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Zinc in PDB 1ldj: Structure of the CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase Complex

Protein crystallography data

The structure of Structure of the CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase Complex, PDB code: 1ldj was solved by N.Zheng, B.A.Schulman, L.Song, J.J.Miller, P.D.Jeffrey, P.Wang, C.Chu, D.M.Koepp, S.J.Elledge, M.Pagano, R.C.Conaway, J.W.Conaway, J.W.Harper, N.P.Pavletich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 113.974, 49.968, 135.883, 90.00, 107.83, 90.00
R / Rfree (%) 24.7 / 28.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase Complex (pdb code 1ldj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of the CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase Complex, PDB code: 1ldj:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1ldj

Go back to Zinc Binding Sites List in 1ldj
Zinc binding site 1 out of 3 in the Structure of the CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase 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 CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:0.8
occ:1.00
ND1 B:HIS80 2.0 96.3 1.0
SG B:CYS83 2.2 0.6 1.0
SG B:CYS45 2.3 0.9 1.0
SG B:CYS42 2.3 91.8 1.0
CB B:CYS83 2.9 0.6 1.0
CE1 B:HIS80 2.9 96.3 1.0
CB B:CYS42 3.0 91.8 1.0
CG B:HIS80 3.1 96.3 1.0
CB B:HIS80 3.5 96.3 1.0
CB B:CYS45 3.6 0.9 1.0
N B:HIS80 3.7 78.2 1.0
CA B:CYS53 4.0 0.3 1.0
NE2 B:HIS80 4.1 96.3 1.0
CB B:CYS53 4.1 0.1 1.0
O B:ILE44 4.2 81.6 1.0
CD2 B:HIS80 4.2 96.3 1.0
CA B:HIS80 4.2 78.2 1.0
CA B:CYS83 4.4 93.6 1.0
C B:ILE44 4.4 81.6 1.0
CA B:CYS42 4.5 0.5 1.0
CA B:CYS45 4.5 96.5 1.0
OD1 B:ASN47 4.6 0.2 1.0
N B:CYS45 4.6 96.5 1.0
N B:ARG46 4.6 0.5 1.0
O B:CYS53 4.7 0.3 1.0
N B:CYS83 4.7 93.6 1.0
C B:CYS53 4.8 0.3 1.0
C B:PHE79 4.8 73.4 1.0
C B:CYS45 4.8 96.5 1.0
CB B:PHE79 4.8 97.1 1.0
N B:ILE44 5.0 81.6 1.0
N B:ALA43 5.0 87.2 1.0

Zinc binding site 2 out of 3 in 1ldj

Go back to Zinc Binding Sites List in 1ldj
Zinc binding site 2 out of 3 in the Structure of the CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase 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 CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:0.8
occ:1.00
ND1 B:HIS77 2.0 0.9 1.0
OD1 B:ASP97 2.2 20.0 1.0
SG B:CYS94 2.3 96.4 1.0
SG B:CYS75 2.3 82.6 1.0
CB B:CYS75 2.9 82.6 1.0
CG B:HIS77 2.9 0.9 1.0
CB B:HIS77 3.1 0.9 1.0
CE1 B:HIS77 3.1 0.9 1.0
CG B:ASP97 3.2 20.0 1.0
CB B:CYS94 3.7 96.4 1.0
CB B:ASP97 3.8 0.8 1.0
OD2 B:ASP97 4.0 20.0 1.0
N B:HIS77 4.1 0.2 1.0
CA B:CYS75 4.1 1.0 1.0
CD2 B:HIS77 4.1 0.9 1.0
CA B:HIS77 4.2 0.2 1.0
CZ3 B:TRP101 4.2 84.2 1.0
NE2 B:HIS77 4.2 0.9 1.0
C B:CYS75 4.3 1.0 1.0
N B:ASP97 4.5 0.7 1.0
N B:CYS75 4.6 1.0 1.0
N B:ASN76 4.6 0.5 1.0
CB B:LEU96 4.6 0.8 1.0
CZ B:PHE79 4.7 97.1 1.0
CE1 B:PHE79 4.7 97.1 1.0
O B:CYS75 4.8 1.0 1.0
CA B:ASP97 4.9 0.7 1.0
CE3 B:TRP101 5.0 84.2 1.0

Zinc binding site 3 out of 3 in 1ldj

Go back to Zinc Binding Sites List in 1ldj
Zinc binding site 3 out of 3 in the Structure of the CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase 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 CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:96.7
occ:1.00
ND1 B:HIS82 2.0 0.2 1.0
SG B:CYS56 2.3 62.5 1.0
SG B:CYS53 2.3 0.1 1.0
SG B:CYS68 2.3 98.6 1.0
CE1 B:HIS82 2.9 0.2 1.0
CG B:HIS82 3.2 0.2 1.0
CB B:CYS56 3.3 62.5 1.0
CB B:CYS53 3.6 0.1 1.0
CB B:HIS82 3.6 0.2 1.0
CB B:CYS68 3.9 98.6 1.0
N B:CYS56 4.0 0.6 1.0
NE2 B:HIS82 4.1 0.2 1.0
CA B:CYS56 4.2 0.6 1.0
O B:LEU52 4.2 0.9 1.0
CD2 B:HIS82 4.2 0.2 1.0
O B:THR64 4.5 0.9 1.0
CA B:CYS68 4.5 97.4 1.0
CA B:CYS53 4.9 0.3 1.0
C B:GLU55 5.0 0.2 1.0

Reference:

N.Zheng, B.A.Schulman, L.Song, J.J.Miller, P.D.Jeffrey, P.Wang, C.Chu, D.M.Koepp, S.J.Elledge, M.Pagano, R.C.Conaway, J.W.Conaway, J.W.Harper, N.P.Pavletich. Structure of the CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase Complex. Nature V. 416 703 2002.
ISSN: ISSN 0028-0836
PubMed: 11961546
DOI: 10.1038/416703A
Page generated: Wed Dec 16 02:56:08 2020

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