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Zinc in PDB 8h35: Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric Complex

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

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

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric Complex (pdb code 8h35). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric Complex, PDB code: 8h35:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 8h35

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Zinc binding site 1 out of 24 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric 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 Octameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn4001

b:104.2
occ:1.00
 ND1 E:HIS80 2.1 112.2 1.0
SG E:CYS45 2.3 137.7 1.0
SG E:CYS83 2.3 118.1 1.0
SG E:CYS42 2.3 136.0 1.0
CE1 E:HIS80 2.8 112.3 1.0
CB E:CYS42 3.0 136.2 1.0
CB E:CYS45 3.0 137.7 1.0
CG E:HIS80 3.2 112.4 1.0
CB E:CYS83 3.6 117.6 1.0
CB E:HIS80 3.7 112.5 1.0
N E:CYS45 3.7 137.4 1.0
CA E:CYS45 3.9 137.8 1.0
NE2 E:HIS80 4.0 112.3 1.0
CD2 E:HIS80 4.2 112.3 1.0
CB E:CYS53 4.2 143.4 1.0
N E:HIS80 4.3 112.2 1.0
CA E:CYS42 4.5 136.3 1.0
C E:CYS45 4.6 138.1 1.0
CA E:HIS80 4.6 112.5 1.0
N E:ARG46 4.6 138.5 1.0
O E:HIS48 4.7 141.4 1.0
C E:ILE44 4.8 137.0 1.0
CA E:CYS53 4.9 143.5 1.0
CB E:ILE44 4.9 136.6 1.0

Zinc binding site 2 out of 24 in 8h35

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Zinc binding site 2 out of 24 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric 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 Octameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn4002

b:92.5
occ:1.00
 OD2 E:ASP97 2.1 131.3 1.0
SG E:CYS75 2.3 115.9 1.0
ND1 E:HIS77 2.3 113.1 1.0
SG E:CYS94 2.3 129.2 1.0
CB E:CYS94 2.9 130.0 1.0
CG E:ASP97 3.1 131.3 1.0
CE1 E:HIS77 3.2 113.2 1.0
CG E:HIS77 3.3 112.9 1.0
OD1 E:ASP97 3.4 131.1 1.0
CB E:CYS75 3.4 116.0 1.0
CB E:HIS77 3.5 112.9 1.0
CE3 E:TRP101 4.3 129.1 1.0
NE2 E:HIS77 4.3 113.1 1.0
CA E:CYS94 4.4 130.1 1.0
CD2 E:HIS77 4.4 113.0 1.0
CZ3 E:TRP101 4.4 128.8 1.0
CB E:ASP97 4.4 131.3 1.0
CZ3 E:TRP35 4.5 160.4 1.0
CE3 E:TRP35 4.7 160.4 1.0
O E:CYS75 4.7 115.6 1.0
CA E:CYS75 4.7 116.0 1.0
C E:CYS94 4.8 130.2 1.0
CA E:HIS77 4.9 112.9 1.0
O E:CYS94 4.9 130.2 1.0
N E:ASP97 4.9 131.1 1.0
C E:CYS75 5.0 115.6 1.0
N E:HIS77 5.0 113.4 1.0

Zinc binding site 3 out of 24 in 8h35

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Zinc binding site 3 out of 24 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric 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 Octameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn4003

b:104.9
occ:1.00
 ND1 E:HIS82 2.1 115.0 1.0
SG E:CYS56 2.3 146.0 1.0
SG E:CYS68 2.3 133.8 1.0
SG E:CYS53 2.3 143.1 1.0
CE1 E:HIS82 2.8 114.9 1.0
CG E:HIS82 3.0 115.1 1.0
CB E:CYS56 3.1 146.0 1.0
NH1 C:ARG751 3.5 170.4 1.0
CB E:HIS82 3.5 115.4 1.0
CB E:CYS68 3.7 134.2 1.0
CB E:CYS53 3.8 143.4 1.0
NE2 E:HIS82 3.9 114.7 1.0
CD2 E:HIS82 4.0 114.8 1.0
N E:CYS53 4.2 143.3 1.0
CA E:CYS56 4.3 146.0 1.0
N E:CYS56 4.3 145.7 1.0
CA E:CYS68 4.6 134.1 1.0
CA E:CYS53 4.6 143.5 1.0
CZ C:ARG751 4.8 170.4 1.0
C E:GLU55 4.9 145.4 1.0
CA E:HIS82 4.9 115.5 1.0
C E:LEU52 5.0 143.2 1.0

