Zinc in PDB 2dw0: Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 Crystal)

The structure of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 Crystal), PDB code: 2dw0 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 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.910, 137.950, 59.240, 90.00, 91.52, 90.00
R / Rfree (%)	17.5 / 22.8

The structure of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 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 2-1 Crystal) (pdb code 2dw0). 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 2-1 Crystal), PDB code: 2dw0:
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 2-1 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 2-1 Crystal) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:13.6 occ:1.00 OAE A:GM6901 2.0 14.9 1.0 NE2 A:HIS333 2.0 10.9 1.0 NE2 A:HIS337 2.0 11.7 1.0 NE2 A:HIS343 2.1 17.4 1.0 OAG A:GM6901 2.3 12.2 1.0 CAD A:GM6901 2.7 13.8 1.0 NAF A:GM6901 2.8 14.8 1.0 CE1 A:HIS333 3.0 7.9 1.0 CD2 A:HIS337 3.0 10.9 1.0 CD2 A:HIS333 3.0 9.0 1.0 CE1 A:HIS343 3.0 14.8 1.0 CE1 A:HIS337 3.0 12.0 1.0 CD2 A:HIS343 3.1 14.4 1.0 ND1 A:HIS333 4.1 10.3 1.0 O A:HOH942 4.1 10.9 1.0 ND1 A:HIS337 4.1 11.5 1.0 CAC A:GM6901 4.1 13.1 1.0 CG A:HIS337 4.1 11.7 1.0 ND1 A:HIS343 4.2 15.7 1.0 CG A:HIS333 4.2 9.7 1.0 CG A:HIS343 4.2 17.5 1.0 OE1 A:GLU334 4.6 12.9 1.0 CAB A:GM6901 4.7 13.3 1.0 O A:HOH1205 4.7 37.4 1.0 CAA A:GM6901 4.7 11.9 1.0 CE A:MET357 4.7 8.0 1.0 O A:HOH968 4.7 22.7 1.0 O A:HOH922 4.8 14.1 1.0 OE2 A:GLU334 4.9 12.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 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 2-1 Crystal) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn700 b:13.5 occ:1.00 NE2 B:HIS343 2.0 15.6 1.0 NE2 B:HIS337 2.0 8.3 1.0 OAE B:GM6901 2.1 12.8 1.0 NE2 B:HIS333 2.1 9.5 1.0 OAG B:GM6901 2.3 16.8 1.0 CAD B:GM6901 2.7 14.6 1.0 NAF B:GM6901 2.9 14.8 1.0 CE1 B:HIS343 2.9 14.0 1.0 CD2 B:HIS333 3.0 10.7 1.0 CE1 B:HIS337 3.0 8.4 1.0 CD2 B:HIS337 3.0 9.5 1.0 CD2 B:HIS343 3.0 15.9 1.0 CE1 B:HIS333 3.1 10.7 1.0 O B:HOH1158 4.0 28.4 1.0 ND1 B:HIS343 4.1 13.6 1.0 O B:HOH936 4.1 12.7 1.0 ND1 B:HIS337 4.1 8.4 1.0 CG B:HIS343 4.2 15.6 1.0 CAC B:GM6901 4.2 13.8 1.0 CG B:HIS337 4.2 9.1 1.0 ND1 B:HIS333 4.2 11.4 1.0 CG B:HIS333 4.2 10.5 1.0 O B:HOH925 4.3 14.4 1.0 OE1 B:GLU334 4.5 11.5 1.0 CAA B:GM6901 4.5 11.7 1.0 CAB B:GM6901 4.6 13.3 1.0 CE B:MET357 4.9 8.2 1.0 OE2 B:GLU334 4.9 11.7 1.0 O A:HOH1147 5.0 30.6 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