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Calcium in PDB 3dsl: The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom.

Enzymatic activity of The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom.

All present enzymatic activity of The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom.:
3.4.24.49;

Protein crystallography data

The structure of The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom., PDB code: 3dsl was solved by J.R.C.Muniz, A.Ambrosio, H.S.Selistre-De-Araujo, G.Oliva, R.C.Garratt, D.H.F.Souza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.44 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.757, 100.271, 133.237, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 29.4

Other elements in 3dsl:

The structure of The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom. (pdb code 3dsl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom., PDB code: 3dsl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3dsl

Go back to Calcium Binding Sites List in 3dsl
Calcium binding site 1 out of 6 in the The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:19.7
occ:1.00
 O A:CYS200 2.5 28.0 1.0
OE1 A:GLU12 2.6 24.8 1.0
OD1 A:ASP96 2.7 25.1 1.0
OD2 A:ASP96 2.7 26.2 1.0
OD1 A:ASN203 2.9 25.4 1.0
CG A:ASP96 3.0 26.4 1.0
ND2 A:ASN203 3.3 26.1 1.0
CD A:GLU12 3.3 25.2 1.0
CG A:GLU12 3.4 23.0 1.0
CG A:ASN203 3.4 25.6 1.0
C A:CYS200 3.7 26.2 1.0
CA A:ILE201 4.2 27.4 1.0
O A:TYR10 4.2 23.4 1.0
N A:ILE201 4.4 26.2 1.0
CB A:GLU12 4.4 33.6 1.0
O A:ASN203 4.4 25.1 1.0
OE2 A:GLU12 4.5 25.4 1.0
CB A:ASP96 4.5 22.6 1.0
C A:ILE201 4.7 29.4 1.0
N A:LEU202 4.8 27.0 1.0
N A:ASN203 4.8 26.5 1.0
CA A:CYS200 4.8 29.4 1.0
CB A:ASN203 4.8 26.5 1.0
SG A:CYS200 4.9 26.8 1.0
N A:GLU12 5.0 23.5 1.0

Calcium binding site 2 out of 6 in 3dsl

Go back to Calcium Binding Sites List in 3dsl
Calcium binding site 2 out of 6 in the The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:26.2
occ:1.00
 O A:LEU220 2.3 28.8 1.0
OD2 A:ASP228 2.4 30.0 1.0
O A:VAL215 2.5 34.0 1.0
OD1 A:ASN218 2.5 32.3 1.0
OE2 A:GLU225 2.6 27.4 1.0
OE1 A:GLU225 2.6 25.7 1.0
OE1 A:GLU222 2.8 25.6 1.0
CD A:GLU225 2.9 26.7 1.0
CG A:ASP228 3.3 30.2 1.0
C A:LEU220 3.4 26.6 1.0
C A:VAL215 3.5 34.5 1.0
CB A:ASP228 3.5 31.0 1.0
CG A:ASN218 3.5 32.5 1.0
CD A:GLU222 3.6 25.3 1.0
CG A:GLU222 3.7 26.4 1.0
N A:LEU220 3.8 26.5 1.0
CA A:CYS216 4.0 28.0 1.0
ND2 A:ASN218 4.1 32.1 1.0
CA A:LEU220 4.1 27.4 1.0
N A:CYS216 4.1 28.9 1.0
N A:GLY217 4.2 35.0 1.0
N A:VAL215 4.3 36.0 1.0
N A:GLU222 4.3 27.8 1.0
CB A:LEU220 4.3 26.0 1.0
N A:ASN218 4.4 27.2 1.0
CG A:GLU225 4.4 26.6 1.0
CB A:GLU222 4.4 26.0 1.0
OD1 A:ASP228 4.4 30.9 1.0
N A:LEU221 4.5 25.8 1.0
CA A:VAL215 4.5 34.7 1.0
C A:CYS216 4.6 27.6 1.0
N A:GLU219 4.6 27.6 1.0
CA A:LEU221 4.7 26.2 1.0
C A:LEU221 4.7 24.8 1.0
CB A:ASN218 4.8 32.6 1.0
OE2 A:GLU222 4.8 27.1 1.0
CA A:ASN218 4.9 26.8 1.0
C A:ASN218 5.0 32.4 1.0

Calcium binding site 3 out of 6 in 3dsl

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Calcium binding site 3 out of 6 in the The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:34.9
occ:1.00
 O A:PRO280 2.6 58.7 1.0
OE1 A:GLU282 2.7 34.5 1.0
OD2 A:ASP279 2.8 47.9 1.0
OD2 A:ASP294 2.8 58.1 1.0
OE2 A:GLU282 2.9 31.2 1.0
O A:VAL295 2.9 0.4 1.0
CD A:GLU282 3.2 33.9 1.0
CG A:ASP294 3.3 56.9 1.0
CG A:ASP279 3.3 49.5 1.0
OD1 A:ASP294 3.4 59.1 1.0
OD1 A:ASP279 3.5 49.1 1.0
C A:PRO280 3.7 58.7 1.0
N A:VAL295 3.7 62.7 1.0
C A:VAL295 3.8 64.7 1.0
C A:ASP279 4.1 54.5 1.0
N A:PRO280 4.1 60.4 1.0
CA A:ASP279 4.3 53.7 1.0
CA A:VAL295 4.3 64.5 1.0
CD2 A:PHE296 4.4 77.7 1.0
CB A:ASP279 4.4 50.0 1.0
CB A:ASP294 4.4 55.5 1.0
CA A:ASP294 4.5 56.9 1.0
C A:ASP294 4.5 58.8 1.0
O A:ASP279 4.5 56.2 1.0
CD A:PRO280 4.5 60.2 1.0
CA A:PRO280 4.5 60.9 1.0
N A:ALA281 4.6 65.8 1.0
CE2 A:PHE296 4.6 72.6 1.0
CA A:ALA281 4.6 64.7 1.0
CG A:GLU282 4.7 35.1 1.0
C A:ALA281 4.7 63.5 1.0
N A:PHE296 4.8 89.7 1.0
N A:GLU282 4.9 40.0 1.0
O A:HOH547 5.0 25.5 1.0
CB A:PRO280 5.0 62.6 1.0

Calcium binding site 4 out of 6 in 3dsl

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Calcium binding site 4 out of 6 in the The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca422

b:24.5
occ:1.00
 ND2 B:ASN203 2.5 42.2 1.0
OD1 B:ASP96 2.5 29.1 1.0
O B:CYS200 2.6 36.2 1.0
OE1 B:GLU12 2.8 31.0 1.0
OD2 B:ASP96 2.9 30.8 1.0
OD1 B:ASN203 2.9 46.4 1.0
O B:HOH430 3.0 64.6 1.0
CG B:ASP96 3.1 32.1 1.0
CG B:ASN203 3.1 45.4 1.0
CD B:GLU12 3.2 29.0 1.0
CG B:GLU12 3.3 30.3 1.0
C B:CYS200 3.7 39.1 1.0
OE2 B:GLU12 4.1 30.8 1.0
CB B:GLU12 4.1 29.3 1.0
O B:TYR10 4.2 31.0 1.0
CA B:ILE201 4.4 30.5 1.0
N B:ILE201 4.5 31.1 1.0
O B:ASN203 4.5 38.2 1.0
CB B:ASP96 4.6 30.4 1.0
CB B:ASN203 4.6 49.5 1.0
O B:HOH436 4.6 38.6 1.0
NZ B:LYS94 4.7 48.3 1.0
CA B:CYS200 4.7 40.2 1.0
CE B:LYS94 4.7 48.2 1.0
N B:GLU12 4.9 30.6 1.0

Calcium binding site 5 out of 6 in 3dsl

Go back to Calcium Binding Sites List in 3dsl
Calcium binding site 5 out of 6 in the The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca423

b:34.9
occ:1.00
 O B:VAL215 2.3 40.4 1.0
O B:LEU220 2.5 31.4 1.0
OE1 B:GLU225 2.7 31.1 1.0
ND2 B:ASN218 2.8 35.8 1.0
OD1 B:ASN218 2.8 32.7 1.0
OE2 B:GLU225 2.9 31.4 1.0
CG B:ASN218 3.0 34.7 1.0
OE1 B:GLU222 3.1 38.7 1.0
CD B:GLU225 3.1 32.3 1.0
OD1 B:ASP228 3.3 49.4 1.0
CG B:ASP228 3.3 52.1 1.0
CD B:GLU222 3.3 35.2 1.0
C B:LEU220 3.5 34.0 1.0
C B:VAL215 3.5 40.6 1.0
OD2 B:ASP228 3.6 52.6 1.0
OE2 B:GLU222 3.8 35.1 1.0
CG B:GLU222 3.9 36.0 1.0
CB B:ASP228 3.9 54.4 1.0
N B:LEU220 4.0 34.5 1.0
CA B:LEU220 4.2 32.2 1.0
N B:VAL215 4.2 34.7 1.0
N B:ASN218 4.3 41.0 1.0
CB B:ASN218 4.3 33.5 1.0
CA B:VAL215 4.4 35.7 1.0
CB B:GLU222 4.4 38.6 1.0
CB B:LEU220 4.4 28.2 1.0
N B:CYS216 4.5 51.1 1.0
CG B:GLU225 4.5 36.9 1.0
CA B:CYS216 4.5 56.7 1.0
N B:LEU221 4.5 28.7 1.0
N B:GLU222 4.5 43.0 1.0
N B:GLY217 4.6 0.9 1.0
CB B:VAL215 4.6 30.5 1.0
N B:GLU219 4.7 41.4 1.0
CA B:ASN218 4.7 35.3 1.0
CA B:LEU221 4.7 29.1 1.0
C B:LEU221 4.7 28.9 1.0
C B:ASN218 4.9 35.3 1.0
C B:CYS216 5.0 55.8 1.0

Calcium binding site 6 out of 6 in 3dsl

Go back to Calcium Binding Sites List in 3dsl
Calcium binding site 6 out of 6 in the The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca424

b:72.3
occ:1.00
 OE1 B:GLU282 2.6 80.8 1.0
O B:VAL295 2.7 81.2 1.0
OD2 B:ASP279 2.7 54.8 1.0
OD1 B:ASP294 2.9 65.3 1.0
O B:PRO280 3.0 0.3 1.0
C B:PRO280 3.0 0.7 1.0
CG B:GLU282 3.1 81.7 1.0
CD B:GLU282 3.2 79.7 1.0
N B:PRO280 3.3 0.6 1.0
CG B:ASP279 3.3 58.9 1.0
N B:ALA281 3.4 73.9 1.0
O B:ALA281 3.4 62.3 1.0
C B:ALA281 3.5 65.7 1.0
C B:ASP279 3.6 67.8 1.0
CA B:PRO280 3.6 0.5 1.0
CD B:PRO280 3.6 0.3 1.0
C B:VAL295 3.8 77.7 1.0
CA B:ALA281 3.8 70.7 1.0
OD1 B:ASP279 3.8 58.1 1.0
N B:VAL295 4.0 78.3 1.0
O B:ASP279 4.0 70.8 1.0
CB B:PRO280 4.1 0.4 1.0
CA B:ASP279 4.1 60.3 1.0
N B:GLU282 4.1 84.0 1.0
CG B:ASP294 4.2 62.7 1.0
CB B:ASP279 4.3 61.0 1.0
CA B:VAL295 4.3 76.8 1.0
CB B:GLU282 4.4 78.6 1.0
OE2 B:GLU282 4.4 76.5 1.0
CG B:PRO280 4.5 0.7 1.0
CB B:VAL295 4.5 80.4 1.0
C B:ASP294 4.5 55.2 1.0
CA B:ASP294 4.7 58.6 1.0
CG B:ARG272 4.8 82.0 1.0
CA B:GLU282 4.8 81.5 1.0
N B:PHE296 4.9 65.3 1.0
O B:ALA273 4.9 0.9 1.0
OD2 B:ASP294 5.0 63.0 1.0

Reference:

J.R.Muniz, A.L.Ambrosio, H.S.Selistre-De-Araujo, M.R.Cominetti, A.M.Moura-Da-Silva, G.Oliva, R.C.Garratt, D.H.Souza. The Three-Dimensional Structure of Bothropasin, the Main Hemorrhagic Factor From Bothrops Jararaca Venom: Insights For A New Classification of Snake Venom Metalloprotease Subgroups. Toxicon V. 52 807 2008.
ISSN: ISSN 0041-0101
PubMed: 18831982
DOI: 10.1016/J.TOXICON.2008.08.021
Page generated: Sat Dec 12 04:09:11 2020

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