Zinc in PDB 5w2m: APOBEC3F Catalytic Domain Complex with A Single-Stranded Dna

The structure of APOBEC3F Catalytic Domain Complex with A Single-Stranded Dna, PDB code: 5w2m was solved by Y.Fang, X.Xiao, S.-X.Li, A.Wolfe, X.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	68.194, 108.489, 108.549, 79.60, 71.80, 71.75
R / Rfree (%)	25 / 26.7

The binding sites of Zinc atom in the APOBEC3F Catalytic Domain Complex with A Single-Stranded Dna (pdb code 5w2m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the APOBEC3F Catalytic Domain Complex with A Single-Stranded Dna, PDB code: 5w2m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the APOBEC3F Catalytic Domain Complex with A Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of APOBEC3F Catalytic Domain Complex with A Single-Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:0.1 occ:1.00 NE2 A:HIS249 2.8 0.8 1.0 CE1 A:HIS247 2.9 0.7 1.0 ND1 A:HIS247 2.9 0.6 1.0 NE2 A:HIS247 3.2 0.2 1.0 CG A:HIS247 3.3 0.8 1.0 ND1 C:HIS228 3.3 0.3 1.0 CD2 A:HIS247 3.4 1.0 1.0 CD2 A:HIS249 3.6 0.7 1.0 CG C:HIS228 3.6 0.9 1.0 CB C:HIS228 3.7 1.0 1.0 O A:HIS247 3.8 0.3 1.0 CE1 A:HIS249 3.8 0.8 1.0 CE1 C:HIS228 4.1 0.7 1.0 CB A:HIS247 4.2 0.6 1.0 CA C:HIS228 4.5 0.1 1.0 CD2 C:HIS228 4.6 0.7 1.0 NE2 C:HIS228 4.8 0.1 1.0 NH1 A:ARG252 4.8 0.5 1.0 CG A:HIS249 4.8 0.0 1.0 C A:HIS247 4.8 0.8 1.0 ND1 A:HIS249 4.9 0.8 1.0

Zinc binding site 2 out of 4 in the APOBEC3F Catalytic Domain Complex with A Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of APOBEC3F Catalytic Domain Complex with A Single-Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn801 b:1.0 occ:1.00 NE2 B:HIS249 2.8 0.2 1.0 CE1 B:HIS247 3.0 0.7 1.0 ND1 B:HIS247 3.0 0.6 1.0 NE2 B:HIS247 3.2 0.3 1.0 CG B:HIS247 3.3 0.8 1.0 ND1 D:HIS228 3.3 0.4 1.0 CD2 B:HIS247 3.4 0.1 1.0 CD2 B:HIS249 3.6 0.9 1.0 CG D:HIS228 3.7 0.4 1.0 O B:HIS247 3.8 0.8 1.0 CB D:HIS228 3.8 0.8 1.0 CE1 B:HIS249 3.8 0.1 1.0 CE1 D:HIS228 4.1 0.5 1.0 CB B:HIS247 4.1 0.6 1.0 CD2 D:HIS228 4.6 0.2 1.0 CA D:HIS228 4.6 0.8 1.0 NH1 B:ARG252 4.7 0.9 1.0 NE2 D:HIS228 4.8 0.8 1.0 C B:HIS247 4.8 0.3 1.0 CG B:HIS249 4.8 0.2 1.0 ND1 B:HIS249 4.9 0.3 1.0

Zinc binding site 3 out of 4 in the APOBEC3F Catalytic Domain Complex with A Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of APOBEC3F Catalytic Domain Complex with A Single-Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn801 b:0.5 occ:1.00 NE2 J:HIS249 2.8 0.9 1.0 CE1 J:HIS247 2.9 0.9 1.0 ND1 J:HIS247 2.9 0.8 1.0 NE2 J:HIS247 3.2 0.8 1.0 CG J:HIS247 3.2 0.3 1.0 ND1 L:HIS228 3.3 0.0 1.0 CD2 J:HIS247 3.4 0.3 1.0 CD2 J:HIS249 3.6 0.2 1.0 CG L:HIS228 3.6 0.9 1.0 CB L:HIS228 3.7 0.1 1.0 O J:HIS247 3.8 0.5 1.0 CE1 J:HIS249 3.9 0.5 1.0 CE1 L:HIS228 4.0 0.9 1.0 CB J:HIS247 4.1 0.1 1.0 CD2 L:HIS228 4.5 0.4 1.0 CA L:HIS228 4.6 0.7 1.0 NE2 L:HIS228 4.7 0.5 1.0 NH1 J:ARG252 4.8 0.6 1.0 C J:HIS247 4.8 0.3 1.0 CG J:HIS249 4.9 0.6 1.0 ND1 J:HIS249 4.9 0.7 1.0

Zinc binding site 4 out of 4 in the APOBEC3F Catalytic Domain Complex with A Single-Stranded Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of APOBEC3F Catalytic Domain Complex with A Single-Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn801 b:0.9 occ:1.00 NE2 K:HIS249 2.8 0.5 1.0 CE1 K:HIS247 2.9 0.6 1.0 ND1 K:HIS247 3.0 0.5 1.0 NE2 K:HIS247 3.2 0.7 1.0 ND1 M:HIS228 3.2 0.7 1.0 CG K:HIS247 3.4 0.5 1.0 CD2 K:HIS247 3.5 0.8 1.0 CG M:HIS228 3.6 1.0 1.0 CD2 K:HIS249 3.6 0.0 1.0 CB M:HIS228 3.7 0.1 1.0 CE1 K:HIS249 3.8 1.0 1.0 O K:HIS247 4.0 0.2 1.0 CE1 M:HIS228 4.1 0.6 1.0 CB K:HIS247 4.3 0.9 1.0 CA M:HIS228 4.5 0.1 1.0 CD2 M:HIS228 4.6 0.4 1.0 NE2 M:HIS228 4.8 0.6 1.0 CG K:HIS249 4.9 0.2 1.0 ND1 K:HIS249 4.9 0.2 1.0 NH1 K:ARG252 5.0 0.1 1.0 C K:HIS247 5.0 0.6 1.0

Y.Fang, X.Xiao, S.X.Li, A.Wolfe, X.S.Chen. Molecular Interactions of A Dna Modifying Enzyme APOBEC3F Catalytic Domain with A Single-Stranded Dna. J. Mol. Biol. V. 430 87 2018.
ISSN: ESSN 1089-8638
PubMed: 29191651
DOI: 10.1016/J.JMB.2017.11.007