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

The structure of Structure of the CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase Complex, PDB code: 1ldk 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)	20.00 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	219.378, 50.529, 158.610, 90.00, 90.00, 90.00
R / Rfree (%)	28.9 / 33.1

The binding sites of Zinc atom in the Structure of the CUL1-RBX1-SKP1-F BOXSKP2 Scf Ubiquitin Ligase Complex (pdb code 1ldk). 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: 1ldk:
Jump to Zinc binding site number: 1; 2; 3;

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 C:Zn4001 b:84.4 occ:1.00 ND1 C:HIS1080 2.1 0.9 0.0 SG C:CYS1083 2.3 56.0 0.0 SG C:CYS1042 2.3 0.1 0.0 SG C:CYS1045 2.3 0.5 0.0 CE1 C:HIS1080 2.9 0.9 0.0 CG C:HIS1080 3.2 0.7 0.0 CB C:CYS1042 3.3 0.3 0.0 CA C:CYS1053 3.5 0.1 0.0 NH2 C:ARG1086 3.5 95.0 0.0 CB C:HIS1080 3.6 0.8 0.0 CB C:CYS1045 3.7 0.2 0.0 CB C:CYS1053 3.9 0.5 0.0 N C:CYS1053 4.0 0.1 0.0 CB C:CYS1083 4.1 55.5 0.0 NE2 C:HIS1080 4.1 0.4 0.0 CD2 C:HIS1080 4.3 0.1 0.0 CA C:CYS1042 4.6 0.5 0.0 N C:HIS1080 4.7 0.5 0.0 C C:CYS1053 4.7 0.8 0.0 CZ C:ARG1086 4.7 95.3 0.0 N C:CYS1042 4.7 0.6 0.0 CA C:HIS1080 4.8 0.1 0.0 N C:CYS1045 4.8 0.9 0.0 CA C:CYS1045 4.9 0.6 0.0 CA C:CYS1083 5.0 0.9 0.0

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 C:Zn4002 b:83.9 occ:1.00 CE1 C:HIS1077 1.3 0.7 0.0 ND1 C:HIS1077 2.0 0.1 0.0 SG C:CYS1075 2.3 0.2 0.0 SG C:CYS1094 2.3 0.2 0.0 NE2 C:HIS1077 2.6 0.6 0.0 OD1 C:ASP1097 2.6 20.0 1.0 CB C:CYS1075 3.2 0.4 0.0 CG C:HIS1077 3.3 0.2 0.0 CD2 C:HIS1077 3.5 0.2 0.0 CB C:CYS1094 3.6 0.2 0.0 CG C:ASP1097 3.7 20.0 1.0 CB C:ASP1097 4.1 88.2 0.0 O C:CYS1075 4.2 0.2 0.0 O C:PRO1095 4.2 0.2 0.0 CA C:CYS1075 4.4 0.6 0.0 C C:CYS1075 4.4 0.7 0.0 CB C:HIS1077 4.5 0.4 0.0 O C:ASP1097 4.7 0.3 0.0 OD2 C:ASP1097 4.8 20.0 1.0 O C:ASN1076 4.9 0.7 0.0 CA C:CYS1094 4.9 0.9 0.0 N C:ASP1097 5.0 0.2 0.0

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 C:Zn4003 b:89.0 occ:1.00 ND1 C:HIS1082 2.1 0.4 0.0 SG C:CYS1056 2.3 0.1 0.0 SG C:CYS1068 2.3 0.4 0.0 SG C:CYS1053 2.3 0.1 0.0 CE1 C:HIS1082 3.0 0.7 0.0 CG C:HIS1082 3.1 0.5 0.0 CB C:CYS1056 3.3 0.7 0.0 CB C:HIS1082 3.5 0.1 0.0 CB C:CYS1053 3.6 0.5 0.0 CB C:CYS1068 3.9 0.0 0.0 NE2 C:HIS1082 4.2 0.5 0.0 O C:THR1064 4.2 95.7 0.0 CD2 C:HIS1082 4.2 0.3 0.0 OG1 C:THR1064 4.4 96.5 0.0 CA C:CYS1056 4.6 0.7 0.0 O C:GLU1067 4.6 0.7 0.0 N C:CYS1056 4.7 1.0 0.0 CA C:CYS1068 4.9 94.5 0.0 C C:THR1064 5.0 95.7 0.0 CA C:HIS1082 5.0 0.7 0.0 CA C:CYS1053 5.0 0.1 0.0

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