Atomistry » Zinc » PDB 3kry-3l2v » 3ky9
Atomistry »
  Zinc »
    PDB 3kry-3l2v »
      3ky9 »

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 Aug 20 11:08:49 2025

Last articles

Zn in 4GBN
Zn in 4GBD
Zn in 4GBL
Zn in 4GBK
Zn in 4GBI
Zn in 4GB0
Zn in 4GBC
Zn in 4G9L
Zn in 4GAA
Zn in 4GAT
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy