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Cadmium in PDB 1c1j: Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution

Enzymatic activity of Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution

All present enzymatic activity of Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution:
3.1.1.4;

Protein crystallography data

The structure of Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution, PDB code: 1c1j was solved by H.-L.Zhang, Y.-Q.Zhang, S.-Y.Song, Y.Zhou, Z.-J.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.180, 54.010, 108.490, 90.00, 111.59, 90.00
R / Rfree (%) 20.1 / 28.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution (pdb code 1c1j). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution, PDB code: 1c1j:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 1c1j

Go back to Cadmium Binding Sites List in 1c1j
Cadmium binding site 1 out of 6 in the Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd601

b:37.2
occ:1.00
 ND1 A:HIS48 2.6 27.0 1.0
O A:HOH603 2.7 2.0 1.0
OD2 A:ASP49 2.8 35.0 1.0
O A:HOH604 2.9 25.0 1.0
CE1 A:HIS48 3.4 22.8 1.0
CG A:HIS48 3.6 24.5 1.0
O A:GLY30 3.9 57.0 1.0
CG A:ASP49 3.9 37.9 1.0
CB A:HIS48 4.0 27.9 1.0
O A:CYS45 4.2 29.7 1.0
N A:GLY30 4.4 39.7 1.0
N A:ASP49 4.5 31.8 1.0
C A:HIS48 4.5 31.8 1.0
NE2 A:HIS48 4.5 23.9 1.0
OD1 A:ASP49 4.5 40.7 1.0
C A:GLY30 4.6 56.6 1.0
O A:TYR28 4.7 36.6 1.0
CD2 A:HIS48 4.7 27.8 1.0
CE2 A:PHE5 4.7 21.0 1.0
CA A:ASP49 4.7 28.8 1.0
O A:HIS48 4.8 34.3 1.0
C8' A:BOG600 4.8 28.9 1.0
CB A:ASP49 4.9 32.0 1.0
CA A:HIS48 4.9 28.7 1.0
CA A:GLY30 5.0 49.4 1.0
CA A:CYS45 5.0 23.1 1.0

Cadmium binding site 2 out of 6 in 1c1j

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Cadmium binding site 2 out of 6 in the Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd602

b:59.0
occ:1.00
 O A:GLY26 3.0 25.7 1.0
OD1 A:ASP122 3.1 69.1 1.0
O A:HOH610 3.3 56.1 1.0
O A:TYR120 3.7 35.8 1.0
C A:GLY26 3.9 26.7 1.0
O A:TYR25 4.0 23.9 1.0
CG A:ASP122 4.1 65.1 1.0
CA A:CYS27 4.1 29.3 1.0
O A:PHE24 4.2 19.0 1.0
C A:CYS27 4.3 30.8 1.0
N A:CYS27 4.4 27.4 1.0
O A:CYS27 4.4 31.8 1.0
OD2 A:ASP122 4.4 68.0 1.0
O A:CYS29 4.4 35.2 1.0
C A:PHE24 4.5 17.5 1.0
C A:TYR25 4.7 22.3 1.0
NH1 A:ARG34 4.8 64.8 1.0
C A:TYR120 4.8 32.3 1.0
N A:TYR28 4.9 31.8 1.0
CA A:PHE24 4.9 16.7 1.0

Cadmium binding site 3 out of 6 in 1c1j

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Cadmium binding site 3 out of 6 in the Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd602

b:77.5
occ:1.00
 ND1 B:HIS48 2.8 30.5 1.0
OD2 B:ASP49 2.8 50.7 1.0
O B:HOH610 3.0 24.3 1.0
CE1 B:HIS48 3.5 30.6 1.0
O4 B:BOG601 3.6 43.4 1.0
O6 B:BOG601 3.7 50.0 1.0
CG B:HIS48 3.7 29.0 1.0
O B:CYS29 3.8 50.3 1.0
CG B:ASP49 3.9 53.7 1.0
C6 B:BOG601 4.0 55.5 1.0
CB B:HIS48 4.1 32.0 1.0
C4 B:BOG601 4.2 52.3 1.0
O B:CYS45 4.3 32.0 1.0
OD1 B:ASP49 4.5 60.2 1.0
N B:ASP49 4.5 38.1 1.0
NE2 B:HIS48 4.6 34.2 1.0
CA B:SER31 4.6 72.1 1.0
C B:HIS48 4.6 37.5 1.0
O B:TYR28 4.7 26.5 1.0
C5 B:BOG601 4.7 55.2 1.0
CD2 B:HIS48 4.7 32.9 1.0
CE2 B:PHE5 4.8 13.4 1.0
CA B:ASP49 4.8 40.9 1.0
N B:SER31 4.8 72.5 1.0
C B:CYS29 4.8 49.7 1.0
N B:GLY32 4.9 72.5 1.0
O B:HIS48 4.9 37.0 1.0
CB B:ASP49 4.9 47.9 1.0
CA B:CYS45 5.0 33.3 1.0

Cadmium binding site 4 out of 6 in 1c1j

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Cadmium binding site 4 out of 6 in the Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd134

b:95.2
occ:1.00
 ND1 C:HIS48 2.5 30.9 1.0
O C:HOH144 2.8 66.2 1.0
OD2 C:ASP49 2.9 50.0 1.0
CE1 C:HIS48 3.3 31.6 1.0
O C:HOH143 3.3 48.9 1.0
CG C:HIS48 3.5 31.9 1.0
CB C:HIS48 3.9 32.9 1.0
CG C:ASP49 3.9 47.9 1.0
O C:CYS45 4.2 30.5 1.0
O C:HOH141 4.2 23.5 1.0
N C:ASP49 4.4 36.5 1.0
C C:HIS48 4.4 36.4 1.0
NE2 C:HIS48 4.4 42.6 1.0
CD2 C:HIS48 4.5 41.0 1.0
O C:HIS48 4.6 39.4 1.0
OD1 C:ASP49 4.6 50.6 1.0
CA C:ASP49 4.6 41.4 1.0
CE2 C:PHE5 4.7 23.0 1.0
CA C:HIS48 4.8 36.9 1.0
CB C:ASP49 4.9 45.1 1.0

Cadmium binding site 5 out of 6 in 1c1j

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Cadmium binding site 5 out of 6 in the Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd134

b:55.6
occ:1.00
 O D:HOH147 2.5 6.1 1.0
ND1 D:HIS48 2.5 33.4 1.0
O D:HOH136 2.9 17.7 1.0
OD2 D:ASP49 3.0 60.7 1.0
CE1 D:HIS48 3.3 32.1 1.0
CG D:HIS48 3.5 31.8 1.0
CB D:HIS48 3.9 31.5 1.0
CG D:ASP49 4.1 55.5 1.0
O D:CYS45 4.3 26.1 1.0
NE2 D:HIS48 4.4 36.4 1.0
N D:ASP49 4.5 36.0 1.0
CD2 D:HIS48 4.5 35.9 1.0
C D:HIS48 4.5 32.5 1.0
CE2 D:PHE5 4.6 11.4 1.0
O D:GLY30 4.6 51.7 1.0
OD1 D:ASP49 4.7 59.5 1.0
N D:GLY30 4.7 35.6 1.0
O D:TYR28 4.8 25.6 1.0
CA D:ASP49 4.8 41.0 1.0
O D:HIS48 4.8 33.5 1.0
CA D:HIS48 4.9 34.3 1.0

Cadmium binding site 6 out of 6 in 1c1j

Go back to Cadmium Binding Sites List in 1c1j
Cadmium binding site 6 out of 6 in the Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Cadmium-Substituted Phospholipase A2 From Agkistrondon Halys Pallas at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd135

b:63.5
occ:1.00
 OD1 D:ASP122 3.0 62.8 1.0
O D:GLY26 3.3 27.6 1.0
O D:TYR120 3.8 38.2 1.0
CG D:ASP122 4.0 59.1 1.0
O D:CYS29 4.0 25.6 1.0
C D:GLY26 4.2 24.1 1.0
O D:PHE24 4.2 28.6 1.0
OD2 D:ASP122 4.2 61.4 1.0
NH1 D:ARG34 4.4 90.7 1.0
O D:TYR25 4.4 22.6 1.0
CA D:CYS27 4.4 16.9 1.0
O D:CYS27 4.5 22.9 1.0
OG D:SER31 4.5 49.9 1.0
C D:CYS27 4.5 18.2 1.0
CZ D:ARG34 4.6 87.4 1.0
C D:PHE24 4.6 21.9 1.0
N D:CYS27 4.7 20.1 1.0
NH2 D:ARG34 4.8 90.8 1.0
CA D:PHE24 4.8 18.0 1.0
C D:TYR25 4.9 19.8 1.0
C D:TYR120 4.9 31.9 1.0

Reference:

H.-L.Zhang, Y.-Q.Zhang, S.-Y.Song, Y.Zhou, Z.-J.Lin. Structure of Cadmium-Substituted Phospholipase A2 From Agkistrodon Halys Pallas at 2.8 Angstroms Resolution Protein Pept.Lett. V. 6 185 1999.
ISSN: ISSN 0929-8665
Page generated: Sun Jan 24 09:41:27 2021

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