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

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