Zinc in PDB 6new: Apo Structure of the Activated Truncation of VAV1

The structure of Apo Structure of the Activated Truncation of VAV1, PDB code: 6new was solved by M.S.Knapp, R.A.Elling, E.Ornelas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.70 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.925, 67.693, 178.560, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 25.7

The binding sites of Zinc atom in the Apo Structure of the Activated Truncation of VAV1 (pdb code 6new). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Apo Structure of the Activated Truncation of VAV1, PDB code: 6new:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Apo Structure of the Activated Truncation of VAV1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Apo Structure of the Activated Truncation of VAV1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:31.2 occ:1.00 SG A:CYS557 2.2 31.0 1.0 SG A:CYS529 2.2 30.4 1.0 ND1 A:HIS554 2.3 30.3 1.0 SG A:CYS532 2.3 37.5 1.0 CB A:CYS529 2.9 26.8 1.0 CB A:CYS557 3.1 28.0 1.0 CE1 A:HIS554 3.1 29.0 1.0 CG A:HIS554 3.4 27.7 1.0 CB A:CYS532 3.5 34.4 1.0 CB A:HIS554 3.8 24.8 1.0 N A:CYS532 3.8 34.3 1.0 N A:HIS554 4.1 24.1 1.0 CA A:CYS532 4.2 34.9 1.0 NE2 A:HIS554 4.3 28.5 1.0 O A:HOH846 4.4 52.5 1.0 CA A:CYS529 4.4 27.9 1.0 CD2 A:HIS554 4.4 28.0 1.0 O A:HOH873 4.5 44.5 1.0 CA A:HIS554 4.5 24.3 1.0 CA A:CYS557 4.5 29.1 1.0 CB A:ALA531 4.7 32.4 1.0 N A:CYS557 4.9 29.7 1.0 C A:ALA531 4.9 37.3 1.0 O A:HOH774 4.9 47.0 1.0 C A:CYS529 5.0 33.6 1.0 C A:CYS532 5.0 40.6 1.0

Zinc binding site 2 out of 2 in the Apo Structure of the Activated Truncation of VAV1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Apo Structure of the Activated Truncation of VAV1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:37.0 occ:1.00 ND1 A:HIS516 2.1 26.5 1.0 SG A:CYS546 2.2 38.5 1.0 SG A:CYS549 2.3 40.2 1.0 SG A:CYS564 2.3 43.7 1.0 CE1 A:HIS516 2.9 26.4 1.0 CB A:CYS549 3.1 38.7 1.0 CB A:CYS546 3.2 32.8 1.0 CB A:CYS564 3.2 41.0 1.0 CG A:HIS516 3.3 25.3 1.0 N A:CYS549 3.6 39.6 1.0 CB A:HIS516 3.7 23.4 1.0 CA A:CYS564 3.8 42.7 1.0 CA A:HIS516 3.8 25.9 1.0 CA A:CYS549 4.0 39.2 1.0 NE2 A:HIS516 4.2 26.8 1.0 CD2 A:HIS516 4.3 26.0 1.0 CB A:ARG548 4.4 38.5 1.0 N A:HIS516 4.6 28.2 1.0 CA A:CYS546 4.6 31.9 1.0 O A:GLY515 4.7 34.8 1.0 C A:ARG548 4.7 44.5 1.0 N A:CYS564 4.7 43.0 1.0 C A:CYS549 4.8 43.4 1.0 C A:CYS564 4.8 54.2 1.0 N A:ASP517 4.8 32.3 1.0 N A:GLY565 4.9 56.0 1.0 C A:HIS516 4.9 34.9 1.0 C A:GLY515 4.9 33.8 1.0 CB A:ALA551 5.0 35.1 1.0 N A:ARG550 5.0 39.2 1.0 CA A:ARG548 5.0 39.8 1.0

M.Gerspacher, P.R.Skaanderup. Allosteric Inhibitors of VAV1 Block Guanine Nucleotide Exchange Activity To Be Published.