Zinc binding site 4 out of 24 in 8h35

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Zinc binding site 4 out of 24 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric 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 Octameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4001

b:104.2
occ:1.00
 ND1 D:HIS80 2.1 112.2 1.0
SG D:CYS83 2.3 118.1 1.0
SG D:CYS42 2.3 136.0 1.0
SG D:CYS45 2.3 137.7 1.0
CE1 D:HIS80 2.5 112.3 1.0
CG D:HIS80 3.3 112.4 1.0
CB D:CYS42 3.4 136.2 1.0
CB D:CYS45 3.4 137.7 1.0
NE2 D:HIS80 3.7 112.3 1.0
CB D:CYS83 3.7 117.6 1.0
N D:CYS45 3.9 137.4 1.0
CD2 D:HIS80 4.1 112.3 1.0
CB D:HIS80 4.1 112.5 1.0
CA D:CYS45 4.2 137.8 1.0
N D:HIS80 4.2 112.2 1.0
O D:HIS48 4.3 141.4 1.0
O D:CYS42 4.6 136.3 1.0
CA D:CYS42 4.6 136.3 1.0
C D:CYS45 4.6 138.1 1.0
CB D:ASN47 4.7 139.8 1.0
CB D:CYS53 4.7 143.4 1.0
N D:ARG46 4.8 138.5 1.0
CA D:HIS80 4.8 112.5 1.0
C D:CYS42 4.9 136.2 1.0
N D:ASN47 4.9 139.5 1.0
C D:ILE44 5.0 137.0 1.0

Zinc binding site 5 out of 24 in 8h35

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Zinc binding site 5 out of 24 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric 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 Octameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4002

b:92.5
occ:1.00
 OD2 D:ASP97 2.1 131.3 1.0
ND1 D:HIS77 2.3 113.1 1.0
SG D:CYS94 2.3 129.2 1.0
SG D:CYS75 2.3 115.9 1.0
OD1 D:ASP97 2.6 131.1 1.0
CG D:ASP97 2.7 131.3 1.0
CB D:CYS75 2.7 116.0 1.0
CE1 D:HIS77 3.1 113.2 1.0
CG D:HIS77 3.4 112.9 1.0
CB D:CYS94 3.4 130.0 1.0
CB D:HIS77 3.8 112.9 1.0
O D:CYS75 3.9 115.6 1.0
CA D:CYS75 4.1 116.0 1.0
CB D:ASP97 4.1 131.3 1.0
NE2 D:HIS77 4.3 113.1 1.0
O D:CYS94 4.3 130.2 1.0
C D:CYS75 4.3 115.6 1.0
CD2 D:HIS77 4.4 113.0 1.0
N D:ASP97 4.5 131.1 1.0
CA D:CYS94 4.7 130.1 1.0
CB D:ARG99 4.8 132.2 1.0
N D:HIS77 4.8 113.4 1.0
C D:CYS94 4.9 130.2 1.0
CB D:LEU96 4.9 130.6 1.0
CG D:ARG99 4.9 132.8 1.0
CA D:ASP97 4.9 131.3 1.0
C D:LEU96 4.9 130.8 1.0
CA D:HIS77 4.9 112.9 1.0
N D:CYS75 5.0 116.6 1.0

Zinc binding site 6 out of 24 in 8h35

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Zinc binding site 6 out of 24 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric 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 Octameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4003

b:104.9
occ:1.00
 ND1 D:HIS82 2.1 115.0 1.0
SG D:CYS56 2.3 146.0 1.0
SG D:CYS68 2.3 133.8 1.0
SG D:CYS53 2.3 143.1 1.0
CG D:HIS82 2.9 115.1 1.0
CE1 D:HIS82 3.0 114.9 1.0
CB D:HIS82 3.2 115.4 1.0
NH1 F:ARG751 3.2 204.2 1.0
CB D:CYS56 3.4 146.0 1.0
CB D:CYS68 3.4 134.2 1.0
CB D:CYS53 3.7 143.4 1.0
CD2 D:HIS82 3.9 114.8 1.0
NE2 D:HIS82 4.0 114.7 1.0
N D:CYS56 4.3 145.7 1.0
CA D:CYS56 4.3 146.0 1.0
N D:CYS53 4.4 143.3 1.0
CZ F:ARG751 4.5 204.2 1.0
CA D:CYS68 4.6 134.1 1.0
C D:GLU55 4.6 145.4 1.0
CA D:CYS53 4.6 143.5 1.0
CA D:HIS82 4.6 115.5 1.0
O D:GLU55 4.9 145.5 1.0

Zinc binding site 7 out of 24 in 8h35

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Zinc binding site 7 out of 24 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn4001

b:104.2
occ:1.00
 ND1 L:HIS80 2.1 112.2 1.0
SG L:CYS45 2.3 137.7 1.0
SG L:CYS83 2.3 118.1 1.0
SG L:CYS42 2.3 136.0 1.0
CE1 L:HIS80 2.8 112.3 1.0
CB L:CYS42 3.0 136.2 1.0
CB L:CYS45 3.0 137.7 1.0
CG L:HIS80 3.2 112.4 1.0
CB L:CYS83 3.6 117.6 1.0
CB L:HIS80 3.7 112.5 1.0
N L:CYS45 3.7 137.4 1.0
CA L:CYS45 3.9 137.8 1.0
NE2 L:HIS80 4.0 112.3 1.0
CD2 L:HIS80 4.2 112.3 1.0
CB L:CYS53 4.2 143.4 1.0
N L:HIS80 4.3 112.2 1.0
CA L:CYS42 4.5 136.3 1.0
C L:CYS45 4.6 138.1 1.0
CA L:HIS80 4.6 112.5 1.0
N L:ARG46 4.6 138.5 1.0
O L:HIS48 4.7 141.4 1.0
C L:ILE44 4.8 137.0 1.0
CA L:CYS53 4.9 143.5 1.0
CB L:ILE44 4.9 136.6 1.0

