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Zinc in PDB 3dqv: 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: 3dqv was solved by D.M.Duda, L.A.Borg, D.C.Scott, H.W.Hunt, M.Hammel, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.315, 122.442, 128.647, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 29.9

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 3dqv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structural Insights Into NEDD8 Activation of Cullin-Ring Ligases: Conformational Control of Conjugation, PDB code: 3dqv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3dqv

Go back to Zinc Binding Sites List in 3dqv
Zinc binding site 1 out of 6 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:Zn4004

b:79.4
occ:1.00
 ND1 R:HIS82 2.4 93.2 1.0
SG R:CYS68 2.5 0.0 1.0
SG R:CYS56 2.5 0.4 1.0
SG R:CYS53 2.6 94.2 1.0
CE1 R:HIS82 3.0 93.2 1.0
CB R:CYS68 3.0 1.0 1.0
CB R:CYS56 3.2 0.5 1.0
CG R:HIS82 3.5 92.3 1.0
CB R:CYS53 3.7 91.3 1.0
N R:CYS53 3.9 89.8 1.0
N R:CYS56 4.1 0.4 1.0
CB R:HIS82 4.1 92.3 1.0
NE2 R:HIS82 4.1 93.5 1.0
CA R:CYS68 4.2 1.0 1.0
CA R:CYS56 4.3 0.5 1.0
CA R:CYS53 4.4 91.4 1.0
CD2 R:HIS82 4.4 92.8 1.0
CB R:GLU55 4.9 0.4 1.0
CD2 R:HIS80 4.9 87.8 1.0

Zinc binding site 2 out of 6 in 3dqv

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Zinc binding site 2 out of 6 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:Zn4005

b:72.1
occ:1.00
 SG R:CYS45 2.4 72.9 1.0
SG R:CYS42 2.5 71.5 1.0
ND1 R:HIS80 2.5 88.2 1.0
SG R:CYS83 2.5 99.1 1.0
CB R:CYS83 3.0 96.5 1.0
CB R:CYS45 3.1 76.0 1.0
CB R:CYS42 3.1 74.6 1.0
CG R:HIS80 3.2 87.9 1.0
CE1 R:HIS80 3.3 87.3 1.0
CB R:HIS80 3.5 87.7 1.0
N R:CYS45 3.6 76.0 1.0
CA R:CYS45 3.9 76.5 1.0
CB R:CYS53 4.2 91.3 1.0
CD2 R:HIS80 4.2 87.8 1.0
N R:HIS80 4.2 88.7 1.0
NE2 R:HIS80 4.2 86.8 1.0
CA R:HIS80 4.5 88.5 1.0
CA R:CYS83 4.5 95.5 1.0
CB R:ILE44 4.5 72.5 1.0
CA R:CYS42 4.6 75.4 1.0
C R:ILE44 4.6 75.3 1.0
C R:CYS45 4.7 77.5 1.0
CA R:CYS53 4.8 91.4 1.0
O R:CYS42 4.8 75.2 1.0
CG2 R:ILE44 4.8 72.5 1.0
N R:ARG46 4.9 78.3 1.0

Zinc binding site 3 out of 6 in 3dqv

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Zinc binding site 3 out of 6 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:Zn4006

b:0.3
occ:1.00
 OD1 R:ASP97 2.3 0.7 1.0
SG R:CYS75 2.4 97.8 1.0
SG R:CYS94 2.4 0.0 1.0
ND1 R:HIS77 2.7 0.9 1.0
CB R:CYS75 2.8 0.2 1.0
CG R:ASP97 2.8 0.3 1.0
OD2 R:ASP97 3.0 0.0 1.0
CB R:CYS94 3.2 0.9 1.0
CG R:HIS77 3.4 0.9 1.0
CE1 R:HIS77 3.5 0.8 1.0
CB R:HIS77 3.8 0.2 1.0
CB R:ASP97 3.9 0.1 1.0
CA R:CYS75 4.2 0.0 1.0
NE2 R:HIS77 4.4 0.9 1.0
CD2 R:HIS77 4.4 1.0 1.0
N R:ASP97 4.5 0.5 1.0
C R:CYS75 4.5 0.9 1.0
O R:CYS75 4.6 0.4 1.0
CA R:CYS94 4.6 0.1 1.0
N R:HIS77 4.7 0.3 1.0
O R:CYS94 4.8 0.9 1.0
CA R:ASP97 4.8 0.3 1.0
CZ3 R:TRP101 4.8 0.9 1.0
CB R:LEU96 4.8 0.5 1.0
CA R:HIS77 4.9 0.7 1.0
C R:CYS94 4.9 0.2 1.0
N R:CYS75 5.0 0.8 1.0
CZ R:PHE79 5.0 92.7 1.0

Zinc binding site 4 out of 6 in 3dqv

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Zinc binding site 4 out of 6 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 4 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
Y:Zn4001

b:0.8
occ:1.00
 SG Y:CYS94 2.5 0.8 0.0
OD1 Y:ASP97 2.7 0.8 1.0
ND1 Y:HIS77 2.8 0.8 1.0
CB Y:HIS77 3.3 0.7 1.0
SG Y:CYS75 3.4 0.8 1.0
CG Y:HIS77 3.4 0.8 1.0
CB Y:CYS94 3.5 0.8 0.0
CG Y:ASP97 3.5 0.8 1.0
CB Y:CYS75 3.7 0.7 1.0
CE1 Y:PHE79 3.7 0.8 1.0
O Y:HIS77 3.7 0.8 1.0
O Y:CYS75 3.9 0.8 1.0
CE1 Y:HIS77 3.9 0.8 1.0
OD2 Y:ASP97 4.1 0.7 1.0
CZ3 Y:TRP101 4.2 0.4 1.0
CZ Y:PHE79 4.2 0.8 1.0
CA Y:HIS77 4.3 0.6 1.0
C Y:HIS77 4.4 0.7 1.0
N Y:ASP97 4.5 0.8 1.0
N Y:HIS77 4.5 0.8 1.0
CB Y:ASP97 4.5 0.8 1.0
C Y:CYS75 4.6 0.8 1.0
CB Y:LEU96 4.6 0.8 1.0
CD2 Y:HIS77 4.6 0.8 1.0
CA Y:CYS75 4.8 0.8 1.0
CD1 Y:PHE79 4.8 0.8 1.0
NE2 Y:HIS77 4.8 0.8 1.0
CE3 Y:TRP101 4.9 0.6 1.0
CA Y:CYS94 4.9 0.8 0.0
CH2 Y:TRP101 5.0 0.8 1.0

Zinc binding site 5 out of 6 in 3dqv

Go back to Zinc Binding Sites List in 3dqv
Zinc binding site 5 out of 6 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 5 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
Y:Zn4002

b:0.8
occ:1.00
 SG Y:CYS45 2.5 0.8 1.0
SG Y:CYS83 2.7 0.8 1.0
SG Y:CYS42 2.7 0.6 1.0
CD2 Y:HIS80 2.8 0.3 1.0
CB Y:CYS42 2.8 1.0 1.0
CB Y:CYS45 3.1 0.8 1.0
CB Y:CYS83 3.4 0.7 1.0
N Y:CYS45 3.4 0.7 1.0
CG Y:HIS80 3.7 0.4 1.0
CA Y:CYS45 3.7 0.8 1.0
NE2 Y:HIS80 3.8 0.8 1.0
CB Y:CYS53 4.0 0.8 1.0
CB Y:HIS80 4.0 0.4 1.0
C Y:CYS45 4.1 0.8 1.0
CA Y:CYS42 4.2 0.0 1.0
C Y:ILE44 4.4 0.5 1.0
N Y:HIS80 4.5 0.9 1.0
O Y:CYS45 4.5 0.8 1.0
N Y:ARG46 4.5 0.8 1.0
NH2 Y:ARG86 4.6 0.9 1.0
N Y:ILE44 4.6 0.7 1.0
C Y:CYS42 4.7 0.7 1.0
CB Y:ILE44 4.7 0.8 1.0
CA Y:ILE44 4.8 0.7 1.0
CA Y:CYS83 4.9 0.8 1.0
ND1 Y:HIS80 4.9 0.6 1.0
CE1 Y:HIS80 4.9 0.8 1.0
CA Y:HIS80 4.9 0.3 1.0
N Y:CYS42 5.0 0.9 1.0
CA Y:CYS53 5.0 0.7 1.0

Zinc binding site 6 out of 6 in 3dqv

Go back to Zinc Binding Sites List in 3dqv
Zinc binding site 6 out of 6 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 6 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
Y:Zn4003

b:0.8
occ:1.00
 SG Y:CYS56 2.7 0.8 1.0
ND1 Y:HIS82 3.0 0.8 1.0
SG Y:CYS68 3.0 0.8 1.0
SG Y:CYS53 3.1 0.8 1.0
CB Y:CYS56 3.3 0.4 1.0
CB Y:CYS68 3.3 0.8 1.0
CE1 Y:HIS82 3.5 0.8 1.0
N Y:CYS56 3.8 0.5 1.0
CG Y:HIS82 3.9 0.8 1.0
CA Y:CYS68 4.1 0.8 1.0
CA Y:CYS56 4.1 0.3 1.0
N Y:CYS53 4.3 0.6 1.0
CB Y:HIS82 4.4 0.6 1.0
CB Y:GLU55 4.4 0.3 1.0
CB Y:CYS53 4.4 0.8 1.0
NE2 Y:HIS82 4.4 0.7 1.0
CD2 Y:HIS82 4.7 0.7 1.0
C Y:GLU55 4.7 0.7 1.0
N Y:CYS68 4.9 0.8 1.0
CA Y:CYS53 5.0 0.7 1.0
CA Y:GLU55 5.0 0.6 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: Thu Oct 24 12:18:46 2024

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