dna Cytosine Deaminase APOBEC3G (pdb code 3v4k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the First-in-Class Small Molecule Inhibitors of the Single-Strand Dna Cytosine Deaminase APOBEC3G, PDB code: 3v4k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3v4k

Go back to Magnesium Binding Sites List in 3v4k
Magnesium binding site 1 out of 2 in the First-in-Class Small Molecule Inhibitors of the Single-Strand Dna Cytosine Deaminase APOBEC3G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of First-in-Class Small Molecule Inhibitors of the Single-Strand Dna Cytosine Deaminase APOBEC3G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg381

b:15.2
occ:1.00
OE1 A:GLU209 2.0 16.5 1.0
O A:HOH71 2.0 18.1 1.0
O A:HOH67 2.1 16.3 1.0
NE2 A:HIS367 2.1 15.9 1.0
O A:HOH504 2.1 17.6 1.0
O A:HOH503 2.2 17.4 1.0
CE1 A:HIS367 3.0 14.9 1.0
CD A:GLU209 3.1 16.3 1.0
CD2 A:HIS367 3.2 15.4 1.0
OE2 A:GLU209 3.5 16.8 1.0
ND1 A:HIS367 4.1 14.1 1.0
O A:HOH170 4.2 32.2 1.0
CG A:HIS367 4.3 14.3 1.0
CG A:GLU209 4.4 15.6 1.0
CD A:PRO210 4.6 16.1 1.0
CB A:GLU209 4.8 14.4 1.0
CA A:GLY363 4.9 14.0 1.0
CA A:GLU209 4.9 13.8 1.0

Magnesium binding site 2 out of 2 in 3v4k

Go back to Magnesium Binding Sites List in 3v4k
Magnesium binding site 2 out of 2 in the First-in-Class Small Molecule Inhibitors of the Single-Strand Dna Cytosine Deaminase APOBEC3G


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of First-in-Class Small Molecule Inhibitors of the Single-Strand Dna Cytosine Deaminase APOBEC3G within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg381

b:28.9
occ:1.00
O B:HOH433 1.9 22.0 1.0
O B:HOH464 1.9 28.3 1.0
O B:HOH163 2.1 28.9 1.0
O B:HOH108 2.1 23.2 1.0
NE2 B:HIS367 2.3 19.9 1.0
OE1 B:GLU209 2.3 37.4 1.0
CE1 B:HIS367 3.0 20.0 1.0
CD B:GLU209 3.1 31.4 1.0
OE2 B:GLU209 3.2 34.5 1.0
CD2 B:HIS367 3.3 18.4 1.0
CD B:PRO210 3.5 22.0 1.0
CG B:PRO210 3.8 24.1 1.0
ND1 B:HIS367 4.1 17.8 1.0
CG B:HIS367 4.3 16.6 1.0
CG B:GLU209 4.6 25.5 1.0
N B:PRO210 4.7 20.5 1.0

Reference:

M.Li, S.M.Shandilya, M.A.Carpenter, A.Rathore, W.L.Brown, A.L.Perkins, D.A.Harki, J.Solberg, D.J.Hook, K.K.Pandey, M.A.Parniak, J.R.Johnson, N.J.Krogan, M.Somasundaran, A.Ali, C.A.Schiffer, R.S.Harris. First-in-Class Small Molecule Inhibitors of the Single-Strand Dna Cytosine Deaminase APOBEC3G. Acs Chem.Biol. V. 7 506 2012.
ISSN: ISSN 1554-8929
PubMed: 22181350
DOI: 10.1021/CB200440Y
Page generated: Mon Dec 14 08:57:52 2020

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