Zinc in PDB 2dw1: Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal)

The structure of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal), PDB code: 2dw1 was solved by S.Takeda, T.Igarashi, S.Araki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.670, 118.180, 138.460, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 28.6

The structure of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal) also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal) (pdb code 2dw1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal), PDB code: 2dw1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:22.4 occ:1.00 NE2 A:HIS343 2.0 19.9 1.0 NE2 A:HIS337 2.1 17.0 1.0 OAE A:GM62 2.2 36.4 1.0 NE2 A:HIS333 2.3 26.8 1.0 OAG A:GM62 2.5 44.9 1.0 CAD A:GM62 2.8 34.0 1.0 NAF A:GM62 3.0 36.9 1.0 CE1 A:HIS343 3.0 21.3 1.0 CD2 A:HIS343 3.0 21.0 1.0 CD2 A:HIS333 3.0 23.7 1.0 CD2 A:HIS337 3.0 12.3 1.0 CE1 A:HIS337 3.1 14.7 1.0 CE1 A:HIS333 3.4 23.5 1.0 O A:HOH832 3.7 32.2 1.0 ND1 A:HIS343 4.1 22.1 1.0 CG A:HIS343 4.1 24.8 1.0 CAC A:GM62 4.2 31.2 1.0 ND1 A:HIS337 4.2 13.5 1.0 CG A:HIS337 4.2 15.3 1.0 CG A:HIS333 4.2 26.4 1.0 ND1 A:HIS333 4.4 22.9 1.0 CAB A:GM62 4.6 30.8 1.0 CAA A:GM62 4.6 30.3 1.0 OE1 A:GLU334 4.7 29.7 1.0 OE2 A:GLU334 4.9 28.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn700 b:29.2 occ:1.00 NE2 B:HIS337 2.0 37.3 1.0 NE2 B:HIS333 2.1 17.8 1.0 NE2 B:HIS343 2.1 45.1 1.0 OAG B:GM61 2.1 55.5 1.0 OAE B:GM61 2.5 43.3 1.0 NAF B:GM61 2.7 46.4 1.0 CAD B:GM61 2.9 43.8 1.0 CE1 B:HIS337 2.9 38.4 1.0 CD2 B:HIS333 3.0 15.9 1.0 CD2 B:HIS337 3.0 40.1 1.0 CD2 B:HIS343 3.0 42.1 1.0 CE1 B:HIS343 3.1 41.9 1.0 CE1 B:HIS333 3.1 20.7 1.0 ND1 B:HIS337 4.0 39.7 1.0 CG B:HIS337 4.1 38.6 1.0 CG B:HIS343 4.1 43.3 1.0 ND1 B:HIS343 4.1 41.3 1.0 CG B:HIS333 4.1 21.8 1.0 ND1 B:HIS333 4.2 23.4 1.0 CAC B:GM61 4.3 38.8 1.0 CAA B:GM61 4.5 36.2 1.0 CAB B:GM61 4.7 36.7 1.0 OE2 B:GLU334 4.8 39.5 1.0 CE B:MET357 4.8 31.6 1.0 O B:HOH816 5.0 28.8 1.0

T.Igarashi, S.Araki, H.Mori, S.Takeda. Crystal Structures of Catrocollastatin/VAP2B Reveal A Dynamic, Modular Architecture of Adam/Adamalysin/Reprolysin Family Proteins Febs Lett. V. 581 2416 2007.
ISSN: ISSN 0014-5793
PubMed: 17485084
DOI: 10.1016/J.FEBSLET.2007.04.057