Zinc in PDB 5sxg: Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B

The structure of Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B, PDB code: 5sxg was solved by K.Shi, K.Kurahashi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.48 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.390, 50.800, 76.890, 90.00, 102.86, 90.00
R / Rfree (%)	17.7 / 21

The binding sites of Zinc atom in the Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B (pdb code 5sxg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B, PDB code: 5sxg:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:18.9 occ:1.00 ND1 A:HIS253 2.1 19.6 1.0 SG A:CYS289 2.2 19.6 1.0 O A:HOH503 2.2 20.8 1.0 SG A:CYS284 2.3 19.2 1.0 HB2 A:CYS289 2.8 24.1 1.0 CE1 A:HIS253 3.0 20.1 1.0 H A:CYS284 3.0 18.9 1.0 CB A:CYS289 3.1 20.1 1.0 HB3 A:CYS284 3.1 21.9 1.0 HE1 A:HIS253 3.1 24.1 1.0 CG A:HIS253 3.1 19.9 1.0 CB A:CYS284 3.3 18.3 1.0 HB3 A:HIS253 3.4 22.2 1.0 HB2 A:HIS253 3.4 22.2 1.0 CB A:HIS253 3.5 18.5 1.0 HB2 A:TRP287 3.6 28.7 1.0 H21 A:PDO402 3.6 62.2 1.0 HB3 A:CYS289 3.6 24.1 1.0 H A:CYS289 3.7 30.3 1.0 H22 A:PDO402 3.7 62.2 1.0 O A:HOH557 3.8 28.1 1.0 N A:CYS284 3.8 15.7 1.0 OE2 A:GLU255 3.9 19.3 1.0 O3 A:PDO402 4.0 52.1 1.0 CA A:CYS284 4.1 17.6 1.0 HB2 A:CYS284 4.1 21.9 1.0 C2 A:PDO402 4.1 51.8 1.0 NE2 A:HIS253 4.1 21.2 1.0 CD2 A:HIS253 4.2 20.1 1.0 CA A:CYS289 4.2 22.1 1.0 N A:CYS289 4.3 25.2 1.0 CD A:GLU255 4.3 19.1 1.0 OE1 A:GLU255 4.3 17.4 1.0 O A:HOH510 4.3 29.8 1.0 CB A:TRP287 4.5 23.9 1.0 HA A:CYS289 4.6 26.4 1.0 HO3 A:PDO402 4.6 62.5 1.0 HA A:PRO283 4.6 23.6 1.0 HB3 A:TRP287 4.6 28.7 1.0 O A:CYS284 4.6 21.1 1.0 C A:CYS284 4.7 19.9 1.0 C3 A:PDO402 4.7 52.4 1.0 HE3 A:TRP287 4.7 26.2 1.0 HB2 A:GLU255 4.8 20.4 1.0 H A:TRP287 4.8 29.5 1.0 HA A:CYS284 4.9 21.1 1.0 HE2 A:HIS253 4.9 25.4 1.0 C A:PRO283 4.9 19.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:24.4 occ:1.00 ND1 B:HIS253 2.0 32.1 1.0 SG B:CYS289 2.2 22.4 1.0 O B:HOH509 2.2 23.1 1.0 SG B:CYS284 2.3 28.1 1.0 HB2 B:CYS289 2.8 28.0 1.0 CE1 B:HIS253 2.9 39.7 1.0 H B:CYS284 3.0 20.6 1.0 HE1 B:HIS253 3.0 47.6 1.0 CB B:CYS289 3.1 23.4 1.0 CG B:HIS253 3.1 31.1 1.0 HB3 B:CYS284 3.3 27.2 1.0 HB3 B:HIS253 3.4 29.0 1.0 HB2 B:HIS253 3.4 29.0 1.0 CB B:CYS284 3.4 22.7 1.0 HO1 B:PDO402 3.5 47.7 1.0 CB B:HIS253 3.5 24.2 1.0 H B:CYS289 3.6 42.3 1.0 HB3 B:CYS289 3.6 28.0 1.0 H22 B:PDO402 3.7 56.6 1.0 N B:CYS284 3.8 17.2 1.0 HB2 B:TRP287 3.8 44.4 1.0 H21 B:PDO402 4.0 56.6 1.0 OE2 B:GLU255 4.0 24.9 1.0 NE2 B:HIS253 4.1 42.4 1.0 CA B:CYS284 4.1 21.2 1.0 O1 B:PDO402 4.2 39.8 1.0 CD2 B:HIS253 4.2 37.1 1.0 HB2 B:CYS284 4.2 27.2 1.0 N B:CYS289 4.2 35.3 1.0 CA B:CYS289 4.2 30.2 1.0 C2 B:PDO402 4.2 47.2 1.0 O B:HOH541 4.3 38.2 1.0 CD B:GLU255 4.4 22.6 1.0 OE1 B:GLU255 4.4 23.4 1.0 HA B:PRO283 4.6 28.6 1.0 O B:CYS284 4.6 26.1 1.0 HA B:CYS289 4.6 36.3 1.0 C B:CYS284 4.6 25.4 1.0 CB B:TRP287 4.7 37.0 1.0 HE3 B:TRP287 4.7 35.9 1.0 HB3 B:TRP287 4.8 44.4 1.0 HE2 B:HIS253 4.8 50.8 1.0 HB2 B:GLU255 4.8 28.5 1.0 C1 B:PDO402 4.9 44.1 1.0 C B:PRO283 5.0 26.0 1.0 O B:TRP287 5.0 40.3 1.0 HA B:CYS284 5.0 25.4 1.0

K.Shi, O.Demir, M.A.Carpenter, J.Wagner, K.Kurahashi, R.S.Harris, R.E.Amaro, H.Aihara. Conformational Switch Regulates the Dna Cytosine Deaminase Activity of Human APOBEC3B. Sci Rep V. 7 17415 2017.
ISSN: ESSN 2045-2322
PubMed: 29234087
DOI: 10.1038/S41598-017-17694-3