Zinc in PDB 8wqc: Cryo-Em Structure of Neddylated CUL2-RBX1-Elob-Eloc-FEM1B Bound with the C-Degron of CDK5R1

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 CDK5R1 (pdb code 8wqc). 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 CDK5R1, PDB code: 8wqc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8wqc

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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 CDK5R1


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 CDK5R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn200

b:70.3
occ:1.00
 ND1 F:HIS82 2.3 45.8 1.0
SG F:CYS56 2.3 58.7 1.0
SG F:CYS53 2.3 56.6 1.0
CB F:HIS82 2.3 45.8 1.0
CB F:CYS53 2.5 56.6 1.0
CG F:HIS82 2.5 45.8 1.0
NE2 F:GLN60 3.1 72.8 1.0
N F:CYS56 3.3 58.7 1.0
CE1 F:HIS82 3.5 45.8 1.0
CB F:GLU55 3.6 60.2 1.0
CB F:CYS56 3.7 58.7 1.0
CA F:HIS82 3.8 45.8 1.0
CD2 F:HIS82 3.8 45.8 1.0
CA F:CYS53 3.9 56.6 1.0
C F:GLU55 4.0 60.2 1.0
N F:GLU55 4.0 60.2 1.0
CA F:GLU55 4.1 60.2 1.0
CA F:CYS56 4.1 58.7 1.0
NE2 F:HIS82 4.2 45.8 1.0
C F:CYS53 4.3 56.6 1.0
C F:HIS82 4.3 45.8 1.0
CD F:GLN60 4.4 72.8 1.0
N F:HIS82 4.4 45.8 1.0
N F:CYS83 4.6 37.2 1.0
N F:CYS53 4.6 56.6 1.0
N F:ILE54 4.7 58.2 1.0
CG F:GLU55 4.8 60.2 1.0
NH1 F:ARG86 4.8 33.0 1.0
O F:CYS53 4.9 56.6 1.0
O F:GLU55 4.9 60.2 1.0
OE1 F:GLN60 5.0 72.8 1.0

Zinc binding site 2 out of 6 in 8wqc

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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 CDK5R1


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 CDK5R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:51.6
occ:1.00
 ND1 F:HIS80 2.1 37.7 1.0
SG F:CYS45 2.3 37.0 1.0
SG F:CYS83 2.3 37.2 1.0
SG F:CYS42 2.3 33.0 1.0
CG F:HIS80 2.7 37.7 1.0
CB F:CYS45 2.7 37.0 1.0
CB F:CYS42 2.9 33.0 1.0
CB F:HIS80 2.9 37.7 1.0
CE1 F:HIS80 3.1 37.7 1.0
CB F:CYS83 3.2 37.2 1.0
N F:CYS45 3.6 37.0 1.0
CA F:CYS45 3.7 37.0 1.0
N F:HIS80 3.8 37.7 1.0
CD2 F:HIS80 3.8 37.7 1.0
CA F:HIS80 3.9 37.7 1.0
NE2 F:HIS80 4.0 37.7 1.0
CA F:CYS42 4.3 33.0 1.0
O F:CYS42 4.5 33.0 1.0
C F:CYS42 4.6 33.0 1.0
CA F:CYS83 4.6 37.2 1.0
C F:CYS45 4.7 37.0 1.0
CA F:CYS53 4.7 56.6 1.0
C F:ILE44 4.8 27.1 1.0
SG F:CYS53 4.8 56.6 1.0
N F:ARG46 4.9 36.3 1.0
N F:CYS83 4.9 37.2 1.0
CB F:CYS53 4.9 56.6 1.0
C F:HIS80 4.9 37.7 1.0
O F:HIS80 5.0 37.7 1.0
CB F:ILE44 5.0 27.1 1.0

Zinc binding site 3 out of 6 in 8wqc

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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 CDK5R1


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 CDK5R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn202

b:40.0
occ:1.00
 OD1 F:ASP97 2.1 18.0 1.0
SG F:CYS75 2.3 24.6 1.0
ND1 F:HIS77 2.3 22.0 1.0
SG F:CYS94 2.3 14.9 1.0
CE1 F:HIS77 2.4 22.0 1.0
CG F:ASP97 2.7 18.0 1.0
N F:ASP97 3.0 18.0 1.0
OD2 F:ASP97 3.3 18.0 1.0
CB F:LEU96 3.3 18.8 1.0
CB F:CYS94 3.4 14.9 1.0
CB F:ASP97 3.5 18.0 1.0
C F:LEU96 3.6 18.8 1.0
CG F:HIS77 3.6 22.0 1.0
NE2 F:HIS77 3.6 22.0 1.0
N F:LEU96 3.6 18.8 1.0
CA F:LEU96 3.7 18.8 1.0
CA F:ASP97 3.8 18.0 1.0
CB F:CYS75 3.9 24.6 1.0
CD2 F:HIS77 4.2 22.0 1.0
O F:CYS94 4.3 14.9 1.0
C F:CYS94 4.4 14.9 1.0
O F:LEU96 4.5 18.8 1.0
CG F:LEU96 4.5 18.8 1.0
CA F:CYS94 4.5 14.9 1.0
CB F:HIS77 4.5 22.0 1.0
C F:ASP97 4.6 18.0 1.0
CD1 F:LEU96 4.7 18.8 1.0
N F:ASN98 4.7 15.2 1.0
C F:PRO95 4.8 17.3 1.0
N F:PRO95 4.9 17.3 1.0

