Calcium 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:

Zinc

(Zn)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-5 Crystal), PDB code: 2dw2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-5 Crystal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca701 b:21.0 occ:1.00 O A:CYS388 2.1 21.7 1.0 O A:HOH4 2.1 10.5 1.0 OE1 A:GLU201 2.1 22.3 1.0 OD1 A:ASP285 2.4 21.9 1.0 ND2 A:ASN391 2.4 28.2 1.0 O A:HOH86 2.5 29.7 1.0 OD2 A:ASP285 2.7 31.9 1.0 OD1 A:ASN391 2.8 21.1 1.0 CG A:ASP285 2.8 26.1 1.0 CG A:ASN391 2.9 20.1 1.0 CD A:GLU201 3.1 24.3 1.0 C A:CYS388 3.3 26.7 1.0 CG A:GLU201 3.7 14.2 1.0 OE2 A:GLU201 4.0 27.8 1.0 CA A:ILE389 4.1 25.1 1.0 N A:ILE389 4.2 25.7 1.0 CB A:GLU201 4.3 17.6 1.0 O A:ASN391 4.3 24.5 1.0 CB A:ASP285 4.3 23.7 1.0 CA A:CYS388 4.3 26.6 1.0 O A:PHE199 4.3 22.2 1.0 CB A:ASN391 4.4 17.4 1.0 CB A:CYS388 4.7 29.3 1.0 C A:ILE389 4.7 28.4 1.0 N A:ASN391 4.8 17.2 1.0 N A:GLU201 4.8 24.0 1.0 N A:LEU390 4.9 26.4 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-5 Crystal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 A:Ca702 b:20.9 occ:1.00 O A:VAL403 2.3 10.9 1.0 OE1 A:GLU410 2.3 24.2 1.0 O A:LEU408 2.4 22.2 1.0 OD2 A:ASP416 2.4 31.3 1.0 OD1 A:ASN406 2.4 23.3 1.0 OE1 A:GLU413 2.5 12.6 1.0 OE2 A:GLU413 2.9 17.8 1.0 CD A:GLU413 3.0 21.6 1.0 CD A:GLU410 3.1 22.1 1.0 CG A:ASN406 3.2 20.8 1.0 CG A:ASP416 3.3 27.0 1.0 C A:VAL403 3.4 15.5 1.0 C A:LEU408 3.4 20.2 1.0 ND2 A:ASN406 3.5 19.8 1.0 CG A:GLU410 3.5 18.3 1.0 N A:LEU408 4.0 18.3 1.0 CB A:ASP416 4.0 26.9 1.0 CB A:GLU410 4.0 21.2 1.0 N A:VAL403 4.1 17.3 1.0 N A:GLU410 4.1 18.7 1.0 CA A:LEU408 4.1 18.7 1.0 OE2 A:GLU410 4.1 24.4 1.0 OD1 A:ASP416 4.2 26.5 1.0 CA A:CYS404 4.3 16.3 1.0 CB A:LEU408 4.3 14.0 1.0 N A:CYS404 4.3 17.6 1.0 CA A:VAL403 4.3 13.1 1.0 N A:ASN406 4.4 10.6 1.0 N A:GLY405 4.4 11.9 1.0 CB A:ASN406 4.5 15.6 1.0 N A:LEU409 4.5 20.9 1.0 CG A:GLU413 4.5 19.1 1.0 CA A:LEU409 4.7 20.1 1.0 CA A:GLU410 4.7 16.0 1.0 C A:LEU409 4.7 20.9 1.0 N A:GLU407 4.8 16.2 1.0 C A:CYS404 4.8 13.9 1.0 CA A:ASN406 4.9 8.2 1.0 CB A:VAL403 4.9 19.3 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-5 Crystal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 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:Ca703 b:23.2 occ:1.00 OE1 A:GLU470 2.2 32.5 1.0 OD2 A:ASP482 2.4 10.0 1.0 O A:PRO468 2.4 15.4 1.0 OD2 A:ASP467 2.5 18.1 1.0 OE2 A:GLU470 2.7 33.7 1.0 CD A:GLU470 2.8 32.4 1.0 O A:VAL483 2.9 12.0 1.0 N A:VAL483 3.5 18.3 1.0 C A:PRO468 3.5 10.4 1.0 CG A:ASP482 3.6 18.5 1.0 CG A:ASP467 3.6 18.7 1.0 C A:VAL483 3.8 16.1 1.0 OD1 A:ASP467 4.1 23.9 1.0 CA A:VAL483 4.2 13.2 1.0 CA A:ALA469 4.2 10.2 1.0 CA A:ASP482 4.2 18.0 1.0 C A:ASP482 4.3 18.5 1.0 N A:PRO468 4.3 13.5 1.0 N A:ALA469 4.3 9.2 1.0 CG A:GLU470 4.3 28.7 1.0 C A:ASP467 4.3 14.9 1.0 OD1 A:ASP482 4.4 18.2 1.0 C A:ALA469 4.4 13.4 1.0 CA A:PRO468 4.5 11.9 1.0 O A:ASP467 4.5 15.8 1.0 CB A:ASP482 4.5 13.8 1.0 O A:HOH49 4.5 12.3 1.0 CD2 A:PHE484 4.5 15.1 1.0 N A:GLU470 4.6 15.8 1.0 CE2 A:PHE484 4.6 10.8 1.0 CG A:PRO468 4.6 8.0 1.0 CD A:ARG460 4.6 23.1 1.0 CD A:PRO468 4.7 14.6 1.0 CB A:VAL483 4.8 14.4 1.0 CB A:ASP467 4.8 19.1 1.0 CA A:ASP467 4.8 17.6 1.0 O A:ALA469 5.0 16.4 1.0 O A:HOH84 5.0 11.8 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-5 Crystal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 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:Ca711 b:23.0 occ:1.00 ND2 B:ASN391 2.3 32.7 1.0 OE1 B:GLU201 2.4 26.2 1.0 OD1 B:ASP285 2.4 29.9 1.0 O B:CYS388 2.4 22.4 1.0 OD2 B:ASP285 2.6 27.6 1.0 CG B:ASP285 2.9 23.4 1.0 OD1 B:ASN391 3.0 27.3 1.0 CG B:ASN391 3.1 25.0 1.0 CD B:GLU201 3.4 27.4 1.0 C B:CYS388 3.6 23.6 1.0 CG B:GLU201 4.0 21.3 1.0 CB B:ASP285 4.4 20.8 1.0 CB B:GLU201 4.4 19.2 1.0 CA B:ILE389 4.4 22.7 1.0 OE2 B:GLU201 4.4 25.4 1.0 O B:ASN391 4.4 19.0 1.0 N B:ILE389 4.5 25.2 1.0 CB B:ASN391 4.5 17.2 1.0 CA B:CYS388 4.6 23.7 1.0 CB B:CYS388 4.8 26.8 1.0 O B:PHE199 4.8 23.9 1.0 N B:ASN391 4.9 14.4 1.0 N B:GLU201 4.9 17.5 1.0 C B:ILE389 5.0 24.6 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-5 Crystal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 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:Ca712 b:22.8 occ:1.00 OD2 B:ASP416 2.3 19.6 1.0 OD1 B:ASN406 2.3 34.7 1.0 OE1 B:GLU410 2.3 28.1 1.0 O B:VAL403 2.4 24.6 1.0 O B:LEU408 2.4 21.8 1.0 OE1 B:GLU413 2.5 25.6 1.0 OE2 B:GLU413 2.9 35.9 1.0 CD B:GLU413 3.0 31.8 1.0 CG B:ASP416 3.3 19.6 1.0 CG B:ASN406 3.3 32.4 1.0 CD B:GLU410 3.3 26.4 1.0 C B:VAL403 3.3 25.1 1.0 C B:LEU408 3.6 20.1 1.0 CG B:GLU410 3.8 25.7 1.0 ND2 B:ASN406 3.9 31.0 1.0 CB B:ASP416 3.9 18.1 1.0 N B:VAL403 4.0 20.9 1.0 N B:LEU408 4.0 23.5 1.0 N B:CYS404 4.1 26.3 1.0 CA B:CYS404 4.1 25.0 1.0 OD1 B:ASP416 4.2 16.7 1.0 CA B:LEU408 4.2 20.9 1.0 CA B:VAL403 4.2 22.8 1.0 CB B:GLU410 4.3 20.8 1.0 N B:ASN406 4.3 25.0 1.0 N B:GLU410 4.3 18.1 1.0 OE2 B:GLU410 4.3 30.3 1.0 N B:GLY405 4.4 26.1 1.0 CB B:LEU408 4.4 19.8 1.0 CB B:ASN406 4.5 30.9 1.0 CG B:GLU413 4.5 28.4 1.0 N B:LEU409 4.7 18.0 1.0 C B:CYS404 4.7 24.0 1.0 N B:GLU407 4.8 24.0 1.0 CA B:ASN406 4.8 25.3 1.0 CB B:VAL403 4.9 22.5 1.0 CA B:LEU409 4.9 18.3 1.0 C B:ASN406 5.0 23.3 1.0 CA B:GLU410 5.0 18.3 1.0 C B:LEU409 5.0 16.0 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-5 Crystal)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 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:Ca713 b:20.5 occ:1.00 OD2 B:ASP467 2.2 24.6 1.0 OD1 B:ASP482 2.3 18.5 1.0 O B:PRO468 2.3 15.8 1.0 OE1 B:GLU470 2.4 22.8 1.0 O B:VAL483 2.6 12.2 1.0 OE2 B:GLU470 2.9 29.4 1.0 CD B:GLU470 3.0 22.0 1.0 CG B:ASP467 3.4 19.4 1.0 C B:PRO468 3.4 14.9 1.0 CG B:ASP482 3.5 22.2 1.0 N B:VAL483 3.5 15.7 1.0 C B:VAL483 3.6 16.2 1.0 OD1 B:ASP467 3.9 22.3 1.0 N B:PRO468 4.0 13.2 1.0 CA B:VAL483 4.1 12.4 1.0 C B:ASP467 4.1 18.2 1.0 OD2 B:ASP482 4.2 24.0 1.0 CD B:PRO468 4.3 15.2 1.0 CA B:ALA469 4.3 19.0 1.0 N B:ALA469 4.3 14.8 1.0 O B:HOH124 4.3 23.5 1.0 C B:ASP482 4.3 16.4 1.0 CG B:PRO468 4.4 16.1 1.0 CA B:PRO468 4.4 11.4 1.0 CA B:ASP482 4.4 16.2 1.0 CD2 B:PHE484 4.4 25.4 1.0 CG B:GLU470 4.5 21.5 1.0 O B:ASP467 4.5 23.4 1.0 CB B:ASP467 4.5 16.7 1.0 CA B:ASP467 4.5 16.2 1.0 CB B:ASP482 4.6 15.2 1.0 C B:ALA469 4.6 18.4 1.0 CE2 B:PHE484 4.6 27.3 1.0 CD B:ARG460 4.7 24.9 1.0 N B:GLU470 4.7 21.1 1.0 CB B:VAL483 4.7 14.4 1.0 N B:PHE484 4.8 17.2 1.0 O B:HOH108 4.8 10.8 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