Zinc in PDB 4ayc: RNF8 Ring Domain Structure

The structure of RNF8 Ring Domain Structure, PDB code: 4ayc was solved by F.Mattiroli, J.H.A.Vissers, W.J.Van Dijk, P.Ikpa, E.Citterio, W.Vermeulen, J.A.Marteijn, T.K.Sixma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.29 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	47.374, 213.717, 34.102, 90.00, 90.00, 90.00
R / Rfree (%)	19.973 / 22.948

The structure of RNF8 Ring Domain Structure also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the RNF8 Ring Domain Structure (pdb code 4ayc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the RNF8 Ring Domain Structure, PDB code: 4ayc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the RNF8 Ring Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RNF8 Ring Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1484 b:32.9 occ:1.00 ND1 A:HIS420 2.1 34.1 1.0 SG A:CYS440 2.3 35.1 1.0 SG A:CYS418 2.3 30.0 1.0 SG A:CYS437 2.3 31.9 1.0 CE1 A:HIS420 3.0 38.4 1.0 CB A:CYS437 3.0 31.1 1.0 CG A:HIS420 3.1 35.4 1.0 CB A:CYS418 3.2 30.4 1.0 CB A:CYS440 3.5 38.0 1.0 CB A:HIS420 3.5 29.9 1.0 N A:CYS440 3.7 37.4 1.0 NE2 A:HIS420 4.1 38.6 1.0 CA A:CYS440 4.1 36.5 1.0 CD2 A:HIS420 4.2 36.7 1.0 O A:CYS418 4.4 27.9 1.0 CA A:CYS418 4.5 30.8 1.0 CA A:CYS437 4.5 29.7 1.0 C A:CYS418 4.5 30.4 1.0 CB A:ILE439 4.5 37.0 1.0 N A:HIS420 4.6 26.7 1.0 O A:HOH2015 4.6 37.0 1.0 CA A:HIS420 4.7 29.6 1.0 C A:ILE439 4.8 44.1 1.0 C A:CYS440 4.9 38.3 1.0 N A:ARG441 4.9 39.1 1.0 CA A:ILE439 5.0 37.0 1.0 N A:ILE439 5.0 35.1 1.0

Zinc binding site 2 out of 4 in the RNF8 Ring Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RNF8 Ring Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1485 b:29.8 occ:1.00 SG A:CYS426 2.3 30.1 1.0 SG A:CYS406 2.3 30.0 1.0 SG A:CYS423 2.4 28.2 1.0 SG A:CYS403 2.4 29.9 1.0 CB A:CYS403 2.9 31.1 1.0 CB A:CYS423 3.1 25.8 1.0 CB A:CYS406 3.3 30.8 1.0 CB A:CYS426 3.3 30.5 1.0 N A:CYS406 3.8 31.0 1.0 NH2 A:ARG479 3.9 39.3 1.0 N A:CYS423 4.0 24.6 1.0 NH1 A:ARG479 4.1 36.1 1.0 CA A:CYS423 4.2 24.3 1.0 CA A:CYS406 4.2 32.1 1.0 CA A:CYS403 4.4 29.2 1.0 CZ A:ARG479 4.5 41.6 1.0 CB A:ILE405 4.6 33.0 1.0 CA A:CYS426 4.7 28.7 1.0 C A:ILE405 4.8 36.3 1.0 C A:CYS403 4.8 29.9 1.0 O A:CYS403 4.9 30.6 1.0 N A:CYS426 4.9 27.0 1.0 O A:HOH2021 4.9 41.5 1.0 N A:ILE405 4.9 33.5 1.0 CA A:ILE405 5.0 34.5 1.0

Zinc binding site 3 out of 4 in the RNF8 Ring Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RNF8 Ring Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1486 b:34.9 occ:1.00 ND1 B:HIS420 2.2 36.5 1.0 SG B:CYS418 2.2 33.3 1.0 SG B:CYS440 2.2 38.0 1.0 SG B:CYS437 2.3 37.3 1.0 CB B:CYS437 3.0 35.2 1.0 CE1 B:HIS420 3.2 39.5 1.0 CB B:CYS418 3.2 30.3 1.0 CG B:HIS420 3.2 34.5 1.0 CB B:CYS440 3.5 42.4 1.0 CB B:HIS420 3.5 33.4 1.0 N B:CYS440 3.8 41.6 1.0 CA B:CYS440 4.2 43.5 1.0 NE2 B:HIS420 4.3 43.3 1.0 O B:CYS418 4.3 30.9 1.0 CD2 B:HIS420 4.3 38.3 1.0 CA B:CYS418 4.4 29.6 1.0 CA B:CYS437 4.5 36.5 1.0 C B:CYS418 4.5 28.8 1.0 N B:HIS420 4.5 29.8 1.0 O B:HOH2011 4.6 30.8 1.0 CB B:ILE439 4.7 41.7 1.0 CA B:HIS420 4.7 31.6 1.0 C B:ILE439 4.8 46.8 1.0 C B:CYS440 4.9 47.7 1.0 N B:ARG441 4.9 46.9 1.0 N B:ILE439 5.0 41.7 1.0

Zinc binding site 4 out of 4 in the RNF8 Ring Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of RNF8 Ring Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1487 b:37.8 occ:1.00 SG B:CYS426 2.3 38.1 1.0 SG B:CYS406 2.3 40.0 1.0 SG B:CYS403 2.3 37.1 1.0 SG B:CYS423 2.3 38.6 1.0 CB B:CYS403 3.0 37.1 1.0 CB B:CYS423 3.1 35.0 1.0 CB B:CYS426 3.2 37.4 1.0 CB B:CYS406 3.3 39.6 1.0 N B:CYS406 3.8 43.3 1.0 N B:CYS423 4.0 30.5 1.0 NH2 B:ARG479 4.0 42.7 1.0 NH1 B:ARG479 4.0 38.9 1.0 CA B:CYS423 4.1 30.8 1.0 CA B:CYS406 4.2 43.8 1.0 CA B:CYS403 4.4 36.1 1.0 CZ B:ARG479 4.5 41.5 1.0 CA B:CYS426 4.6 35.3 1.0 CB B:ILE405 4.6 42.5 1.0 C B:ILE405 4.8 43.5 1.0 N B:CYS426 4.8 34.5 1.0 C B:CYS403 4.9 38.2 1.0 N B:ILE405 5.0 40.1 1.0

F.Mattiroli, J.H.A.Vissers, W.J.Van Dijk, P.Ikpa, E.Citterio, W.Vermeulen, J.A.Marteijn, T.K.Sixma. RNF168 Ubiquitinates K13-15 on H2A/H2AX to Drive Dna Damage Signaling Cell(Cambridge,Mass.) V. 150 1182 2012.
ISSN: ISSN 0092-8674
PubMed: 22980979
DOI: 10.1016/J.CELL.2012.08.005