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Calcium in PDB 2dw1: Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal)

Protein crystallography data

The structure of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal), PDB code: 2dw1 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 (°) 57.670, 118.180, 138.460, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 28.6

Other elements in 2dw1:

The structure of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 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 2-2 Crystal) (pdb code 2dw1). 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 2-2 Crystal), PDB code: 2dw1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2dw1

Go back to Calcium Binding Sites List in 2dw1
Calcium binding site 1 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 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 2-2 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:35.9
occ:1.00
 O A:HOH886 2.1 23.5 1.0
OD1 A:ASN391 2.2 39.8 1.0
O A:CYS388 2.3 36.8 1.0
OD1 A:ASP285 2.5 22.9 1.0
O A:HOH814 2.5 32.4 1.0
OE1 A:GLU201 2.5 33.2 1.0
OD2 A:ASP285 2.5 23.6 1.0
CG A:ASP285 2.8 24.2 1.0
CG A:ASN391 3.3 41.3 1.0
CD A:GLU201 3.3 30.3 1.0
C A:CYS388 3.5 38.2 1.0
CG A:GLU201 3.5 25.7 1.0
ND2 A:ASN391 3.7 38.4 1.0
CB A:GLU201 4.2 22.9 1.0
O A:HOH915 4.2 46.2 1.0
O A:ASN391 4.2 38.9 1.0
CB A:ASP285 4.3 22.4 1.0
O A:PHE199 4.4 30.3 1.0
CA A:CYS388 4.4 43.0 1.0
CA A:ILE389 4.4 34.9 1.0
OE2 A:GLU201 4.4 35.8 1.0
N A:ILE389 4.5 35.2 1.0
CB A:CYS388 4.5 44.2 1.0
CB A:ASN391 4.6 37.5 1.0
N A:GLU201 4.8 23.0 1.0
N A:ASN391 4.9 37.8 1.0
SG A:CYS388 5.0 49.4 1.0

Calcium binding site 2 out of 6 in 2dw1

Go back to Calcium Binding Sites List in 2dw1
Calcium binding site 2 out of 6 in the Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 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 2-2 Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:38.1
occ:1.00
 O A:LEU408 2.3 28.1 1.0
O A:VAL403 2.4 33.0 1.0
OE1 A:GLU410 2.4 44.9 1.0
OE1 A:GLU413 2.6 34.4 1.0
OD2 A:ASP416 2.6 40.0 1.0
OD1 A:ASN406 2.6 32.1 1.0
OE2 A:GLU413 2.7 33.0 1.0
CD A:GLU413 3.0 34.9 1.0
CD A:GLU410 3.3 43.9 1.0
CG A:ASN406 3.3 33.7 1.0
C A:VAL403 3.3 33.0 1.0
C A:LEU408 3.5 32.5 1.0
ND2 A:ASN406 3.5 26.3 1.0
CG A:ASP416 3.6 37.4 1.0
CG A:GLU410 3.7 39.9 1.0
CA A:CYS404 3.9 35.6 1.0
N A:CYS404 4.0 35.6 1.0
N A:LEU408 4.1 34.0 1.0
N A:VAL403 4.1 31.4 1.0
CB A:ASP416 4.1 38.0 1.0
OE2 A:GLU410 4.2 47.5 1.0
N A:GLU410 4.2 38.2 1.0
CA A:LEU408 4.3 33.1 1.0
N A:GLY405 4.3 35.0 1.0
CB A:GLU410 4.3 37.6 1.0
CA A:VAL403 4.3 34.2 1.0
N A:ASN406 4.4 35.1 1.0
OD1 A:ASP416 4.5 35.6 1.0
CG A:GLU413 4.5 35.8 1.0
CB A:LEU408 4.5 34.7 1.0
N A:LEU409 4.5 32.2 1.0
C A:CYS404 4.6 34.4 1.0
CB A:ASN406 4.6 31.4 1.0
CA A:LEU409 4.7 33.9 1.0
C A:LEU409 4.9 36.7 1.0
N A:GLU407 4.9 32.9 1.0
CA A:ASN406 4.9 34.0 1.0
CA A:GLU410 4.9 39.6 1.0
CB A:VAL403 5.0 34.3 1.0

Calcium binding site 3 out of 6 in 2dw1

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

b:40.8
occ:1.00
 OD2 A:ASP482 2.2 34.7 1.0
OE1 A:GLU470 2.2 36.9 1.0
OD2 A:ASP467 2.3 38.4 1.0
O A:HOH882 2.5 19.8 1.0
O A:VAL483 2.5 33.8 1.0
O A:PRO468 2.6 37.5 1.0
OE2 A:GLU470 2.9 30.4 1.0
CD A:GLU470 2.9 37.2 1.0
N A:VAL483 3.2 35.3 1.0
CG A:ASP482 3.4 33.9 1.0
CG A:ASP467 3.4 38.9 1.0
C A:VAL483 3.5 34.8 1.0
C A:PRO468 3.7 36.8 1.0
CA A:VAL483 3.9 34.5 1.0
OD1 A:ASP467 4.0 39.3 1.0
O A:HOH815 4.1 27.3 1.0
C A:ASP482 4.1 35.1 1.0
CA A:ASP482 4.2 34.0 1.0
OD1 A:ASP482 4.2 37.7 1.0
CD2 A:PHE484 4.2 28.9 1.0
N A:PRO468 4.3 37.9 1.0
CE2 A:PHE484 4.3 32.2 1.0
CG A:GLU470 4.3 38.2 1.0
C A:ASP467 4.4 37.8 1.0
CB A:ASP482 4.4 31.6 1.0
CA A:ALA469 4.5 38.2 1.0
CB A:VAL483 4.5 34.5 1.0
N A:ALA469 4.5 36.1 1.0
CD A:PRO468 4.5 37.2 1.0
CG A:PRO468 4.6 38.7 1.0
CA A:PRO468 4.6 36.7 1.0
N A:PHE484 4.6 34.4 1.0
C A:ALA469 4.6 41.4 1.0
CB A:ASP467 4.6 37.8 1.0
CD A:ARG460 4.6 32.4 1.0
O A:ASP467 4.7 39.4 1.0
CA A:ASP467 4.7 36.6 1.0
N A:GLU470 4.8 42.5 1.0
NH1 A:ARG460 5.0 34.3 1.0

Calcium binding site 4 out of 6 in 2dw1

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

b:43.1
occ:1.00
 O B:HOH849 2.1 22.0 1.0
O B:HOH812 2.3 29.1 1.0
OE1 B:GLU201 2.4 32.2 1.0
O B:CYS388 2.4 40.9 1.0
OD1 B:ASP285 2.5 32.2 1.0
OD2 B:ASP285 2.6 30.1 1.0
OD1 B:ASN391 2.8 47.0 1.0
CG B:ASP285 2.9 34.4 1.0
ND2 B:ASN391 2.9 46.0 1.0
CG B:ASN391 3.2 46.7 1.0
CD B:GLU201 3.3 33.5 1.0
CG B:GLU201 3.6 31.0 1.0
C B:CYS388 3.7 44.3 1.0
CB B:GLU201 4.1 32.1 1.0
O B:PHE199 4.2 44.4 1.0
CE B:LYS283 4.2 59.2 1.0
O B:ASN391 4.2 46.1 1.0
OE2 B:GLU201 4.3 37.6 1.0
CB B:ASP285 4.4 33.1 1.0
CA B:ILE389 4.4 44.2 1.0
N B:ILE389 4.5 42.5 1.0
N B:GLU201 4.6 31.6 1.0
CA B:CYS388 4.6 48.4 1.0
CB B:ASN391 4.7 45.4 1.0
CB B:CYS388 4.8 49.2 1.0
CD B:LYS283 4.9 57.1 1.0
N B:ASP285 4.9 32.5 1.0

