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Calcium in PDB 3jr8: Crystal Structure of Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions

Enzymatic activity of Crystal Structure of Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions

All present enzymatic activity of Crystal Structure of Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure of Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions, PDB code: 3jr8 was solved by R.J.Borges, J.I.Dos Santos, M.R.M.Fontes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.44 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.236, 100.879, 47.166, 90.00, 126.00, 90.00
R / Rfree (%) 21.7 / 24.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions (pdb code 3jr8). 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 Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions, PDB code: 3jr8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3jr8

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Calcium binding site 1 out of 4 in the Crystal Structure of Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions


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 Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca134

b:55.3
occ:0.88
 OH A:TYR22 2.7 28.0 0.8
O A:PHE106 2.8 32.1 1.0
OG1 A:THR41 3.2 32.6 1.0
CE1 A:TYR22 3.4 25.7 1.0
CZ A:TYR22 3.5 27.4 0.5
CD1 A:TYR113 3.6 34.1 0.7
C A:PHE106 3.6 32.0 0.9
N A:LEU110 3.7 37.9 0.9
O A:ASN109 3.7 39.0 1.0
C A:ASN109 3.7 37.8 1.0
CG2 A:THR41 3.8 32.2 1.0
CA A:LEU110 3.8 37.3 1.0
CA A:PHE106 3.9 30.8 1.0
CD2 A:LEU110 3.9 35.6 0.6
CB A:THR41 4.1 32.6 1.0
CB A:TYR113 4.1 35.9 1.0
CG A:LEU110 4.1 36.7 0.2
CB A:PHE106 4.2 31.5 1.0
CG A:TYR113 4.3 34.4 1.0
CB A:LEU110 4.6 37.7 0.9
CE1 A:TYR113 4.6 34.6 1.0
CB A:ASN109 4.6 37.0 1.0
CA A:ASN109 4.6 37.5 1.0
CD1 A:PHE106 4.7 32.1 1.0
CD1 A:TYR22 4.7 27.9 0.8
N A:ARG107 4.8 32.4 1.0
CA A:THR41 4.8 32.4 0.7
CE2 A:TYR22 4.8 28.7 1.0
CG A:PHE106 4.9 31.4 1.0
NZ A:LYS16 4.9 35.5 0.4

Calcium binding site 2 out of 4 in 3jr8

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Calcium binding site 2 out of 4 in the Crystal Structure of Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions


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 Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca135

b:63.3
occ:0.92
 OG1 A:THR41 2.4 32.6 1.0
OD2 A:ASP39 2.6 38.7 1.0
N A:THR41 2.9 32.7 1.0
OG1 A:THR112 3.0 39.0 1.0
CB A:THR41 3.1 32.6 1.0
CG A:ASP39 3.3 37.1 0.8
O A:THR112 3.6 36.6 1.0
CA A:THR41 3.6 32.4 0.7
C A:THR112 3.6 37.9 0.1
OD1 A:ASP39 3.6 35.9 1.0
O A:ASN109 3.7 39.0 1.0
N A:ALA40 3.8 34.6 1.0
N A:TYR113 3.9 38.0 1.0
CB A:THR112 3.9 38.6 0.9
OH A:TYR25 4.0 37.3 0.9
C A:ALA40 4.0 32.8 1.0
CA A:TYR113 4.1 37.9 1.0
CB A:ALA40 4.2 32.5 1.0
CA A:ALA40 4.2 33.2 0.3
CB A:ASN109 4.2 37.0 1.0
CA A:THR112 4.3 38.1 1.0
CB A:ASP39 4.3 37.8 1.0
CG2 A:THR41 4.5 32.2 1.0
C A:ASP39 4.7 36.0 1.0
C A:ASN109 4.7 37.8 1.0
CZ A:TYR25 4.7 34.3 1.0
N A:THR112 4.8 38.5 1.0
C A:THR41 4.8 32.0 1.0
CE1 A:TYR25 4.9 33.9 1.0
N A:ASP42 4.9 32.8 1.0
CB A:TYR113 5.0 35.9 1.0
CG A:ASN109 5.0 37.9 0.7

Calcium binding site 3 out of 4 in 3jr8

Go back to Calcium Binding Sites List in 3jr8
Calcium binding site 3 out of 4 in the Crystal Structure of Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions


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 Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca134

b:59.7
occ:1.00
 O B:PHE106 2.8 33.3 1.0
OH B:TYR22 2.9 33.3 1.0
OG1 B:THR41 2.9 39.0 1.0
N B:LEU110 3.5 39.3 1.0
C B:PHE106 3.6 34.4 1.0
CE1 B:TYR22 3.6 31.6 1.0
C B:ASN109 3.7 38.9 1.0
CZ B:TYR22 3.7 32.3 0.4
O B:ASN109 3.8 38.2 0.7
CA B:PHE106 3.8 34.7 1.0
CD2 B:LEU110 3.8 42.4 1.0
CA B:LEU110 3.8 39.3 1.0
CG2 B:THR41 3.9 37.1 1.0
CD1 B:TYR113 3.9 38.8 1.0
CB B:THR41 3.9 36.1 0.7
CG B:LEU110 4.1 40.9 0.2
CB B:TYR113 4.2 36.9 1.0
CB B:PHE106 4.3 33.7 1.0
CB B:ASN109 4.4 40.0 1.0
CA B:ASN109 4.5 39.0 1.0
CB B:LEU110 4.5 41.1 1.0
CG B:TYR113 4.6 37.2 1.0
CD1 B:PHE106 4.6 35.8 1.0
N B:ASN109 4.7 38.8 1.0
N B:ARG107 4.7 35.2 1.0
CA B:THR41 4.7 36.3 1.0
CG B:PHE106 4.8 35.1 1.0
CD1 B:TYR22 4.9 31.1 1.0
CE1 B:TYR113 4.9 36.2 0.7

Calcium binding site 4 out of 4 in 3jr8

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Calcium binding site 4 out of 4 in the Crystal Structure of Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions


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 Bthtx-II (ASP49-PLA2 From Bothrops Jararacussu Snake Venom) with Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca135

b:59.9
occ:0.79
 OD2 B:ASP39 2.8 38.7 1.0
OG1 B:THR112 2.8 40.5 0.9
OG1 B:THR41 2.9 39.0 1.0
N B:THR41 3.0 36.5 1.0
CG B:ASP39 3.1 40.3 1.0
CB B:THR41 3.4 36.1 0.7
OD1 B:ASP39 3.4 39.8 0.8
O B:THR112 3.5 39.2 1.0
N B:ALA40 3.7 38.5 0.9
C B:THR112 3.7 38.8 1.0
CA B:THR41 3.8 36.3 1.0
O B:HOH149 3.8 46.5 1.0
O B:ASN109 3.9 38.2 0.7
CB B:ASP39 4.0 40.2 1.0
OH B:TYR25 4.0 36.9 1.0
C B:ALA40 4.0 36.7 1.0
CB B:THR112 4.0 39.1 1.0
N B:TYR113 4.0 37.9 1.0
CA B:ALA40 4.0 37.5 0.8
NZ B:LYS114 4.1 41.8 1.0
CB B:ALA40 4.1 36.7 1.0
CA B:TYR113 4.2 37.5 1.0
C B:ASP39 4.3 39.7 0.7
CB B:ASN109 4.4 40.0 1.0
CA B:THR112 4.4 38.8 1.0
CZ B:TYR25 4.8 35.4 0.6
CG2 B:THR41 4.8 37.1 1.0
CA B:ASP39 4.8 40.3 1.0
CE1 B:TYR25 4.8 34.5 0.8
N B:ASP42 4.9 35.1 1.0
C B:ASN109 4.9 38.9 1.0
C B:THR41 4.9 35.7 1.0
N B:THR112 5.0 38.7 1.0

Reference:

J.I.Dos Santos, M.Cintra-Francischinelli, R.J.Borges, C.A.Fernandes, P.Pizzo, A.C.Cintra, A.S.Braz, A.M.Soares, M.R.Fontes. Structural, Functional, and Bioinformatics Studies Reveal A New Snake Venom Homologue Phospholipase A2 Class. Proteins V. 79 61 2011.
ISSN: ISSN 0887-3585
PubMed: 20878713
DOI: 10.1002/PROT.22858
Page generated: Tue Jul 8 13:32:23 2025

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