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Calcium in PDB 1vl9: Atomic Resolution (0.97A) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A2

Enzymatic activity of Atomic Resolution (0.97A) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A2

All present enzymatic activity of Atomic Resolution (0.97A) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A2:
3.1.1.4;

Protein crystallography data

The structure of Atomic Resolution (0.97A) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A2, PDB code: 1vl9 was solved by K.Sekar, D.Velmurugan, V.Rajakannan, D.Gayathri, M.-J.Poi, M.-D.Tsai, M.Dauter, Z.Dauter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 0.97
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 36.934, 23.863, 65.931, 90.00, 101.47, 90.00
R / Rfree (%) 11.4 / 13.4

Other elements in 1vl9:

The structure of Atomic Resolution (0.97A) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A2 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Atomic Resolution (0.97A) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A2 (pdb code 1vl9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Atomic Resolution (0.97A) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A2, PDB code: 1vl9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1vl9

Go back to Calcium Binding Sites List in 1vl9
Calcium binding site 1 out of 2 in the Atomic Resolution (0.97A) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Atomic Resolution (0.97A) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca124

b:7.9
occ:1.00
 O A:GLY30 2.3 9.2 1.0
O A:TYR28 2.3 7.5 1.0
O A:GLY32 2.3 9.2 1.0
O A:HOH204 2.4 9.7 1.0
O A:HOH206 2.4 8.5 1.0
OD2 A:ASP49 2.4 8.4 1.0
OD1 A:ASP49 2.5 8.0 1.0
CG A:ASP49 2.8 7.8 1.0
C A:TYR28 3.5 7.2 1.0
C A:GLY30 3.5 8.9 1.0
C A:GLY32 3.5 9.8 1.0
N A:GLY32 3.8 10.6 1.0
N A:GLY30 3.8 8.0 1.0
O A:HOH430 4.2 8.0 0.7
CA A:TYR28 4.2 7.5 1.0
CA A:GLY32 4.2 12.3 1.0
CB A:ASP49 4.3 8.3 1.0
O A:HOH220 4.3 14.4 1.0
C A:LEU31 4.3 11.2 1.0
CA A:GLY30 4.3 9.1 1.0
C5 A:MPD1602 4.4 17.6 0.5
N A:LEU31 4.4 10.8 1.0
O A:HOH205 4.5 9.8 1.0
CA A:LEU31 4.5 11.1 1.0
N A:CYS29 4.5 7.2 1.0
N A:GLY33 4.5 11.7 1.0
C A:CYS29 4.6 7.9 1.0
CA A:CYS29 4.6 7.3 1.0
O A:HOH243 4.6 19.0 1.0
CB A:TYR28 4.6 7.6 1.0
O4 A:MRD1604 4.6 20.1 0.8
C5 A:MPD1601 4.7 19.0 0.5
O A:HOH430 4.7 10.8 0.3
CA A:GLY33 4.8 13.2 1.0
O A:CYS45 4.8 7.9 1.0
O2 A:MPD1601 4.9 27.6 0.5

Calcium binding site 2 out of 2 in 1vl9

Go back to Calcium Binding Sites List in 1vl9
Calcium binding site 2 out of 2 in the Atomic Resolution (0.97A) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Atomic Resolution (0.97A) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca125

b:8.5
occ:1.00
 OD1 A:ASN71 2.3 9.6 1.0
O A:HOH431 2.3 11.4 0.7
OE2 A:GLU92 2.3 9.1 1.0
O A:HOH212 2.4 12.1 1.0
O A:ASN72 2.4 9.3 1.0
O A:HOH431 2.4 10.2 0.3
O A:HOH207 2.5 9.0 1.0
CD A:GLU92 3.4 8.2 1.0
C A:ASN72 3.5 7.7 1.0
CG A:ASN71 3.5 8.2 1.0
N A:ASN72 3.6 7.5 1.0
CG A:GLU92 3.7 8.4 1.0
CA A:ASN72 4.0 8.0 1.0
C A:ASN71 4.1 7.9 1.0
O A:HOH211 4.2 12.2 1.0
O A:HOH253 4.2 23.5 1.0
ND2 A:ASN71 4.3 8.8 1.0
CA A:ASN71 4.4 8.0 1.0
O A:HOH240 4.4 22.3 1.0
O A:HOH297 4.4 37.6 1.0
O A:HOH263 4.4 19.5 1.0
CB A:ASN72 4.5 8.4 1.0
OE1 A:GLU92 4.5 9.2 1.0
CB A:ASN71 4.5 9.1 1.0
O A:HOH218 4.6 14.2 1.0
N A:TYR73 4.6 8.7 1.0
O A:ASN71 4.8 9.1 1.0

Reference:

K.Sekar, V.Rajakannan, D.Gayathri, D.Velmurugan, M.J.Poi, M.Dauter, Z.Dauter, M.D.Tsai. Atomic Resolution (0.97 A) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A2. Acta Crystallogr.,Sect.F V. 61 3 2005.
ISSN: ESSN 1744-3091
PubMed: 16508077
DOI: 10.1107/S1744309104021748
Page generated: Fri Jul 12 06:55:33 2024

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