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Calcium in PDB 1dji: Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium

Enzymatic activity of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium

All present enzymatic activity of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium:
3.1.4.11;

Protein crystallography data

The structure of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium, PDB code: 1dji was solved by L.-O.Essen, O.Perisic, R.L.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.50
Space group F 41 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 398.030, 398.030, 398.030, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 28

Calcium Binding Sites:

The binding sites of Calcium atom in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium (pdb code 1dji). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium, PDB code: 1dji:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1dji

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Calcium binding site 1 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:53.1
occ:0.50
 OD1 A:ASN312 2.5 19.9 1.0
O A:HOH1052 2.8 64.2 1.0
OD1 A:ASP343 3.0 47.5 1.0
OE1 A:GLU341 3.1 29.2 1.0
OD2 A:ASP343 3.4 54.3 1.0
O A:HOH1055 3.5 57.2 1.0
CG A:ASP343 3.6 48.3 1.0
CG A:ASN312 3.7 28.7 1.0
CD A:GLU341 3.9 41.5 1.0
OE1 A:GLU390 4.0 92.0 1.0
O A:HOH1053 4.1 43.6 1.0
NH2 A:ARG549 4.3 32.7 1.0
CB A:GLU341 4.3 20.6 1.0
CD A:GLU390 4.4 76.1 1.0
O A:HOH1054 4.4 38.4 1.0
ND2 A:ASN312 4.4 16.7 1.0
CG A:GLU341 4.4 23.9 1.0
OE2 A:GLU390 4.6 94.1 1.0
N A:ASN312 4.7 19.5 1.0
CA A:ASN312 4.7 17.9 1.0
OE2 A:GLU341 4.8 22.0 1.0
CD2 A:HIS311 4.8 23.1 1.0
CB A:ASN312 4.8 21.6 1.0
NE2 A:HIS311 4.8 21.6 1.0

Calcium binding site 2 out of 6 in 1dji

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Calcium binding site 2 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:55.9
occ:0.60
 O A:HOH778 1.2 71.1 1.0
OD1 A:ASN677 2.0 80.5 1.0
O A:ILE651 2.4 55.0 1.0
OD1 A:ASP653 2.6 48.9 1.0
OD2 A:ASP653 2.7 59.5 1.0
O A:HOH777 2.8 59.2 1.0
CG A:ASP653 3.1 49.2 1.0
CG A:ASN677 3.3 83.2 1.0
C A:ILE651 3.6 55.2 1.0
N A:ILE651 4.0 59.4 1.0
ND2 A:ASN677 4.1 79.8 1.0
CA A:ASN677 4.2 39.3 1.0
N A:ASN677 4.2 37.8 1.0
CA A:ILE651 4.2 56.0 1.0
CB A:ASN677 4.3 46.1 1.0
OG A:SER650 4.4 0.5 1.0
CB A:ILE651 4.4 58.6 1.0
C A:VAL652 4.6 47.1 1.0
CB A:ASP653 4.6 36.5 1.0
O A:VAL652 4.6 47.9 1.0
N A:VAL652 4.6 48.0 1.0
N A:ASP653 4.8 37.1 1.0
CA A:VAL652 4.9 47.5 1.0

Calcium binding site 3 out of 6 in 1dji

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Calcium binding site 3 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:67.1
occ:0.60
 O A:TYR707 2.1 47.6 1.0
OD1 A:ASP706 2.8 41.5 1.0
OD2 A:ASP653 3.0 59.5 1.0
C A:TYR707 3.2 52.5 1.0
CG A:ASP706 3.5 42.0 1.0
O A:HOH779 3.6 47.5 1.0
OD2 A:ASP708 3.7 0.1 1.0
OD2 A:ASP706 3.8 49.3 1.0
CA A:ASP708 3.9 63.2 1.0
N A:ASP708 3.9 58.5 1.0
CG A:ASP653 4.0 49.2 1.0
CB A:ASP708 4.0 66.7 1.0
CG A:ASP708 4.1 95.9 1.0
CB A:ASP653 4.2 36.5 1.0
C A:ASP706 4.2 38.1 1.0
N A:TYR707 4.2 42.5 1.0
O A:ASP706 4.2 36.9 1.0
CA A:TYR707 4.2 45.6 1.0
O A:HOH778 4.3 71.1 1.0
CB A:ASP706 4.6 32.1 1.0
N A:ASP653 4.7 37.1 1.0
CA A:ASP706 4.9 30.8 1.0
OD1 A:ASP708 4.9 94.4 1.0

