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Zinc in PDB 5n4w: Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex

Protein crystallography data

The structure of Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex, PDB code: 5n4w was solved by T.A.F.Cardote, M.S.Gadd, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.48 / 3.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 86.038, 190.962, 238.885, 90.00, 90.00, 90.00
R / Rfree (%) 30.2 / 34.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex (pdb code 5n4w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex, PDB code: 5n4w:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5n4w

Go back to Zinc Binding Sites List in 5n4w
Zinc binding site 1 out of 3 in the Crystal Structure of the CUL2-RBX1-Elobc-Vhl 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 Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn201

b:0.4
occ:1.00
SG R:CYS45 2.7 0.4 1.0
SG R:CYS83 2.9 0.7 1.0
ND1 R:HIS80 3.2 0.2 1.0
CB R:CYS83 3.3 0.9 1.0
SG R:CYS42 3.3 0.6 1.0
CB R:HIS80 3.4 0.9 1.0
CG R:HIS80 3.5 0.4 1.0
CB R:CYS45 4.0 0.6 1.0
CE1 R:HIS80 4.1 0.2 1.0
N R:HIS80 4.2 0.1 1.0
CB R:CYS42 4.2 0.0 1.0
O R:CYS42 4.3 0.2 1.0
N R:CYS45 4.3 0.9 1.0
CB R:CYS53 4.3 0.8 1.0
CA R:HIS80 4.4 0.8 1.0
CD2 R:HIS80 4.5 0.3 1.0
CA R:CYS45 4.7 0.6 1.0
CB R:ILE44 4.7 0.8 1.0
NE2 R:HIS80 4.8 0.5 1.0
CA R:CYS83 4.8 0.7 1.0
O R:HIS80 5.0 0.2 1.0
CG2 R:ILE44 5.0 0.2 1.0

Zinc binding site 2 out of 3 in 5n4w

Go back to Zinc Binding Sites List in 5n4w
Zinc binding site 2 out of 3 in the Crystal Structure of the CUL2-RBX1-Elobc-Vhl 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 Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn202

b:0.9
occ:1.00
CE1 R:HIS82 2.2 0.2 1.0
NE2 R:HIS82 2.3 0.7 1.0
SG R:CYS56 2.4 1.0 1.0
SG R:CYS53 2.5 0.4 1.0
CB R:CYS56 3.0 0.3 1.0
SG R:CYS68 3.2 0.1 1.0
ND1 R:HIS82 3.5 1.0 1.0
CD2 R:HIS82 3.7 0.8 1.0
CB R:CYS53 3.9 0.8 1.0
CB R:CYS68 4.1 0.5 1.0
N R:CYS53 4.1 0.1 1.0
CA R:CYS56 4.2 0.3 1.0
N R:CYS56 4.2 0.7 1.0
CG R:HIS82 4.3 0.6 1.0
CA R:CYS53 4.5 0.1 1.0
C R:CYS53 5.0 0.2 1.0

Zinc binding site 3 out of 3 in 5n4w

Go back to Zinc Binding Sites List in 5n4w
Zinc binding site 3 out of 3 in the Crystal Structure of the CUL2-RBX1-Elobc-Vhl 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 Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn203

b:0.4
occ:1.00
SG R:CYS75 2.5 0.2 1.0
CB R:CYS75 3.2 0.0 1.0
CD2 R:HIS77 3.3 0.2 1.0
OD2 R:ASP97 3.3 0.5 1.0
SG R:CYS94 3.4 0.9 1.0
O R:CYS75 3.7 0.9 1.0
CB R:HIS77 3.8 0.7 1.0
CG R:HIS77 3.8 0.4 1.0
CG R:ASP97 4.1 0.1 1.0
C R:CYS75 4.2 0.9 1.0
CB R:ASP97 4.3 0.8 1.0
CA R:CYS75 4.3 0.6 1.0
NE2 R:HIS77 4.5 0.2 1.0
CB R:CYS94 4.5 0.1 1.0
N R:HIS77 4.5 0.3 1.0
CA R:HIS77 4.8 0.0 1.0

Reference:

T.A.F.Cardote, M.S.Gadd, A.Ciulli. Crystal Structure of the CUL2-RBX1-Elobc-Vhl Ubiquitin Ligase Complex. Structure V. 25 901 2017.
ISSN: ISSN 1878-4186
PubMed: 28591624
DOI: 10.1016/J.STR.2017.04.009
Page generated: Wed Dec 16 06:34:25 2020

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