Zinc in PDB 8wqh: Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2)

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 8wqh

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


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 Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn200

b:52.8
occ:1.00
 ND1 J:HIS82 2.1 36.3 1.0
SG J:CYS68 2.3 44.3 1.0
SG J:CYS56 2.3 46.8 1.0
SG J:CYS53 2.3 40.0 1.0
CB J:CYS56 2.4 46.8 1.0
CE1 J:HIS82 2.8 36.3 1.0
CG J:HIS82 2.9 36.3 1.0
CB J:HIS82 3.4 36.3 1.0
CB J:CYS53 3.6 40.0 1.0
CA J:CYS56 3.7 46.8 1.0
N J:CYS56 3.8 46.8 1.0
CB J:CYS68 3.8 44.3 1.0
NE2 J:HIS82 3.8 36.3 1.0
CD2 J:HIS82 3.9 36.3 1.0
CA J:CYS68 4.2 44.3 1.0
N J:CYS53 4.3 40.0 1.0
CA J:CYS53 4.5 40.0 1.0
O J:CYS53 4.7 40.0 1.0
C J:CYS56 4.7 46.8 1.0
N J:CYS68 4.7 44.3 1.0
CA J:HIS82 4.8 36.3 1.0
C J:CYS53 4.8 40.0 1.0
C J:GLU55 4.9 46.2 1.0
N J:HIS82 5.0 36.3 1.0

Zinc binding site 2 out of 6 in 8wqh

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


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 Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn201

b:26.9
occ:1.00
 ND1 J:HIS80 2.1 29.4 1.0
SG J:CYS45 2.3 27.4 1.0
SG J:CYS42 2.3 27.8 1.0
SG J:CYS83 2.3 32.1 1.0
CB J:CYS42 2.9 27.8 1.0
CG J:HIS80 3.0 29.4 1.0
CE1 J:HIS80 3.1 29.4 1.0
CB J:HIS80 3.2 29.4 1.0
CB J:CYS45 3.3 27.4 1.0
CB J:CYS83 3.3 32.1 1.0
N J:HIS80 3.9 29.4 1.0
CB J:CYS53 4.0 40.0 1.0
N J:CYS45 4.0 27.4 1.0
CD2 J:HIS80 4.1 29.4 1.0
CA J:HIS80 4.2 29.4 1.0
NE2 J:HIS80 4.2 29.4 1.0
CA J:CYS45 4.3 27.4 1.0
CA J:CYS42 4.4 27.8 1.0
CA J:CYS53 4.5 40.0 1.0
CA J:CYS83 4.7 32.1 1.0
O J:CYS42 4.9 27.8 1.0
C J:CYS42 4.9 27.8 1.0
CB J:ILE44 4.9 26.0 1.0
N J:CYS83 5.0 32.1 1.0

Zinc binding site 3 out of 6 in 8wqh

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2)


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 Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn202

b:49.3
occ:1.00
 SG J:CYS75 2.3 38.0 1.0
SG J:CYS94 2.3 37.2 1.0
ND1 J:HIS77 2.3 34.0 1.0
CE1 J:HIS77 3.0 34.0 1.0
CB J:CYS94 3.1 37.2 1.0
CB J:CYS75 3.2 38.0 1.0
CB J:ASP97 3.2 42.7 1.0
CG J:HIS77 3.5 34.0 1.0
N J:ASP97 3.8 42.7 1.0
O J:ASP97 3.9 42.7 1.0
CA J:ASP97 4.0 42.7 1.0
CB J:HIS77 4.0 34.0 1.0
NE2 J:HIS77 4.2 34.0 1.0
CG J:ASP97 4.4 42.7 1.0
C J:ASP97 4.4 42.7 1.0
CD2 J:HIS77 4.5 34.0 1.0
OD2 J:ASP97 4.5 42.7 1.0
CA J:CYS94 4.6 37.2 1.0
CA J:CYS75 4.6 38.0 1.0
CZ3 J:TRP101 4.7 35.2 1.0
O J:CYS75 4.7 38.0 1.0
CE3 J:TRP101 4.8 35.2 1.0
C J:LEU96 4.9 36.8 1.0
CB J:LEU96 5.0 36.8 1.0
C J:CYS75 5.0 38.0 1.0
C J:CYS94 5.0 37.2 1.0

Zinc binding site 4 out of 6 in 8wqh

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2)


