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Calcium in PDB 1djy: Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2,4,5-Trisphosphate

Enzymatic activity of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2,4,5-Trisphosphate

All present enzymatic activity of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2,4,5-Trisphosphate:
3.1.4.11;

Protein crystallography data

The structure of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2,4,5-Trisphosphate, PDB code: 1djy 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 / 2.80
Space group F 41 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 397.130, 397.130, 397.130, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26

Calcium Binding Sites:

The binding sites of Calcium atom in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2,4,5-Trisphosphate (pdb code 1djy). 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 Inositol-2,4,5-Trisphosphate, PDB code: 1djy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1djy

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Calcium binding site 1 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2,4,5-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-2,4,5-Trisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:25.0
occ:1.00
 OE1 A:GLU390 1.9 32.3 1.0
OE2 A:GLU341 2.2 16.8 1.0
OD2 A:ASP343 2.4 21.1 1.0
O22 A:I2P1 2.4 26.7 1.0
OD1 A:ASP343 2.4 11.0 1.0
OD1 A:ASN312 2.6 12.0 1.0
CG A:ASP343 2.7 14.7 1.0
CD A:GLU390 3.0 38.1 1.0
O2 A:I2P1 3.0 16.8 1.0
P2 A:I2P1 3.2 26.5 1.0
CD A:GLU341 3.3 30.8 1.0
CG A:ASN312 3.6 18.6 1.0
OE2 A:GLU390 3.6 39.8 1.0
ND2 A:ASN312 3.9 6.9 1.0
CG A:GLU341 4.0 15.8 1.0
O A:HOH922 4.2 18.9 1.0
OE1 A:GLU341 4.2 27.1 1.0
CG A:GLU390 4.2 25.0 1.0
OH A:TYR314 4.3 12.4 1.0
CB A:ASP343 4.3 10.8 1.0
C2 A:I2P1 4.3 21.7 1.0
O3 A:I2P1 4.4 29.2 1.0
O21 A:I2P1 4.4 33.0 1.0
O23 A:I2P1 4.4 27.4 1.0
CB A:GLU390 4.5 16.8 1.0
C4 A:I2P1 4.6 23.5 1.0
C3 A:I2P1 4.6 24.3 1.0
O A:HOH923 4.7 27.7 1.0
CB A:ASN312 4.9 6.5 1.0
C6 A:I2P1 5.0 28.8 1.0

Calcium binding site 2 out of 6 in 1djy

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Calcium binding site 2 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2,4,5-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-2,4,5-Trisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:58.3
occ:1.00
 OD1 A:ASN677 2.3 76.8 1.0
O A:ILE651 2.4 43.0 1.0
OD1 A:ASP653 2.7 28.9 1.0
OD2 A:ASP653 3.0 49.1 1.0
CG A:ASP653 3.2 30.9 1.0
CG A:ASN677 3.4 74.9 1.0
OG A:SER650 3.5 95.5 0.0
C A:ILE651 3.6 41.4 1.0
CA A:CA4 3.9 89.4 1.0
N A:ILE651 4.0 50.5 1.0
ND2 A:ASN677 4.1 67.0 1.0
CA A:ILE651 4.2 45.8 1.0
N A:ASN677 4.3 30.7 1.0
CA A:ASN677 4.3 32.1 1.0
O A:VAL652 4.3 21.2 1.0
CB A:ASN677 4.4 39.8 1.0
CB A:ILE651 4.5 48.6 1.0
C A:VAL652 4.5 22.2 1.0
CB A:ASP653 4.6 15.7 1.0
N A:VAL652 4.6 30.0 1.0
CB A:SER650 4.8 86.9 0.0
N A:ASP653 4.9 12.4 1.0
CA A:VAL652 4.9 27.5 1.0
C A:SER650 5.0 67.5 1.0

Calcium binding site 3 out of 6 in 1djy

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Calcium binding site 3 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2,4,5-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-2,4,5-Trisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:89.4
occ:1.00
 OD1 A:ASP708 2.8 97.1 0.0
O A:TYR707 3.0 20.3 1.0
OD1 A:ASP706 3.0 40.7 1.0
OD2 A:ASP653 3.0 49.1 1.0
CG A:ASP653 3.6 30.9 1.0
CG A:ASP706 3.9 38.6 1.0
CA A:CA3 3.9 58.3 1.0
OD2 A:ASP706 4.1 50.0 1.0
CG A:ASP708 4.1 92.7 0.0
CB A:ASP653 4.1 15.7 1.0
C A:TYR707 4.2 29.9 1.0
O A:ILE651 4.3 43.0 1.0
OD1 A:ASP653 4.4 28.9 1.0
N A:ASP653 4.6 12.4 1.0
OD2 A:ASP708 4.8 97.7 0.0
CA A:ASP708 4.8 45.8 1.0
N A:ASP708 5.0 40.0 1.0

