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

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

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

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 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 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

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