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Calcium in PDB 1bjj: Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas

Enzymatic activity of Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas

All present enzymatic activity of Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas:
3.1.1.4;

Protein crystallography data

The structure of Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas, PDB code: 1bjj was solved by L.Tang, Y.Zhou, Z.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.750, 105.800, 110.030, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 26

Calcium Binding Sites:

The binding sites of Calcium atom in the Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas (pdb code 1bjj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas, PDB code: 1bjj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1bjj

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Calcium binding site 1 out of 8 in the Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca134

b:17.4
occ:1.00
 OD1 E:ASP71 2.4 31.0 1.0
OD1 A:ASP71 2.4 26.7 1.0
O A:ILE72 2.4 19.3 1.0
O E:ILE72 2.4 22.7 1.0
OE2 E:GLU92 2.5 25.9 1.0
OE2 A:GLU92 2.6 16.1 1.0
CD E:GLU92 3.4 23.2 1.0
C A:ILE72 3.4 20.1 1.0
N A:ILE72 3.4 19.2 1.0
C E:ILE72 3.5 20.7 1.0
CD A:GLU92 3.5 20.5 1.0
CG E:ASP71 3.6 23.6 1.0
N E:ILE72 3.6 21.1 1.0
CG A:ASP71 3.6 23.8 1.0
CG E:GLU92 3.7 21.6 1.0
CA A:ILE72 3.8 17.8 1.0
CG A:GLU92 3.9 17.5 1.0
CA E:ILE72 3.9 20.2 1.0
CB A:ILE72 4.1 21.8 1.0
OD2 E:ASP71 4.1 23.4 1.0
CB E:ILE72 4.2 22.5 1.0
C A:ASP71 4.3 19.6 1.0
OD2 A:ASP71 4.3 24.0 1.0
OE1 E:GLU92 4.4 20.9 1.0
C E:ASP71 4.4 19.0 1.0
N A:TYR73 4.5 18.1 1.0
OE1 A:GLU92 4.5 22.3 1.0
CA A:ASP71 4.5 20.1 1.0
N E:TYR73 4.6 19.1 1.0
CA E:ASP71 4.7 18.5 1.0
CB A:ASP71 4.7 21.7 1.0
CB E:ASP71 4.7 20.2 1.0
CA A:TYR73 4.9 15.8 1.0

Calcium binding site 2 out of 8 in 1bjj

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Calcium binding site 2 out of 8 in the Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca11

b:39.8
occ:1.00
 O A:TYR28 2.5 23.9 1.0
O A:GLY32 2.7 49.4 1.0
O A:GLY30 2.8 32.4 1.0
OD1 A:ASP49 2.8 55.7 1.0
OD2 A:ASP49 2.9 54.0 1.0
CG A:ASP49 3.2 51.2 1.0
O A:HOH136 3.4 52.2 1.0
C A:TYR28 3.7 29.4 1.0
C A:GLY32 3.9 50.7 1.0
C A:GLY30 3.9 36.8 1.0
N A:GLY30 4.2 34.8 1.0
CA A:TYR28 4.3 31.1 1.0
N A:GLY32 4.5 50.3 1.0
C A:TRP31 4.6 51.2 1.0
CB A:ASP49 4.6 39.8 1.0
N A:CYS29 4.7 30.0 1.0
CB A:TYR28 4.7 35.7 1.0
C A:CYS29 4.7 36.9 1.0
O A:CYS45 4.7 23.1 1.0
CA A:GLY30 4.7 35.8 1.0
CA A:GLY33 4.7 47.9 1.0
N A:GLY33 4.8 50.6 1.0
CA A:GLY32 4.8 50.6 1.0
CA A:CYS29 4.8 32.1 1.0
O A:TRP31 4.9 51.1 1.0
N A:TRP31 4.9 44.7 1.0
CA A:TRP31 4.9 50.6 1.0
CD1 A:TYR28 4.9 31.2 1.0
O A:HOH137 5.0 59.3 1.0

Calcium binding site 3 out of 8 in 1bjj

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Calcium binding site 3 out of 8 in the Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca134

b:33.6
occ:1.00
 O B:GLY30 2.6 35.7 1.0
O B:TYR28 2.7 30.6 1.0
OD1 B:ASP49 3.1 41.5 1.0
O B:GLY32 3.1 45.7 1.0
OD2 B:ASP49 3.2 38.0 1.0
CG B:ASP49 3.6 36.0 1.0
C B:GLY32 3.6 44.6 1.0
N B:GLY32 3.6 38.8 1.0
C B:GLY30 3.8 28.5 1.0
C B:TYR28 3.9 28.2 1.0
CA B:GLY32 3.9 41.3 1.0
O B:HOH136 4.0 20.9 1.0
N B:GLY30 4.1 28.8 1.0
N B:GLY33 4.4 44.8 1.0
C B:TRP31 4.5 36.6 1.0
O B:HOH137 4.5 25.2 1.0
CA B:TYR28 4.5 27.5 1.0
CA B:GLY30 4.6 27.2 1.0
N B:TRP31 4.8 30.0 1.0
CA B:TRP31 4.9 37.0 1.0
N B:CYS29 4.9 24.4 1.0
C B:CYS29 4.9 29.1 1.0
CA B:GLY33 4.9 41.3 1.0
CB B:TYR28 5.0 23.9 1.0
CA B:CYS29 5.0 24.4 1.0

Calcium binding site 4 out of 8 in 1bjj

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Calcium binding site 4 out of 8 in the Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca134

b:19.0
occ:1.00
 OE2 D:GLU92 2.4 25.8 1.0
OD1 C:ASP71 2.4 18.8 1.0
O C:ILE72 2.5 11.4 1.0
O D:ILE72 2.5 24.9 1.0
OE2 C:GLU92 2.5 33.9 1.0
OD1 D:ASP71 2.6 13.0 1.0
CD D:GLU92 3.3 28.5 1.0
C C:ILE72 3.5 14.1 1.0
CD C:GLU92 3.5 25.4 1.0
CG C:ASP71 3.5 19.6 1.0
C D:ILE72 3.5 24.2 1.0
N C:ILE72 3.6 23.0 1.0
CG D:GLU92 3.6 23.1 1.0
N D:ILE72 3.8 22.6 1.0
CG D:ASP71 3.8 17.8 1.0
CG C:GLU92 3.8 28.1 1.0
CA C:ILE72 3.9 18.9 1.0
OD2 C:ASP71 4.1 23.6 1.0
CA D:ILE72 4.1 22.9 1.0
CB C:ILE72 4.3 16.5 1.0
CB D:ILE72 4.3 20.8 1.0
C C:ASP71 4.3 21.5 1.0
OD2 D:ASP71 4.4 24.6 1.0
OE1 D:GLU92 4.5 25.7 1.0
C D:ASP71 4.5 18.2 1.0
OE1 C:GLU92 4.6 20.3 1.0
N D:TYR73 4.6 24.8 1.0
N C:TYR73 4.6 15.7 1.0
CA C:ASP71 4.6 19.1 1.0
CB C:ASP71 4.7 15.0 1.0
CA D:ASP71 4.9 19.3 1.0
CA D:TYR73 4.9 17.5 1.0
CB D:ASP71 4.9 18.2 1.0

Calcium binding site 5 out of 8 in 1bjj

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Calcium binding site 5 out of 8 in the Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca134

b:44.3
occ:1.00
 O D:TYR28 2.6 30.2 1.0
O D:GLY30 2.8 50.3 1.0
OD2 D:ASP49 3.2 49.7 1.0
C D:GLY32 3.3 39.3 1.0
OD1 D:ASP49 3.3 41.6 1.0
CA D:GLY32 3.5 44.1 1.0
C D:TYR28 3.5 28.8 1.0
N D:GLY32 3.5 49.9 1.0
O D:GLY32 3.6 41.7 1.0
N D:GLY33 3.6 37.0 1.0
CG D:ASP49 3.7 38.2 1.0
C D:GLY30 3.9 47.8 1.0
CA D:TYR28 4.1 26.8 1.0
N D:GLY30 4.1 39.6 1.0
CA D:GLY33 4.3 37.3 1.0
C D:TRP31 4.4 53.0 1.0
N D:CYS29 4.5 32.7 1.0
C D:CYS29 4.5 35.1 1.0
CB D:TYR28 4.6 23.3 1.0
CA D:GLY30 4.6 44.6 1.0
CA D:CYS29 4.7 32.4 1.0
CD2 D:TYR28 4.9 23.7 1.0
N D:TRP31 4.9 52.4 1.0

