Zinc in PDB 3v4j: 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: 3v4j 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)	28.01 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.080, 67.764, 64.472, 90.00, 107.38, 90.00
R / Rfree (%)	22.8 / 27.6

The binding sites of Zinc atom in the First-in-Class Small Molecule Inhibitors of the Single-Strand Dna Cytosine Deaminase APOBEC3G (pdb code 3v4j). 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: 3v4j:
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:Zn401 b:58.5 occ:1.00 NE2 A:HIS250 2.1 63.3 1.0 ND1 A:HIS248 2.3 54.5 1.0 CE1 A:HIS250 3.0 65.3 1.0 CD2 A:HIS250 3.1 62.8 1.0 CE1 A:HIS248 3.3 57.1 1.0 CG A:HIS248 3.3 57.3 1.0 CB A:HIS248 3.6 56.2 1.0 O A:HOH555 4.1 53.9 1.0 ND1 A:HIS250 4.2 63.8 1.0 CG A:HIS250 4.2 66.0 1.0 NE2 A:HIS248 4.4 57.8 1.0 CD2 A:HIS248 4.4 59.9 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:Zn402 b:57.3 occ:1.00 ND1 A:HIS257 2.2 53.8 1.0 SG A:CYS288 2.2 60.8 1.0 SG A:CYS291 2.3 52.7 1.0 CB A:CYS291 3.1 52.6 1.0 CE1 A:HIS257 3.1 57.0 1.0 CG A:HIS257 3.2 55.0 1.0 CB A:CYS288 3.4 57.2 1.0 CB A:HIS257 3.5 54.5 1.0 OE2 A:GLU259 3.8 51.2 1.0 N A:CYS288 4.0 51.1 1.0 N A:CYS291 4.0 53.8 1.0 O A:HOH548 4.0 49.5 1.0 CA A:CYS291 4.1 53.4 1.0 CA A:CYS288 4.2 56.0 1.0 NE2 A:HIS257 4.3 58.3 1.0 CD2 A:HIS257 4.3 55.5 1.0 CD A:GLU259 4.5 53.1 1.0 O A:CYS288 4.6 51.3 1.0 C A:CYS288 4.6 57.0 1.0 OG A:SER290 4.6 56.0 0.5 O A:HOH505 4.9 48.5 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:Zn401 b:57.6 occ:1.00 NE2 B:HIS250 2.1 59.7 1.0 ND1 B:HIS248 2.2 55.2 1.0 CD2 B:HIS250 3.1 57.8 1.0 CE1 B:HIS250 3.1 59.0 1.0 CE1 B:HIS248 3.2 55.6 1.0 CG B:HIS248 3.2 53.1 1.0 CB B:HIS248 3.5 55.4 1.0 O B:HOH545 4.2 52.2 1.0 CG B:HIS250 4.3 56.7 1.0 ND1 B:HIS250 4.3 54.7 1.0 NE2 B:HIS248 4.3 53.5 1.0 CD2 B:HIS248 4.3 54.0 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:Zn402 b:61.0 occ:1.00 ND1 B:HIS257 2.1 57.4 1.0 SG B:CYS291 2.1 58.3 1.0 SG B:CYS288 2.3 59.7 1.0 CB B:CYS291 3.0 60.1 1.0 CG B:HIS257 3.1 55.2 1.0 CE1 B:HIS257 3.1 59.2 1.0 CB B:HIS257 3.4 55.0 1.0 CB B:CYS288 3.4 56.8 1.0 OE2 B:GLU259 3.7 53.5 1.0 N B:CYS291 3.9 58.8 1.0 O B:HOH544 4.0 56.6 1.0 CA B:CYS291 4.0 58.0 1.0 N B:CYS288 4.1 53.9 1.0 NE2 B:HIS257 4.2 57.4 1.0 CD2 B:HIS257 4.2 56.5 1.0 CA B:CYS288 4.3 54.6 1.0 CD B:GLU259 4.5 57.7 1.0 OG B:SER290 4.6 64.5 1.0 O B:CYS288 4.7 56.0 1.0 C B:CYS288 4.7 57.1 1.0 O B:HOH526 4.9 45.8 1.0 CA B:HIS257 4.9 52.1 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