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 Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:67.0
occ:1.00
 ND1 B:HIS82 2.1 48.8 1.0
SG B:CYS68 2.3 60.4 1.0
SG B:CYS53 2.3 56.2 1.0
SG B:CYS56 2.3 63.3 1.0
CE1 B:HIS82 2.5 48.8 1.0
CB B:CYS56 2.6 63.3 1.0
CG B:HIS82 3.4 48.8 1.0
CB B:CYS53 3.4 56.2 1.0
NE2 B:HIS82 3.8 48.8 1.0
CA B:CYS56 3.8 63.3 1.0
N B:CYS56 3.8 63.3 1.0
CB B:CYS68 3.8 60.4 1.0
N B:CYS53 4.0 56.2 1.0
CB B:HIS82 4.1 48.8 1.0
CA B:CYS68 4.1 60.4 1.0
CD2 B:HIS82 4.2 48.8 1.0
CA B:CYS53 4.2 56.2 1.0
N B:CYS68 4.6 60.4 1.0
O B:CYS53 4.7 56.2 1.0
C B:CYS53 4.8 56.2 1.0
C B:GLU55 4.9 64.6 1.0
C B:CYS56 4.9 63.3 1.0

Zinc binding site 5 out of 6 in 8wqh

Go back to Zinc Binding Sites List in 8wqh
Zinc binding site 5 out of 6 in the Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2)


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 Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:54.8
occ:1.00
 ND1 B:HIS80 2.1 42.4 1.0
SG B:CYS83 2.3 42.8 1.0
SG B:CYS45 2.3 40.7 1.0
SG B:CYS42 2.3 40.5 1.0
CE1 B:HIS80 2.7 42.4 1.0
CB B:CYS45 2.9 40.7 1.0
CB B:CYS42 3.4 40.5 1.0
CG B:HIS80 3.4 42.4 1.0
CB B:CYS83 3.4 42.8 1.0
CB B:CYS53 3.9 56.2 1.0
NE2 B:HIS80 4.0 42.4 1.0
OD1 B:ASN47 4.0 44.4 1.0
CB B:HIS80 4.0 42.4 1.0
N B:CYS45 4.0 40.7 1.0
CA B:CYS45 4.1 40.7 1.0
CA B:CYS53 4.2 56.2 1.0
CD2 B:HIS80 4.3 42.4 1.0
N B:ILE54 4.5 56.6 1.0
N B:HIS80 4.6 42.4 1.0
CA B:CYS83 4.8 42.8 1.0
CA B:CYS42 4.8 40.5 1.0
CA B:HIS80 4.9 42.4 1.0
CB B:ILE44 4.9 36.4 1.0
C B:CYS53 5.0 56.2 1.0

Zinc binding site 6 out of 6 in 8wqh

Go back to Zinc Binding Sites List in 8wqh
Zinc binding site 6 out of 6 in the Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2)


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 Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:71.3
occ:1.00
 OD1 B:ASP97 2.1 56.8 1.0
SG B:CYS75 2.3 57.7 1.0
SG B:CYS94 2.3 50.4 1.0
ND1 B:HIS77 2.3 49.4 1.0
CG B:ASP97 3.0 56.8 1.0
CB B:CYS75 3.1 57.7 1.0
CE1 B:HIS77 3.2 49.4 1.0
CG B:HIS77 3.3 49.4 1.0
OD2 B:ASP97 3.3 56.8 1.0
CB B:CYS94 3.5 50.4 1.0
CB B:HIS77 3.6 49.4 1.0
N B:ASP97 4.1 56.8 1.0
O B:ASP97 4.3 56.8 1.0
CB B:ASP97 4.4 56.8 1.0
NE2 B:HIS77 4.4 49.4 1.0
CD2 B:HIS77 4.4 49.4 1.0
CB B:LEU96 4.5 49.9 1.0
CA B:CYS75 4.5 57.7 1.0
CZ3 B:TRP101 4.6 48.3 1.0
O B:CYS75 4.6 57.7 1.0
CE3 B:TRP101 4.7 48.3 1.0
CA B:ASP97 4.7 56.8 1.0
C B:CYS75 4.8 57.7 1.0
CA B:CYS94 4.8 50.4 1.0
CA B:HIS77 4.9 49.4 1.0
N B:LEU96 4.9 49.9 1.0
N B:HIS77 5.0 49.4 1.0

Reference:

X.Chen, K.Zhang, C.Xu. Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CCDC89 (Conformation 2) To Be Published.
Page generated: Thu Oct 31 13:39:38 2024

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