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Calcium in PDB 3fvi: Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates

Enzymatic activity of Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates

All present enzymatic activity of Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates:
3.1.1.4;

Protein crystallography data

The structure of Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates, PDB code: 3fvi was solved by Y.H.Pan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.54 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.988, 82.061, 123.824, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 27.5

Other elements in 3fvi:

The structure of Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates (pdb code 3fvi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates, PDB code: 3fvi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3fvi

Go back to Calcium Binding Sites List in 3fvi
Calcium binding site 1 out of 4 in the Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates


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 Complex of Phospholipase A2 with Octyl Sulfates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca125

b:33.1
occ:1.00
 OD2 A:ASP49 2.1 18.0 1.0
O A:GLY30 2.2 19.8 1.0
O A:TYR28 2.3 17.6 1.0
O A:GLY32 2.6 19.9 1.0
CG A:ASP49 2.9 15.9 1.0
OD1 A:ASP49 3.0 17.7 1.0
CL A:CL126 3.3 29.1 1.0
C A:GLY30 3.3 20.1 1.0
C A:TYR28 3.5 18.1 1.0
N A:GLY30 3.5 18.1 1.0
C A:GLY32 3.6 19.5 1.0
N A:GLY32 3.7 20.6 1.0
CA A:GLY32 4.0 19.9 1.0
CA A:GLY30 4.1 18.9 1.0
C A:LEU31 4.2 21.0 1.0
CA A:TYR28 4.3 18.8 1.0
CB A:ASP49 4.4 14.2 1.0
N A:LEU31 4.4 20.8 1.0
N A:CYS29 4.5 17.8 1.0
C A:CYS29 4.5 16.7 1.0
CA A:CYS29 4.5 16.4 1.0
O A:HOH147 4.5 21.0 1.0
CA A:LEU31 4.6 21.4 1.0
CB A:TYR28 4.7 20.0 1.0
N A:GLY33 4.8 18.0 1.0
O A:CYS45 4.9 15.6 1.0
O A:LEU31 4.9 21.5 1.0

Calcium binding site 2 out of 4 in 3fvi

Go back to Calcium Binding Sites List in 3fvi
Calcium binding site 2 out of 4 in the Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates


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 Complex of Phospholipase A2 with Octyl Sulfates within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca125

b:20.5
occ:1.00
 O B:GLY32 2.2 21.3 1.0
O B:GLY30 2.3 22.4 1.0
O B:TYR28 2.3 17.1 1.0
OD1 B:ASP49 2.6 15.4 1.0
OD2 B:ASP49 2.8 15.6 1.0
CG B:ASP49 3.0 16.0 1.0
O2 B:OSF127 3.2 29.0 1.0
O4 B:OSF127 3.2 30.0 1.0
C B:GLY32 3.4 22.0 1.0
C B:GLY30 3.5 22.4 1.0
C B:TYR28 3.5 18.0 1.0
N B:GLY30 3.7 20.0 1.0
N B:GLY32 3.8 22.9 1.0
S B:OSF127 3.8 25.8 1.0
CA B:GLY32 4.1 22.1 1.0
CA B:GLY30 4.2 21.4 1.0
CA B:TYR28 4.2 18.5 1.0
C B:LEU31 4.3 23.7 1.0
N B:GLY33 4.5 22.1 1.0
N B:LEU31 4.5 22.9 1.0
C B:CYS29 4.5 19.3 1.0
N B:CYS29 4.5 17.3 1.0
CB B:ASP49 4.5 16.0 1.0
CB B:TYR28 4.5 18.0 1.0
CA B:CYS29 4.6 18.0 1.0
CA B:LEU31 4.7 24.0 1.0
CA B:GLY33 4.7 22.4 1.0
O1 B:OSF127 4.8 26.6 1.0
O B:CYS45 4.8 15.1 1.0
OH B:TYR69 4.8 25.4 1.0
O B:LEU31 4.9 24.4 1.0

Calcium binding site 3 out of 4 in 3fvi

Go back to Calcium Binding Sites List in 3fvi
Calcium binding site 3 out of 4 in the Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates


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 Complex of Phospholipase A2 with Octyl Sulfates within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca125

b:19.0
occ:1.00
 O C:TYR28 2.3 17.9 1.0
O C:GLY30 2.3 17.5 1.0
OD2 C:ASP49 2.3 19.7 1.0
O C:GLY32 2.5 12.7 1.0
OD1 C:ASP49 2.7 20.9 1.0
CG C:ASP49 2.9 18.4 1.0
O4 C:OSF128 3.1 28.9 1.0
C C:TYR28 3.4 18.4 1.0
C C:GLY30 3.4 16.9 1.0
O2 C:OSF128 3.6 27.1 1.0
N C:GLY30 3.6 17.7 1.0
C C:GLY32 3.6 12.9 1.0
S C:OSF128 4.0 25.6 1.0
CA C:TYR28 4.1 17.3 1.0
CA C:GLY30 4.1 17.5 1.0
C C:LEU31 4.2 15.3 1.0
N C:GLY32 4.2 14.9 1.0
O C:LEU31 4.4 17.3 1.0
CB C:ASP49 4.4 16.1 1.0
N C:CYS29 4.5 19.5 1.0
CA C:GLY32 4.5 13.0 1.0
N C:LEU31 4.5 17.2 1.0
N C:GLY33 4.5 12.7 1.0
C C:CYS29 4.5 18.4 1.0
CA C:GLY33 4.6 12.9 1.0
CA C:CYS29 4.7 19.0 1.0
CB C:TYR28 4.7 18.2 1.0
CA C:LEU31 4.7 15.2 1.0
O3 C:OSF128 4.8 27.7 1.0
O C:HOH130 4.9 13.8 1.0
O C:CYS45 5.0 17.4 1.0

Calcium binding site 4 out of 4 in 3fvi

Go back to Calcium Binding Sites List in 3fvi
Calcium binding site 4 out of 4 in the Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Complex of Phospholipase A2 with Octyl Sulfates within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca125

b:18.6
occ:1.00
 O D:TYR28 2.3 26.6 1.0
OD2 D:ASP49 2.4 13.9 1.0
O D:GLY32 2.4 22.9 1.0
O D:GLY30 2.5 26.4 1.0
OD1 D:ASP49 2.7 17.1 1.0
CG D:ASP49 2.9 15.2 1.0
O2 D:OSF129 3.0 49.2 1.0
O4 D:OSF129 3.3 49.3 1.0
C D:TYR28 3.5 25.5 1.0
C D:GLY30 3.7 26.4 1.0
C D:GLY32 3.7 23.1 1.0
S D:OSF129 3.8 48.2 1.0
N D:GLY30 3.8 27.9 1.0
CA D:TYR28 4.2 24.5 1.0
CA D:GLY30 4.4 27.3 1.0
N D:GLY32 4.4 24.4 1.0
C D:LEU31 4.4 25.2 1.0
CB D:ASP49 4.4 15.3 1.0
C D:CYS29 4.5 27.7 1.0
N D:CYS29 4.5 25.8 1.0
CA D:GLY33 4.5 23.0 1.0
N D:GLY33 4.5 22.7 1.0
O D:LEU31 4.5 26.2 1.0
CA D:CYS29 4.6 26.7 1.0
CA D:GLY32 4.6 23.2 1.0
N D:LEU31 4.7 25.6 1.0
CB D:TYR28 4.7 22.8 1.0
O3 D:OSF129 4.7 48.0 1.0
CA D:LEU31 4.8 25.4 1.0

Reference:

Y.H.Pan, B.J.Bahnson. Structure of A Premicellar Complex of Alkyl Sulfates with the Interfacial Binding Surfaces of Four Subunits of Phospholipase A2. Biochim.Biophys.Acta V.1804 1443 2010.
ISSN: ISSN 0006-3002
PubMed: 20302975
DOI: 10.1016/J.BBAPAP.2010.03.004
Page generated: Sat Jul 13 10:17:32 2024

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