Zinc binding site 8 out of 24 in 8h35

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Zinc binding site 8 out of 24 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn4002

b:92.5
occ:1.00
 SG L:CYS75 2.3 115.9 1.0
ND1 L:HIS77 2.3 113.1 1.0
CB L:CYS94 2.9 130.0 1.0
CE1 L:HIS77 3.2 113.2 1.0
CG L:HIS77 3.3 112.9 1.0
CB L:CYS75 3.4 116.0 1.0
CB L:HIS77 3.5 112.9 1.0
CE3 L:TRP101 4.3 129.1 1.0
NE2 L:HIS77 4.3 113.1 1.0
CA L:CYS94 4.4 130.1 1.0
CD2 L:HIS77 4.4 113.0 1.0
CZ3 L:TRP101 4.4 128.8 1.0
CB L:ASP97 4.4 131.3 1.0
CZ3 L:TRP35 4.5 160.4 1.0
CE3 L:TRP35 4.7 160.4 1.0
O L:CYS75 4.7 115.6 1.0
CA L:CYS75 4.7 116.0 1.0
C L:CYS94 4.8 130.2 1.0
CA L:HIS77 4.9 112.9 1.0
O L:CYS94 4.9 130.2 1.0
N L:ASP97 4.9 131.1 1.0
C L:CYS75 5.0 115.6 1.0
N L:HIS77 5.0 113.4 1.0

Zinc binding site 9 out of 24 in 8h35

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Zinc binding site 9 out of 24 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn4003

b:104.9
occ:1.00
 ND1 L:HIS82 2.1 115.0 1.0
SG L:CYS56 2.3 146.0 1.0
SG L:CYS68 2.3 133.8 1.0
SG L:CYS53 2.3 143.1 1.0
CE1 L:HIS82 2.8 114.9 1.0
CG L:HIS82 3.0 115.1 1.0
CB L:CYS56 3.1 146.0 1.0
NH1 I:ARG751 3.5 170.4 1.0
CB L:HIS82 3.5 115.4 1.0
CB L:CYS68 3.7 134.2 1.0
CB L:CYS53 3.8 143.4 1.0
NE2 L:HIS82 3.9 114.7 1.0
CD2 L:HIS82 4.0 114.8 1.0
N L:CYS53 4.2 143.3 1.0
CA L:CYS56 4.3 146.0 1.0
N L:CYS56 4.3 145.7 1.0
CA L:CYS68 4.6 134.1 1.0
CA L:CYS53 4.6 143.5 1.0
CZ I:ARG751 4.8 170.4 1.0
C L:GLU55 4.9 145.4 1.0
CA L:HIS82 4.9 115.5 1.0
C L:LEU52 5.0 143.2 1.0

Zinc binding site 10 out of 24 in 8h35

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Zinc binding site 10 out of 24 in the Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn4001

b:104.2
occ:1.00
 ND1 K:HIS80 2.1 112.2 1.0
CB K:CYS42 2.2 136.2 1.0
SG K:CYS45 2.3 137.7 1.0
SG K:CYS83 2.3 118.1 1.0
SG K:CYS42 2.3 136.0 1.0
CE1 K:HIS80 2.5 112.3 1.0
CB K:CYS45 2.8 137.7 1.0
CG K:HIS80 3.3 112.4 1.0
N K:CYS45 3.4 137.4 1.0
NE2 K:HIS80 3.7 112.3 1.0
CA K:CYS45 3.7 137.8 1.0
CB K:CYS83 3.7 117.6 1.0
CA K:CYS42 3.7 136.3 1.0
CD2 K:HIS80 4.1 112.3 1.0
CB K:HIS80 4.1 112.5 1.0
N K:HIS80 4.2 112.2 1.0
C K:CYS42 4.3 136.2 1.0
C K:CYS45 4.4 138.1 1.0
O K:HIS48 4.4 141.4 1.0
N K:ARG46 4.5 138.5 1.0
N K:CYS42 4.5 136.5 1.0
C K:ILE44 4.5 137.0 1.0
O K:CYS42 4.6 136.3 1.0
CB K:ILE44 4.7 136.6 1.0
CB K:CYS53 4.7 143.4 1.0
N K:ILE44 4.7 136.5 1.0
CA K:HIS80 4.8 112.5 1.0
ND2 K:ASN47 4.9 139.8 1.0
CA K:ILE44 4.9 136.8 1.0

Reference:

Y.Hu, Q.Mao, Z.Chen, L.Sun. Cryo-Em Structure of the KBTBD2-CUL3-RBX1 Octameric Complex To Be Published.
Page generated: Fri Aug 22 10:37:32 2025

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