Atomistry » Calcium » PDB 1y1x-1ydy » 1y6p
Atomistry »
  Calcium »
    PDB 1y1x-1ydy »
      1y6p »

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: Fri Jul 12 08:00:58 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy