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Calcium in PDB 2phi: A Large Conformational Change Is Found in the Crystal Structure of the Porcine Pancreatic Phospholipase A2 Point Mutant F63V

Enzymatic activity of A Large Conformational Change Is Found in the Crystal Structure of the Porcine Pancreatic Phospholipase A2 Point Mutant F63V

All present enzymatic activity of A Large Conformational Change Is Found in the Crystal Structure of the Porcine Pancreatic Phospholipase A2 Point Mutant F63V:
3.1.1.4;

Protein crystallography data

The structure of A Large Conformational Change Is Found in the Crystal Structure of the Porcine Pancreatic Phospholipase A2 Point Mutant F63V, PDB code: 2phi was solved by B.W.Dijkstra, M.M.G.M.Thunnissen, K.H.Kalk, J.Drenth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.880, 65.230, 52.620, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the A Large Conformational Change Is Found in the Crystal Structure of the Porcine Pancreatic Phospholipase A2 Point Mutant F63V (pdb code 2phi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the A Large Conformational Change Is Found in the Crystal Structure of the Porcine Pancreatic Phospholipase A2 Point Mutant F63V, PDB code: 2phi:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2phi

Go back to Calcium Binding Sites List in 2phi
Calcium binding site 1 out of 3 in the A Large Conformational Change Is Found in the Crystal Structure of the Porcine Pancreatic Phospholipase A2 Point Mutant F63V


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A Large Conformational Change Is Found in the Crystal Structure of the Porcine Pancreatic Phospholipase A2 Point Mutant F63V within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca125

b:17.4
occ:1.00
 O A:TYR28 2.3 7.7 1.0
O A:HOH220 2.3 16.6 1.0
O A:GLY32 2.3 20.4 1.0
O A:HOH168 2.4 8.9 1.0
O A:GLY30 2.4 14.2 1.0
OD2 A:ASP49 2.5 22.0 1.0
OD1 A:ASP49 2.6 22.2 1.0
CG A:ASP49 2.9 21.7 1.0
C A:TYR28 3.4 8.3 1.0
C A:GLY32 3.5 20.4 1.0
C A:GLY30 3.6 14.6 1.0
N A:GLY30 3.7 12.7 1.0
O A:HOH126 4.1 19.6 1.0
CA A:TYR28 4.2 9.6 1.0
C A:LEU31 4.2 19.9 1.0
N A:GLY32 4.2 20.2 1.0
O A:LEU31 4.2 20.1 1.0
CA A:GLY32 4.3 20.5 1.0
CB A:ASP49 4.3 11.3 1.0
CA A:GLY30 4.4 13.8 1.0
N A:CYS29 4.4 9.3 1.0
O A:HOH199 4.5 51.5 1.0
N A:GLY33 4.5 20.6 1.0
CA A:CYS29 4.5 11.2 1.0
C A:CYS29 4.6 12.2 1.0
N A:LEU31 4.6 16.7 1.0
CB A:TYR28 4.7 10.4 1.0
O A:HOH221 4.7 12.3 1.0
CA A:GLY33 4.7 20.5 1.0
CA A:LEU31 4.8 18.7 1.0
O A:HOH169 4.8 39.5 1.0
O A:HOH161 4.9 39.9 1.0
O A:CYS45 4.9 11.8 1.0

Calcium binding site 2 out of 3 in 2phi

Go back to Calcium Binding Sites List in 2phi
Calcium binding site 2 out of 3 in the A Large Conformational Change Is Found in the Crystal Structure of the Porcine Pancreatic Phospholipase A2 Point Mutant F63V


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A Large Conformational Change Is Found in the Crystal Structure of the Porcine Pancreatic Phospholipase A2 Point Mutant F63V within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca125

b:22.9
occ:1.00
 OE2 B:GLU92 2.4 17.6 1.0
OE2 B:GLU71 2.4 25.0 1.0
OE2 A:GLU92 2.4 27.3 1.0
O B:SER72 2.4 14.3 1.0
O A:SER72 2.4 16.9 1.0
OE2 A:GLU71 2.6 24.5 1.0
CD B:GLU71 3.3 34.4 1.0
CD A:GLU92 3.4 21.8 1.0
CD B:GLU92 3.5 16.2 1.0
C A:SER72 3.5 16.7 1.0
C B:SER72 3.5 15.0 1.0
CD A:GLU71 3.7 17.6 1.0
CG A:GLU92 3.9 16.0 1.0
OE1 B:GLU71 4.0 24.4 1.0
OG A:SER72 4.0 47.9 1.0
N A:SER72 4.1 18.5 1.0
CG B:GLU92 4.1 12.0 1.0
N B:SER72 4.1 17.8 1.0
OG B:SER72 4.1 51.8 1.0
CA A:SER72 4.2 17.5 1.0
CG B:GLU71 4.3 47.2 1.0
CA B:SER72 4.3 16.3 1.0
CG A:GLU71 4.4 17.1 1.0
OE1 B:GLU92 4.5 18.2 1.0
N A:TYR73 4.5 15.7 1.0
OE1 A:GLU92 4.6 27.5 1.0
N B:TYR73 4.6 14.1 1.0
OE1 A:GLU71 4.6 25.1 1.0
CA A:TYR73 4.6 15.3 1.0
CA B:TYR73 4.8 12.9 1.0
CB B:SER72 4.8 15.8 1.0
CB A:SER72 4.8 17.3 1.0
C A:GLU71 4.9 20.0 1.0
C B:GLU71 4.9 19.5 1.0

Calcium binding site 3 out of 3 in 2phi

Go back to Calcium Binding Sites List in 2phi
Calcium binding site 3 out of 3 in the A Large Conformational Change Is Found in the Crystal Structure of the Porcine Pancreatic Phospholipase A2 Point Mutant F63V


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A Large Conformational Change Is Found in the Crystal Structure of the Porcine Pancreatic Phospholipase A2 Point Mutant F63V within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca126

b:12.8
occ:1.00
 O B:GLY32 2.3 17.9 1.0
O B:TYR28 2.3 7.8 1.0
O B:HOH128 2.4 16.1 1.0
O B:HOH127 2.4 6.7 1.0
O B:GLY30 2.4 13.6 1.0
OD2 B:ASP49 2.5 17.4 1.0
OD1 B:ASP49 2.6 17.5 1.0
CG B:ASP49 2.9 6.2 1.0
C B:GLY32 3.4 17.9 1.0
C B:TYR28 3.5 8.5 1.0
C B:GLY30 3.6 14.0 1.0
N B:GLY30 3.9 11.7 1.0
O B:HOH140 4.1 19.4 1.0
C B:LEU31 4.2 17.2 1.0
CA B:TYR28 4.2 9.5 1.0
N B:GLY32 4.2 17.2 1.0
CA B:GLY32 4.2 17.5 1.0
O B:LEU31 4.3 17.6 1.0
CB B:ASP49 4.4 8.9 1.0
CA B:GLY30 4.4 12.3 1.0
N B:GLY33 4.4 17.3 1.0
N B:CYS29 4.5 8.7 1.0
N B:LEU31 4.6 15.7 1.0
CA B:CYS29 4.6 10.4 1.0
C B:CYS29 4.7 11.2 1.0
CB B:TYR28 4.7 10.1 1.0
CA B:GLY33 4.7 16.5 1.0
CA B:LEU31 4.8 17.0 1.0
O B:HOH129 4.9 14.7 1.0
O B:HOH163 5.0 44.8 1.0

Reference:

M.M.Thunnissen, P.A.Franken, G.H.De Haas, J.Drenth, K.H.Kalk, H.M.Verheij, B.W.Dijkstra. Crystal Structure of A Porcine Pancreatic Phospholipase A2 Mutant. A Large Conformational Change Caused By the F63V Point Mutation. J.Mol.Biol. V. 232 839 1993.
ISSN: ISSN 0022-2836
PubMed: 8355274
DOI: 10.1006/JMBI.1993.1435
Page generated: Fri Jul 12 15:09:43 2024

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