Zinc in PDB 3bji: Structural Basis of Promiscuous Guanine Nucleotide Exchange By the T-Cell Essential VAV1

The structure of Structural Basis of Promiscuous Guanine Nucleotide Exchange By the T-Cell Essential VAV1, PDB code: 3bji was solved by J.E.Chrencik, A.Brooun, P.Kuhn, Accelerated Technologies Centerfor Gene To 3D Structure (Atcg3D), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.948, 75.079, 114.857, 90.00, 103.87, 90.00
R / Rfree (%)	22.1 / 29.3

The binding sites of Zinc atom in the Structural Basis of Promiscuous Guanine Nucleotide Exchange By the T-Cell Essential VAV1 (pdb code 3bji). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Basis of Promiscuous Guanine Nucleotide Exchange By the T-Cell Essential VAV1, PDB code: 3bji:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structural Basis of Promiscuous Guanine Nucleotide Exchange By the T-Cell Essential VAV1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of Promiscuous Guanine Nucleotide Exchange By the T-Cell Essential VAV1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:32.1 occ:1.00 SG A:CYS529 2.1 29.6 1.0 SG A:CYS557 2.2 30.6 1.0 ND1 A:HIS554 2.2 29.2 1.0 SG A:CYS532 2.3 37.1 1.0 CB A:CYS529 3.0 31.7 1.0 CB A:CYS557 3.0 30.4 1.0 CE1 A:HIS554 3.0 28.2 1.0 CB A:CYS532 3.2 37.3 1.0 CG A:HIS554 3.3 30.2 1.0 CB A:HIS554 3.7 29.4 1.0 N A:CYS532 3.9 36.6 1.0 N A:HIS554 4.0 28.7 1.0 NE2 A:HIS554 4.2 30.1 1.0 CA A:CYS532 4.2 37.1 1.0 CD2 A:HIS554 4.3 30.8 1.0 CA A:CYS529 4.5 31.9 1.0 CA A:HIS554 4.5 29.1 1.0 CA A:CYS557 4.5 30.4 1.0 O A:HOH578 4.8 27.5 1.0 N A:GLN533 4.8 38.1 1.0 C A:CYS532 4.9 37.5 1.0 CB A:ALA531 5.0 35.1 1.0 N A:CYS557 5.0 30.7 1.0

Zinc binding site 2 out of 4 in the Structural Basis of Promiscuous Guanine Nucleotide Exchange By the T-Cell Essential VAV1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of Promiscuous Guanine Nucleotide Exchange By the T-Cell Essential VAV1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4 b:32.9 occ:1.00 SG A:CYS549 2.0 33.7 1.0 ND1 A:HIS516 2.0 23.2 1.0 SG A:CYS546 2.0 29.2 1.0 SG A:CYS564 2.5 40.8 1.0 CB A:CYS564 2.9 41.8 1.0 CG A:HIS516 2.9 25.1 1.0 CB A:CYS546 3.1 29.7 1.0 CE1 A:HIS516 3.1 23.6 1.0 CB A:HIS516 3.2 26.9 1.0 CA A:HIS516 3.3 27.5 1.0 CB A:CYS549 3.3 32.7 1.0 N A:CYS549 3.5 32.5 1.0 CA A:CYS549 4.0 32.8 1.0 CD2 A:HIS516 4.1 22.7 1.0 N A:HIS516 4.1 28.5 1.0 NE2 A:HIS516 4.2 22.8 1.0 N A:ASP517 4.3 28.6 1.0 CA A:CYS564 4.3 41.2 1.0 C A:HIS516 4.3 27.9 1.0 CB A:ARG548 4.5 31.7 1.0 CA A:CYS546 4.5 29.4 1.0 C A:ARG548 4.6 32.1 1.0 N A:CYS564 4.7 40.2 1.0 C A:GLY515 4.9 29.0 1.0 N A:ARG548 4.9 31.4 1.0 CA A:ARG548 4.9 31.6 1.0 C A:CYS546 5.0 29.2 1.0