Calcium binding site 6 out of 8 in 1bjj

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Calcium binding site 6 out of 8 in the Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca134

b:44.4
occ:1.00
 O E:TYR28 2.5 26.8 1.0
O E:GLY30 2.7 50.4 1.0
O E:GLY32 2.8 45.7 1.0
OD2 E:ASP49 2.8 41.7 1.0
OD1 E:ASP49 3.1 38.7 1.0
CG E:ASP49 3.3 34.8 1.0
C E:TYR28 3.6 28.5 1.0
C E:GLY30 3.9 48.8 1.0
C E:GLY32 4.0 43.0 1.0
N E:GLY30 4.1 43.2 1.0
CA E:TYR28 4.2 27.1 1.0
CB E:TYR28 4.5 32.4 1.0
CA E:GLY30 4.6 46.0 1.0
C E:TRP31 4.7 56.9 1.0
N E:GLY32 4.7 50.3 1.0
CA E:GLY33 4.7 32.8 1.0
N E:CYS29 4.7 31.8 1.0
CB E:ASP49 4.8 30.9 1.0
O E:TRP31 4.8 62.6 1.0
N E:GLY33 4.8 40.2 1.0
C E:CYS29 4.9 37.9 1.0
CA E:GLY32 4.9 46.0 1.0
N E:TRP31 4.9 53.6 1.0
CA E:CYS29 5.0 32.9 1.0

Calcium binding site 7 out of 8 in 1bjj

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Calcium binding site 7 out of 8 in the Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca134

b:12.6
occ:1.00
 OE2 B:GLU92 2.3 16.1 1.0
O F:ILE72 2.4 9.3 1.0
O B:ILE72 2.4 17.4 1.0
OD1 F:ASP71 2.5 7.3 1.0
OE2 F:GLU92 2.5 16.8 1.0
OD1 B:ASP71 2.5 23.6 1.0
CD B:GLU92 3.4 18.6 1.0
C F:ILE72 3.4 12.3 1.0
CD F:GLU92 3.4 20.2 1.0
N F:ILE72 3.5 14.4 1.0
C B:ILE72 3.5 15.2 1.0
N B:ILE72 3.6 15.5 1.0
CG F:GLU92 3.7 16.8 1.0
CG F:ASP71 3.7 9.7 1.0
CG B:ASP71 3.7 13.9 1.0
CA F:ILE72 3.8 11.9 1.0
CG B:GLU92 3.9 9.2 1.0
CA B:ILE72 4.0 13.1 1.0
CB F:ILE72 4.2 11.4 1.0
CB B:ILE72 4.2 13.3 1.0
C F:ASP71 4.2 16.4 1.0
OD2 B:ASP71 4.4 22.1 1.0
OD2 F:ASP71 4.4 17.1 1.0
C B:ASP71 4.4 13.4 1.0
OE1 B:GLU92 4.5 14.3 1.0
CA F:ASP71 4.6 15.3 1.0
N F:TYR73 4.6 13.2 1.0
OE1 F:GLU92 4.6 18.1 1.0
CA B:ASP71 4.7 12.5 1.0
N B:TYR73 4.7 13.9 1.0
CB F:ASP71 4.7 11.9 1.0
CB B:ASP71 4.8 6.1 1.0
CG2 F:ILE72 4.9 2.0 1.0
CA F:TYR73 5.0 8.5 1.0

Calcium binding site 8 out of 8 in 1bjj

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Calcium binding site 8 out of 8 in the Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Agkistrodotoxin, A Phospholipase A2-Type Presynaptic Neurotoxin From Agkistrodon Halys Pallas within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca135

b:50.4
occ:1.00
 O F:TYR28 2.5 31.7 1.0
OD2 F:ASP49 2.6 50.6 1.0
O F:GLY32 2.7 38.7 1.0
OD1 F:ASP49 2.8 52.0 1.0
CG F:ASP49 3.0 45.1 1.0
O F:GLY30 3.1 29.1 1.0
C F:TYR28 3.7 31.1 1.0
C F:GLY32 3.8 41.5 1.0
N F:GLY32 4.3 47.9 1.0
CA F:TYR28 4.3 31.1 1.0
N F:GLY30 4.3 29.5 1.0
C F:GLY30 4.3 32.3 1.0
CB F:ASP49 4.4 35.4 1.0
O F:CYS45 4.4 25.5 1.0
CB F:TYR28 4.5 31.1 1.0
CA F:GLY32 4.5 45.4 1.0
N F:CYS29 4.7 28.7 1.0
N F:GLY33 4.8 41.1 1.0
CD2 F:TYR28 4.8 37.5 1.0
CA F:CYS29 4.9 28.7 1.0
CB F:CYS45 5.0 25.7 1.0
CA F:GLY33 5.0 38.7 1.0
C F:CYS45 5.0 24.7 1.0

Reference:

L.Tang, Y.C.Zhou, Z.J.Lin. Structure of Agkistrodotoxin in An Orthorhombic Crystal Form with Six Molecules Per Asymmetric Unit. Acta Crystallogr.,Sect.D V. 55 1986 1999.
ISSN: ISSN 0907-4449
PubMed: 10666574
DOI: 10.1107/S0907444999012603
Page generated: Sat Dec 12 02:49:50 2020

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