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Zinc in PDB 4a0c: Structure of the CAND1-CUL4B-RBX1 Complex

Protein crystallography data

The structure of Structure of the CAND1-CUL4B-RBX1 Complex, PDB code: 4a0c was solved by A.Scrima, E.S.Fischer, M.Faty, H.Gut, N.H.Thoma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.76 / 3.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.090, 152.360, 263.010, 90.00, 89.37, 90.00
R / Rfree (%) 23.8 / 31.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the CAND1-CUL4B-RBX1 Complex (pdb code 4a0c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the CAND1-CUL4B-RBX1 Complex, PDB code: 4a0c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4a0c

Go back to Zinc Binding Sites List in 4a0c
Zinc binding site 1 out of 6 in the Structure of the CAND1-CUL4B-RBX1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the CAND1-CUL4B-RBX1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4001

b:0.2
occ:1.00
 ND1 D:HIS80 2.0 0.2 1.0
SG D:CYS42 2.0 1.0 1.0
SG D:CYS45 2.4 0.7 1.0
SG D:CYS83 2.6 0.1 1.0
CE1 D:HIS80 3.0 0.3 1.0
CB D:CYS42 3.0 0.2 1.0
CG D:HIS80 3.0 0.4 1.0
CB D:CYS83 3.2 0.6 1.0
CB D:CYS45 3.4 0.7 1.0
CB D:HIS80 3.4 0.5 1.0
N D:CYS45 3.9 0.4 1.0
N D:HIS80 4.0 0.2 1.0
NE2 D:HIS80 4.1 0.3 1.0
CB D:CYS53 4.1 0.4 1.0
CD2 D:HIS80 4.1 0.3 1.0
CA D:CYS45 4.2 0.8 1.0
CA D:HIS80 4.3 0.5 1.0
CA D:CYS42 4.4 0.3 1.0
CA D:CYS83 4.6 0.7 1.0
O D:CYS42 4.7 0.3 1.0
C D:CYS42 4.8 0.2 1.0
CB D:ILE44 4.8 0.6 1.0
CA D:CYS53 4.9 0.5 1.0
C D:ILE44 4.9 0.0 1.0
C D:CYS45 4.9 0.1 1.0
N D:ARG46 5.0 0.5 1.0
N D:CYS83 5.0 0.9 1.0
O D:HIS80 5.0 0.9 1.0

Zinc binding site 2 out of 6 in 4a0c

Go back to Zinc Binding Sites List in 4a0c
Zinc binding site 2 out of 6 in the Structure of the CAND1-CUL4B-RBX1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the CAND1-CUL4B-RBX1 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 0.1 1.0
SG D:CYS75 2.4 0.9 1.0
SG D:CYS94 2.6 0.2 1.0
OD1 D:ASP97 2.8 0.1 1.0
CE1 D:HIS77 2.9 0.2 1.0
OD2 D:ASP97 3.0 0.3 1.0
CB D:CYS75 3.0 0.0 1.0
CG D:ASP97 3.1 0.3 1.0
CG D:HIS77 3.2 0.9 1.0
CB D:HIS77 3.7 0.9 1.0
CB D:CYS94 3.9 1.0 1.0
NE2 D:HIS77 4.1 0.1 1.0
CD2 D:HIS77 4.3 0.0 1.0
CA D:CYS75 4.4 0.0 1.0
O D:CYS75 4.4 0.6 1.0
CB D:ASP97 4.4 0.3 1.0
C D:CYS75 4.5 0.6 1.0
CB D:LEU96 4.6 0.6 1.0
N D:HIS77 4.7 0.4 1.0
N D:ASP97 4.7 0.1 1.0
C D:LEU96 4.7 0.8 1.0
CA D:HIS77 4.8 0.9 1.0
CA D:LEU96 5.0 0.6 1.0

Zinc binding site 3 out of 6 in 4a0c

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Zinc binding site 3 out of 6 in the Structure of the CAND1-CUL4B-RBX1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the CAND1-CUL4B-RBX1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4003

b:0.9
occ:1.00
 SG D:CYS56 2.3 0.0 1.0
SG D:CYS53 2.6 0.1 1.0
SG D:CYS68 2.8 0.8 1.0
CG D:HIS82 3.1 0.1 1.0
CD2 D:HIS82 3.1 0.8 1.0
CB D:HIS82 3.5 0.4 1.0
CB D:CYS56 3.5 0.0 1.0
ND1 D:HIS82 3.6 0.0 1.0
CB D:CYS68 3.6 0.2 1.0
NE2 D:HIS82 3.6 0.7 1.0
CE1 D:HIS82 3.9 0.9 1.0
CB D:CYS53 3.9 0.4 1.0
N D:CYS53 4.4 0.3 1.0
O D:GLU55 4.4 0.5 1.0
C D:GLU55 4.5 0.4 1.0
N D:CYS56 4.5 0.7 1.0
CA D:CYS56 4.6 0.0 1.0
CA D:CYS68 4.6 0.1 1.0
CA D:CYS53 4.7 0.5 1.0
CA D:HIS82 4.9 0.5 1.0

Zinc binding site 4 out of 6 in 4a0c

Go back to Zinc Binding Sites List in 4a0c
Zinc binding site 4 out of 6 in the Structure of the CAND1-CUL4B-RBX1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the CAND1-CUL4B-RBX1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn4001

b:0.1
occ:1.00
 SG F:CYS45 1.7 0.9 1.0
SG F:CYS42 2.4 0.5 1.0
ND1 F:HIS80 2.5 0.1 1.0
CG F:HIS80 3.0 0.3 1.0
CB F:HIS80 3.1 0.4 1.0
CB F:CYS42 3.2 0.7 1.0
CB F:CYS45 3.2 0.8 1.0
CE1 F:HIS80 3.5 0.1 1.0
SG F:CYS83 3.5 0.9 1.0
N F:CYS45 3.8 0.3 1.0
CB F:CYS83 3.8 0.8 1.0
CB F:CYS53 3.9 0.7 1.0
N F:HIS80 3.9 0.8 1.0
CA F:CYS45 4.0 0.8 1.0
CD2 F:HIS80 4.1 0.2 1.0
CA F:HIS80 4.1 0.5 1.0
NE2 F:HIS80 4.3 0.0 1.0
CA F:CYS42 4.7 0.8 1.0
C F:CYS45 4.7 0.1 1.0
O F:LEU52 4.8 0.5 1.0
CA F:CYS53 4.8 0.7 1.0
N F:ARG46 4.8 0.5 1.0
O F:HIS80 4.9 0.1 1.0
C F:ILE44 5.0 0.7 1.0
C F:HIS80 5.0 1.0 1.0

Zinc binding site 5 out of 6 in 4a0c

Go back to Zinc Binding Sites List in 4a0c
Zinc binding site 5 out of 6 in the Structure of the CAND1-CUL4B-RBX1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the CAND1-CUL4B-RBX1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn4002

b:0.2
occ:1.00
 SG F:CYS75 2.1 0.8 1.0
SG F:CYS94 2.4 0.7 1.0
ND1 F:HIS77 2.7 0.3 1.0
CB F:CYS94 2.9 0.8 1.0
CB F:ASP97 3.0 0.7 1.0
OD2 F:ASP97 3.1 0.6 1.0
CB F:CYS75 3.2 0.5 1.0
CE1 F:HIS77 3.3 0.3 1.0
N F:ASP97 3.3 0.7 1.0
CG F:ASP97 3.5 0.8 1.0
CG F:HIS77 3.6 0.1 1.0
CA F:ASP97 3.8 0.7 1.0
CB F:HIS77 4.1 0.0 1.0
CA F:CYS94 4.3 0.7 1.0
NE2 F:HIS77 4.4 0.2 1.0
C F:LEU96 4.4 0.7 1.0
CZ3 F:TRP101 4.5 0.6 1.0
CB F:LEU96 4.5 0.7 1.0
CD2 F:HIS77 4.5 0.1 1.0
N F:LEU96 4.6 0.9 1.0
CA F:CYS75 4.6 0.5 1.0
OD1 F:ASP97 4.7 0.0 1.0
C F:CYS94 4.7 0.5 1.0
C F:ASP97 4.7 0.7 1.0
CA F:LEU96 4.7 0.7 1.0
CE3 F:TRP101 4.8 0.8 1.0
C F:CYS75 4.9 0.6 1.0
O F:CYS94 4.9 0.5 1.0
N F:HIS77 4.9 1.0 1.0

Zinc binding site 6 out of 6 in 4a0c

Go back to Zinc Binding Sites List in 4a0c
Zinc binding site 6 out of 6 in the Structure of the CAND1-CUL4B-RBX1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the CAND1-CUL4B-RBX1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn4003

b:0.1
occ:1.00
 SG F:CYS68 2.5 0.9 1.0
SG F:CYS56 2.5 0.1 1.0
SG F:CYS53 2.7 0.9 1.0
CB F:CYS56 3.0 0.2 1.0
CD2 F:HIS82 3.1 0.3 1.0
CB F:CYS68 3.2 0.1 1.0
NE2 F:HIS82 3.5 0.6 1.0
CG F:HIS82 3.6 0.9 1.0
CA F:CYS68 3.9 0.1 1.0
N F:CYS53 4.0 0.1 1.0
CB F:CYS53 4.1 0.7 1.0
CE1 F:HIS82 4.2 0.6 1.0
ND1 F:HIS82 4.2 0.4 1.0
CB F:HIS82 4.2 0.4 1.0
CA F:CYS56 4.4 0.2 1.0
C F:LEU52 4.5 0.6 1.0
CA F:LEU52 4.5 0.2 1.0
CA F:CYS53 4.6 0.7 1.0
CD2 F:HIS80 4.7 0.2 1.0
O F:GLU55 4.7 0.1 1.0
N F:CYS56 4.9 0.2 1.0
N F:CYS68 4.9 0.2 1.0
C F:CYS68 5.0 0.0 1.0

Reference:

A.Scrima, E.S.Fischer, S.Iwai, H.Gut, N.H.Thoma. The Molecular Basis of CRL4(DDB2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation Cell(Cambridge,Mass.) V. 147 1024 2011.
ISSN: ISSN 0092-8674
PubMed: 22118460
DOI: 10.1016/J.CELL.2011.10.035
Page generated: Sat Oct 26 18:45:57 2024

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