Zinc in PDB 9ipu: Cryo-Em Structure of the RNF168(1-193)/UBCH5C-Ub Ubiquitylation Module Bound to H1.0-K63-UB3 Modified Chromatosome

Enzymatic activity of Cryo-Em Structure of the RNF168(1-193)/UBCH5C-Ub Ubiquitylation Module Bound to H1.0-K63-UB3 Modified Chromatosome

All present enzymatic activity of Cryo-Em Structure of the RNF168(1-193)/UBCH5C-Ub Ubiquitylation Module Bound to H1.0-K63-UB3 Modified Chromatosome:
2.3.2.23; 2.3.2.24; 2.3.2.27;

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the RNF168(1-193)/UBCH5C-Ub Ubiquitylation Module Bound to H1.0-K63-UB3 Modified Chromatosome (pdb code 9ipu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of the RNF168(1-193)/UBCH5C-Ub Ubiquitylation Module Bound to H1.0-K63-UB3 Modified Chromatosome, PDB code: 9ipu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 9ipu

Go back to Zinc Binding Sites List in 9ipu
Zinc binding site 1 out of 2 in the Cryo-Em Structure of the RNF168(1-193)/UBCH5C-Ub Ubiquitylation Module Bound to H1.0-K63-UB3 Modified Chromatosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the RNF168(1-193)/UBCH5C-Ub Ubiquitylation Module Bound to H1.0-K63-UB3 Modified Chromatosome within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn201

b:257.7
occ:1.00
CE1 L:HIS33 2.0 224.0 1.0
ND1 L:HIS33 2.1 224.0 1.0
SG L:CYS51 2.3 210.1 1.0
SG L:CYS31 2.3 218.0 1.0
SG L:CYS54 2.3 213.5 1.0
NE2 L:HIS33 2.8 224.0 1.0
CG L:HIS33 3.0 224.0 1.0
CB L:CYS31 3.2 218.0 1.0
CD2 L:HIS33 3.4 224.0 1.0
CB L:CYS51 3.5 210.1 1.0
N L:CYS54 3.6 213.5 1.0
CB L:CYS54 3.7 213.5 1.0
CB L:PHE53 3.8 217.7 1.0
CD2 L:PHE53 3.9 217.7 1.0
CB L:HIS33 4.1 224.0 1.0
CA L:CYS54 4.1 213.5 1.0
O L:CYS31 4.3 218.0 1.0
CG L:PHE53 4.3 217.7 1.0
C L:PHE53 4.4 217.7 1.0
CA L:PHE53 4.5 217.7 1.0
CB L:ARG56 4.5 191.9 1.0
CA L:CYS31 4.6 218.0 1.0
N L:PHE53 4.6 217.7 1.0
C L:CYS54 4.7 213.5 1.0
C L:CYS31 4.8 218.0 1.0
CD1 L:LEU29 4.8 216.7 1.0
CA L:CYS51 4.9 210.1 1.0

Zinc binding site 2 out of 2 in 9ipu

Go back to Zinc Binding Sites List in 9ipu
Zinc binding site 2 out of 2 in the Cryo-Em Structure of the RNF168(1-193)/UBCH5C-Ub Ubiquitylation Module Bound to H1.0-K63-UB3 Modified Chromatosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the RNF168(1-193)/UBCH5C-Ub Ubiquitylation Module Bound to H1.0-K63-UB3 Modified Chromatosome within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn202

b:299.0
occ:1.00
SG L:CYS36 2.3 253.7 1.0
SG L:CYS16 2.3 283.0 1.0
SG L:CYS39 2.3 248.3 1.0
SG L:CYS19 2.3 282.5 1.0
CB L:CYS19 2.8 282.5 1.0
CB L:CYS16 2.9 283.0 1.0
CB L:CYS39 3.0 248.3 1.0
N L:CYS19 3.3 282.5 1.0
CA L:CYS19 3.6 282.5 1.0
CB L:CYS36 3.7 253.7 1.0
N L:CYS36 4.2 253.7 1.0
CA L:CYS39 4.2 248.3 1.0
N L:CYS39 4.2 248.3 1.0
CA L:CYS16 4.4 283.0 1.0
C L:CYS19 4.5 282.5 1.0
C L:ILE18 4.5 270.0 1.0
CA L:CYS36 4.5 253.7 1.0
CB L:ILE18 4.6 270.0 1.0
N L:MET20 4.7 282.3 1.0
N L:ILE18 4.7 270.0 1.0
CA L:ILE18 4.9 270.0 1.0
C L:CYS16 5.0 283.0 1.0

Reference:

Q.Shi, Z.H.Deng, L.Y.Zhang, Z.B.Tong, G.-C.Chu, H.S.Ai, L.Liu. Chemically and Site-Specifically Ubiquitylated Linker Histone H1 Facilitates RNF168-Mediated Nucleosomal H2A Ubiquitylation To Be Published.
Page generated: Thu Oct 31 15:41:39 2024

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