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Zinc in PDB 8wqa: Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) (pdb code 8wqa). 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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1), PDB code: 8wqa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8wqa

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)


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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn200

b:74.5
occ:1.00
 CB J:CYS53 2.0 56.4 1.0
ND1 J:HIS82 2.1 45.4 1.0
SG J:CYS68 2.3 55.0 1.0
SG J:CYS56 2.3 66.8 1.0
SG J:CYS53 2.3 56.4 1.0
CG J:HIS82 3.0 45.4 1.0
CE1 J:HIS82 3.1 45.4 1.0
CB J:HIS82 3.3 45.4 1.0
CA J:CYS53 3.5 56.4 1.0
CB J:CYS56 3.6 66.8 1.0
N J:CYS56 3.9 66.8 1.0
CB J:CYS68 4.0 55.0 1.0
C J:CYS53 4.1 56.4 1.0
N J:CYS53 4.1 56.4 1.0
CD2 J:HIS82 4.2 45.4 1.0
NE2 J:HIS82 4.2 45.4 1.0
CA J:CYS56 4.4 66.8 1.0
O J:CYS53 4.5 56.4 1.0
CB J:GLU55 4.6 57.2 1.0
N J:GLU55 4.7 57.2 1.0
CA J:HIS82 4.7 45.4 1.0
C J:GLU55 4.8 57.2 1.0
N J:ILE54 4.8 53.3 1.0
CA J:GLU55 4.9 57.2 1.0

Zinc binding site 2 out of 6 in 8wqa

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)


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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn201

b:39.2
occ:1.00
 ND1 J:HIS80 2.1 36.4 1.0
SG J:CYS45 2.3 30.9 1.0
SG J:CYS83 2.3 36.4 1.0
SG J:CYS42 2.3 30.5 1.0
CE1 J:HIS80 3.0 36.4 1.0
CG J:HIS80 3.1 36.4 1.0
CB J:CYS42 3.2 30.5 1.0
CB J:CYS83 3.4 36.4 1.0
CB J:HIS80 3.4 36.4 1.0
CB J:CYS45 3.6 30.9 1.0
N J:CYS45 4.1 30.9 1.0
NE2 J:HIS80 4.1 36.4 1.0
CD2 J:HIS80 4.2 36.4 1.0
N J:HIS80 4.2 36.4 1.0
O J:CYS42 4.2 30.5 1.0
CA J:HIS80 4.5 36.4 1.0
CA J:CYS45 4.5 30.9 1.0
CA J:CYS42 4.5 30.5 1.0
C J:CYS42 4.7 30.5 1.0
CA J:CYS83 4.8 36.4 1.0
CB J:ILE44 4.8 25.7 1.0
O J:ASN47 4.9 32.4 1.0

Zinc binding site 3 out of 6 in 8wqa

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)


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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn202

b:70.5
occ:1.00
 CG J:HIS77 2.0 42.9 1.0
CD2 J:HIS77 2.1 42.9 1.0
SG J:CYS94 2.3 42.3 1.0
SG J:CYS75 2.3 46.5 1.0
ND1 J:HIS77 2.3 42.9 1.0
NE2 J:HIS77 2.5 42.9 1.0
CE1 J:HIS77 2.6 42.9 1.0
CB J:HIS77 2.8 42.9 1.0
OD1 J:ASP97 3.7 48.1 1.0
CB J:CYS75 3.9 46.5 1.0
CB J:CYS94 4.1 42.3 1.0
CA J:HIS77 4.2 42.9 1.0
O J:CYS75 4.5 46.5 1.0
CZ3 J:TRP101 4.6 38.4 1.0
CG J:ASP97 4.7 48.1 1.0
CE3 J:TRP101 4.8 38.4 1.0
CA J:CYS75 4.8 46.5 1.0
C J:CYS75 4.8 46.5 1.0
OD2 J:ASP97 4.9 48.1 1.0
C J:HIS77 4.9 42.9 1.0

Zinc binding site 4 out of 6 in 8wqa

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)


