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

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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

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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

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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

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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

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