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Zinc in PDB 3ky9: Autoinhibited VAV1

Protein crystallography data

The structure of Autoinhibited VAV1, PDB code: 3ky9 was solved by D.R.Tomchick, M.K.Rosen, M.Machius, B.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.29 / 2.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.376, 58.738, 160.721, 90.00, 97.31, 90.00
R / Rfree (%) 22.3 / 27.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Autoinhibited VAV1 (pdb code 3ky9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Autoinhibited VAV1, PDB code: 3ky9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3ky9

Go back to Zinc Binding Sites List in 3ky9
Zinc binding site 1 out of 4 in the Autoinhibited VAV1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Autoinhibited VAV1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:0.9
occ:1.00
SG A:CYS532 2.2 0.9 1.0
ND1 A:HIS554 2.3 85.4 1.0
SG A:CYS557 2.5 0.7 1.0
CB A:CYS529 2.5 88.6 1.0
SG A:CYS529 2.5 0.5 1.0
CG A:HIS554 3.1 82.8 1.0
CB A:CYS557 3.2 96.6 1.0
CE1 A:HIS554 3.3 67.0 1.0
CB A:HIS554 3.3 79.9 1.0
N A:HIS554 3.4 77.4 1.0
CB A:CYS532 3.8 98.5 1.0
N A:CYS532 3.9 0.3 1.0
CA A:HIS554 4.0 80.6 1.0
CA A:CYS529 4.0 80.9 1.0
CA A:CYS532 4.3 0.0 1.0
CD2 A:HIS554 4.3 0.1 1.0
NE2 A:HIS554 4.4 0.2 1.0
C A:ALA553 4.4 81.6 1.0
O A:MET534 4.5 0.1 1.0
CD1 A:LEU536 4.5 0.5 1.0
CA A:ALA553 4.6 83.1 1.0
CA A:CYS557 4.6 90.6 1.0
N A:CYS529 4.7 85.3 1.0
C A:CYS529 4.8 98.5 1.0
C A:CYS532 4.9 0.7 1.0
N A:GLN533 5.0 0.8 1.0
CB A:ALA553 5.0 87.3 1.0
C A:HIS554 5.0 84.3 1.0
N A:CYS557 5.0 0.3 1.0

Zinc binding site 2 out of 4 in 3ky9

Go back to Zinc Binding Sites List in 3ky9
Zinc binding site 2 out of 4 in the Autoinhibited VAV1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Autoinhibited VAV1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:0.3
occ:1.00
ND1 A:HIS516 2.0 0.5 1.0
CE1 A:HIS516 2.5 0.4 1.0
SG A:CYS549 2.6 0.5 1.0
SG A:CYS564 2.6 0.3 1.0
CB A:CYS564 2.8 0.5 1.0
SG A:CYS546 3.0 0.3 1.0
CG A:HIS516 3.1 0.6 1.0
CA A:CYS564 3.1 0.5 1.0
CB A:CYS549 3.1 0.1 1.0
NE2 A:HIS516 3.6 0.6 1.0
CB A:CYS546 3.8 0.1 1.0
CB A:HIS516 3.8 0.0 1.0
CA A:HIS516 3.8 0.1 1.0
CD2 A:HIS516 3.9 0.6 1.0
N A:CYS564 4.0 0.3 1.0
N A:CYS549 4.1 0.1 1.0
CA A:CYS549 4.2 0.3 1.0
C A:CYS564 4.3 0.8 1.0
N A:HIS516 4.5 0.9 1.0
C A:PRO563 4.8 0.2 1.0
CB A:ALA551 5.0 0.2 1.0
CB A:ARG548 5.0 0.3 1.0
C A:HIS516 5.0 0.5 1.0
O A:PRO563 5.0 0.9 1.0

