Zinc in PDB 8grm: Cryo-Em Structure of PRC1 Bound to H2AK119-UBCH5B-Ub Nucleosome

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of PRC1 Bound to H2AK119-UBCH5B-Ub Nucleosome (pdb code 8grm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of PRC1 Bound to H2AK119-UBCH5B-Ub Nucleosome, PDB code: 8grm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8grm

Go back to Zinc Binding Sites List in 8grm
Zinc binding site 1 out of 4 in the Cryo-Em Structure of PRC1 Bound to H2AK119-UBCH5B-Ub Nucleosome


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 PRC1 Bound to H2AK119-UBCH5B-Ub Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:56.3
occ:1.00
SG M:CYS39 2.5 36.0 1.0
SG M:CYS42 2.7 38.0 1.0
CB M:CYS39 3.0 36.0 1.0
SG M:CYS18 3.1 42.8 1.0
CB M:CYS21 3.7 42.7 1.0
SG M:CYS21 3.8 42.7 1.0
CB M:CYS18 3.8 42.8 1.0
N M:CYS39 4.0 36.0 1.0
CA M:CYS39 4.1 36.0 1.0
CB M:CYS42 4.3 38.0 1.0
O M:TYR24 4.5 41.7 1.0
N M:CYS21 4.8 42.7 1.0
NH2 N:ARG26 4.8 46.8 1.0
CA M:CYS21 4.8 42.7 1.0

Zinc binding site 2 out of 4 in 8grm

Go back to Zinc Binding Sites List in 8grm
Zinc binding site 2 out of 4 in the Cryo-Em Structure of PRC1 Bound to H2AK119-UBCH5B-Ub Nucleosome


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 PRC1 Bound to H2AK119-UBCH5B-Ub Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn202

b:42.8
occ:1.00
ND1 M:HIS36 2.2 31.5 1.0
SG M:CYS34 2.4 28.9 1.0
SG M:CYS56 2.4 36.9 1.0
SG M:CYS53 2.4 36.4 1.0
CE1 M:HIS36 2.9 31.5 1.0
CB M:CYS34 2.9 28.9 1.0
CB M:CYS53 3.1 36.4 1.0
CG M:HIS36 3.2 31.5 1.0
CB M:HIS36 3.7 31.5 1.0
CB M:CYS56 3.8 36.9 1.0
N M:CYS56 3.8 36.9 1.0
NE2 M:HIS36 3.9 31.5 1.0
CD2 M:HIS36 4.1 31.5 1.0
CA M:CYS56 4.3 36.9 1.0
CA M:CYS34 4.3 28.9 1.0
CB M:ILE55 4.4 38.0 1.0
CA M:CYS53 4.6 36.4 1.0
C M:CYS34 4.6 28.9 1.0
O M:CYS34 4.6 28.9 1.0
N M:HIS36 4.7 31.5 1.0
C M:ILE55 4.8 38.0 1.0
N M:ILE55 4.8 38.0 1.0
CA M:HIS36 4.9 31.5 1.0
C M:CYS56 4.9 36.9 1.0
CA M:ILE55 4.9 38.0 1.0
CG2 M:ILE55 4.9 38.0 1.0
N M:ASP57 4.9 38.3 1.0

Zinc binding site 3 out of 4 in 8grm

Go back to Zinc Binding Sites List in 8grm
Zinc binding site 3 out of 4 in the Cryo-Em Structure of PRC1 Bound to H2AK119-UBCH5B-Ub Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of PRC1 Bound to H2AK119-UBCH5B-Ub Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn401

b:42.1
occ:1.00
SG N:CYS54 2.5 38.1 1.0
SG N:CYS75 2.5 30.0 1.0
SG N:CYS51 2.5 35.7 1.0
SG N:CYS72 2.5 30.8 1.0
CB N:CYS72 3.0 30.8 1.0
CB N:CYS51 3.1 35.7 1.0
CB N:CYS54 3.4 38.1 1.0
CB N:CYS75 3.7 30.0 1.0
N N:CYS54 3.9 38.1 1.0
N N:CYS72 4.0 30.8 1.0
CA N:CYS72 4.1 30.8 1.0
CA N:CYS54 4.3 38.1 1.0
CA N:CYS51 4.6 35.7 1.0
NZ N:LYS59 4.8 32.4 1.0
CB N:ILE53 4.9 34.8 1.0

Zinc binding site 4 out of 4 in 8grm

Go back to Zinc Binding Sites List in 8grm
Zinc binding site 4 out of 4 in the Cryo-Em Structure of PRC1 Bound to H2AK119-UBCH5B-Ub Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of PRC1 Bound to H2AK119-UBCH5B-Ub Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn402

b:40.1
occ:1.00
SG N:CYS87 2.5 27.2 1.0
SG N:CYS90 2.5 32.5 1.0
CB N:CYS67 2.5 24.8 1.0
ND1 N:HIS69 2.9 25.0 1.0
SG N:CYS67 2.9 24.8 1.0
CB N:CYS90 3.0 32.5 1.0
CB N:CYS87 3.4 27.2 1.0
CG N:HIS69 3.6 25.0 1.0
CE1 N:HIS69 3.6 25.0 1.0
CB N:HIS69 3.9 25.0 1.0
CA N:CYS67 4.0 24.8 1.0
CG2 N:THR89 4.1 32.0 1.0
N N:CYS90 4.1 32.5 1.0
CA N:CYS90 4.1 32.5 1.0
OG1 N:THR64 4.3 22.0 1.0
C N:CYS67 4.4 24.8 1.0
NE2 N:HIS69 4.5 25.0 1.0
C N:THR89 4.5 32.0 1.0
CD2 N:HIS69 4.5 25.0 1.0
O N:CYS67 4.6 24.8 1.0
O N:THR89 4.8 32.0 1.0
CA N:CYS87 4.9 27.2 1.0
N N:CYS67 4.9 24.8 1.0
N N:HIS69 5.0 25.0 1.0
CG2 N:THR64 5.0 22.0 1.0

Reference:

H.S.Ai, Z.Tong, Z.Deng, J.Tian, L.Zhang, M.Sun, Y.Du, Z.Xu, Q.Shi, L.Liang, Q.Zheng, J.B.Li, M.Pan, L.Liu. Synthetic E2-Ub-Nucleosome Conjugates For Studying Nucleosome Ubiquitination. Chem 2023.
ISSN: ESSN 2451-9294
DOI: 10.1016/J.CHEMPR.2023.01.012
Page generated: Wed Apr 26 00:45:18 2023

Last articles

Ca in 5YLJ
Ca in 5YL2
Ca in 5YL4
Ca in 5YJH
Ca in 5YJ7
Ca in 5YL1
Ca in 5YJD
Ca in 5Y2Z
Ca in 5XYR
Ca in 5XVZ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy