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Calcium in PDB 2b04: Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate

Enzymatic activity of Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate

All present enzymatic activity of Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate, PDB code: 2b04 was solved by Y.H.Pan, 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) 24.07 / 2.50
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.156, 69.156, 67.043, 90.00, 90.00, 120.00
R / Rfree (%) 21.1 / 24.4

Other elements in 2b04:

The structure of Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate (pdb code 2b04). 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 Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate, PDB code: 2b04:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2b04

Go back to Calcium Binding Sites List in 2b04
Calcium binding site 1 out of 3 in the Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate


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 Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca130

b:46.9
occ:1.00
O A:GLY32 2.3 45.8 1.0
O A:TYR28 2.4 40.7 1.0
O A:HOH238 2.4 37.1 1.0
OD2 A:ASP49 2.4 38.9 1.0
O A:GLY30 2.5 47.1 1.0
OD1 A:ASP49 2.5 35.7 1.0
O A:HOH239 2.6 47.4 1.0
CG A:ASP49 2.8 36.9 1.0
C A:GLY32 3.5 45.8 1.0
C A:TYR28 3.5 40.0 1.0
C A:GLY30 3.6 46.4 1.0
N A:GLY32 3.7 46.5 1.0
N A:GLY30 3.9 44.8 1.0
CA A:GLY32 4.1 46.3 1.0
CA A:TYR28 4.1 39.9 1.0
C A:LEU31 4.2 46.6 1.0
CB A:ASP49 4.3 35.1 1.0
O A:HOH243 4.4 36.4 1.0
CA A:GLY30 4.5 45.4 1.0
CA A:LEU31 4.5 46.2 1.0
N A:LEU31 4.5 46.2 1.0
N A:CYS29 4.5 41.7 1.0
N A:GLY33 4.6 44.9 1.0
O A:HOH202 4.6 22.6 1.0
CB A:TYR28 4.6 37.8 1.0
O A:HOH241 4.6 55.0 1.0
O A:HOH201 4.7 10.6 1.0
CA A:CYS29 4.7 43.6 1.0
C A:CYS29 4.7 44.7 1.0
O A:HOH206 4.7 46.1 1.0
O A:LEU31 4.8 47.3 1.0
CD1 A:TYR28 4.8 36.0 1.0
CA A:GLY33 4.9 43.9 1.0
O A:CYS45 5.0 40.1 1.0

Calcium binding site 2 out of 3 in 2b04

Go back to Calcium Binding Sites List in 2b04
Calcium binding site 2 out of 3 in the Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate


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 Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca131

b:9.4
occ:0.50
OE1 A:GLU92 2.1 37.7 1.0
OE1 A:GLU71 2.2 34.2 1.0
O A:SER72 2.4 34.2 1.0
CD A:GLU92 3.2 38.2 1.0
CD A:GLU71 3.2 35.3 1.0
C A:SER72 3.4 36.3 1.0
N A:SER72 3.5 36.5 1.0
CG A:GLU92 3.7 36.2 1.0
OE2 A:GLU71 3.8 34.2 1.0
CA A:SER72 3.9 36.0 1.0
O A:HOH212 4.1 20.3 1.0
CB A:SER72 4.2 35.8 1.0
CG A:GLU71 4.3 32.8 1.0
OE2 A:GLU92 4.3 37.9 1.0
C A:GLU71 4.4 36.8 1.0
N A:TYR73 4.6 36.8 1.0
CA A:GLU71 4.7 36.2 1.0

Calcium binding site 3 out of 3 in 2b04

Go back to Calcium Binding Sites List in 2b04
Calcium binding site 3 out of 3 in the Crystal Structure of Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate


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 Porcine Pancreatic Phospholipase A2 in Complex with Glycochenodeoxycholate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca132

b:36.3
occ:0.50
O A:LYS62 2.1 47.4 1.0
CL A:CL135 2.6 41.9 0.5
O A:HOH214 2.9 42.9 1.0
C A:LYS62 3.3 47.2 1.0
CB A:LYS62 3.7 49.9 1.0
CA A:LYS62 3.9 47.8 1.0
N A:LYS62 4.1 46.9 1.0
N A:PHE63 4.4 45.4 1.0
CG A:LYS62 4.4 52.8 1.0
CA A:PHE63 4.6 44.2 1.0

Reference:

Y.H.Pan, B.J.Bahnson. Structural Basis For Bile Salt Inhibition of Pancreatic Phospholipase A2. J.Mol.Biol. V. 369 439 2007.
ISSN: ISSN 0022-2836
PubMed: 17434532
DOI: 10.1016/J.JMB.2007.03.034
Page generated: Fri Jul 12 08:55:58 2024

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