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Zinc in PDB 8h36: Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex

Enzymatic activity of Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex

All present enzymatic activity of Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex:
2.3.2.27; 2.3.2.32;

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex (pdb code 8h36). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex, PDB code: 8h36:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8h36

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex


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 KBTBD2-CUL3-RBX1-P85A Dimeric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn4001

b:104.2
occ:1.00
 ND1 E:HIS80 2.0 112.2 1.0
SG E:CYS42 2.3 136.0 1.0
SG E:CYS45 2.4 137.7 1.0
SG E:CYS83 2.6 118.1 1.0
CE1 E:HIS80 3.0 112.3 1.0
CG E:HIS80 3.0 112.4 1.0
CB E:CYS83 3.2 117.6 1.0
CB E:CYS42 3.3 136.2 1.0
CB E:CYS45 3.4 137.7 1.0
CB E:HIS80 3.4 112.5 1.0
N E:CYS45 3.9 137.4 1.0
N E:HIS80 4.0 112.2 1.0
NE2 E:HIS80 4.1 112.3 1.0
CD2 E:HIS80 4.1 112.3 1.0
CA E:CYS45 4.2 137.8 1.0
CB E:CYS53 4.3 143.4 1.0
CA E:HIS80 4.3 112.5 1.0
CA E:CYS53 4.3 143.5 1.0
CA E:CYS83 4.6 117.7 1.0
CA E:CYS42 4.7 136.3 1.0
CB E:ILE44 4.8 136.6 1.0
N E:ARG46 4.9 138.5 1.0
C E:ILE44 4.9 137.0 1.0
C E:CYS45 4.9 138.1 1.0
N E:CYS83 5.0 116.9 1.0
O E:HIS80 5.0 112.9 1.0

Zinc binding site 2 out of 6 in 8h36

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex


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 KBTBD2-CUL3-RBX1-P85A Dimeric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn4002

b:92.5
occ:1.00
 ND1 E:HIS77 2.1 113.1 1.0
SG E:CYS75 2.4 115.9 1.0
SG E:CYS94 2.6 129.2 1.0
OD1 E:ASP97 2.8 131.1 1.0
CE1 E:HIS77 2.9 113.2 1.0
OD2 E:ASP97 3.0 131.3 1.0
CB E:CYS75 3.0 116.0 1.0
CG E:ASP97 3.1 131.3 1.0
CG E:HIS77 3.2 112.9 1.0
CB E:HIS77 3.7 112.9 1.0
CB E:CYS94 3.9 130.0 1.0
NE2 E:HIS77 4.1 113.1 1.0
CD2 E:HIS77 4.3 113.0 1.0
CA E:CYS75 4.4 116.0 1.0
O E:CYS75 4.4 115.6 1.0
CB E:ASP97 4.4 131.3 1.0
C E:CYS75 4.5 115.6 1.0
CE3 E:TRP101 4.6 129.1 1.0
CB E:LEU96 4.6 130.6 1.0
N E:HIS77 4.7 113.4 1.0
N E:ASP97 4.7 131.1 1.0
C E:LEU96 4.7 130.8 1.0
CZ3 E:TRP101 4.8 128.8 1.0
CA E:HIS77 4.8 112.9 1.0
CA E:LEU96 5.0 130.6 1.0

Zinc binding site 3 out of 6 in 8h36

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex


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 KBTBD2-CUL3-RBX1-P85A Dimeric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn4003

b:104.9
occ:1.00
 SG E:CYS68 2.2 133.8 1.0
SG E:CYS56 2.3 146.0 1.0
SG E:CYS53 2.3 143.1 1.0
ND1 E:HIS82 2.4 115.0 1.0
CG E:HIS82 3.1 115.1 1.0
CE1 E:HIS82 3.2 114.9 1.0
CB E:CYS56 3.3 146.0 1.0
CB E:HIS82 3.4 115.4 1.0
CB E:CYS53 3.4 143.4 1.0
NH1 C:ARG751 3.5 170.4 1.0
CB E:CYS68 3.7 134.2 1.0
N E:CYS53 4.0 143.3 1.0
CD2 E:HIS82 4.1 114.8 1.0
NE2 E:HIS82 4.1 114.7 1.0
N E:CYS56 4.1 145.7 1.0
CA E:CYS56 4.3 146.0 1.0
CA E:CYS53 4.4 143.5 1.0
CA E:CYS68 4.8 134.1 1.0
CZ C:ARG751 4.8 170.4 1.0
CA E:HIS82 4.9 115.5 1.0

Zinc binding site 4 out of 6 in 8h36

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex


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 KBTBD2-CUL3-RBX1-P85A Dimeric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4001

b:104.2
occ:1.00
 ND1 D:HIS80 2.0 112.2 1.0
SG D:CYS42 2.3 136.0 1.0
SG D:CYS45 2.4 137.7 1.0
SG D:CYS83 2.6 118.1 1.0
CE1 D:HIS80 3.0 112.3 1.0
CG D:HIS80 3.0 112.4 1.0
CB D:CYS83 3.2 117.6 1.0
CB D:CYS42 3.3 136.2 1.0
CB D:CYS45 3.4 137.7 1.0
CB D:HIS80 3.4 112.5 1.0
N D:CYS45 3.9 137.4 1.0
N D:HIS80 4.0 112.2 1.0
NE2 D:HIS80 4.1 112.3 1.0
CB D:CYS53 4.1 143.4 1.0
CD2 D:HIS80 4.1 112.3 1.0
CA D:CYS45 4.2 137.8 1.0
CA D:HIS80 4.3 112.5 1.0
CA D:CYS83 4.6 117.7 1.0
CA D:CYS42 4.7 136.3 1.0
CB D:ILE44 4.8 136.6 1.0
CA D:CYS53 4.9 143.5 1.0
C D:ILE44 4.9 137.0 1.0
C D:CYS45 4.9 138.1 1.0
N D:ARG46 5.0 138.5 1.0
N D:CYS83 5.0 116.9 1.0
O D:HIS80 5.0 112.9 1.0

Zinc binding site 5 out of 6 in 8h36

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4002

b:92.5
occ:1.00
 ND1 D:HIS77 2.1 113.1 1.0
SG D:CYS75 2.4 115.9 1.0
SG D:CYS94 2.6 129.2 1.0
OD1 D:ASP97 2.8 131.1 1.0
CE1 D:HIS77 2.9 113.2 1.0
OD2 D:ASP97 3.0 131.3 1.0
CB D:CYS75 3.0 116.0 1.0
CG D:ASP97 3.1 131.3 1.0
CG D:HIS77 3.2 112.9 1.0
CB D:HIS77 3.7 112.9 1.0
CB D:CYS94 3.9 130.0 1.0
NE2 D:HIS77 4.1 113.1 1.0
CD2 D:HIS77 4.3 113.0 1.0
CA D:CYS75 4.4 116.0 1.0
O D:CYS75 4.4 115.6 1.0
CB D:ASP97 4.4 131.3 1.0
C D:CYS75 4.5 115.6 1.0
CB D:LEU96 4.6 130.6 1.0
N D:HIS77 4.7 113.4 1.0
N D:ASP97 4.7 131.1 1.0
C D:LEU96 4.7 130.8 1.0
CA D:HIS77 4.8 112.9 1.0
CA D:LEU96 5.0 130.6 1.0

Zinc binding site 6 out of 6 in 8h36

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Zinc binding site 6 out of 6 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4003

b:104.9
occ:1.00
 SG D:CYS53 2.2 143.1 1.0
SG D:CYS68 2.2 133.8 1.0
SG D:CYS56 2.3 146.0 1.0
ND1 D:HIS82 2.3 115.0 1.0
CG D:HIS82 3.1 115.1 1.0
CE1 D:HIS82 3.2 114.9 1.0
CB D:HIS82 3.4 115.4 1.0
CB D:CYS56 3.4 146.0 1.0
CB D:CYS68 3.7 134.2 1.0
CB D:CYS53 3.8 143.4 1.0
O D:GLU55 3.9 145.5 1.0
C D:GLU55 4.0 145.4 1.0
CD2 D:HIS82 4.1 114.8 1.0
N D:CYS56 4.1 145.7 1.0
NE2 D:HIS82 4.1 114.7 1.0
CA D:CYS56 4.3 146.0 1.0
N D:CYS53 4.4 143.3 1.0
CD1 D:LEU52 4.5 143.4 1.0
CB D:GLU55 4.5 145.1 1.0
CA D:CYS53 4.6 143.5 1.0
CA D:GLU55 4.7 145.1 1.0
CA D:CYS68 4.8 134.1 1.0
N D:GLU55 4.8 144.8 1.0
CA D:HIS82 4.9 115.5 1.0

Reference:

Y.Hu, Q.Mao, Z.Chen, L.Sun. Cryo-Em Structure of the KBTBD2-CUL3-RBX1-P85A Dimeric Complex To Be Published.
Page generated: Fri Aug 22 10:38:37 2025

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