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Calcium in PDB 2dw0: Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 Crystal)

Protein crystallography data

The structure of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 Crystal), PDB code: 2dw0 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 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.910, 137.950, 59.240, 90.00, 91.52, 90.00
R / Rfree (%) 17.5 / 22.8

Other elements in 2dw0:

The structure of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 Crystal) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 Crystal) (pdb code 2dw0). 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 2-1 Crystal), PDB code: 2dw0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2dw0

Go back to Calcium Binding Sites List in 2dw0
Calcium binding site 1 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 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 2-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:15.6
occ:1.00
 O A:HOH946 2.1 17.8 1.0
O A:CYS388 2.3 19.2 1.0
O A:HOH1093 2.4 9.2 1.0
OD2 A:ASP285 2.4 11.7 1.0
OD1 A:ASP285 2.4 11.2 1.0
OE1 A:GLU201 2.5 15.3 1.0
OD1 A:ASN391 2.5 22.2 1.0
CG A:ASP285 2.7 10.9 1.0
C A:CYS388 3.5 18.6 1.0
CD A:GLU201 3.5 17.7 1.0
CG A:ASN391 3.5 21.2 1.0
ND2 A:ASN391 3.8 19.5 1.0
CG A:GLU201 3.8 15.6 1.0
CB A:ASP285 4.2 12.8 1.0
CB A:GLU201 4.3 13.6 1.0
CA A:CYS388 4.3 20.2 1.0
N A:ILE389 4.4 18.1 1.0
CA A:ILE389 4.4 17.4 1.0
CB A:CYS388 4.5 20.4 1.0
O A:PHE199 4.6 13.2 1.0
OE2 A:GLU201 4.6 18.6 1.0
O A:ASN391 4.8 24.6 1.0
N A:GLU201 4.8 11.3 1.0
CB A:ASN391 4.9 21.8 1.0
N A:ASP285 4.9 12.6 1.0
SG A:CYS388 4.9 19.8 1.0

Calcium binding site 2 out of 6 in 2dw0

Go back to Calcium Binding Sites List in 2dw0
Calcium binding site 2 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 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 2-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:18.0
occ:1.00
 O A:LEU408 2.2 14.4 1.0
OE1 A:GLU410 2.3 16.0 1.0
OD2 A:ASP416 2.3 15.3 1.0
O A:VAL403 2.4 16.0 1.0
OD1 A:ASN406 2.5 18.2 1.0
OE2 A:GLU413 2.6 17.1 1.0
OE1 A:GLU413 2.6 15.1 1.0
CD A:GLU413 3.0 15.1 1.0
CD A:GLU410 3.3 17.8 1.0
CG A:ASP416 3.4 13.0 1.0
C A:VAL403 3.4 16.1 1.0
C A:LEU408 3.4 16.0 1.0
CG A:ASN406 3.4 18.9 1.0
CG A:GLU410 3.8 16.4 1.0
ND2 A:ASN406 3.8 18.4 1.0
CB A:ASP416 3.9 15.0 1.0
N A:LEU408 4.0 17.1 1.0
CB A:GLU410 4.1 15.5 1.0
CA A:CYS404 4.1 17.9 1.0
N A:GLU410 4.1 16.1 1.0
N A:CYS404 4.1 16.8 1.0
N A:VAL403 4.1 16.5 1.0
CA A:LEU408 4.2 16.5 1.0
N A:GLY405 4.3 17.1 1.0
N A:ASN406 4.3 18.1 1.0
CA A:VAL403 4.3 16.8 1.0
OE2 A:GLU410 4.4 16.9 1.0
OD1 A:ASP416 4.4 15.9 1.0
N A:LEU409 4.4 16.3 1.0
CG A:GLU413 4.5 16.6 1.0
CB A:LEU408 4.5 15.0 1.0
CA A:LEU409 4.6 17.5 1.0
CB A:ASN406 4.7 17.8 1.0
C A:LEU409 4.7 16.7 1.0
C A:CYS404 4.7 16.8 1.0
N A:GLU407 4.8 18.7 1.0
CA A:GLU410 4.8 16.4 1.0
CB A:VAL403 4.9 16.0 1.0
CA A:ASN406 4.9 18.9 1.0

