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

Go back to Zinc Binding Sites List in 8grq
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

Go back to Zinc Binding Sites List in 8grq
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

Go back to Zinc Binding Sites List in 8grq
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

Go back to Zinc Binding Sites List in 8grq
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

Last articles

Cl in 4NHT
Cl in 4NO7
Cl in 4NML
Cl in 4NN3
Cl in 4NMW
Cl in 4NM7
Cl in 4NM5
Cl in 4NM3
Cl in 4NM0
Cl in 4NHQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy