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Fluorine 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:

Calcium (Ca) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 6 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 1y6o

Go back to Fluorine Binding Sites List in 1y6o
Fluorine binding site 1 out of 6 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 Fluorine with other atoms in the F 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:F217

b:42.7
occ:1.00
 F31 A:MJI217 0.0 42.7 1.0
C32 A:MJI217 1.4 42.5 1.0
F32 A:MJI217 2.1 43.1 1.0
F33 A:MJI217 2.2 42.2 1.0
C31 A:MJI217 2.5 43.3 1.0
O3 A:MJI217 2.8 43.7 1.0
CD1 A:LEU2 3.5 16.1 1.0
C3 A:MJI217 3.8 43.4 1.0
CD2 A:PHE5 3.9 14.5 1.0
N A:ARG6 4.5 11.8 1.0
CG A:PHE5 4.5 12.0 1.0
CD2 A:LEU19 4.5 16.8 1.0
CE2 A:PHE5 4.5 13.9 1.0
CA A:ARG6 4.6 13.1 1.0
O A:LEU2 4.6 12.9 1.0
CB A:PHE5 4.6 11.9 1.0
CG A:LEU2 4.6 14.4 1.0
CB A:ARG6 4.7 13.8 1.0
C2 A:MJI217 4.7 42.8 1.0
CB A:PRO18 4.8 12.2 1.0
C A:PHE5 4.9 12.7 1.0

Fluorine binding site 2 out of 6 in 1y6o

Go back to Fluorine Binding Sites List in 1y6o
Fluorine binding site 2 out of 6 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 Fluorine with other atoms in the F 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
A:F217

b:43.1
occ:1.00
 F32 A:MJI217 0.0 43.1 1.0
C32 A:MJI217 1.3 42.5 1.0
F33 A:MJI217 2.1 42.2 1.0
F31 A:MJI217 2.1 42.7 1.0
C31 A:MJI217 2.3 43.3 1.0
C A:PRO18 3.3 14.2 1.0
N A:LEU19 3.3 15.0 1.0
CB A:PRO18 3.4 12.2 1.0
O A:PRO18 3.4 14.9 1.0
CD2 A:LEU19 3.4 16.8 1.0
O3 A:MJI217 3.5 43.7 1.0
CA A:LEU19 3.6 15.9 1.0
CG A:LEU19 3.8 14.8 1.0
CA A:PRO18 3.9 13.6 1.0
CB A:LEU19 4.3 14.2 1.0
C3 A:MJI217 4.4 43.4 1.0
CB A:ARG6 4.7 13.8 1.0
CG A:PRO18 4.8 12.1 1.0
CA A:ARG6 4.8 13.1 1.0
CG A:ARG6 4.9 12.3 1.0
C A:LEU19 4.9 16.9 1.0
CB A:ASN23 4.9 20.8 1.0

Fluorine binding site 3 out of 6 in 1y6o

Go back to Fluorine Binding Sites List in 1y6o
Fluorine binding site 3 out of 6 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 Fluorine with other atoms in the F binding site number 3 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:F217

b:42.2
occ:1.00
 F33 A:MJI217 0.0 42.2 1.0
C32 A:MJI217 1.3 42.5 1.0
F32 A:MJI217 2.1 43.1 1.0
F31 A:MJI217 2.2 42.7 1.0
C31 A:MJI217 2.4 43.3 1.0
O3 A:MJI217 3.0 43.7 1.0
CB A:PRO18 3.9 12.2 1.0
O A:PRO18 4.0 14.9 1.0
C A:PRO18 4.2 14.2 1.0
CD2 A:PHE5 4.3 14.5 1.0
C2P A:MJI217 4.4 43.1 1.0
C3 A:MJI217 4.4 43.4 1.0
CE2 A:PHE5 4.4 13.9 1.0
CG1 A:ILE9 4.4 16.6 1.0
CA A:PRO18 4.4 13.6 1.0
CB A:PHE22 4.5 18.1 1.0
N A:LEU19 4.9 15.0 1.0
CG A:PHE5 4.9 12.0 1.0
CZ A:PHE5 4.9 11.6 1.0
CD2 A:PHE22 5.0 14.8 1.0
CE2 A:PHE106 5.0 16.5 1.0

Fluorine binding site 4 out of 6 in 1y6o

Go back to Fluorine Binding Sites List in 1y6o
Fluorine binding site 4 out of 6 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 Fluorine with other atoms in the F binding site number 4 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:F218

b:41.8
occ:1.00
 F31 B:MJI218 0.0 41.8 1.0
C32 B:MJI218 1.4 43.4 1.0
F33 B:MJI218 2.2 43.1 1.0
F32 B:MJI218 2.2 45.1 1.0
C31 B:MJI218 2.4 43.5 1.0
O3 B:MJI218 3.0 45.3 1.0
CD2 B:PHE5 3.9 13.9 1.0
CA B:ARG6 4.2 11.6 1.0
CD1 B:LEU2 4.2 16.1 1.0
N B:ARG6 4.2 11.3 1.0
CD1 B:ILE9 4.2 10.9 1.0
CB B:ARG6 4.3 11.0 1.0
CB B:PRO18 4.3 15.1 1.0
C3 B:MJI218 4.3 43.5 1.0
CG B:PHE5 4.5 11.7 1.0
CE2 B:PHE5 4.5 12.7 1.0
CB B:PHE5 4.6 12.8 1.0
C B:PHE5 4.7 12.7 1.0
O B:LEU2 4.7 10.8 1.0
CD2 B:LEU19 4.7 18.5 1.0

Fluorine binding site 5 out of 6 in 1y6o

Go back to Fluorine Binding Sites List in 1y6o
Fluorine binding site 5 out of 6 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 Fluorine with other atoms in the F binding site number 5 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:F218

b:45.1
occ:1.00
 F32 B:MJI218 0.0 45.1 1.0
C32 B:MJI218 1.3 43.4 1.0
F33 B:MJI218 2.1 43.1 1.0
F31 B:MJI218 2.2 41.8 1.0
C31 B:MJI218 2.4 43.5 1.0
O3 B:MJI218 2.9 45.3 1.0
CD2 B:LEU19 3.3 18.5 1.0
N B:LEU19 3.5 17.6 1.0
CA B:LEU19 3.5 17.4 1.0
C B:PRO18 3.6 16.3 1.0
O B:PRO18 3.6 16.9 1.0
C3 B:MJI218 3.7 43.5 1.0
CG B:LEU19 3.9 16.1 1.0
CB B:PRO18 4.1 15.1 1.0
CB B:ASN23 4.3 21.7 1.0
CB B:LEU19 4.3 15.9 1.0
CA B:PRO18 4.4 15.7 1.0
N B:ASN23 4.5 20.9 1.0
C B:LEU19 4.7 17.8 1.0
CA B:ASN23 4.7 20.9 1.0
O B:LEU19 5.0 19.8 1.0

Fluorine binding site 6 out of 6 in 1y6o

Go back to Fluorine Binding Sites List in 1y6o
Fluorine binding site 6 out of 6 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 Fluorine with other atoms in the F binding site number 6 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:F218

b:43.1
occ:1.00
 F33 B:MJI218 0.0 43.1 1.0
C32 B:MJI218 1.3 43.4 1.0
F32 B:MJI218 2.1 45.1 1.0
F31 B:MJI218 2.2 41.8 1.0
C31 B:MJI218 2.3 43.5 1.0
CD1 B:ILE9 3.2 10.9 1.0
CB B:PRO18 3.4 15.1 1.0
O3 B:MJI218 3.5 45.3 1.0
O B:PRO18 3.7 16.9 1.0
C B:PRO18 3.7 16.3 1.0
CA B:PRO18 3.9 15.7 1.0
CB B:PHE22 4.1 18.1 1.0
N B:LEU19 4.3 17.6 1.0
C3 B:MJI218 4.5 43.5 1.0
CG B:PRO18 4.6 15.1 1.0
CG1 B:ILE9 4.6 13.0 1.0
CD2 B:PHE22 4.7 16.8 1.0
CE2 B:PHE5 4.8 12.7 1.0
CD2 B:PHE5 4.8 13.9 1.0
CA B:LEU19 4.9 17.4 1.0
CG B:PHE22 4.9 17.2 1.0
N B:ASN23 4.9 20.9 1.0
C B:PHE22 5.0 20.5 1.0
CA B:PHE22 5.0 19.1 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: Wed Jul 31 13:32:47 2024

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