Calcium in PDB 2ero: Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form)

The structure of Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form), PDB code: 2ero 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 (°)	86.710, 93.270, 137.740, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.8

The structure of Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form) also contains other interesting chemical elements:

Cobalt	(Co)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form) (pdb code 2ero). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form), PDB code: 2ero:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form)


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 Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:44.3 occ:1.00 OD1 A:ASN408 2.1 45.9 1.0 O A:PHE410 2.3 43.1 1.0 OE1 A:GLU415 2.4 49.2 1.0 O A:VAL405 2.4 41.1 1.0 OD1 A:ASP418 2.4 39.2 1.0 OE1 A:GLU412 2.4 53.8 1.0 OE2 A:GLU415 2.9 52.6 1.0 CD A:GLU415 3.0 50.8 1.0 CG A:ASN408 3.2 44.6 1.0 CD A:GLU412 3.5 51.3 1.0 C A:VAL405 3.5 42.1 1.0 C A:PHE410 3.5 40.6 1.0 CG A:ASP418 3.5 36.4 1.0 ND2 A:ASN408 3.7 43.2 1.0 CG A:GLU412 3.9 47.5 1.0 CB A:ASP418 4.0 36.2 1.0 N A:GLU412 4.1 45.0 1.0 N A:PHE410 4.2 41.9 1.0 N A:VAL405 4.2 42.1 1.0 CA A:CYS406 4.3 41.5 1.0 N A:CYS406 4.3 43.3 1.0 CB A:GLU412 4.3 44.8 1.0 N A:ASN408 4.3 41.6 1.0 CA A:PHE410 4.3 41.9 1.0 CB A:ASN408 4.4 40.2 1.0 CA A:VAL405 4.4 40.7 1.0 N A:VAL411 4.5 39.8 1.0 N A:GLY407 4.5 41.5 1.0 OE2 A:GLU412 4.5 54.0 1.0 CG A:GLU415 4.5 47.2 1.0 CA A:VAL411 4.5 39.0 1.0 OD2 A:ASP418 4.6 35.9 1.0 CB A:PHE410 4.7 40.7 1.0 C A:VAL411 4.8 42.2 1.0 CA A:ASN408 4.8 42.1 1.0 CA A:GLU412 4.9 47.4 1.0 C A:CYS406 4.9 41.7 1.0 C A:ASN408 4.9 43.2 1.0 CB A:VAL405 5.0 41.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form)


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 Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:38.8 occ:1.00 OD1 A:ASP483 2.4 42.9 1.0 O A:ARG484 2.4 46.5 1.0 O A:MET470 2.4 39.5 1.0 OD2 A:ASP472 2.5 40.9 1.0 OD2 A:ASP469 2.5 39.0 1.0 OD1 A:ASP472 2.6 42.7 1.0 O A:HOH815 2.6 34.9 1.0 CG A:ASP472 2.8 42.4 1.0 N A:ARG484 3.3 48.2 1.0 C A:ARG484 3.4 49.2 1.0 CG A:ASP483 3.5 46.9 1.0 C A:MET470 3.5 42.5 1.0 CG A:ASP469 3.6 36.0 1.0 N A:MET470 3.8 43.6 1.0 C A:ASP483 3.9 46.2 1.0 OD1 A:ASP469 3.9 32.8 1.0 CA A:ARG484 3.9 51.2 1.0 CA A:ASP483 4.1 47.1 1.0 CA A:MET470 4.2 44.7 1.0 CB A:ASP472 4.2 40.0 1.0 CG A:ARG484 4.3 64.5 1.0 OD2 A:ASP483 4.3 48.3 1.0 N A:ASP472 4.4 39.8 1.0 CB A:ASP483 4.4 44.8 1.0 CD2 A:PHE485 4.5 38.7 1.0 N A:PHE485 4.5 47.3 1.0 C A:ALA471 4.5 41.0 1.0 N A:ALA471 4.6 42.1 1.0 CE2 A:PHE485 4.7 42.8 1.0 CB A:ARG484 4.7 57.6 1.0 NH1 A:ARG462 4.8 39.4 1.0 CB A:MET470 4.8 46.8 1.0 CA A:ASP472 4.8 39.0 1.0 CA A:ALA471 4.8 41.9 1.0 O A:ASP483 4.8 43.7 1.0 CD A:ARG462 4.8 39.3 1.0 CA A:PHE485 4.9 46.6 1.0 C A:ASP469 4.9 44.5 1.0 CB A:ASP469 4.9 40.6 1.0 O A:ARG462 4.9 34.4 1.0 O A:ALA471 4.9 40.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form)


