Zinc in PDB 8x7k: Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Activity-Based Chemical Trapping Strategy (Adjacent H2AK13/15 Dual-Monoubiquitination)

Enzymatic activity of Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Activity-Based Chemical Trapping Strategy (Adjacent H2AK13/15 Dual-Monoubiquitination)

All present enzymatic activity of Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Activity-Based Chemical Trapping Strategy (Adjacent H2AK13/15 Dual-Monoubiquitination):
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 Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Activity-Based Chemical Trapping Strategy (Adjacent H2AK13/15 Dual-Monoubiquitination) (pdb code 8x7k). 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 Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Activity-Based Chemical Trapping Strategy (Adjacent H2AK13/15 Dual-Monoubiquitination), PDB code: 8x7k:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8x7k

Go back to Zinc Binding Sites List in 8x7k
Zinc binding site 1 out of 2 in the Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Activity-Based Chemical Trapping Strategy (Adjacent H2AK13/15 Dual-Monoubiquitination)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Activity-Based Chemical Trapping Strategy (Adjacent H2AK13/15 Dual-Monoubiquitination) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn201

b:281.1
occ:1.00
 ND1 L:HIS33 2.1 263.6 1.0
CE1 L:HIS33 2.3 263.6 1.0
SG L:CYS51 2.3 256.9 1.0
SG L:CYS31 2.3 258.4 1.0
SG L:CYS54 2.3 257.6 1.0
CG L:HIS33 3.0 263.6 1.0
NE2 L:HIS33 3.2 263.6 1.0
CB L:CYS51 3.2 256.9 1.0
CB L:CYS31 3.3 258.4 1.0
CB L:CYS54 3.3 257.6 1.0
N L:CYS54 3.4 257.6 1.0
CD2 L:HIS33 3.5 263.6 1.0
CA L:CYS54 3.8 257.6 1.0
CB L:HIS33 3.8 263.6 1.0
CB L:ARG56 3.9 238.4 1.0
CB L:PHE53 4.1 265.4 1.0
C L:CYS54 4.3 257.6 1.0
O L:CYS31 4.3 258.4 1.0
C L:PHE53 4.4 265.4 1.0
CD1 L:LEU29 4.4 255.0 1.0
N L:ARG56 4.5 238.4 1.0
CA L:CYS31 4.5 258.4 1.0
CA L:PHE53 4.6 265.4 1.0
CA L:CYS51 4.7 256.9 1.0
C L:CYS31 4.7 258.4 1.0
N L:PHE53 4.7 265.4 1.0
N L:ARG55 4.7 246.4 1.0
O L:CYS54 4.9 257.6 1.0
CA L:ARG56 4.9 238.4 1.0
CG L:ARG56 4.9 238.4 1.0

Zinc binding site 2 out of 2 in 8x7k

Go back to Zinc Binding Sites List in 8x7k
Zinc binding site 2 out of 2 in the Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Activity-Based Chemical Trapping Strategy (Adjacent H2AK13/15 Dual-Monoubiquitination)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structures of RNF168/UBCH5C-Ub in Complex with H2AK13UB Nucleosomes Determined By Activity-Based Chemical Trapping Strategy (Adjacent H2AK13/15 Dual-Monoubiquitination) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn202

b:301.0
occ:1.00
 SG L:CYS19 2.3 278.9 1.0
SG L:CYS36 2.3 279.9 1.0
SG L:CYS16 2.3 277.2 1.0
SG L:CYS39 2.3 280.0 1.0
CB L:CYS19 2.5 278.9 1.0
CB L:CYS39 2.6 280.0 1.0
CB L:CYS16 2.8 277.2 1.0
N L:CYS19 3.2 278.9 1.0
CB L:CYS36 3.3 279.9 1.0
CA L:CYS19 3.4 278.9 1.0
CA L:CYS39 3.8 280.0 1.0
N L:CYS39 3.9 280.0 1.0
N L:CYS36 4.2 279.9 1.0
CA L:CYS36 4.3 279.9 1.0
CA L:CYS16 4.3 277.2 1.0
C L:CYS19 4.3 278.9 1.0
C L:ILE18 4.5 277.8 1.0
N L:MET20 4.5 269.5 1.0
O L:CYS36 4.5 279.9 1.0
C L:CYS36 4.7 279.9 1.0
CB L:ILE18 4.8 277.8 1.0
N L:ILE18 4.9 277.8 1.0
CA L:ILE18 5.0 277.8 1.0
C L:CYS39 5.0 280.0 1.0
C L:CYS16 5.0 277.2 1.0

Reference:

H.Ai, Z.Tong, Z.Deng, Q.Shi, S.Tao, J.Liang, M.Sun, X.Wu, Q.Zheng, L.Liang, J.B.Li, S.Gao, C.Tian, L.Liu, M.Pan. Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated By the Monomeric E3 Ligase RNF168 Biorxiv 2024.
ISSN: ISSN 2692-8205
DOI: 10.1101/2024.01.02.573964
Page generated: Thu Oct 31 13:51:16 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy