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

The structure of Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B, PDB code: 5cqd 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)	46.14 / 2.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.440, 50.840, 70.150, 90.00, 100.83, 90.00
R / Rfree (%)	18.8 / 22.7

The binding sites of Zinc atom in the Crystal Structure of the Cancer Genomic Dna Mutator APOBEC3B (pdb code 5cqd). 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: 5cqd:
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:Zn501 b:44.5 occ:1.00 ND1 A:HIS253 2.0 45.1 1.0 O A:HOH603 2.1 44.0 1.0 SG A:CYS289 2.2 39.8 1.0 SG A:CYS284 2.2 41.5 1.0 HB2 A:CYS289 2.8 49.0 1.0 CE1 A:HIS253 2.9 44.8 1.0 HE1 A:HIS253 3.0 53.7 1.0 H A:CYS284 3.0 49.7 1.0 CB A:CYS289 3.1 40.9 1.0 HO3 A:GOL502 3.1 63.3 1.0 HB3 A:CYS284 3.1 48.9 1.0 CG A:HIS253 3.1 44.0 1.0 CB A:CYS284 3.3 40.7 1.0 HB3 A:HIS253 3.4 49.9 1.0 H A:CYS289 3.5 51.9 1.0 HB2 A:HIS253 3.5 49.9 1.0 CB A:HIS253 3.6 41.6 1.0 O3 A:GOL502 3.6 52.7 1.0 HB2 A:TRP287 3.7 58.7 1.0 HB3 A:CYS289 3.7 49.0 1.0 N A:CYS284 3.8 41.5 1.0 OE2 A:GLU255 3.9 41.7 1.0 NE2 A:HIS253 4.1 43.8 1.0 HB2 A:CYS284 4.1 48.9 1.0 CA A:CYS284 4.1 42.5 1.0 N A:CYS289 4.1 43.2 1.0 CA A:CYS289 4.2 40.9 1.0 CD2 A:HIS253 4.2 44.4 1.0 OE1 A:GLU255 4.3 44.2 1.0 CD A:GLU255 4.3 40.9 1.0 O A:HOH601 4.4 51.8 1.0 CB A:TRP287 4.5 49.0 1.0 HA A:CYS289 4.5 49.1 1.0 O A:CYS284 4.6 38.8 1.0 HA A:PRO283 4.6 49.9 1.0 C A:CYS284 4.6 39.4 1.0 HB3 A:TRP287 4.6 58.7 1.0 HB2 A:GLU255 4.7 48.5 1.0 H32 A:GOL502 4.8 61.1 1.0 C3 A:GOL502 4.8 50.9 1.0 HE2 A:HIS253 4.8 52.6 1.0 H A:TRP287 4.8 58.7 1.0 HE3 A:TRP287 4.9 63.3 1.0 C A:TRP287 4.9 46.0 1.0 HA A:CYS284 4.9 51.0 1.0 C A:PRO283 5.0 42.2 1.0 O A:TRP287 5.0 44.1 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 C:Zn501 b:45.3 occ:1.00 ND1 C:HIS253 2.0 41.7 1.0 SG C:CYS289 2.2 44.7 1.0 SG C:CYS284 2.2 42.9 1.0 O C:HOH602 2.3 36.2 1.0 HB2 C:CYS289 2.7 52.5 1.0 CE1 C:HIS253 2.9 43.3 1.0 HE1 C:HIS253 3.0 52.0 1.0 CB C:CYS289 3.0 43.7 1.0 H C:CYS284 3.1 50.0 1.0 CG C:HIS253 3.1 43.8 1.0 HB3 C:HIS253 3.4 49.2 1.0 HB3 C:CYS284 3.4 50.8 1.0 CB C:CYS284 3.5 42.3 1.0 HB2 C:HIS253 3.5 49.2 1.0 HB2 C:TRP287 3.5 74.6 1.0 CB C:HIS253 3.6 41.0 1.0 O C:HOH607 3.6 57.0 1.0 H C:CYS289 3.6 54.1 1.0 HB3 C:CYS289 3.6 52.5 1.0 O3 C:GOL502 3.8 50.8 1.0 N C:CYS284 3.9 41.7 1.0 OE2 C:GLU255 4.0 43.5 1.0 NE2 C:HIS253 4.0 42.7 1.0 H32 C:GOL502 4.1 60.1 1.0 CD2 C:HIS253 4.2 40.9 1.0 CA C:CYS284 4.2 42.6 1.0 CA C:CYS289 4.2 43.8 1.0 HO3 C:GOL502 4.2 61.0 1.0 N C:CYS289 4.2 45.1 1.0 OE1 C:GLU255 4.2 44.1 1.0 HB2 C:CYS284 4.2 50.8 1.0 CD C:GLU255 4.3 41.9 1.0 CB C:TRP287 4.4 62.1 1.0 HB3 C:TRP287 4.5 74.6 1.0 HA C:CYS289 4.5 52.5 1.0 C3 C:GOL502 4.5 50.1 1.0 HE3 C:TRP287 4.6 87.5 1.0 HA C:PRO283 4.6 54.2 1.0 HB2 C:GLU255 4.6 47.3 1.0 O C:CYS284 4.7 42.4 1.0 C C:CYS284 4.7 41.8 1.0 H C:TRP287 4.8 65.9 1.0 HE2 C:HIS253 4.8 51.2 1.0 O C:TRP287 4.9 54.1 1.0 C C:TRP287 4.9 55.2 1.0

K.Shi, M.A.Carpenter, K.Kurahashi, R.S.Harris, H.Aihara. Crystal Structure of the Dna Deaminase APOBEC3B Catalytic Domain. J.Biol.Chem. V. 290 28120 2015.
ISSN: ESSN 1083-351X
PubMed: 26416889
DOI: 10.1074/JBC.M115.679951