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Calcium in PDB 1djx: Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-1,4,5-Trisphosphate

Enzymatic activity of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-1,4,5-Trisphosphate

All present enzymatic activity of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-1,4,5-Trisphosphate:
3.1.4.11;

Protein crystallography data

The structure of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-1,4,5-Trisphosphate, PDB code: 1djx 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 / 2.30
Space group F 41 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 397.540, 397.540, 397.540, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 27

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 1djx

Go back to Calcium Binding Sites List in 1djx
Calcium binding site 1 out of 4 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-1,4,5-Trisphosphate


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 Inositol-1,4,5-Trisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:46.7
occ:1.00
 OE1 A:GLU390 2.3 53.8 1.0
OD1 A:ASN312 2.4 27.3 1.0
O2 A:I3P1 2.4 52.4 1.0
OD2 A:ASP343 2.4 30.2 1.0
OE2 A:GLU341 2.5 29.3 1.0
OD1 A:ASP343 2.5 29.5 1.0
CG A:ASP343 2.8 29.1 1.0
O A:HOH1070 3.1 53.4 1.0
CD A:GLU341 3.2 45.0 1.0
CD A:GLU390 3.3 44.6 1.0
CG A:ASN312 3.4 30.9 1.0
O11 A:I3P1 3.7 0.1 1.0
C2 A:I3P1 3.7 39.0 1.0
ND2 A:ASN312 3.8 20.7 1.0
OE2 A:GLU390 3.9 44.9 1.0
CG A:GLU341 3.9 34.0 1.0
OE1 A:GLU341 4.0 34.3 1.0
O3 A:I3P1 4.2 42.5 1.0
OH A:TYR314 4.2 25.2 1.0
O A:HOH1034 4.2 43.4 1.0
CB A:ASP343 4.3 24.5 1.0
C3 A:I3P1 4.3 43.2 1.0
CB A:GLU390 4.3 31.8 1.0
CG A:GLU390 4.4 38.1 1.0
C4 A:I3P1 4.5 33.0 1.0
C1 A:I3P1 4.6 49.9 1.0
O1 A:I3P1 4.6 47.1 1.0
CB A:ASN312 4.7 18.2 1.0
C6 A:I3P1 4.7 35.5 1.0
O A:HOH1067 4.8 26.2 1.0
P1 A:I3P1 4.8 50.7 1.0
CA A:ASN312 4.9 21.6 1.0
CE1 A:TYR314 4.9 17.7 1.0

Calcium binding site 2 out of 4 in 1djx

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Calcium binding site 2 out of 4 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-1,4,5-Trisphosphate


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 Inositol-1,4,5-Trisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:79.1
occ:1.00
 O A:ILE651 2.1 62.1 1.0
O A:HOH1002 2.7 87.5 1.0
OD1 A:ASN677 2.7 73.6 1.0
OD1 A:ASP653 2.8 55.7 1.0
OD2 A:ASP653 2.8 69.8 1.0
O A:HOH1003 2.9 73.4 1.0
CG A:ASP653 3.1 56.5 1.0
C A:ILE651 3.3 61.7 1.0
OG A:SER650 3.4 0.5 1.0
N A:ILE651 3.7 65.5 1.0
CG A:ASN677 3.9 84.6 1.0
O A:HOH1001 3.9 53.0 1.0
CA A:ILE651 4.0 64.0 1.0
C A:VAL652 4.2 46.6 1.0
N A:VAL652 4.3 52.9 1.0
O A:VAL652 4.3 46.7 1.0
CB A:ASP653 4.5 40.1 1.0
N A:ASP653 4.5 38.0 1.0
CA A:VAL652 4.5 50.3 1.0
CB A:ILE651 4.5 69.0 1.0
N A:ASN677 4.6 40.5 1.0
CA A:ASN677 4.6 42.5 1.0
CB A:SER650 4.7 89.4 1.0
ND2 A:ASN677 4.7 85.5 1.0
C A:SER650 4.7 75.9 1.0
CB A:ASN677 4.9 55.4 1.0
CA A:ASP653 5.0 37.2 1.0