Calcium binding site 5 out of 6 in 2dw1

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

b:52.9
occ:1.00
 OD1 B:ASN406 2.2 57.8 1.0
O B:LEU408 2.4 48.8 1.0
O B:VAL403 2.4 50.2 1.0
OE1 B:GLU413 2.5 40.0 1.0
OE2 B:GLU413 2.6 40.3 1.0
OE1 B:GLU410 2.7 62.0 1.0
OD2 B:ASP416 2.7 67.7 1.0
CD B:GLU413 2.9 45.3 1.0
CG B:ASN406 3.3 57.6 1.0
CD B:GLU410 3.4 61.3 1.0
C B:LEU408 3.5 51.0 1.0
C B:VAL403 3.6 51.7 1.0
CG B:ASP416 3.6 67.4 1.0
CG B:GLU410 3.7 58.3 1.0
ND2 B:ASN406 3.8 57.1 1.0
N B:LEU408 4.0 54.0 1.0
CB B:ASP416 4.0 66.3 1.0
CB B:GLU410 4.2 55.2 1.0
N B:GLU410 4.2 53.3 1.0
CA B:CYS404 4.2 52.3 1.0
CA B:LEU408 4.2 51.9 1.0
N B:CYS404 4.4 52.8 1.0
N B:ASN406 4.4 56.1 1.0
N B:GLY405 4.4 53.0 1.0
OE2 B:GLU410 4.4 64.7 1.0
CG B:GLU413 4.4 48.2 1.0
N B:VAL403 4.5 48.8 1.0
N B:LEU409 4.5 51.3 1.0
CB B:LEU408 4.5 51.2 1.0
OD1 B:ASP416 4.6 68.8 1.0
CB B:ASN406 4.6 56.9 1.0
CA B:VAL403 4.6 50.7 1.0
CA B:LEU409 4.7 50.9 1.0
N B:GLU407 4.8 56.5 1.0
C B:CYS404 4.8 52.7 1.0
C B:LEU409 4.8 52.4 1.0
CA B:GLU410 4.9 54.7 1.0
CA B:ASN406 4.9 56.9 1.0
C B:ASN406 5.0 58.0 1.0

Calcium binding site 6 out of 6 in 2dw1

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

b:42.2
occ:1.00
 O B:PRO468 2.2 37.7 1.0
OD2 B:ASP467 2.2 37.5 1.0
OE2 B:GLU470 2.4 38.0 1.0
OD1 B:ASP482 2.5 40.5 1.0
O B:HOH871 2.6 18.9 1.0
O B:VAL483 2.6 36.6 1.0
OE1 B:GLU470 2.7 36.7 1.0
CD B:GLU470 2.9 41.1 1.0
CG B:ASP467 3.4 35.1 1.0
C B:PRO468 3.5 39.5 1.0
N B:VAL483 3.7 36.9 1.0
C B:VAL483 3.7 38.0 1.0
CG B:ASP482 3.7 39.0 1.0
OD1 B:ASP467 3.9 37.3 1.0
N B:PRO468 4.1 35.4 1.0
C B:ASP467 4.2 35.1 1.0
CD2 B:PHE484 4.2 38.4 1.0
CA B:VAL483 4.3 37.7 1.0
C B:ASP482 4.3 39.3 1.0
CE2 B:PHE484 4.4 38.5 1.0
N B:ALA469 4.4 40.8 1.0
CA B:PRO468 4.4 38.2 1.0
CA B:ALA469 4.4 41.5 1.0
CA B:ASP482 4.4 39.0 1.0
CG B:GLU470 4.4 43.1 1.0
O B:ASP467 4.5 36.2 1.0
OD2 B:ASP482 4.5 38.3 1.0
CG B:PRO468 4.5 36.7 1.0
CD B:PRO468 4.5 37.5 1.0
N B:GLU470 4.6 40.9 1.0
CB B:ASP467 4.6 33.5 1.0
CA B:ASP467 4.6 36.0 1.0
CB B:ASP482 4.6 37.9 1.0
C B:ALA469 4.7 40.5 1.0
CD B:ARG460 4.7 47.1 1.0
N B:PHE484 4.8 36.6 1.0
O B:ARG460 4.9 45.8 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 10:00:14 2024

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