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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn200

b:57.6
occ:1.00
 ND1 I:HIS82 2.1 35.1 1.0
SG I:CYS68 2.3 48.7 1.0
SG I:CYS53 2.3 38.6 1.0
SG I:CYS56 2.3 48.3 1.0
CB I:CYS56 2.6 48.3 1.0
CE1 I:HIS82 2.6 35.1 1.0
CG I:HIS82 3.1 35.1 1.0
CB I:CYS68 3.7 48.7 1.0
NE2 I:HIS82 3.7 35.1 1.0
CB I:HIS82 3.8 35.1 1.0
CA I:CYS56 3.9 48.3 1.0
CB I:CYS53 3.9 38.6 1.0
CD2 I:HIS82 4.0 35.1 1.0
N I:CYS56 4.0 48.3 1.0
CA I:CYS68 4.2 48.7 1.0
N I:CYS53 4.4 38.6 1.0
N I:CYS68 4.6 48.7 1.0
CA I:CYS53 4.7 38.6 1.0
O I:CYS53 4.9 38.6 1.0
C I:CYS56 4.9 48.3 1.0

Zinc binding site 5 out of 6 in 8wqa

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)


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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:22.5
occ:1.00
 ND1 I:HIS80 2.1 23.9 1.0
SG I:CYS45 2.3 24.2 1.0
SG I:CYS83 2.3 27.1 1.0
SG I:CYS42 2.3 23.2 1.0
CE1 I:HIS80 2.9 23.9 1.0
CB I:CYS42 3.1 23.2 1.0
CG I:HIS80 3.1 23.9 1.0
CB I:CYS45 3.2 24.2 1.0
CB I:CYS83 3.2 27.1 1.0
CB I:HIS80 3.5 23.9 1.0
N I:CYS45 3.8 24.2 1.0
CA I:CYS45 4.1 24.2 1.0
N I:HIS80 4.1 23.9 1.0
NE2 I:HIS80 4.1 23.9 1.0
CB I:CYS53 4.2 38.6 1.0
CD2 I:HIS80 4.2 23.9 1.0
CA I:HIS80 4.4 23.9 1.0
CA I:CYS42 4.5 23.2 1.0
O I:CYS42 4.5 23.2 1.0
CA I:CYS83 4.7 27.1 1.0
CA I:CYS53 4.7 38.6 1.0
CB I:ILE44 4.7 18.7 1.0
C I:CYS42 4.8 23.2 1.0
C I:CYS45 4.9 24.2 1.0
C I:ILE44 4.9 18.7 1.0

Zinc binding site 6 out of 6 in 8wqa

Go back to Zinc Binding Sites List in 8wqa
Zinc binding site 6 out of 6 in the Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1)


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 CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:56.6
occ:1.00
 SG I:CYS94 2.3 32.7 1.0
SG I:CYS75 2.3 34.6 1.0
ND1 I:HIS77 2.3 31.5 1.0
CB I:CYS75 2.5 34.6 1.0
CE1 I:HIS77 2.9 31.5 1.0
CB I:CYS94 3.4 32.7 1.0
CG I:HIS77 3.5 31.5 1.0
CB I:ASP97 3.6 37.5 1.0
O I:ASP97 3.7 37.5 1.0
CA I:CYS75 4.0 34.6 1.0
N I:ASP97 4.0 37.5 1.0
O I:CYS75 4.1 34.6 1.0
NE2 I:HIS77 4.1 31.5 1.0
CB I:HIS77 4.2 31.5 1.0
CA I:ASP97 4.2 37.5 1.0
NH2 I:ARG99 4.3 38.7 1.0
C I:CYS75 4.4 34.6 1.0
C I:ASP97 4.4 37.5 1.0
CD2 I:HIS77 4.5 31.5 1.0
CA I:CYS94 4.8 32.7 1.0
N I:CYS75 4.9 34.6 1.0
CG I:ASP97 4.9 37.5 1.0

Reference:

X.Chen, K.Zhang, C.Xu. Cryo-Em Structure of CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 1) To Be Published.
Page generated: Fri Aug 22 15:17:26 2025

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