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Calcium in PDB 1y6p: Crystal Structure of Disulfide Engineered Porcine Pancratic Phospholipase A2 to Group-X Isozyme

Enzymatic activity of Crystal Structure of Disulfide Engineered Porcine Pancratic Phospholipase A2 to Group-X Isozyme

All present enzymatic activity of Crystal Structure of Disulfide Engineered Porcine Pancratic Phospholipase A2 to Group-X Isozyme:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure of Disulfide Engineered Porcine Pancratic Phospholipase A2 to Group-X Isozyme, PDB code: 1y6p 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) 19.80 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.988, 88.383, 38.560, 90.00, 105.65, 90.00
R / Rfree (%) 18.8 / 26.1

Other elements in 1y6p:

The structure of Crystal Structure of Disulfide Engineered Porcine Pancratic Phospholipase A2 to Group-X Isozyme also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Disulfide Engineered Porcine Pancratic Phospholipase A2 to Group-X Isozyme (pdb code 1y6p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Disulfide Engineered Porcine Pancratic Phospholipase A2 to Group-X Isozyme, PDB code: 1y6p:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1y6p

Go back to Calcium Binding Sites List in 1y6p
Calcium binding site 1 out of 3 in the Crystal Structure of Disulfide Engineered Porcine Pancratic Phospholipase A2 to Group-X Isozyme


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 Pancratic Phospholipase A2 to Group-X Isozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca217

b:53.7
occ:1.00
 O A:HOH323 2.2 30.4 1.0
O A:GLY30 2.2 22.4 1.0
O A:TYR28 2.5 18.2 1.0
O A:GLY32 2.7 29.9 1.0
N A:GLY32 2.8 27.9 1.0
C A:GLY32 3.0 29.1 1.0
CA A:GLY32 3.1 29.1 1.0
C A:GLY30 3.4 22.4 1.0
C A:TYR28 3.6 19.1 1.0
C A:LEU31 3.6 26.7 1.0
N A:GLY30 3.8 19.2 1.0
N A:GLY33 4.0 29.8 1.0
CA A:LEU31 4.2 25.4 1.0
CA A:TYR28 4.2 20.1 1.0
N A:LEU31 4.2 23.3 1.0
O A:HOH249 4.3 25.6 1.0
CA A:GLY30 4.3 21.0 1.0
O A:LEU31 4.4 26.0 1.0
OD2 A:ASP49 4.4 29.4 1.0
CB A:TYR28 4.6 20.7 1.0
O A:CYS45 4.6 13.1 1.0
N A:CYS29 4.6 18.9 1.0
CA A:GLY33 4.7 29.4 1.0
CB A:ASP49 4.7 21.8 1.0
C A:CYS29 4.7 18.1 1.0
CA A:CYS29 4.8 18.0 1.0
OH A:TYR69 4.9 23.6 1.0
CG A:ASP49 5.0 24.2 1.0

Calcium binding site 2 out of 3 in 1y6p

Go back to Calcium Binding Sites List in 1y6p
Calcium binding site 2 out of 3 in the Crystal Structure of Disulfide Engineered Porcine Pancratic Phospholipase A2 to Group-X Isozyme


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 Pancratic Phospholipase A2 to Group-X Isozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca218

b:48.4
occ:1.00
 OD2 B:ASP49 2.2 19.8 1.0
O B:GLY30 2.3 26.1 1.0
O B:TYR28 2.4 17.7 1.0
O B:GLY32 2.4 30.0 1.0
CG B:ASP49 2.9 18.4 1.0
OD1 B:ASP49 3.0 20.5 1.0
O B:HOH290 3.3 24.5 1.0
C B:TYR28 3.5 16.6 1.0
C B:GLY30 3.5 26.6 1.0
C B:GLY32 3.6 30.7 1.0
N B:GLY30 3.9 21.9 1.0
C B:LEU31 4.0 31.8 1.0
CA B:TYR28 4.0 16.4 1.0
O B:LEU31 4.1 32.7 1.0
N B:GLY32 4.2 31.4 1.0
CB B:TYR28 4.3 14.8 1.0
CA B:GLY30 4.4 25.2 1.0
N B:LEU31 4.4 29.6 1.0
CA B:LEU31 4.4 31.9 1.0
CB B:ASP49 4.4 17.1 1.0
CA B:GLY33 4.4 28.0 1.0
N B:GLY33 4.5 28.7 1.0
CA B:GLY32 4.5 30.9 1.0
N B:CYS29 4.6 17.0 1.0
O B:HOH273 4.7 17.3 1.0
C B:CYS29 4.7 19.7 1.0
CD2 B:TYR28 4.8 14.8 1.0
CA B:CYS29 4.8 16.9 1.0

Calcium binding site 3 out of 3 in 1y6p

Go back to Calcium Binding Sites List in 1y6p
Calcium binding site 3 out of 3 in the Crystal Structure of Disulfide Engineered Porcine Pancratic Phospholipase A2 to Group-X Isozyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Disulfide Engineered Porcine Pancratic Phospholipase A2 to Group-X Isozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca219

b:15.0
occ:1.00
 OE2 A:GLU71 2.2 12.5 1.0
OE2 A:GLU92 2.3 10.0 1.0
OE1 B:GLU92 2.3 17.2 1.0
O B:SER72 2.3 14.4 1.0
OE2 B:GLU71 2.4 15.6 1.0
O A:SER72 2.5 13.5 1.0
C B:SER72 3.4 14.2 1.0
CD A:GLU92 3.4 12.9 1.0
CD B:GLU92 3.4 17.2 1.0
CD A:GLU71 3.4 13.4 1.0
C A:SER72 3.5 13.6 1.0
N B:SER72 3.6 13.6 1.0
CD B:GLU71 3.7 16.3 1.0
N A:SER72 3.8 13.7 1.0
CG B:GLU92 3.8 14.7 1.0
CA B:SER72 3.9 14.7 1.0
CG A:GLU92 4.0 12.7 1.0
CA A:SER72 4.0 14.7 1.0
CB B:SER72 4.1 15.4 1.0
O A:HOH230 4.1 9.8 1.0
O A:HOH255 4.1 10.9 1.0
OE1 A:GLU71 4.2 15.7 1.0
CB A:SER72 4.2 15.7 1.0
CG A:GLU71 4.3 12.9 1.0
OE1 A:GLU92 4.4 15.1 1.0
OE2 B:GLU92 4.5 11.5 1.0
OE1 B:GLU71 4.5 19.2 1.0
C B:GLU71 4.5 14.3 1.0
N B:TYR73 4.6 14.6 1.0
CG B:GLU71 4.6 17.0 1.0
N A:TYR73 4.7 13.3 1.0
C A:GLU71 4.7 14.1 1.0
CA B:GLU71 4.9 15.3 1.0
CA B:TYR73 5.0 14.5 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 03:28:24 2020

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