Calcium binding site 3 out of 6 in 2dw0

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Calcium binding site 3 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 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 2-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:15.1
occ:1.00
 OD2 A:ASP482 2.3 18.7 1.0
OD2 A:ASP467 2.3 17.5 1.0
O A:PRO468 2.3 14.8 1.0
O A:HOH1094 2.3 18.6 1.0
OE2 A:GLU470 2.4 15.0 1.0
O A:VAL483 2.5 18.2 1.0
OE1 A:GLU470 2.7 15.9 1.0
CD A:GLU470 2.9 16.7 1.0
CG A:ASP467 3.4 19.2 1.0
CG A:ASP482 3.4 18.5 1.0
N A:VAL483 3.5 19.4 1.0
C A:PRO468 3.5 18.0 1.0
C A:VAL483 3.5 17.5 1.0
OD1 A:ASP467 3.9 16.1 1.0
CA A:VAL483 4.1 18.4 1.0
N A:PRO468 4.1 17.4 1.0
OD1 A:ASP482 4.1 22.1 1.0
C A:ASP482 4.2 19.4 1.0
C A:ASP467 4.3 17.1 1.0
CA A:ASP482 4.3 18.1 1.0
O A:HOH963 4.3 21.6 1.0
CD A:PRO468 4.4 16.2 1.0
CG A:PRO468 4.4 17.4 1.0
CA A:PRO468 4.4 17.5 1.0
CG A:GLU470 4.4 15.6 1.0
N A:ALA469 4.5 17.3 1.0
CB A:ASP482 4.5 18.0 1.0
CD2 A:PHE484 4.5 15.1 1.0
CA A:ALA469 4.5 17.8 1.0
O A:HOH959 4.6 19.0 1.0
CB A:VAL483 4.6 21.2 1.0
CB A:ASP467 4.6 16.1 1.0
O A:ASP467 4.7 18.8 1.0
CD A:ARG460 4.7 17.6 1.0
C A:ALA469 4.7 17.1 1.0
N A:PHE484 4.7 16.8 1.0
N A:GLU470 4.7 17.0 1.0
CA A:ASP467 4.7 18.0 1.0
CE2 A:PHE484 4.7 17.6 1.0
CB A:PRO468 5.0 16.8 1.0

Calcium binding site 4 out of 6 in 2dw0

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Calcium binding site 4 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 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 2-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca711

b:12.9
occ:1.00
 O B:HOH1113 2.2 9.2 1.0
O B:CYS388 2.2 19.5 1.0
OE1 B:GLU201 2.2 16.0 1.0
O B:HOH1114 2.3 11.0 1.0
OD1 B:ASP285 2.4 10.1 1.0
OD1 B:ASN391 2.4 15.9 1.0
OD2 B:ASP285 2.5 10.6 1.0
CG B:ASP285 2.8 12.3 1.0
CD B:GLU201 3.3 17.4 1.0
CG B:ASN391 3.3 16.9 1.0
C B:CYS388 3.5 17.4 1.0
ND2 B:ASN391 3.6 12.8 1.0
CG B:GLU201 3.7 15.1 1.0
CB B:GLU201 4.1 13.0 1.0
O B:HOH1092 4.1 36.9 1.0
CB B:ASP285 4.3 11.2 1.0
CA B:ILE389 4.3 15.2 1.0
N B:ILE389 4.4 15.6 1.0
CA B:CYS388 4.4 18.9 1.0
O B:ASN391 4.4 21.6 1.0
OE2 B:GLU201 4.4 17.9 1.0
O B:PHE199 4.4 18.4 1.0
O B:HOH1086 4.5 28.6 1.0
CB B:CYS388 4.6 17.0 1.0
CB B:ASN391 4.7 17.6 1.0
N B:GLU201 4.8 13.2 1.0
O B:HOH1097 4.9 25.0 1.0
O B:HOH1201 5.0 37.5 1.0
N B:ASN391 5.0 19.7 1.0
SG B:CYS388 5.0 18.9 1.0

Calcium binding site 5 out of 6 in 2dw0

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Calcium binding site 5 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 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 2-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca712

b:12.4
occ:1.00
 OE1 B:GLU410 2.3 12.6 1.0
O B:LEU408 2.3 11.6 1.0
OE2 B:GLU413 2.3 9.1 1.0
O B:VAL403 2.4 12.0 1.0
OD2 B:ASP416 2.4 9.7 1.0
OE1 B:GLU413 2.5 9.5 1.0
OD1 B:ASN406 2.5 11.9 1.0
CD B:GLU413 2.8 10.3 1.0
CD B:GLU410 3.3 14.8 1.0
C B:VAL403 3.4 13.2 1.0
CG B:ASP416 3.5 13.7 1.0
CG B:ASN406 3.5 16.6 1.0
C B:LEU408 3.5 12.3 1.0
CG B:GLU410 3.8 12.5 1.0
CB B:ASP416 3.9 14.8 1.0
ND2 B:ASN406 4.0 13.4 1.0
N B:VAL403 4.1 13.8 1.0
CA B:CYS404 4.1 13.2 1.0
N B:LEU408 4.1 12.9 1.0
N B:CYS404 4.2 13.2 1.0
CB B:GLU410 4.2 13.6 1.0
N B:GLU410 4.2 12.4 1.0
CG B:GLU413 4.3 10.9 1.0
OE2 B:GLU410 4.3 13.2 1.0
CA B:LEU408 4.3 13.7 1.0
N B:GLY405 4.3 14.5 1.0
CA B:VAL403 4.3 13.6 1.0
N B:ASN406 4.4 14.3 1.0
OD1 B:ASP416 4.5 13.0 1.0
CB B:LEU408 4.5 12.7 1.0
N B:LEU409 4.5 12.3 1.0
CA B:LEU409 4.6 12.2 1.0
CB B:ASN406 4.7 13.7 1.0
C B:CYS404 4.7 14.2 1.0
C B:LEU409 4.7 13.0 1.0
CA B:GLU410 4.9 12.3 1.0
N B:GLU407 4.9 13.4 1.0
CB B:VAL403 4.9 14.8 1.0
CA B:ASN406 4.9 15.4 1.0

Calcium binding site 6 out of 6 in 2dw0

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Calcium binding site 6 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-1 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 2-1 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca713

b:13.6
occ:1.00
 OD2 B:ASP482 2.2 15.6 1.0
O B:HOH1115 2.3 15.3 1.0
OE2 B:GLU470 2.3 11.0 1.0
O B:PRO468 2.3 13.4 1.0
OD2 B:ASP467 2.4 16.9 1.0
O B:VAL483 2.6 14.2 1.0
OE1 B:GLU470 2.6 10.2 1.0
CD B:GLU470 2.8 13.0 1.0
CG B:ASP482 3.4 18.5 1.0
CG B:ASP467 3.4 19.1 1.0
C B:PRO468 3.5 16.1 1.0
N B:VAL483 3.5 18.6 1.0
C B:VAL483 3.7 16.9 1.0
OD1 B:ASP467 3.9 18.0 1.0
N B:PRO468 4.2 17.1 1.0
CA B:ASP482 4.2 17.5 1.0
C B:ASP482 4.2 18.1 1.0
C B:ASP467 4.2 17.3 1.0
OD1 B:ASP482 4.2 19.9 1.0
CA B:VAL483 4.2 18.1 1.0
CG B:GLU470 4.3 13.5 1.0
O B:HOH1037 4.3 30.9 1.0
CD2 B:PHE484 4.4 15.6 1.0
CB B:ASP482 4.4 17.2 1.0
CA B:PRO468 4.4 16.6 1.0
O B:ASP467 4.5 20.4 1.0
N B:ALA469 4.5 15.8 1.0
CD B:PRO468 4.5 16.7 1.0
CA B:ALA469 4.5 16.7 1.0
CE2 B:PHE484 4.6 15.8 1.0
C B:ALA469 4.6 15.4 1.0
N B:GLU470 4.6 16.8 1.0
CG2 B:VAL483 4.6 20.9 1.0
CB B:ASP467 4.6 17.2 1.0
CA B:ASP467 4.7 16.6 1.0
CD B:ARG460 4.7 17.7 1.0
N B:PHE484 4.8 15.7 1.0
CB B:PRO468 4.9 17.5 1.0

Reference:

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
Page generated: Fri Jul 12 09:58:02 2024

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