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Calcium in PDB 2rd4: Design of Specific Inhibitors of Phospholipase A2: Crystal Structure of the Complex of Phospholipase A2 with Pentapeptide Leu-Val-Phe-Phe- Ala at 2.9 A Resolution

Enzymatic activity of Design of Specific Inhibitors of Phospholipase A2: Crystal Structure of the Complex of Phospholipase A2 with Pentapeptide Leu-Val-Phe-Phe- Ala at 2.9 A Resolution

All present enzymatic activity of Design of Specific Inhibitors of Phospholipase A2: Crystal Structure of the Complex of Phospholipase A2 with Pentapeptide Leu-Val-Phe-Phe- Ala at 2.9 A Resolution:
3.1.1.4;

Protein crystallography data

The structure of Design of Specific Inhibitors of Phospholipase A2: Crystal Structure of the Complex of Phospholipase A2 with Pentapeptide Leu-Val-Phe-Phe- Ala at 2.9 A Resolution, PDB code: 2rd4 was solved by Z.Mirza, A.Kaur, N.Singh, M.Sinha, S.Sharma, A.Srinivasan, P.Kaur, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.97
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 65.540, 65.540, 58.551, 90.00, 90.00, 90.00
R / Rfree (%) 25.1 / 27.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Design of Specific Inhibitors of Phospholipase A2: Crystal Structure of the Complex of Phospholipase A2 with Pentapeptide Leu-Val-Phe-Phe- Ala at 2.9 A Resolution (pdb code 2rd4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Design of Specific Inhibitors of Phospholipase A2: Crystal Structure of the Complex of Phospholipase A2 with Pentapeptide Leu-Val-Phe-Phe- Ala at 2.9 A Resolution, PDB code: 2rd4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2rd4

Go back to Calcium Binding Sites List in 2rd4
Calcium binding site 1 out of 2 in the Design of Specific Inhibitors of Phospholipase A2: Crystal Structure of the Complex of Phospholipase A2 with Pentapeptide Leu-Val-Phe-Phe- Ala at 2.9 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Design of Specific Inhibitors of Phospholipase A2: Crystal Structure of the Complex of Phospholipase A2 with Pentapeptide Leu-Val-Phe-Phe- Ala at 2.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:24.5
occ:1.00
 OD2 B:ASP24 2.5 29.0 1.0
O B:HOH430 2.6 44.5 1.0
OD1 A:ASP24 2.6 22.4 1.0
OD2 A:ASP24 2.8 23.2 1.0
O A:HOH405 2.8 63.4 1.0
OD1 A:ASN112 2.9 31.5 1.0
ND2 B:ASN112 2.9 27.2 1.0
OD1 B:ASN112 3.1 29.3 1.0
CG A:ASP24 3.1 21.6 1.0
CG B:ASN112 3.2 26.6 1.0
CA A:ASN112 3.6 23.4 1.0
CG B:ASP24 3.7 27.4 1.0
CG A:ASN112 3.8 28.8 1.0
C A:ASN112 4.0 22.4 1.0
O A:ILE113 4.1 17.0 1.0
CB A:ASN112 4.1 25.7 1.0
OD1 B:ASP24 4.3 30.2 1.0
CB B:ASN112 4.5 26.5 1.0
O A:ASN112 4.5 23.6 1.0
N A:ILE113 4.5 20.7 1.0
CB A:ASP24 4.6 20.2 1.0
CA B:ASN112 4.6 28.1 1.0
O A:ASP24 4.7 18.5 1.0
CB B:ASP24 4.7 22.9 1.0
N A:ASN112 4.8 24.4 1.0
ND2 A:ASN112 5.0 31.4 1.0
O B:ILE113 5.0 30.0 1.0

Calcium binding site 2 out of 2 in 2rd4

Go back to Calcium Binding Sites List in 2rd4
Calcium binding site 2 out of 2 in the Design of Specific Inhibitors of Phospholipase A2: Crystal Structure of the Complex of Phospholipase A2 with Pentapeptide Leu-Val-Phe-Phe- Ala at 2.9 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Design of Specific Inhibitors of Phospholipase A2: Crystal Structure of the Complex of Phospholipase A2 with Pentapeptide Leu-Val-Phe-Phe- Ala at 2.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:53.2
occ:1.00
 O B:GLY30 2.5 34.5 1.0
O B:GLY32 2.5 34.1 1.0
OD1 B:ASP49 2.7 26.2 1.0
OD2 B:ASP49 2.8 25.4 1.0
O B:TYR28 2.9 28.4 1.0
CG B:ASP49 3.0 25.1 1.0
O B:ARG31 3.5 34.6 1.0
C B:GLY30 3.5 33.0 1.0
C B:ARG31 3.5 34.7 1.0
C B:GLY32 3.6 33.8 1.0
N B:GLY32 3.9 34.3 1.0
CA B:ARG31 4.0 35.6 1.0
C B:TYR28 4.0 27.1 1.0
CB C:ALA6 4.2 77.1 1.0
N B:ARG31 4.2 35.2 1.0
N B:GLY30 4.2 27.5 1.0
CA B:GLY32 4.3 34.4 1.0
CB B:ASP49 4.4 24.2 1.0
CA B:GLY30 4.6 30.2 1.0
CA C:ALA6 4.6 77.3 1.0
O B:HOH410 4.7 39.7 1.0
CA B:TYR28 4.7 26.8 1.0
O C:ALA6 4.7 78.7 1.0
N B:GLY33 4.7 33.6 1.0
C C:ALA6 4.8 77.7 1.0
N C:ALA6 4.8 77.3 1.0
C B:CYS29 4.9 25.1 1.0
CA B:GLY33 4.9 34.3 1.0
O B:CYS45 5.0 20.8 1.0

Reference:

Z.Mirza, A.Kaur, N.Singh, M.Sinha, S.Sharma, A.Srinivasan, P.Kaur, T.P.Singh. Design of Specific Inhibitors of Phospholipase A2: Crystal Structure of the Complex of Phospholipase A2 with Pentapeptide Leu-Val-Phe-Phe-Ala at 2.9 A Resolution To Be Published.
Page generated: Tue Jul 8 08:11:31 2025

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