Zinc binding site 3 out of 4 in 3ky9

Go back to Zinc Binding Sites List in 3ky9
Zinc binding site 3 out of 4 in the Autoinhibited VAV1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Autoinhibited VAV1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:0.1
occ:1.00
SG B:CYS532 2.1 0.3 1.0
SG B:CYS529 2.3 95.6 1.0
CB B:CYS529 2.4 80.8 1.0
SG B:CYS557 2.4 89.3 1.0
ND1 B:HIS554 2.6 71.8 1.0
CB B:CYS557 3.1 84.2 1.0
CG B:HIS554 3.5 75.3 1.0
CB B:CYS532 3.6 86.0 1.0
N B:CYS532 3.6 97.6 1.0
CE1 B:HIS554 3.6 44.7 1.0
N B:HIS554 3.6 62.0 1.0
CB B:HIS554 3.6 68.5 1.0
CA B:CYS529 3.9 68.8 1.0
CA B:CYS532 4.0 98.7 1.0
CA B:HIS554 4.3 67.4 1.0
CA B:ALA553 4.5 69.1 1.0
CA B:CYS557 4.6 86.5 1.0
C B:ALA553 4.6 69.9 1.0
O B:MET534 4.6 0.3 1.0
C B:CYS532 4.6 0.9 1.0
N B:CYS529 4.6 79.5 1.0
C B:CYS529 4.6 81.4 1.0
CD2 B:HIS554 4.7 95.9 1.0
N B:GLN533 4.7 0.5 1.0
NE2 B:HIS554 4.7 0.9 1.0
C B:ALA531 4.7 0.2 1.0
CD1 B:LEU536 4.7 99.6 1.0
CB B:ALA531 4.8 90.4 1.0
N B:ALA531 4.8 86.9 1.0
CB B:ALA553 4.9 72.2 1.0

Zinc binding site 4 out of 4 in 3ky9

Go back to Zinc Binding Sites List in 3ky9
Zinc binding site 4 out of 4 in the Autoinhibited VAV1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Autoinhibited VAV1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:99.4
occ:1.00
ND1 B:HIS516 2.3 72.5 1.0
SG B:CYS546 2.4 80.1 1.0
SG B:CYS549 2.4 98.4 1.0
SG B:CYS564 2.7 95.5 1.0
CB B:CYS549 3.0 99.7 1.0
CE1 B:HIS516 3.1 97.3 1.0
CB B:CYS546 3.2 69.5 1.0
CB B:CYS564 3.3 0.0 1.0
CG B:HIS516 3.4 79.3 1.0
N B:CYS549 3.6 1.0 1.0
CA B:CYS564 3.7 1.0 1.0
CB B:HIS516 3.8 91.8 1.0
CA B:HIS516 3.8 90.8 1.0
CA B:CYS549 3.9 0.5 1.0
NE2 B:HIS516 4.2 0.9 1.0
CD2 B:HIS516 4.4 0.5 1.0
CB B:ARG548 4.5 0.1 1.0
C B:ARG548 4.5 0.0 1.0
CA B:CYS546 4.6 73.9 1.0
N B:CYS564 4.7 0.6 1.0
N B:ASP517 4.7 81.8 1.0
C B:CYS549 4.7 0.9 1.0
N B:HIS516 4.7 0.6 1.0
N B:GLY565 4.7 0.5 1.0
C B:CYS564 4.8 1.0 1.0
C B:HIS516 4.9 88.0 1.0
O B:CYS546 4.9 0.7 1.0
CB B:ALA551 4.9 89.1 1.0
CA B:ARG548 4.9 0.2 1.0
N B:ARG548 4.9 0.9 1.0
C B:CYS546 5.0 87.3 1.0

Reference:

B.Yu, I.R.Martins, P.Li, G.K.Amarasinghe, J.Umetani, M.E.Fernandez-Zapico, D.D.Billadeau, M.Machius, D.R.Tomchick, M.K.Rosen. Structural and Energetic Mechanisms of Cooperative Autoinhibition and Activation of VAV1 Cell(Cambridge,Mass.) V. 140 246 2010.
ISSN: ISSN 0092-8674
PubMed: 20141838
DOI: 10.1016/J.CELL.2009.12.033
Page generated: Wed Dec 16 04:31:19 2020

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