Calcium binding site 4 out of 6 in 1djy

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Calcium binding site 4 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2,4,5-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-2,4,5-Trisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:13.3
occ:1.00
 OE1 B:GLU390 1.9 33.1 1.0
OE2 B:GLU341 2.1 17.8 1.0
O22 B:I2P1 2.3 12.3 1.0
OD2 B:ASP343 2.3 18.9 1.0
OD1 B:ASP343 2.4 5.8 1.0
OD1 B:ASN312 2.5 13.5 1.0
CG B:ASP343 2.7 12.1 1.0
O2 B:I2P1 2.9 19.9 1.0
CD B:GLU390 3.0 37.7 1.0
P2 B:I2P1 3.1 14.8 1.0
CD B:GLU341 3.2 30.2 1.0
CG B:ASN312 3.5 20.1 1.0
OE2 B:GLU390 3.7 38.9 1.0
CG B:GLU341 3.8 14.1 1.0
ND2 B:ASN312 3.9 6.3 1.0
O3 B:I2P1 4.0 15.1 1.0
OE1 B:GLU341 4.1 25.8 1.0
O21 B:I2P1 4.1 15.2 1.0
CG B:GLU390 4.1 25.5 1.0
CB B:ASP343 4.2 11.0 1.0
C2 B:I2P1 4.3 24.3 1.0
OH B:TYR314 4.3 12.4 1.0
O B:HOH898 4.3 15.9 1.0
CB B:GLU390 4.4 17.2 1.0
O23 B:I2P1 4.5 17.3 1.0
C3 B:I2P1 4.7 20.4 1.0
C4 B:I2P1 4.7 25.1 1.0
CB B:ASN312 4.9 8.7 1.0
CA B:ASP343 5.0 8.3 1.0

Calcium binding site 5 out of 6 in 1djy

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Calcium binding site 5 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2,4,5-Trisphosphate


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 Inositol-2,4,5-Trisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:68.5
occ:1.00
 O B:ILE651 2.4 37.1 1.0
OD1 B:ASN677 2.4 77.0 1.0
OD1 B:ASP653 2.6 44.3 1.0
CG B:ASP653 3.4 44.9 1.0
C B:ILE651 3.5 36.5 1.0
CG B:ASN677 3.6 74.9 1.0
OD2 B:ASP653 3.6 64.3 1.0
N B:ILE651 4.0 42.6 1.0
CA B:ILE651 4.2 37.2 1.0
ND2 B:ASN677 4.4 67.1 1.0
OG B:SER650 4.5 64.3 1.0
CA B:ASN677 4.5 31.3 1.0
N B:ASN677 4.6 29.9 1.0
N B:VAL652 4.6 29.1 1.0
CA B:CA4 4.6 72.9 1.0
CB B:ASN677 4.6 39.7 1.0
CB B:ILE651 4.7 37.9 1.0
C B:VAL652 4.7 24.3 1.0
O B:VAL652 4.8 27.4 1.0
CB B:ASP653 4.9 22.3 1.0
N B:ASP653 4.9 15.1 1.0
CA B:VAL652 4.9 25.2 1.0

Calcium binding site 6 out of 6 in 1djy

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Calcium binding site 6 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2,4,5-Trisphosphate


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 Inositol-2,4,5-Trisphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4

b:72.9
occ:1.00
 O B:TYR707 2.0 34.6 1.0
OD1 B:ASP708 2.2 77.8 1.0
OD1 B:ASP706 2.7 40.9 1.0
C B:TYR707 3.2 34.8 1.0
CG B:ASP708 3.4 70.4 1.0
CG B:ASP653 3.5 44.9 1.0
OD2 B:ASP653 3.5 64.3 1.0
CG B:ASP706 3.7 39.1 1.0
CA B:ASP708 3.8 32.0 1.0
OD1 B:ASP653 3.8 44.3 1.0
CB B:ASP653 3.9 22.3 1.0
N B:ASP708 3.9 33.7 1.0
CB B:ASP708 4.1 35.2 1.0
OD2 B:ASP706 4.1 50.2 1.0
CA B:TYR707 4.2 21.4 1.0
N B:TYR707 4.3 18.4 1.0
OD2 B:ASP708 4.3 79.2 1.0
C B:ASP706 4.5 22.5 1.0
N B:ASP653 4.5 15.1 1.0
O B:ASP706 4.6 24.4 1.0
CA B:CA3 4.6 68.5 1.0
CA B:ASP653 4.8 18.1 1.0
CD1 B:TYR707 4.9 31.7 1.0
CB B:ASP706 4.9 17.6 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: Thu Jul 11 07:34:21 2024

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