Zinc in PDB 7lyb: Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C

Enzymatic activity of Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C

All present enzymatic activity of Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C:
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 Structure of the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C (pdb code 7lyb). 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 the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C, PDB code: 7lyb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7lyb

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Zinc binding site 1 out of 4 in the Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C


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 the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:161.3
occ:1.00
SG M:CYS24 2.3 119.9 1.0
SG M:CYS44 2.3 120.0 1.0
SG M:CYS27 2.3 123.0 1.0
SG M:CYS47 2.3 121.0 1.0
CB M:CYS44 2.9 120.0 1.0
CB M:CYS24 3.0 119.9 1.0
CB M:CYS47 3.4 121.0 1.0
NZ M:LYS32 3.4 122.7 1.0
CB M:CYS27 3.7 123.0 1.0
N M:CYS44 3.7 120.0 1.0
N M:CYS27 3.9 123.0 1.0
CA M:CYS44 3.9 120.0 1.0
CA M:CYS27 4.3 123.0 1.0
CA M:CYS24 4.4 119.9 1.0
CE M:LYS32 4.5 122.7 1.0
N M:CYS47 4.6 121.0 1.0
C M:PHE43 4.6 112.6 1.0
CA M:CYS47 4.6 121.0 1.0
CB M:ILE26 4.8 117.3 1.0
C M:CYS44 4.9 120.0 1.0
C M:CYS27 4.9 123.0 1.0
N M:LEU28 4.9 121.5 1.0
CA M:PHE43 5.0 112.6 1.0
C M:ILE26 5.0 117.3 1.0

Zinc binding site 2 out of 4 in 7lyb

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Zinc binding site 2 out of 4 in the Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C


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 the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn202

b:138.4
occ:1.00
CD2 M:HIS41 1.5 109.5 1.0
NE2 M:HIS41 2.0 109.5 1.0
SG M:CYS39 2.3 106.0 1.0
SG M:CYS61 2.3 109.9 1.0
SG M:CYS64 2.3 113.5 1.0
CG M:HIS41 2.8 109.5 1.0
CB M:CYS39 3.1 106.0 1.0
CE1 M:HIS41 3.3 109.5 1.0
CB M:CYS61 3.6 109.9 1.0
ND1 M:HIS41 3.6 109.5 1.0
CB M:CYS64 3.7 113.5 1.0
N M:CYS64 3.7 113.5 1.0
CB M:HIS41 3.9 109.5 1.0
N M:LYS65 4.0 110.2 1.0
CG M:LYS65 4.0 110.2 1.0
CA M:CYS64 4.1 113.5 1.0
NZ M:LYS65 4.3 110.2 1.0
CB M:LEU63 4.4 110.0 1.0
OG1 M:THR37 4.5 103.2 1.0
CA M:CYS39 4.5 106.0 1.0
C M:CYS64 4.6 113.5 1.0
CB M:LYS65 4.6 110.2 1.0
CD M:LYS65 4.7 110.2 1.0
O M:CYS39 4.7 106.0 1.0
C M:LEU63 4.7 110.0 1.0
C M:CYS39 4.8 106.0 1.0
N M:LEU63 4.8 110.0 1.0
CA M:LYS65 4.9 110.2 1.0
CA M:LEU63 4.9 110.0 1.0
CA M:CYS61 4.9 109.9 1.0
CG M:LEU63 5.0 110.0 1.0

Zinc binding site 3 out of 4 in 7lyb

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Zinc binding site 3 out of 4 in the Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C


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 the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn201

b:158.9
occ:1.00
SG N:CYS50 2.3 121.6 1.0
SG N:CYS53 2.3 125.0 1.0
SG N:CYS71 2.4 123.8 1.0
SG N:CYS74 2.4 122.8 1.0
CB N:CYS71 2.6 123.8 1.0
N N:CYS71 2.8 123.8 1.0
CB N:CYS53 2.9 125.0 1.0
CA N:CYS71 3.2 123.8 1.0
N N:CYS53 3.3 125.0 1.0
CB N:CYS50 3.5 121.6 1.0
CA N:CYS53 3.7 125.0 1.0
CB N:CYS74 3.9 122.8 1.0
C N:PHE70 3.9 120.7 1.0
O N:CYS71 4.0 123.8 1.0
C N:CYS71 4.0 123.8 1.0
CB N:PHE70 4.3 120.7 1.0
CA N:PHE70 4.4 120.7 1.0
C N:ARG52 4.4 118.4 1.0
CB N:ARG52 4.4 118.4 1.0
CA N:ARG52 4.8 118.4 1.0
N N:ARG52 4.8 118.4 1.0
CA N:CYS50 4.9 121.6 1.0
N N:CYS74 4.9 122.8 1.0
CD1 N:PHE70 4.9 120.7 1.0
C N:CYS53 5.0 125.0 1.0
O N:PHE70 5.0 120.7 1.0

Zinc binding site 4 out of 4 in 7lyb

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Zinc binding site 4 out of 4 in the Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C


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 the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn202

b:130.0
occ:1.00
ND1 N:HIS68 2.1 107.3 1.0
SG N:CYS86 2.3 92.1 1.0
SG N:CYS83 2.3 96.3 1.0
SG N:CYS66 2.3 98.0 1.0
CG N:HIS68 2.7 107.3 1.0
CB N:HIS68 2.9 107.3 1.0
CB N:CYS66 3.1 98.0 1.0
CE1 N:HIS68 3.1 107.3 1.0
CB N:CYS86 3.2 92.1 1.0
CB N:CYS83 3.4 96.3 1.0
CD2 N:HIS68 3.8 107.3 1.0
N N:CYS86 3.9 92.1 1.0
N N:HIS68 3.9 107.3 1.0
NE2 N:HIS68 4.0 107.3 1.0
CA N:HIS68 4.0 107.3 1.0
CA N:CYS86 4.1 92.1 1.0
CA N:CYS66 4.5 98.0 1.0
N N:GLU67 4.6 107.1 1.0
C N:CYS66 4.7 98.0 1.0
CB N:VAL85 4.8 93.8 1.0
CA N:CYS83 4.8 96.3 1.0
C N:VAL85 5.0 93.8 1.0
C N:HIS68 5.0 107.3 1.0

Reference:

Q.Hu, M.V.Botuyan, D.Zhao, D.Cui, E.Mer, G.Mer. Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with BRCA1-BARD1-UBCH5C To Be Published.
Page generated: Sun Aug 22 09:48:16 2021

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