Zinc 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:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the First-in-Class Small Molecule Inhibitors of the Single-Strand Dna Cytosine Deaminase APOBEC3G, PDB code: 3v4k:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn382 b:17.6 occ:1.00 O A:HOH506 2.0 22.2 1.0 ND1 A:HIS248 2.0 19.2 1.0 NE2 A:HIS250 2.0 20.2 1.0 CE1 A:HIS248 2.9 21.8 1.0 CE1 A:HIS250 3.0 20.8 1.0 CD2 A:HIS250 3.0 19.4 1.0 CG A:HIS248 3.1 18.6 1.0 CB A:HIS248 3.6 19.0 1.0 NE2 A:HIS248 4.0 22.6 1.0 ND1 A:HIS250 4.1 21.6 1.0 CD2 A:HIS248 4.1 20.3 1.0 CG A:HIS250 4.2 21.1 1.0 O A:HOH402 4.7 29.4 1.0

Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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 A:Zn2 b:17.8 occ:1.00 O A:HOH90 1.9 17.1 1.0 ND1 A:HIS257 2.0 19.1 1.0 SG A:CYS291 2.3 20.1 1.0 SG A:CYS288 2.3 19.0 1.0 CE1 A:HIS257 2.9 21.1 1.0 CG A:HIS257 3.1 18.2 1.0 CB A:CYS291 3.1 18.4 1.0 CB A:CYS288 3.4 17.9 1.0 CB A:HIS257 3.4 16.3 1.0 O A:HOH147 3.8 24.1 1.0 OE2 A:GLU259 3.9 18.8 1.0 N A:CYS288 4.0 15.5 1.0 O A:HOH507 4.0 30.0 1.0 N A:CYS291 4.0 18.2 1.0 NE2 A:HIS257 4.1 20.4 1.0 CA A:CYS291 4.1 18.6 1.0 CD2 A:HIS257 4.2 19.1 1.0 CA A:CYS288 4.2 15.6 1.0 CD A:GLU259 4.5 17.7 1.0 O A:HOH495 4.5 33.3 1.0 OG A:SER290 4.6 27.8 1.0 C A:CYS288 4.7 16.6 1.0 O A:CYS288 4.7 16.0 1.0 O A:HOH430 4.9 37.2 1.0 CA A:HIS257 4.9 15.1 1.0 OE1 A:GLU259 5.0 20.5 1.0 O A:HOH20 5.0 16.4 1.0

Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn binding site number 3 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:Zn3 b:16.7 occ:1.00 O B:HOH497 1.9 20.1 1.0 ND1 B:HIS248 2.0 18.1 1.0 NE2 B:HIS250 2.0 18.8 1.0 CE1 B:HIS248 2.9 19.4 1.0 CE1 B:HIS250 3.0 20.8 1.0 CD2 B:HIS250 3.0 20.5 1.0 CG B:HIS248 3.1 17.7 1.0 CB B:HIS248 3.6 17.8 1.0 O B:HOH430 4.0 31.0 1.0 NE2 B:HIS248 4.0 19.0 1.0 ND1 B:HIS250 4.1 21.8 1.0 CD2 B:HIS248 4.2 18.3 1.0 CG B:HIS250 4.2 21.6 1.0 O B:HOH475 4.8 26.2 1.0

Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn binding site number 4 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:Zn4 b:16.4 occ:1.00 O B:HOH140 2.0 17.9 1.0 ND1 B:HIS257 2.0 16.6 1.0 SG B:CYS288 2.3 17.0 1.0 SG B:CYS291 2.3 18.4 1.0 CE1 B:HIS257 3.0 18.7 1.0 CG B:HIS257 3.1 17.3 1.0 CB B:CYS291 3.1 16.7 1.0 CB B:CYS288 3.4 15.2 1.0 CB B:HIS257 3.5 15.9 1.0 O B:HOH144 3.8 21.9 1.0 O B:HOH411 3.9 29.3 1.0 N B:CYS288 4.0 13.8 1.0 OE2 B:GLU259 4.0 18.0 1.0 N B:CYS291 4.0 16.9 1.0 NE2 B:HIS257 4.1 20.0 1.0 CA B:CYS291 4.2 16.2 1.0 CA B:CYS288 4.2 14.4 1.0 CD2 B:HIS257 4.2 18.8 1.0 CD B:GLU259 4.6 16.8 1.0 O B:HOH498 4.6 33.9 1.0 OG B:SER290 4.6 24.9 1.0 C B:CYS288 4.6 14.4 1.0 O B:CYS288 4.7 13.8 1.0 O B:HOH19 4.9 15.0 1.0 OE1 B:GLU259 5.0 18.8 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