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Zinc in PDB 3dpl: Structural Insights Into NEDD8 Activation of Cullin-Ring Ligases: Conformational Control of Conjugation.

Protein crystallography data

The structure of Structural Insights Into NEDD8 Activation of Cullin-Ring Ligases: Conformational Control of Conjugation., PDB code: 3dpl was solved by D.M.Duda, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.965, 65.510, 141.116, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 27.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Insights Into NEDD8 Activation of Cullin-Ring Ligases: Conformational Control of Conjugation. (pdb code 3dpl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structural Insights Into NEDD8 Activation of Cullin-Ring Ligases: Conformational Control of Conjugation., PDB code: 3dpl:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3dpl

Go back to Zinc Binding Sites List in 3dpl
Zinc binding site 1 out of 3 in the Structural Insights Into NEDD8 Activation of Cullin-Ring Ligases: Conformational Control of Conjugation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Insights Into NEDD8 Activation of Cullin-Ring Ligases: Conformational Control of Conjugation. within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn201

b:57.7
occ:1.00
SG R:CYS45 1.8 60.2 1.0
ND1 R:HIS80 2.2 43.0 1.0
SG R:CYS42 2.3 69.5 1.0
CB R:CYS42 2.5 72.3 1.0
CG R:HIS80 2.6 39.4 1.0
SG R:CYS83 2.6 48.1 1.0
CB R:HIS80 2.8 34.0 1.0
CE1 R:HIS80 3.1 42.9 1.0
N R:HIS80 3.5 30.9 1.0
CD2 R:HIS80 3.6 42.7 1.0
CB R:CYS83 3.6 40.9 1.0
CB R:CYS45 3.6 64.7 1.0
CA R:HIS80 3.7 32.8 1.0
NE2 R:HIS80 3.8 45.4 1.0
CA R:CYS42 4.0 74.1 1.0
CB R:CYS53 4.0 80.8 1.0
N R:CYS45 4.5 67.8 1.0
O R:HIS80 4.6 35.3 1.0
CA R:CYS45 4.6 68.6 1.0
C R:HIS80 4.6 32.7 1.0
C R:PHE79 4.7 31.1 1.0
N R:CYS42 4.7 78.1 1.0
N R:ARG46 4.9 73.3 1.0
CA R:CYS83 4.9 36.3 1.0
C R:CYS42 4.9 72.7 1.0
SG R:CYS53 4.9 80.3 1.0
N R:CYS83 4.9 36.8 1.0
O R:ASN47 4.9 79.5 1.0
CB R:PHE79 5.0 30.2 1.0

Zinc binding site 2 out of 3 in 3dpl

Go back to Zinc Binding Sites List in 3dpl
Zinc binding site 2 out of 3 in the Structural Insights Into NEDD8 Activation of Cullin-Ring Ligases: Conformational Control of Conjugation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Insights Into NEDD8 Activation of Cullin-Ring Ligases: Conformational Control of Conjugation. within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn202

b:34.1
occ:1.00
OD1 R:ASP97 2.1 47.8 1.0
ND1 R:HIS77 2.1 28.7 1.0
SG R:CYS75 2.4 34.1 1.0
SG R:CYS94 2.4 27.7 1.0
CG R:HIS77 3.0 30.1 1.0
CE1 R:HIS77 3.1 28.4 1.0
CG R:ASP97 3.1 48.8 1.0
CB R:CYS75 3.2 28.3 1.0
CB R:CYS94 3.2 30.2 1.0
CB R:HIS77 3.3 31.3 1.0
OD2 R:ASP97 3.5 48.8 1.0
CD2 R:HIS77 4.1 30.4 1.0
NE2 R:HIS77 4.2 31.9 1.0
O R:CYS75 4.3 30.3 1.0
N R:ASP97 4.4 45.3 1.0
CB R:ASP97 4.4 48.5 1.0
CA R:CYS75 4.5 30.0 1.0
CA R:HIS77 4.5 32.0 1.0
C R:CYS75 4.5 30.9 1.0
N R:HIS77 4.5 31.6 1.0
CA R:CYS94 4.7 32.1 1.0
CZ3 R:TRP101 4.7 27.4 1.0
CB R:LEU96 4.7 41.7 1.0

Zinc binding site 3 out of 3 in 3dpl

Go back to Zinc Binding Sites List in 3dpl
Zinc binding site 3 out of 3 in the Structural Insights Into NEDD8 Activation of Cullin-Ring Ligases: Conformational Control of Conjugation.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Insights Into NEDD8 Activation of Cullin-Ring Ligases: Conformational Control of Conjugation. within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn203

b:65.6
occ:1.00
SG R:CYS68 2.1 81.8 1.0
ND1 R:HIS82 2.3 37.6 1.0
SG R:CYS56 2.4 85.2 1.0
SG R:CYS53 2.5 80.3 1.0
CG R:HIS82 2.9 37.1 1.0
CE1 R:HIS82 3.1 37.4 1.0
CB R:HIS82 3.2 34.8 1.0
CB R:CYS68 3.4 75.6 1.0
CA R:CYS68 3.7 72.4 1.0
CD2 R:HIS82 3.9 38.0 1.0
NE2 R:HIS82 4.0 38.5 1.0
CB R:CYS56 4.0 88.2 1.0
N R:CYS68 4.1 74.0 1.0
N R:CYS56 4.1 88.9 1.0
CB R:CYS53 4.2 80.8 1.0
CB R:GLU55 4.5 89.0 1.0
CA R:CYS56 4.6 90.3 1.0
CA R:HIS82 4.7 35.3 1.0
C R:GLU55 4.9 87.8 1.0
N R:CYS53 4.9 80.6 1.0
O R:CYS53 4.9 82.2 1.0
CA R:CYS53 5.0 81.1 1.0

Reference:

D.M.Duda, L.A.Borg, D.C.Scott, H.W.Hunt, M.Hammel, B.A.Schulman. Structural Insights Into NEDD8 Activation of Cullin-Ring Ligases: Conformational Control of Conjugation. Cell(Cambridge,Mass.) V. 134 995 2008.
ISSN: ISSN 0092-8674
PubMed: 18805092
DOI: 10.1016/J.CELL.2008.07.022
Page generated: Sat Sep 26 06:02:31 2020
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