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

The structure of Crystal Structure of Vascular Apoptosis-Inducing Protein-1(Tetragonal Crystal Form), PDB code: 2erq 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 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.940, 93.940, 244.820, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 26.9

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

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Vascular Apoptosis-Inducing Protein-1(Tetragonal Crystal Form) (pdb code 2erq). 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(Tetragonal Crystal Form), PDB code: 2erq:
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(Tetragonal 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(Tetragonal Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:35.0 occ:1.00 OE1 A:GLU412 2.4 45.6 1.0 O A:PHE410 2.4 23.0 1.0 OE1 A:GLU415 2.4 37.2 1.0 O A:VAL405 2.5 38.7 1.0 OD1 A:ASN408 2.6 38.8 1.0 OE2 A:GLU415 2.7 37.6 1.0 OD1 A:ASP418 2.8 38.0 1.0 CD A:GLU415 2.9 39.8 1.0 CD A:GLU412 3.1 45.3 1.0 CG A:ASN408 3.2 37.2 1.0 C A:VAL405 3.5 40.8 1.0 ND2 A:ASN408 3.5 37.4 1.0 C A:PHE410 3.6 28.2 1.0 CG A:GLU412 3.7 42.4 1.0 CG A:ASP418 3.8 37.4 1.0 OE2 A:GLU412 3.9 51.2 1.0 N A:VAL405 4.1 34.7 1.0 N A:PHE410 4.1 31.0 1.0 CB A:ASP418 4.2 39.3 1.0 N A:CYS406 4.2 43.9 1.0 CA A:CYS406 4.2 44.6 1.0 N A:ASN408 4.2 41.3 1.0 N A:GLU412 4.3 38.6 1.0 CA A:PHE410 4.4 28.9 1.0 CB A:GLU412 4.4 40.0 1.0 N A:GLY407 4.4 41.5 1.0 CA A:VAL405 4.4 36.1 1.0 CG A:GLU415 4.4 35.1 1.0 CB A:ASN408 4.4 37.1 1.0 N A:VAL411 4.6 32.0 1.0 CA A:VAL411 4.7 34.0 1.0 CB A:PHE410 4.7 31.6 1.0 C A:CYS406 4.8 41.7 1.0 CA A:ASN408 4.8 40.1 1.0 OD2 A:ASP418 4.8 36.5 1.0 O A:HOH759 4.8 42.0 1.0 CB A:VAL405 4.9 37.7 1.0 C A:ASN408 4.9 37.9 1.0 N A:TYR409 4.9 36.4 1.0 C A:VAL411 4.9 36.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Vascular Apoptosis-Inducing Protein-1(Tetragonal 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(Tetragonal Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:58.9 occ:1.00 O A:ARG484 2.2 53.5 1.0 O A:MET470 2.3 59.6 1.0 O A:HOH788 2.3 36.0 1.0 OD1 A:ASP483 2.3 60.9 1.0 OD2 A:ASP469 2.4 48.4 1.0 OD2 A:ASP472 2.6 60.0 1.0 OD1 A:ASP472 2.7 55.5 1.0 CG A:ASP472 3.0 58.6 1.0 C A:ARG484 3.3 58.6 1.0 CG A:ASP469 3.4 48.4 1.0 C A:MET470 3.4 56.6 1.0 N A:ARG484 3.4 59.4 1.0 CG A:ASP483 3.6 61.6 1.0 N A:MET470 3.7 57.9 1.0 OD1 A:ASP469 3.8 50.1 1.0 CA A:ARG484 4.0 60.2 1.0 C A:ASP483 4.1 59.8 1.0 CA A:MET470 4.1 57.5 1.0 CA A:ASP483 4.3 61.0 1.0 N A:PHE485 4.4 58.7 1.0 OD2 A:ASP483 4.4 62.3 1.0 CD2 A:PHE485 4.4 47.6 1.0 CB A:ASP472 4.4 55.9 1.0 C A:ALA471 4.5 54.8 1.0 N A:ALA471 4.5 55.5 1.0 CB A:ASP483 4.5 60.7 1.0 N A:ASP472 4.6 56.0 1.0 CA A:PHE485 4.6 58.7 1.0 CB A:MET470 4.6 57.4 1.0 CA A:ALA471 4.7 55.3 1.0 C A:ASP469 4.7 58.9 1.0 CB A:ASP469 4.7 54.8 1.0 O A:ALA471 4.7 53.6 1.0 CE2 A:PHE485 4.8 45.4 1.0 CA A:ASP469 4.8 56.7 1.0 NH1 A:ARG462 4.9 50.7 1.0 CD A:ARG462 4.9 48.0 1.0 O A:ASP483 5.0 59.9 1.0 CA A:ASP472 5.0 56.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Vascular Apoptosis-Inducing Protein-1(Tetragonal 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(Tetragonal Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:33.1 occ:1.00 O B:VAL405 2.3 34.3 1.0 OD1 B:ASN408 2.4 35.1 1.0 OD1 B:ASP418 2.4 39.8 1.0 OE1 B:GLU415 2.5 37.5 1.0 OE1 B:GLU412 2.5 40.1 1.0 O B:PHE410 2.5 32.5 1.0 OE2 B:GLU415 2.7 34.2 1.0 CD B:GLU415 2.9 35.1 1.0 CG B:ASN408 3.3 35.1 1.0 C B:VAL405 3.3 34.3 1.0 CD B:GLU412 3.4 42.5 1.0 CG B:ASP418 3.5 37.8 1.0 C B:PHE410 3.6 34.9 1.0 ND2 B:ASN408 3.8 36.3 1.0 CB B:ASP418 4.0 34.3 1.0 CA B:CYS406 4.1 35.1 1.0 N B:VAL405 4.1 35.6 1.0 N B:CYS406 4.1 33.2 1.0 CG B:GLU412 4.2 43.4 1.0 N B:PHE410 4.2 34.0 1.0 OE2 B:GLU412 4.2 46.3 1.0 N B:ASN408 4.2 33.1 1.0 N B:GLY407 4.2 34.4 1.0 CA B:VAL405 4.3 32.9 1.0 N B:GLU412 4.4 41.1 1.0 CA B:PHE410 4.4 33.9 1.0 CG B:GLU415 4.5 31.8 1.0 CB B:ASN408 4.5 29.9 1.0 OD2 B:ASP418 4.5 39.0 1.0 CB B:GLU412 4.5 39.6 1.0 C B:CYS406 4.6 35.9 1.0 N B:VAL411 4.6 36.3 1.0 CA B:VAL411 4.7 38.6 1.0 CA B:ASN408 4.8 33.7 1.0 CB B:PHE410 4.8 35.4 1.0 CB B:VAL405 4.8 34.0 1.0 C B:ASN408 4.9 33.3 1.0 C B:VAL411 4.9 40.0 1.0 N B:TYR409 5.0 32.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Vascular Apoptosis-Inducing Protein-1(Tetragonal 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(Tetragonal Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:82.5 occ:1.00 O B:ARG484 2.1 72.1 1.0 O B:MET470 2.1 76.5 1.0 OD1 B:ASP483 2.3 61.3 1.0 OD2 B:ASP469 2.4 81.3 1.0 OD1 B:ASP472 2.6 79.4 1.0 OD2 B:ASP472 3.1 79.4 1.0 CG B:ASP472 3.2 80.6 1.0 C B:ARG484 3.2 74.2 1.0 C B:MET470 3.3 79.1 1.0 N B:ARG484 3.4 71.6 1.0 CG B:ASP469 3.4 81.5 1.0 N B:MET470 3.6 78.3 1.0 CG B:ASP483 3.6 65.4 1.0 C B:ASP483 3.7 69.7 1.0 OD1 B:ASP469 3.8 82.3 1.0 CA B:ARG484 3.9 73.7 1.0 CA B:MET470 3.9 79.8 1.0 CA B:ASP483 4.0 69.4 1.0 CG B:ARG484 4.1 78.6 1.0 N B:PHE485 4.3 74.3 1.0 N B:ALA471 4.3 79.6 1.0 CD2 B:PHE485 4.4 68.4 1.0 CB B:ASP483 4.4 66.8 1.0 O B:ASP483 4.4 69.1 1.0 OD2 B:ASP483 4.5 66.7 1.0 N B:ASP472 4.5 81.1 1.0 CB B:MET470 4.5 79.0 1.0 CB B:ARG484 4.6 75.2 1.0 CA B:PHE485 4.6 73.1 1.0 C B:ALA471 4.6 80.1 1.0 CB B:ASP472 4.6 81.7 1.0 C B:ASP469 4.6 79.2 1.0 CA B:ALA471 4.6 79.9 1.0 CB B:ASP469 4.7 80.7 1.0 CE2 B:PHE485 4.7 69.0 1.0 CA B:ASP469 4.9 80.8 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