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 Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:32.9 occ:1.00 OD1 B:ASN408 2.3 32.2 1.0 O B:VAL405 2.3 34.5 1.0 OE1 B:GLU412 2.3 36.0 1.0 OD2 B:ASP418 2.3 25.2 1.0 O B:PHE410 2.4 31.4 1.0 OE1 B:GLU415 2.5 45.0 1.0 OE2 B:GLU415 2.9 43.5 1.0 CD B:GLU415 3.1 43.6 1.0 CG B:ASN408 3.2 30.6 1.0 CD B:GLU412 3.3 36.2 1.0 C B:VAL405 3.4 34.2 1.0 CG B:ASP418 3.5 24.6 1.0 C B:PHE410 3.6 31.5 1.0 ND2 B:ASN408 3.7 19.1 1.0 CG B:GLU412 4.0 38.1 1.0 CB B:ASP418 4.0 28.9 1.0 N B:VAL405 4.1 30.5 1.0 OE2 B:GLU412 4.1 36.7 1.0 N B:PHE410 4.1 32.8 1.0 N B:CYS406 4.2 35.6 1.0 CA B:CYS406 4.2 39.2 1.0 N B:ASN408 4.2 29.7 1.0 N B:GLY407 4.3 36.5 1.0 CA B:VAL405 4.3 31.9 1.0 N B:GLU412 4.3 35.0 1.0 CA B:PHE410 4.4 32.2 1.0 CB B:ASN408 4.4 26.3 1.0 OD1 B:ASP418 4.4 26.1 1.0 CB B:GLU412 4.5 35.9 1.0 N B:VAL411 4.6 31.8 1.0 CG B:GLU415 4.6 45.5 1.0 CA B:VAL411 4.7 32.5 1.0 CA B:ASN408 4.7 30.3 1.0 C B:CYS406 4.7 38.1 1.0 CB B:PHE410 4.8 32.7 1.0 N B:TYR409 4.8 30.8 1.0 C B:ASN408 4.8 29.1 1.0 CB B:VAL405 4.9 33.9 1.0 C B:VAL411 4.9 34.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form)


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 Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:57.8 occ:1.00 O B:MET470 2.2 67.9 1.0 O B:ARG484 2.3 64.0 1.0 OD2 B:ASP469 2.3 65.0 1.0 OD1 B:ASP483 2.7 62.6 1.0 OD2 B:ASP472 2.7 65.1 1.0 OD1 B:ASP472 2.9 69.2 1.0 CG B:ASP472 3.0 67.8 1.0 CG B:ASP469 3.3 66.4 1.0 C B:MET470 3.3 67.6 1.0 C B:ARG484 3.4 65.6 1.0 N B:ARG484 3.5 67.2 1.0 OD1 B:ASP469 3.6 68.1 1.0 N B:MET470 3.6 66.3 1.0 CG B:ASP483 3.8 64.4 1.0 CA B:ARG484 4.0 67.1 1.0 CA B:MET470 4.0 68.4 1.0 N B:ASP472 4.2 64.7 1.0 O B:HOH713 4.2 33.2 1.0 CG B:ARG484 4.2 73.2 1.0 N B:ALA471 4.3 66.3 1.0 C B:ALA471 4.3 63.3 1.0 CB B:ASP472 4.3 65.9 1.0 C B:ASP483 4.4 65.8 1.0 OD2 B:ASP483 4.5 64.5 1.0 CA B:ASP483 4.5 65.2 1.0 N B:PHE485 4.5 65.9 1.0 CA B:ALA471 4.6 63.5 1.0 CB B:ASP469 4.6 64.6 1.0 CB B:MET470 4.6 69.9 1.0 CA B:ASP472 4.6 65.9 1.0 C B:ASP469 4.6 64.7 1.0 CB B:ARG484 4.7 70.0 1.0 CB B:ASP483 4.8 63.6 1.0 CA B:PHE485 4.8 65.1 1.0 O B:ALA471 4.8 61.5 1.0 CA B:ASP469 4.9 63.8 1.0

S.Takeda, T.Igarashi, H.Mori, S.Araki. Crystal Structures of VAP1 Reveal Adams' Mdc Domain Architecture and Its Unique C-Shaped Scaffold Embo J. V. 25 2388 2006.
ISSN: ISSN 0261-4189
PubMed: 16688218
DOI: 10.1038/SJ.EMBOJ.7601131