Calcium binding site 4 out of 6 in 1dji

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Calcium binding site 4 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:54.1
occ:0.80
 OD2 B:ASP343 2.5 54.2 1.0
O B:HOH1052 2.5 64.7 1.0
OD1 B:ASN312 2.8 21.8 1.0
OD1 B:ASP343 3.0 46.4 1.0
CG B:ASP343 3.1 47.6 1.0
OE1 B:GLU390 3.2 91.9 1.0
CD B:GLU390 3.6 75.9 1.0
CG B:ASN312 3.8 29.2 1.0
OE2 B:GLU390 3.8 93.6 1.0
O B:HOH988 4.0 44.7 1.0
ND2 B:ASN312 4.1 17.8 1.0
O B:HOH989 4.3 36.8 1.0
O B:HOH1053 4.3 56.4 1.0
O B:HOH1051 4.4 49.0 1.0
OH B:TYR314 4.5 23.3 1.0
CB B:ASP343 4.5 29.8 1.0
OE1 B:GLU341 4.6 29.1 1.0
O B:HOH986 4.6 55.1 1.0
CG B:GLU390 4.7 44.9 1.0
CB B:GLU390 4.9 37.2 1.0

Calcium binding site 5 out of 6 in 1dji

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Calcium binding site 5 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:69.1
occ:0.80
 OD1 B:ASP653 2.6 53.2 1.0
OD1 B:ASN677 2.6 81.0 1.0
O B:ILE651 2.7 52.9 1.0
O B:HOH1106 2.7 46.3 1.0
CG B:ASP653 3.3 45.0 1.0
O B:HOH1105 3.3 76.3 1.0
OD2 B:ASP653 3.4 53.7 1.0
CG B:ASN677 3.8 83.5 1.0
C B:ILE651 3.9 54.2 1.0
CA B:CA3 4.4 57.1 0.6
ND2 B:ASN677 4.6 79.8 1.0
CA B:ILE651 4.6 66.5 1.0
CB B:ASP653 4.7 27.0 1.0
C B:VAL652 4.7 30.2 1.0
CB B:ILE651 4.7 69.4 1.0
O B:VAL652 4.7 26.9 1.0
CA B:ASN677 4.7 38.9 1.0
O B:SER650 4.7 94.5 1.0
N B:ASN677 4.8 37.7 1.0
N B:ILE651 4.8 74.6 1.0
C B:SER650 4.8 87.6 1.0
CB B:ASN677 4.9 46.0 1.0
N B:VAL652 4.9 41.4 1.0
N B:ASP653 4.9 24.9 1.0
OG B:SER650 4.9 91.1 1.0

Calcium binding site 6 out of 6 in 1dji

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Calcium binding site 6 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Calcium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:57.1
occ:0.60
 O B:TYR707 2.1 38.5 1.0
O B:HOH1105 2.6 76.3 1.0
OD1 B:ASP706 2.7 41.0 1.0
OD1 B:ASP708 2.9 81.1 1.0
C B:TYR707 3.2 42.4 1.0
CG B:ASP706 3.4 41.5 1.0
OD2 B:ASP706 3.6 48.7 1.0
CG B:ASP653 3.8 45.0 1.0
CG B:ASP708 3.8 75.9 1.0
CB B:ASP653 3.8 27.0 1.0
N B:ASP708 4.0 47.1 1.0
CA B:ASP708 4.1 50.4 1.0
OD1 B:ASP653 4.1 53.2 1.0
OD2 B:ASP653 4.1 53.7 1.0
N B:TYR707 4.1 33.9 1.0
CA B:TYR707 4.2 34.1 1.0
C B:ASP706 4.4 37.0 1.0
N B:ASP653 4.4 24.9 1.0
CA B:CA2 4.4 69.1 0.8
OD2 B:ASP708 4.5 72.2 1.0
CB B:ASP708 4.5 53.0 1.0
CB B:ASP706 4.6 32.3 1.0
O B:ASP706 4.6 36.7 1.0
CA B:ASP653 4.7 25.1 1.0
CA B:ASP706 5.0 30.7 1.0
O B:ILE651 5.0 52.9 1.0

Reference:

L.O.Essen, O.Perisic, D.E.Lynch, M.Katan, R.L.Williams. A Ternary Metal Binding Site in the C2 Domain of Phosphoinositide-Specific Phospholipase C-DELTA1. Biochemistry V. 36 2753 1997.
ISSN: ISSN 0006-2960
PubMed: 9062102
DOI: 10.1021/BI962466T
Page generated: Mon Jul 7 14:25:44 2025

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