Atomistry » Cadmium » PDB 1a4k-1dmf » 1c1j
Atomistry »
  Cadmium »
    PDB 1a4k-1dmf »
      1c1j »

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

Go back to Cadmium Binding Sites List in 1c1j
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

Go back to Cadmium Binding Sites List in 1c1j
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

Go back to Cadmium Binding Sites List in 1c1j
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

Go back to Cadmium Binding Sites List in 1c1j
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: Fri Jul 19 13:04:57 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy