Zinc in PDB 6w9a: RNF12 Ring Domain in Complex with UBE2E2

All present enzymatic activity of RNF12 Ring Domain in Complex with UBE2E2:
2.3.2.23; 2.3.2.27;

The structure of RNF12 Ring Domain in Complex with UBE2E2, PDB code: 6w9a was solved by A.J.Middleton, C.L.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.30 / 2.30
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	81.355, 81.355, 98.247, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 21.9

The binding sites of Zinc atom in the RNF12 Ring Domain in Complex with UBE2E2 (pdb code 6w9a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the RNF12 Ring Domain in Complex with UBE2E2, PDB code: 6w9a:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the RNF12 Ring Domain in Complex with UBE2E2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RNF12 Ring Domain in Complex with UBE2E2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:55.6 occ:1.00 ND1 B:HIS593 2.2 59.3 1.0 SG B:CYS570 2.2 48.5 1.0 SG B:CYS596 2.3 59.0 1.0 SG B:CYS573 2.3 58.4 1.0 CG B:HIS593 3.1 66.5 1.0 CB B:CYS570 3.1 51.7 1.0 CE1 B:HIS593 3.2 58.3 1.0 CB B:CYS573 3.3 55.1 1.0 CB B:HIS593 3.3 54.3 1.0 CB B:CYS596 3.3 54.5 1.0 N B:CYS573 3.7 56.7 1.0 CA B:CYS573 4.1 53.7 1.0 N B:HIS593 4.1 63.0 1.0 CD2 B:HIS593 4.2 62.0 1.0 NE2 B:HIS593 4.3 65.6 1.0 CA B:HIS593 4.3 62.9 1.0 NE2 B:HIS595 4.5 83.2 1.0 CA B:CYS570 4.5 47.0 1.0 O B:CYS570 4.7 58.0 1.0 C B:VAL572 4.7 53.6 1.0 CA B:CYS596 4.7 58.8 1.0 CB B:VAL572 4.8 54.5 1.0 C B:CYS570 4.8 65.1 1.0 CE1 B:HIS595 4.9 83.5 1.0 C B:CYS573 4.9 52.6 1.0 N B:VAL572 5.0 49.2 1.0

Zinc binding site 2 out of 4 in the RNF12 Ring Domain in Complex with UBE2E2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RNF12 Ring Domain in Complex with UBE2E2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:70.4 occ:1.00 ND1 B:HIS590 2.0 78.1 1.0 SG B:CYS610 2.2 67.7 1.0 SG B:CYS588 2.4 84.0 1.0 SG B:CYS607 2.4 64.4 1.0 CE1 B:HIS590 2.8 69.1 1.0 CB B:CYS588 3.1 76.8 1.0 CB B:CYS607 3.2 58.8 1.0 CG B:HIS590 3.2 69.2 1.0 CB B:CYS610 3.3 68.0 1.0 CB B:HIS590 3.7 63.2 1.0 N B:CYS610 3.8 68.3 1.0 NE2 B:HIS590 4.0 73.5 1.0 CA B:CYS610 4.1 68.2 1.0 CD2 B:HIS590 4.2 67.7 1.0 O B:CYS588 4.4 81.3 1.0 CA B:CYS588 4.4 80.7 1.0 N B:HIS590 4.5 73.8 1.0 C B:CYS588 4.6 80.7 1.0 CA B:CYS607 4.6 66.1 1.0 CB B:ILE609 4.7 67.8 1.0 CA B:HIS590 4.8 59.9 1.0 C B:CYS610 4.8 70.2 1.0 C B:ILE609 4.9 67.2 1.0

Zinc binding site 3 out of 4 in the RNF12 Ring Domain in Complex with UBE2E2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RNF12 Ring Domain in Complex with UBE2E2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:54.0 occ:1.00 ND1 D:HIS593 2.1 64.1 1.0 SG D:CYS570 2.3 49.7 1.0 SG D:CYS596 2.3 53.6 1.0 SG D:CYS573 2.3 50.3 1.0 CB D:CYS570 2.9 43.5 1.0 CG D:HIS593 3.0 71.0 1.0 CE1 D:HIS593 3.1 61.8 1.0 CB D:HIS593 3.2 44.5 1.0 CB D:CYS596 3.3 58.7 1.0 CB D:CYS573 3.4 44.4 1.0 N D:CYS573 3.7 40.9 1.0 N D:HIS593 4.0 61.9 1.0 CD2 D:HIS593 4.1 69.5 1.0 CA D:CYS573 4.1 42.8 1.0 NE2 D:HIS593 4.2 66.3 1.0 CA D:HIS593 4.2 61.9 1.0 CA D:CYS570 4.4 48.6 1.0 CB D:VAL572 4.7 51.0 1.0 C D:VAL572 4.7 54.5 1.0 NE2 D:HIS595 4.7 84.5 1.0 CA D:CYS596 4.7 57.2 1.0 C D:CYS570 4.8 52.4 1.0 O D:CYS570 4.8 55.3 1.0 N D:VAL572 4.9 56.8 1.0 CA D:VAL572 5.0 53.4 1.0 C D:CYS573 5.0 47.2 1.0

Zinc binding site 4 out of 4 in the RNF12 Ring Domain in Complex with UBE2E2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of RNF12 Ring Domain in Complex with UBE2E2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn702 b:65.8 occ:1.00 ND1 D:HIS590 2.1 72.9 1.0 SG D:CYS610 2.1 77.4 1.0 SG D:CYS607 2.3 63.2 1.0 SG D:CYS588 2.4 80.2 1.0 CE1 D:HIS590 2.9 67.0 1.0 CB D:CYS588 3.2 80.3 1.0 CB D:CYS607 3.2 66.7 1.0 CG D:HIS590 3.2 68.8 1.0 CB D:CYS610 3.3 70.0 1.0 CB D:HIS590 3.7 61.2 1.0 N D:CYS610 3.7 55.2 1.0 CA D:CYS610 4.1 59.1 1.0 NE2 D:HIS590 4.1 67.2 1.0 CD2 D:HIS590 4.3 65.8 1.0 CA D:CYS588 4.5 81.7 1.0 N D:HIS590 4.6 69.2 1.0 CA D:CYS607 4.6 61.3 1.0 C D:CYS588 4.7 80.1 1.0 CB D:ILE609 4.7 55.4 1.0 C D:CYS610 4.7 62.8 1.0 O D:CYS588 4.8 82.0 1.0 CA D:HIS590 4.8 65.2 1.0 OH D:TYR592 4.8 64.2 1.0 C D:ILE609 4.8 63.8 1.0 N D:ARG611 4.8 66.0 1.0 N D:ILE609 5.0 50.4 1.0

A.J.Middleton, J.Zhu, C.L.Day. The Ring Domain of Ring Finger 12 Efficiently Builds Degradative Ubiquitin Chains J.Mol.Biol..
ISSN: ESSN 1089-8638
DOI: 10.1016/J.JMB.2020.05.001