Calcium binding site 3 out of 4 in 1djx

Go back to Calcium Binding Sites List in 1djx
Calcium binding site 3 out of 4 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-1,4,5-Trisphosphate


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 Inositol-1,4,5-Trisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:43.2
occ:1.00
 O2 B:I3P1 2.1 35.4 1.0
OE1 B:GLU390 2.3 53.2 1.0
OD2 B:ASP343 2.3 30.2 1.0
OD1 B:ASP343 2.4 28.9 1.0
OD1 B:ASN312 2.5 28.1 1.0
OE2 B:GLU341 2.6 28.6 1.0
O B:HOH1176 2.7 47.9 1.0
CG B:ASP343 2.7 28.7 1.0
CD B:GLU390 3.3 44.0 1.0
CD B:GLU341 3.3 44.2 1.0
CG B:ASN312 3.5 32.1 1.0
O11 B:I3P1 3.5 60.8 1.0
C2 B:I3P1 3.5 36.0 1.0
CG B:GLU341 3.9 33.3 1.0
OE2 B:GLU390 3.9 44.6 1.0
ND2 B:ASN312 3.9 20.8 1.0
O3 B:I3P1 4.0 31.0 1.0
OE1 B:GLU341 4.2 34.0 1.0
C3 B:I3P1 4.2 26.8 1.0
CB B:ASP343 4.2 24.3 1.0
OH B:TYR314 4.2 23.8 1.0
CB B:GLU390 4.2 32.5 1.0
CG B:GLU390 4.3 38.1 1.0
C4 B:I3P1 4.4 29.2 1.0
C1 B:I3P1 4.4 35.9 1.0
O1 B:I3P1 4.5 42.1 1.0
C6 B:I3P1 4.5 73.4 1.0
O B:HOH971 4.6 26.5 1.0
P1 B:I3P1 4.7 44.2 1.0
O B:HOH1031 4.8 39.6 1.0
CB B:ASN312 4.8 18.3 1.0
CE1 B:TYR314 4.9 17.4 1.0

Calcium binding site 4 out of 4 in 1djx

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Calcium binding site 4 out of 4 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-1,4,5-Trisphosphate


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 Inositol-1,4,5-Trisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:72.0
occ:1.00
 OD1 B:ASP653 2.2 50.1 1.0
O B:ILE651 2.3 47.0 1.0
O B:HOH793 2.4 66.1 1.0
O B:HOH791 2.8 62.9 1.0
OD1 B:ASN677 2.8 73.9 1.0
O B:HOH794 2.8 57.7 1.0
CG B:ASP653 3.1 53.7 1.0
OD2 B:ASP653 3.3 75.0 1.0
C B:ILE651 3.5 49.0 1.0
CG B:ASN677 3.9 84.8 1.0
O B:HOH792 4.1 50.8 1.0
O B:HOH795 4.3 86.6 1.0
C B:VAL652 4.3 36.0 1.0
N B:ILE651 4.4 61.4 1.0
N B:ASP653 4.4 28.6 1.0
CB B:ASP653 4.4 34.9 1.0
N B:VAL652 4.5 40.1 1.0
CA B:ILE651 4.5 55.9 1.0
O B:VAL652 4.5 39.6 1.0
CA B:ASN677 4.5 42.0 1.0
N B:ASN677 4.5 40.4 1.0
CA B:VAL652 4.6 36.9 1.0
ND2 B:ASN677 4.8 85.2 1.0
CB B:ILE651 4.8 58.8 1.0
CB B:ASN677 4.9 55.5 1.0
CA B:ASP653 4.9 30.7 1.0
OG B:SER650 5.0 89.4 1.0

Reference:

L.O.Essen, O.Perisic, M.Katan, Y.Wu, M.F.Roberts, R.L.Williams. Structural Mapping of the Catalytic Mechanism For A Mammalian Phosphoinositide-Specific Phospholipase C. Biochemistry V. 36 1704 1997.
ISSN: ISSN 0006-2960
PubMed: 9048554
DOI: 10.1021/BI962512P
Page generated: Sat Dec 12 02:53:02 2020

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