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Calcium in PDB 1y6o: Crystal Structure of Disulfide Engineered Porcine Pancreatic Phospholipase A2 to Group-X Isozyme in Complex with Inhibitor MJ33 and Phosphate Ions

Enzymatic activity of Crystal Structure of Disulfide Engineered Porcine Pancreatic Phospholipase A2 to Group-X Isozyme in Complex with Inhibitor MJ33 and Phosphate Ions

All present enzymatic activity of Crystal Structure of Disulfide Engineered Porcine Pancreatic Phospholipase A2 to Group-X Isozyme in Complex with Inhibitor MJ33 and Phosphate Ions:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure of Disulfide Engineered Porcine Pancreatic Phospholipase A2 to Group-X Isozyme in Complex with Inhibitor MJ33 and Phosphate Ions, PDB code: 1y6o was solved by B.Z.Yu, Y.H.Pan, M.J.W.Jassen, B.J.Bahnson, M.K.Jain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.64 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.534, 85.921, 38.554, 90.00, 94.76, 90.00
R / Rfree (%) 19.6 / 24.5

Other elements in 1y6o:

The structure of Crystal Structure of Disulfide Engineered Porcine Pancreatic Phospholipase A2 to Group-X Isozyme in Complex with Inhibitor MJ33 and Phosphate Ions also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Disulfide Engineered Porcine Pancreatic Phospholipase A2 to Group-X Isozyme in Complex with Inhibitor MJ33 and Phosphate Ions (pdb code 1y6o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Disulfide Engineered Porcine Pancreatic Phospholipase A2 to Group-X Isozyme in Complex with Inhibitor MJ33 and Phosphate Ions, PDB code: 1y6o:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1y6o

Go back to Calcium Binding Sites List in 1y6o
Calcium binding site 1 out of 2 in the Crystal Structure of Disulfide Engineered Porcine Pancreatic Phospholipase A2 to Group-X Isozyme in Complex with Inhibitor MJ33 and Phosphate 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 Disulfide Engineered Porcine Pancreatic Phospholipase A2 to Group-X Isozyme in Complex with Inhibitor MJ33 and Phosphate Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:25.0
occ:1.00
 O A:GLY30 2.3 25.4 1.0
O A:HOH218 2.3 29.9 1.0
O A:TYR28 2.4 14.9 1.0
O A:GLY32 2.4 23.9 1.0
OD2 A:ASP49 2.5 17.1 1.0
OD1 A:ASP49 2.6 19.9 1.0
O21 A:MJI217 2.7 43.7 1.0
CG A:ASP49 2.9 18.1 1.0
C A:GLY30 3.5 25.5 1.0
C A:TYR28 3.5 15.4 1.0
C A:GLY32 3.5 23.2 1.0
N A:GLY30 3.7 21.0 1.0
N A:GLY32 3.9 26.8 1.0
P2 A:MJI217 3.9 44.9 1.0
O A:HOH285 4.1 34.7 1.0
CA A:TYR28 4.2 14.2 1.0
C A:LEU31 4.2 27.4 1.0
CA A:GLY32 4.2 25.4 1.0
O A:HOH219 4.3 27.2 1.0
CA A:GLY30 4.3 24.0 1.0
O22 A:MJI217 4.3 45.1 1.0
CB A:ASP49 4.4 16.8 1.0
N A:LEU31 4.5 27.0 1.0
O A:HOH227 4.5 27.5 1.0
N A:CYS29 4.6 15.0 1.0
CA A:LEU31 4.6 28.1 1.0
N A:GLY33 4.6 21.3 1.0
CB A:TYR28 4.6 13.7 1.0
C A:CYS29 4.6 19.5 1.0
CA A:CYS29 4.7 18.5 1.0
O2 A:MJI217 4.7 43.4 1.0
O A:CYS45 4.8 16.4 1.0
CA A:GLY33 4.8 18.6 1.0
O A:LEU31 4.8 27.8 1.0

Calcium binding site 2 out of 2 in 1y6o

Go back to Calcium Binding Sites List in 1y6o
Calcium binding site 2 out of 2 in the Crystal Structure of Disulfide Engineered Porcine Pancreatic Phospholipase A2 to Group-X Isozyme in Complex with Inhibitor MJ33 and Phosphate 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 Disulfide Engineered Porcine Pancreatic Phospholipase A2 to Group-X Isozyme in Complex with Inhibitor MJ33 and Phosphate Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca208

b:26.4
occ:1.00
 O B:GLY30 2.2 22.7 1.0
O B:TYR28 2.3 15.8 1.0
O B:HOH228 2.4 24.4 1.0
O B:GLY32 2.5 22.9 1.0
O21 B:MJI218 2.5 44.2 1.0
OD2 B:ASP49 2.5 17.1 1.0
OD1 B:ASP49 2.6 19.3 1.0
CG B:ASP49 2.9 18.6 1.0
C B:GLY30 3.4 22.3 1.0
C B:TYR28 3.5 15.5 1.0
C B:GLY32 3.5 23.0 1.0
P2 B:MJI218 3.7 45.1 1.0
N B:GLY30 3.7 19.1 1.0
N B:GLY32 3.8 25.6 1.0
O22 B:MJI218 4.0 44.5 1.0
C B:LEU31 4.2 25.8 1.0
CA B:GLY32 4.2 24.3 1.0
CA B:GLY30 4.2 21.4 1.0
CA B:TYR28 4.3 15.2 1.0
O B:HOH309 4.3 25.4 1.0
O2 B:MJI218 4.4 43.3 1.0
N B:LEU31 4.4 23.4 1.0
CB B:ASP49 4.4 15.6 1.0
CA B:LEU31 4.5 25.4 1.0
N B:CYS29 4.5 15.2 1.0
C B:CYS29 4.6 18.3 1.0
N B:GLY33 4.6 21.2 1.0
CB B:TYR28 4.6 13.3 1.0
CA B:CYS29 4.7 17.7 1.0
O B:LEU31 4.7 27.3 1.0
CA B:GLY33 4.8 18.8 1.0
O B:CYS45 4.8 14.8 1.0
O B:HOH236 4.8 26.8 1.0
O B:HOH233 4.9 45.3 1.0
O23 B:MJI218 5.0 43.7 1.0

Reference:

B.Z.Yu, Y.H.Pan, M.J.W.Janssen, B.J.Bahnson, M.K.Jain. Kinetic and Structural Properties of Disulfide Engineered Phospholipase A(2): Insight Into the Role of Disulfide Bonding Patterns. Biochemistry V. 44 3369 2005.
ISSN: ISSN 0006-2960
PubMed: 15736947
DOI: 10.1021/BI0482147
Page generated: Sat Dec 12 03:28:23 2020

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