Calcium in PDB 2erp: Crystal Structure of Vascular Apoptosis-Inducing Protein-1(Inhibitor- Bound Form)

The structure of Crystal Structure of Vascular Apoptosis-Inducing Protein-1(Inhibitor- Bound Form), PDB code: 2erp 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 / 2.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.345, 91.379, 136.039, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 26.4

The structure of Crystal Structure of Vascular Apoptosis-Inducing Protein-1(Inhibitor- Bound 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(Inhibitor- Bound Form) (pdb code 2erp). 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(Inhibitor- Bound Form), PDB code: 2erp:
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(Inhibitor- Bound 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(Inhibitor- Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:51.8 occ:1.00 OD1 A:ASN408 2.0 51.8 1.0 OE1 A:GLU415 2.3 52.4 1.0 OD1 A:ASP418 2.4 49.2 1.0 O A:PHE410 2.5 43.5 1.0 OE1 A:GLU412 2.6 66.1 1.0 O A:VAL405 2.6 45.5 1.0 OE2 A:GLU415 2.7 50.7 1.0 CD A:GLU415 2.9 50.8 1.0 CG A:ASN408 3.2 51.2 1.0 CG A:ASP418 3.3 52.0 1.0 C A:PHE410 3.6 34.5 1.0 C A:VAL405 3.6 42.9 1.0 CD A:GLU412 3.7 65.4 1.0 CB A:ASP418 3.7 49.4 1.0 ND2 A:ASN408 3.8 64.1 1.0 N A:GLY407 4.0 44.4 1.0 CA A:CYS406 4.0 47.5 1.0 N A:ASN408 4.1 39.3 1.0 N A:PHE410 4.1 34.7 1.0 N A:CYS406 4.2 44.9 1.0 N A:GLU412 4.2 49.1 1.0 CG A:GLU412 4.3 59.8 1.0 CG A:GLU415 4.4 46.0 1.0 N A:VAL405 4.4 37.3 1.0 CA A:PHE410 4.4 32.9 1.0 CB A:ASN408 4.4 44.4 1.0 OD2 A:ASP418 4.4 50.8 1.0 N A:VAL411 4.4 39.4 1.0 CA A:VAL411 4.5 42.4 1.0 CA A:VAL405 4.6 42.1 1.0 CB A:GLU412 4.6 51.0 1.0 C A:CYS406 4.6 46.3 1.0 CA A:ASN408 4.6 44.7 1.0 OE2 A:GLU412 4.7 72.3 1.0 C A:ASN408 4.7 47.9 1.0 SG A:CYS435 4.8 48.8 1.0 N A:TYR409 4.8 45.7 1.0 CB A:PHE410 4.9 34.3 1.0 C A:VAL411 4.9 45.5 1.0 CB A:GLU415 5.0 43.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Vascular Apoptosis-Inducing Protein-1(Inhibitor- Bound 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(Inhibitor- Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:45.0 occ:1.00 O A:MET470 2.3 59.1 1.0 O A:ARG484 2.4 50.6 1.0 OD1 A:ASP472 2.4 41.2 1.0 OD1 A:ASP483 2.4 55.5 1.0 OD2 A:ASP469 2.4 67.3 1.0 OD2 A:ASP472 2.5 66.8 1.0 CG A:ASP472 2.7 50.6 1.0 CG A:ASP469 3.4 63.6 1.0 N A:ARG484 3.5 60.6 1.0 C A:ARG484 3.5 55.9 1.0 C A:MET470 3.5 54.7 1.0 CG A:ASP483 3.5 52.0 1.0 OD1 A:ASP469 3.8 60.2 1.0 C A:ASP483 3.8 54.4 1.0 N A:MET470 3.8 59.2 1.0 CA A:ASP483 4.0 51.4 1.0 CA A:ARG484 4.1 60.7 1.0 CB A:ASP472 4.1 41.7 1.0 N A:ASP472 4.2 48.5 1.0 CA A:MET470 4.2 56.1 1.0 CB A:ASP483 4.3 51.8 1.0 OD2 A:ASP483 4.3 47.7 1.0 C A:ALA471 4.4 48.8 1.0 CD2 A:PHE485 4.5 38.4 1.0 O A:ASP483 4.5 54.4 1.0 N A:ALA471 4.5 54.4 1.0 CA A:ASP472 4.6 42.9 1.0 N A:PHE485 4.6 54.6 1.0 CE2 A:PHE485 4.7 38.8 1.0 CA A:ALA471 4.7 49.8 1.0 CB A:MET470 4.8 58.8 1.0 CB A:ASP469 4.8 65.5 1.0 CB A:ARG484 4.8 66.2 1.0 C A:ASP469 4.8 60.9 1.0 CD A:ARG462 4.8 38.6 1.0 NH1 A:ARG462 4.9 31.1 1.0 O A:ALA471 4.9 46.0 1.0 O A:ALA463 4.9 40.8 1.0 CA A:PHE485 4.9 53.6 1.0 CA A:ASP469 5.0 61.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Vascular Apoptosis-Inducing Protein-1(Inhibitor- Bound 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(Inhibitor- Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:34.3 occ:1.00 OD1 B:ASN408 2.1 38.6 1.0 OE1 B:GLU415 2.3 50.8 1.0 OD2 B:ASP418 2.3 31.7 1.0 O B:PHE410 2.4 39.0 1.0 O B:VAL405 2.5 41.0 1.0 OE2 B:GLU415 2.6 47.4 1.0 OE1 B:GLU412 2.6 54.1 1.0 CD B:GLU415 2.8 47.9 1.0 CG B:ASN408 3.2 33.8 1.0 CG B:ASP418 3.3 40.6 1.0 C B:VAL405 3.4 38.8 1.0 C B:PHE410 3.5 38.2 1.0 CD B:GLU412 3.6 53.5 1.0 CB B:ASP418 3.8 40.2 1.0 ND2 B:ASN408 3.8 34.2 1.0 CA B:CYS406 4.0 42.9 1.0 N B:CYS406 4.1 42.9 1.0 N B:GLY407 4.1 44.2 1.0 CG B:GLU412 4.1 51.3 1.0 N B:ASN408 4.1 35.0 1.0 N B:PHE410 4.1 36.4 1.0 N B:VAL405 4.2 32.6 1.0 N B:GLU412 4.2 49.1 1.0 CG B:GLU415 4.3 48.2 1.0 OD1 B:ASP418 4.4 44.8 1.0 CA B:PHE410 4.4 37.7 1.0 CB B:ASN408 4.4 30.5 1.0 CA B:VAL405 4.4 33.0 1.0 N B:VAL411 4.5 35.4 1.0 C B:CYS406 4.5 45.0 1.0 CB B:GLU412 4.5 47.0 1.0 CA B:VAL411 4.6 38.7 1.0 OE2 B:GLU412 4.7 57.5 1.0 CA B:ASN408 4.7 35.4 1.0 C B:ASN408 4.8 36.8 1.0 C B:VAL411 4.8 45.5 1.0 N B:TYR409 4.9 35.9 1.0 CB B:PHE410 4.9 38.3 1.0 SG B:CYS435 4.9 48.5 1.0 CB B:GLU415 5.0 48.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Vascular Apoptosis-Inducing Protein-1(Inhibitor- Bound 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(Inhibitor- Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:66.2 occ:1.00 O B:MET470 2.3 87.3 1.0 OD2 B:ASP472 2.4 89.5 1.0 O B:ARG484 2.6 74.3 1.0 OD2 B:ASP469 2.7 90.8 1.0 OD1 B:ASP472 2.8 87.8 1.0 CG B:ASP472 2.8 84.5 1.0 OD1 B:ASP483 3.0 86.2 1.0 N B:ARG484 3.3 79.5 1.0 CG B:ASP483 3.4 84.6 1.0 C B:MET470 3.4 85.3 1.0 OD2 B:ASP483 3.5 86.5 1.0 C B:ARG484 3.6 77.2 1.0 CG B:ASP469 3.7 89.3 1.0 N B:ASP472 3.8 78.1 1.0 OD1 B:ASP469 4.0 91.3 1.0 N B:MET470 4.0 87.0 1.0 CB B:ASP472 4.1 80.2 1.0 CA B:ARG484 4.1 80.5 1.0 CA B:ASP483 4.2 77.3 1.0 C B:ASP483 4.2 78.0 1.0 C B:ALA471 4.2 76.5 1.0 CA B:MET470 4.3 86.7 1.0 CD B:ARG462 4.3 76.4 1.0 N B:ALA471 4.3 82.4 1.0 CA B:ASP472 4.3 77.6 1.0 CB B:ASP483 4.4 81.3 1.0 CA B:ALA471 4.4 77.2 1.0 CB B:ARG484 4.7 89.7 1.0 O B:ALA463 4.8 83.5 1.0 N B:PHE485 4.8 74.3 1.0 O B:ARG462 4.8 82.5 1.0 CG B:ARG462 4.9 75.8 1.0 CB B:MET470 4.9 86.5 1.0 O B:ALA471 4.9 74.6 1.0 C B:ASP469 4.9 86.4 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