Zinc in PDB 2dw2: Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-5 Crystal)

The structure of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-5 Crystal), PDB code: 2dw2 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 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	220.742, 79.475, 58.690, 90.00, 91.73, 90.00
R / Rfree (%)	19.9 / 26

The structure of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-5 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 2-5 Crystal) (pdb code 2dw2). 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 2-5 Crystal), PDB code: 2dw2:
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 2-5 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 2-5 Crystal) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:18.9 occ:1.00 NE2 A:HIS343 1.9 24.4 1.0 O A:HOH153 2.0 4.1 1.0 NE2 A:HIS337 2.1 9.0 1.0 NE2 A:HIS333 2.1 6.6 1.0 CE1 A:HIS343 2.9 26.1 1.0 CD2 A:HIS343 3.0 25.1 1.0 CE1 A:HIS337 3.0 12.7 1.0 CD2 A:HIS333 3.0 7.5 1.0 CE1 A:HIS333 3.2 7.7 1.0 CD2 A:HIS337 3.2 12.3 1.0 ND1 A:HIS343 4.0 21.6 1.0 CG A:HIS343 4.1 23.5 1.0 ND1 A:HIS337 4.2 18.0 1.0 CG A:HIS333 4.2 13.3 1.0 ND1 A:HIS333 4.2 7.7 1.0 CG A:HIS337 4.3 15.9 1.0 OE2 A:GLU334 4.5 22.8 1.0 CE A:MET357 4.7 23.9 1.0 O A:PRO359 4.8 29.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-5 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 2-5 Crystal) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn700 b:17.3 occ:1.00 NE2 B:HIS343 2.0 23.8 1.0 NE2 B:HIS333 2.0 13.1 1.0 NE2 B:HIS337 2.1 8.1 1.0 O B:HOH155 2.2 5.3 1.0 CE1 B:HIS343 2.8 24.7 1.0 CD2 B:HIS333 3.0 10.7 1.0 CE1 B:HIS333 3.1 13.8 1.0 CD2 B:HIS343 3.1 20.5 1.0 CE1 B:HIS337 3.1 18.7 1.0 CD2 B:HIS337 3.2 20.6 1.0 ND1 B:HIS343 4.0 18.2 1.0 CG B:HIS343 4.1 20.6 1.0 CG B:HIS333 4.1 18.3 1.0 ND1 B:HIS333 4.1 9.4 1.0 ND1 B:HIS337 4.2 24.0 1.0 CG B:HIS337 4.3 20.4 1.0 O B:HOH11 4.7 12.9 1.0 CE B:MET357 4.7 25.2 1.0 OE2 B:GLU334 4.8 15.7 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