Zinc in PDB 8grq: Cryo-Em Structure of BRCA1/BARD1 Bound to H2AK127-UBCH5C-Ub Nucleosome

Enzymatic activity of Cryo-Em Structure of BRCA1/BARD1 Bound to H2AK127-UBCH5C-Ub Nucleosome

All present enzymatic activity of Cryo-Em Structure of BRCA1/BARD1 Bound to H2AK127-UBCH5C-Ub Nucleosome:
2.3.2.27;

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of BRCA1/BARD1 Bound to H2AK127-UBCH5C-Ub Nucleosome (pdb code 8grq). 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 BRCA1/BARD1 Bound to H2AK127-UBCH5C-Ub Nucleosome, PDB code: 8grq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8grq

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Zinc binding site 1 out of 4 in the Cryo-Em Structure of BRCA1/BARD1 Bound to H2AK127-UBCH5C-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 BRCA1/BARD1 Bound to H2AK127-UBCH5C-Ub Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn101

b:228.3
occ:1.00
 CB K:CYS27 1.8 177.8 1.0
SG K:CYS44 2.3 172.3 1.0
SG K:CYS27 2.3 177.8 1.0
SG K:CYS47 2.3 176.1 1.0
SG K:CYS24 2.3 172.7 1.0
CA K:CYS27 3.3 177.8 1.0
CB K:CYS24 3.6 172.7 1.0
CB K:CYS44 3.6 172.3 1.0
N K:CYS27 3.8 177.8 1.0
N K:CYS44 4.0 172.3 1.0
CG2 K:ILE26 4.1 182.5 1.0
CB K:CYS47 4.1 176.1 1.0
C K:CYS27 4.1 177.8 1.0
CA K:CYS44 4.3 172.3 1.0
O K:LYS45 4.4 169.6 1.0
CE1 K:PHE46 4.5 179.3 1.0
CB K:GLU29 4.5 168.9 1.0
O K:CYS27 4.6 177.8 1.0
C K:ILE26 4.6 182.5 1.0
C K:CYS44 4.7 172.3 1.0
CZ K:PHE46 4.7 179.3 1.0
N K:LEU28 4.8 164.8 1.0
O K:CYS44 4.9 172.3 1.0
N K:GLU29 4.9 168.9 1.0

Zinc binding site 2 out of 4 in 8grq

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Zinc binding site 2 out of 4 in the Cryo-Em Structure of BRCA1/BARD1 Bound to H2AK127-UBCH5C-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 BRCA1/BARD1 Bound to H2AK127-UBCH5C-Ub Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn102

b:204.5
occ:1.00
 CB K:CYS64 1.3 187.4 1.0
NE2 K:HIS41 2.2 155.8 1.0
CE1 K:HIS41 2.2 155.8 1.0
SG K:CYS39 2.3 151.2 1.0
SG K:CYS61 2.3 176.7 1.0
SG K:CYS64 2.3 187.4 1.0
CA K:CYS64 2.7 187.4 1.0
N K:CYS64 3.1 187.4 1.0
OD2 K:ASP67 3.3 191.4 1.0
C K:CYS64 3.5 187.4 1.0
ND1 K:HIS41 3.5 155.8 1.0
CD2 K:HIS41 3.6 155.8 1.0
CB K:CYS39 3.8 151.2 1.0
N K:LYS65 3.8 192.8 1.0
CB K:CYS61 3.8 176.7 1.0
CG K:HIS41 4.2 155.8 1.0
CG K:ASP67 4.4 191.4 1.0
O K:CYS64 4.4 187.4 1.0
C K:LEU63 4.4 179.3 1.0
CB K:ASP67 4.7 191.4 1.0

Zinc binding site 3 out of 4 in 8grq

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Zinc binding site 3 out of 4 in the Cryo-Em Structure of BRCA1/BARD1 Bound to H2AK127-UBCH5C-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 BRCA1/BARD1 Bound to H2AK127-UBCH5C-Ub Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:368.6
occ:1.00
 SG M:CYS74 2.3 335.2 1.0
SG M:CYS53 2.3 349.3 1.0
SG M:CYS71 2.3 330.7 1.0
SG M:CYS50 2.3 315.2 1.0
CB M:CYS53 2.7 349.3 1.0
N M:CYS71 3.1 330.7 1.0
CB M:CYS71 3.1 330.7 1.0
N M:CYS53 3.4 349.3 1.0
CB M:CYS50 3.4 315.2 1.0
CA M:CYS71 3.7 330.7 1.0
CA M:CYS53 3.7 349.3 1.0
NH2 M:ARG58 3.8 321.1 1.0
C M:PHE70 4.1 309.4 1.0
CB M:CYS74 4.1 335.2 1.0
OD1 M:ASN73 4.2 336.6 1.0
CA M:PHE70 4.3 309.4 1.0
CZ M:ARG58 4.3 321.1 1.0
NH1 M:ARG58 4.4 321.1 1.0
CB M:ARG52 4.5 337.6 1.0
C M:ARG52 4.5 337.6 1.0
CB M:PHE70 4.6 309.4 1.0
C M:CYS71 4.7 330.7 1.0
CA M:CYS50 4.8 315.2 1.0
CD1 M:LEU57 4.9 312.1 1.0
C M:CYS53 4.9 349.3 1.0
CA M:ARG52 4.9 337.6 1.0
O M:CYS71 4.9 330.7 1.0

Zinc binding site 4 out of 4 in 8grq

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Zinc binding site 4 out of 4 in the Cryo-Em Structure of BRCA1/BARD1 Bound to H2AK127-UBCH5C-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 BRCA1/BARD1 Bound to H2AK127-UBCH5C-Ub Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn202

b:353.5
occ:1.00
 CE1 M:HIS68 1.5 299.1 1.0
ND1 M:HIS68 2.1 299.1 1.0
CB M:CYS66 2.3 288.6 1.0
SG M:CYS83 2.3 333.4 1.0
SG M:CYS86 2.3 326.8 1.0
SG M:CYS66 2.3 288.6 1.0
NE2 M:HIS68 2.8 299.1 1.0
CB M:CYS86 2.9 326.8 1.0
CG M:HIS68 3.3 299.1 1.0
N M:CYS86 3.6 326.8 1.0
CA M:CYS66 3.6 288.6 1.0
CD2 M:HIS68 3.7 299.1 1.0
CB M:CYS83 3.7 333.4 1.0
CA M:CYS86 3.8 326.8 1.0
C M:CYS66 4.0 288.6 1.0
N M:GLU67 4.4 276.3 1.0
O M:CYS66 4.5 288.6 1.0
CB M:HIS68 4.5 299.1 1.0
C M:VAL85 4.7 324.4 1.0
N M:CYS66 4.7 288.6 1.0
N M:VAL85 4.8 324.4 1.0
CB M:VAL85 4.9 324.4 1.0
C M:CYS86 4.9 326.8 1.0
CA M:CYS83 5.0 333.4 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 00:45:17 2023

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