Zinc in PDB 5sww: Crystal Structure of Human APOBEC3A Complexed with Ssdna

The structure of Crystal Structure of Human APOBEC3A Complexed with Ssdna, PDB code: 5sww was solved by K.Shi, S.Banerjee, K.Kurahashi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.42 / 3.15
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	90.148, 90.199, 167.257, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 26.3

The binding sites of Zinc atom in the Crystal Structure of Human APOBEC3A Complexed with Ssdna (pdb code 5sww). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human APOBEC3A Complexed with Ssdna, PDB code: 5sww:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human APOBEC3A Complexed with Ssdna


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 Human APOBEC3A Complexed with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:60.6 occ:1.00 ND1 A:HIS70 2.0 94.0 1.0 SG A:CYS106 2.3 68.9 1.0 SG A:CYS101 2.3 54.4 1.0 CB A:CYS106 2.9 81.0 1.0 CG A:HIS70 3.0 69.4 1.0 CE1 A:HIS70 3.1 74.6 1.0 CB A:HIS70 3.2 75.7 1.0 CB A:CYS101 3.5 63.7 1.0 N A:CYS101 3.6 56.2 1.0 CA A:CYS101 4.1 64.0 1.0 CD2 A:HIS70 4.1 69.4 1.0 N4 E:DC0 4.1 58.0 1.0 NE2 A:HIS70 4.2 70.4 1.0 CA A:CYS106 4.2 79.4 1.0 C4 E:DC0 4.2 51.6 1.0 N3 E:DC0 4.2 51.0 1.0 N A:CYS106 4.4 88.5 1.0 C A:CYS101 4.7 68.5 1.0 C A:PRO100 4.7 64.1 1.0 O A:CYS101 4.7 76.3 1.0 CA A:HIS70 4.7 68.7 1.0 CA A:PRO100 4.8 49.4 1.0 CB A:TRP104 4.9 86.8 1.0 C2 E:DC0 4.9 48.6 1.0 C5 E:DC0 4.9 57.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human APOBEC3A Complexed with Ssdna


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 Human APOBEC3A Complexed with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:52.7 occ:1.00 ND1 B:HIS70 2.0 92.3 1.0 SG B:CYS106 2.2 63.6 1.0 SG B:CYS101 2.3 50.8 1.0 CB B:CYS106 2.9 80.1 1.0 CG B:HIS70 3.0 58.9 1.0 CE1 B:HIS70 3.1 64.0 1.0 CB B:HIS70 3.2 61.9 1.0 CB B:CYS101 3.5 65.7 1.0 N B:CYS101 3.6 48.4 1.0 CA B:CYS101 4.1 58.6 1.0 CD2 B:HIS70 4.1 59.4 1.0 NE2 B:HIS70 4.2 61.3 1.0 N4 F:DC0 4.2 61.9 1.0 CA B:CYS106 4.2 85.7 1.0 C4 F:DC0 4.3 58.6 1.0 N3 F:DC0 4.3 54.4 1.0 N B:CYS106 4.4 91.7 1.0 C B:CYS101 4.7 57.6 1.0 C B:PRO100 4.7 57.4 1.0 O B:CYS101 4.7 55.8 1.0 CA B:HIS70 4.8 56.4 1.0 CA B:PRO100 4.8 44.1 1.0 CB B:TRP104 4.9 70.0 1.0 C2 F:DC0 4.9 45.2 1.0 C5 F:DC0 5.0 60.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human APOBEC3A Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human APOBEC3A Complexed with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:60.0 occ:1.00 ND1 C:HIS70 2.0 67.2 1.0 SG C:CYS106 2.2 68.5 1.0 SG C:CYS101 2.3 38.5 1.0 CG C:HIS70 2.9 62.9 1.0 CE1 C:HIS70 3.1 58.5 1.0 CB C:HIS70 3.2 65.1 1.0 CB C:CYS106 3.2 49.6 1.0 CB C:CYS101 3.4 47.7 1.0 N C:CYS101 3.7 33.9 1.0 C4 G:DC0 3.7 72.3 1.0 N4 G:DC0 3.8 75.2 1.0 N3 G:DC0 3.8 72.0 1.0 CD2 C:HIS70 4.1 62.2 1.0 CA C:CYS101 4.1 35.8 1.0 NE2 C:HIS70 4.1 64.8 1.0 C5 G:DC0 4.3 58.7 1.0 C2 G:DC0 4.4 66.2 1.0 CA C:CYS106 4.5 51.3 1.0 CA C:HIS70 4.7 61.4 1.0 N C:CYS106 4.7 53.5 1.0 C C:PRO100 4.8 52.6 1.0 C6 G:DC0 4.8 50.4 1.0 C C:CYS101 4.9 44.9 1.0 N1 G:DC0 4.9 56.5 1.0 CA C:PRO100 4.9 51.6 1.0 O C:CYS101 5.0 45.3 1.0 CB C:TRP104 5.0 48.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human APOBEC3A Complexed with Ssdna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human APOBEC3A Complexed with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:72.2 occ:1.00 ND1 D:HIS70 2.0 68.1 1.0 SG D:CYS106 2.3 66.1 1.0 SG D:CYS101 2.3 50.2 1.0 CG D:HIS70 2.9 78.5 1.0 CE1 D:HIS70 3.1 61.5 1.0 CB D:CYS106 3.2 53.5 1.0 CB D:HIS70 3.2 80.8 1.0 CB D:CYS101 3.4 49.0 1.0 N D:CYS101 3.7 32.8 1.0 C4 H:DC0 3.8 77.0 1.0 N4 H:DC0 3.9 81.4 1.0 N3 H:DC0 3.9 69.2 1.0 CD2 D:HIS70 4.1 75.9 1.0 CA D:CYS101 4.1 36.3 1.0 NE2 D:HIS70 4.1 65.4 1.0 C5 H:DC0 4.3 57.6 1.0 CA D:CYS106 4.5 61.6 1.0 C2 H:DC0 4.5 57.4 1.0 N D:CYS106 4.6 59.0 1.0 CA D:HIS70 4.7 66.7 1.0 C D:PRO100 4.8 41.8 1.0 C D:CYS101 4.8 41.6 1.0 CB D:TRP104 4.9 48.1 1.0 C6 H:DC0 4.9 46.5 1.0 O D:CYS101 4.9 55.5 1.0 CA D:PRO100 5.0 44.9 1.0 N1 H:DC0 5.0 45.9 1.0

K.Shi, M.A.Carpenter, S.Banerjee, N.M.Shaban, K.Kurahashi, D.J.Salamango, J.L.Mccann, G.J.Starrett, J.V.Duffy, O.Demir, R.E.Amaro, D.A.Harki, R.S.Harris, H.Aihara. Structural Basis For Targeted Dna Cytosine Deamination and Mutagenesis By APOBEC3A and APOBEC3B. Nat. Struct. Mol. Biol. V. 24 131 2017.
ISSN: ESSN 1545-9985
PubMed: 27991903
DOI: 10.1038/NSMB.3344