Zinc binding site 3 out of 4 in the Structural Basis of Promiscuous Guanine Nucleotide Exchange By the T-Cell Essential VAV1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis of Promiscuous Guanine Nucleotide Exchange By the T-Cell Essential VAV1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:44.3 occ:1.00 ND1 B:HIS516 1.8 34.9 1.0 SG B:CYS549 2.3 41.7 1.0 SG B:CYS564 2.3 39.9 1.0 SG B:CYS546 2.3 37.0 1.0 CE1 B:HIS516 2.8 35.5 1.0 CG B:HIS516 2.8 36.1 1.0 CB B:CYS546 3.2 39.2 1.0 CB B:HIS516 3.2 36.6 1.0 CB B:CYS564 3.3 40.6 1.0 CA B:HIS516 3.4 37.0 1.0 N B:CYS549 3.7 45.4 1.0 CB B:CYS549 3.8 45.5 1.0 NE2 B:HIS516 3.9 34.5 1.0 CD2 B:HIS516 3.9 35.5 1.0 CA B:CYS564 4.0 40.7 1.0 CB B:ARG548 4.1 45.2 1.0 N B:ASP517 4.3 36.5 1.0 CA B:CYS549 4.3 45.4 1.0 N B:HIS516 4.3 37.2 1.0 O B:GLY515 4.3 38.3 1.0 C B:HIS516 4.4 36.8 1.0 O B:CYS549 4.4 46.7 1.0 CA B:CYS546 4.6 39.2 1.0 C B:ARG548 4.6 45.1 1.0 CB B:ALA551 4.7 44.0 1.0 C B:GLY515 4.7 37.9 1.0 CA B:ARG548 4.8 44.9 1.0 C B:CYS549 4.8 46.2 1.0 N B:ARG548 4.8 44.4 1.0 CG B:ARG548 4.9 46.3 1.0 N B:CYS564 4.9 39.9 1.0

Zinc binding site 4 out of 4 in the Structural Basis of Promiscuous Guanine Nucleotide Exchange By the T-Cell Essential VAV1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis of Promiscuous Guanine Nucleotide Exchange By the T-Cell Essential VAV1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3 b:31.1 occ:1.00 ND1 B:HIS554 1.9 24.8 1.0 SG B:CYS557 2.0 32.7 1.0 SG B:CYS529 2.3 28.8 1.0 SG B:CYS532 2.4 37.3 1.0 CE1 B:HIS554 2.7 25.3 1.0 CB B:CYS532 2.8 34.8 1.0 CB B:CYS529 3.0 30.8 1.0 CG B:HIS554 3.0 29.5 1.0 CB B:CYS557 3.2 33.3 1.0 CB B:HIS554 3.6 31.4 1.0 NE2 B:HIS554 3.8 24.3 1.0 CD2 B:HIS554 4.0 28.3 1.0 N B:HIS554 4.1 32.6 1.0 CA B:CYS532 4.3 34.7 1.0 CA B:CYS529 4.5 31.1 1.0 CA B:HIS554 4.5 32.3 1.0 CB B:ALA531 4.5 33.5 1.0 CA B:CYS557 4.6 33.5 1.0 N B:CYS532 4.8 34.5 1.0 N B:CYS557 4.9 33.1 1.0 C B:CYS529 5.0 31.5 1.0

J.E.Chrencik, A.Brooun, H.Zhang, I.I.Mathews, G.L.Hura, S.A.Foster, J.J.Perry, M.Streiff, P.Ramage, H.Widmer, G.M.Bokoch, J.A.Tainer, G.Weckbecker, P.Kuhn. Structural Basis of Guanine Nucleotide Exchange Mediated By the T-Cell Essential VAV1. J.Mol.Biol. V. 380 828 2008.
ISSN: ISSN 0022-2836
PubMed: 18589439
DOI: 10.1016/J.JMB.2008.05.024