Zinc binding site 4 out of 6 in 8wqc

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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 CDK5R1


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 CDK5R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn200

b:97.9
occ:1.00
 CD2 J:HIS82 1.8 48.0 1.0
NE2 J:HIS82 2.1 48.0 1.0
SG J:CYS56 2.3 53.6 1.0
SG J:CYS53 2.3 55.3 1.0
SG J:CYS68 2.3 50.4 1.0
CG J:HIS82 2.8 48.0 1.0
OE2 J:GLU55 3.0 57.1 1.0
CE1 J:HIS82 3.1 48.0 1.0
CB J:CYS56 3.1 53.6 1.0
ND1 J:HIS82 3.4 48.0 1.0
CB J:HIS82 3.8 48.0 1.0
CB J:CYS53 4.0 55.3 1.0
CD J:GLU55 4.0 57.1 1.0
CB J:CYS68 4.1 50.4 1.0
N J:CYS56 4.2 53.6 1.0
CA J:CYS56 4.2 53.6 1.0
CG J:GLU55 4.6 57.1 1.0
N J:CYS53 4.7 55.3 1.0
CA J:CYS68 4.8 50.4 1.0
CD1 J:LEU52 4.8 56.3 1.0
CA J:CYS53 4.9 55.3 1.0
CG J:LEU52 4.9 56.3 1.0
OE1 J:GLU55 5.0 57.1 1.0
O J:CYS53 5.0 55.3 1.0

Zinc binding site 5 out of 6 in 8wqc

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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 CDK5R1


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 CDK5R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn201

b:51.9
occ:1.00
 ND1 J:HIS80 2.1 41.3 1.0
SG J:CYS42 2.3 38.1 1.0
SG J:CYS83 2.3 36.8 1.0
SG J:CYS45 2.3 36.6 1.0
CG J:HIS80 2.9 41.3 1.0
CB J:CYS42 3.0 38.1 1.0
CB J:HIS80 3.0 41.3 1.0
CB J:CYS45 3.1 36.6 1.0
CB J:CYS83 3.1 36.8 1.0
CE1 J:HIS80 3.2 41.3 1.0
N J:CYS45 3.9 36.6 1.0
CB J:CYS53 3.9 55.3 1.0
O J:CYS42 3.9 38.1 1.0
N J:HIS80 4.0 41.3 1.0
CD2 J:HIS80 4.1 41.3 1.0
CA J:CYS45 4.1 36.6 1.0
CA J:HIS80 4.1 41.3 1.0
NE2 J:HIS80 4.2 41.3 1.0
CA J:CYS42 4.3 38.1 1.0
C J:CYS42 4.4 38.1 1.0
CA J:CYS83 4.5 36.8 1.0
CA J:CYS53 4.5 55.3 1.0
N J:CYS83 4.7 36.8 1.0
O J:HIS80 4.9 41.3 1.0
C J:HIS80 4.9 41.3 1.0
C J:CYS45 5.0 36.6 1.0
C J:ILE44 5.0 28.2 1.0

Zinc binding site 6 out of 6 in 8wqc

Go back to Zinc Binding Sites List in 8wqc
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 CDK5R1


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 CDK5R1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn202

b:42.3
occ:1.00
 CB J:CYS75 2.2 26.6 1.0
ND1 J:HIS77 2.3 21.0 1.0
SG J:CYS94 2.3 17.2 1.0
SG J:CYS75 2.3 26.6 1.0
OD1 J:ASP97 2.4 16.1 1.0
CB J:CYS94 2.8 17.2 1.0
CE1 J:HIS77 3.1 21.0 1.0
CG J:HIS77 3.4 21.0 1.0
CG J:ASP97 3.6 16.1 1.0
CA J:CYS75 3.7 26.6 1.0
CB J:HIS77 3.8 21.0 1.0
OD2 J:ASP97 4.0 16.1 1.0
CZ3 J:TRP101 4.2 31.9 1.0
NE2 J:HIS77 4.3 21.0 1.0
C J:CYS75 4.3 26.6 1.0
O J:CYS75 4.3 26.6 1.0
CA J:CYS94 4.4 17.2 1.0
CD2 J:HIS77 4.4 21.0 1.0
N J:CYS75 4.4 26.6 1.0
CE3 J:TRP101 4.5 31.9 1.0
O J:ASP97 4.6 16.1 1.0
N J:ASP97 4.8 16.1 1.0
CB J:ASP97 4.8 16.1 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 CDK5R1 To Be Published.
Page generated: Thu Oct 31 13:37:37 2024

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