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Calcium in PDB 1djw: Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2-Methylene-1,2-Cyclic- Monophosphonate

Enzymatic activity of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2-Methylene-1,2-Cyclic- Monophosphonate

All present enzymatic activity of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2-Methylene-1,2-Cyclic- Monophosphonate:
3.1.4.11;

Protein crystallography data

The structure of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2-Methylene-1,2-Cyclic- Monophosphonate, PDB code: 1djw 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 / 2.45
Space group F 41 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 397.030, 397.030, 397.030, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 27.3

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 1djw

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Calcium binding site 1 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2-Methylene-1,2-Cyclic- Monophosphonate


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-Methylene-1,2-Cyclic- Monophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:50.5
occ:1.00
 OD1 A:ASP343 2.4 31.9 1.0
OD2 A:ASP343 2.5 34.5 1.0
P A:CIP1 2.5 55.7 0.7
O2P A:CIP1 2.5 54.4 0.7
C7 A:CIP1 2.5 53.2 0.7
OD1 A:ASN312 2.6 21.5 1.0
O1P A:CIP1 2.7 54.8 0.7
OE1 A:GLU341 2.7 52.1 1.0
CG A:ASP343 2.8 33.9 1.0
OE1 A:GLU390 2.8 54.5 1.0
O A:HOH840 3.0 50.8 1.0
CD A:GLU390 3.6 60.2 1.0
CG A:ASN312 3.7 38.3 1.0
OE2 A:GLU390 3.9 55.9 1.0
CD A:GLU341 3.9 66.0 1.0
C2 A:CIP1 3.9 52.5 0.7
O1 A:CIP1 4.1 56.0 0.7
ND2 A:ASN312 4.3 24.0 1.0
OH A:TYR314 4.3 24.4 1.0
CB A:ASP343 4.3 27.8 1.0
O3 A:CIP1 4.5 44.8 0.7
C3 A:CIP1 4.5 46.8 0.7
CB A:GLU390 4.5 37.4 1.0
C1 A:CIP1 4.5 54.4 0.7
O A:HOH854 4.6 35.4 1.0
CG A:GLU390 4.7 48.1 1.0
C4 A:CIP1 4.7 43.9 0.7
OE2 A:GLU341 4.7 58.3 1.0
CE1 A:TYR314 4.8 15.8 1.0
CG A:GLU341 4.8 41.6 1.0
C6 A:CIP1 4.9 49.1 0.7
CB A:ASN312 4.9 21.3 1.0
CA A:ASN312 5.0 21.6 1.0

Calcium binding site 2 out of 6 in 1djw

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Calcium binding site 2 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2-Methylene-1,2-Cyclic- Monophosphonate


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-Methylene-1,2-Cyclic- Monophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:56.0
occ:0.60
 O A:ILE651 2.3 66.5 1.0
OD1 A:ASN677 2.4 76.5 1.0
OD1 A:ASP653 2.6 50.9 1.0
OD2 A:ASP653 2.7 62.7 1.0
CG A:ASP653 3.0 52.5 1.0
C A:ILE651 3.5 64.8 1.0
CG A:ASN677 3.6 81.8 1.0
OG A:SER650 3.6 0.3 1.0
N A:ILE651 4.0 72.8 1.0
CA A:ILE651 4.1 71.0 1.0
N A:ASN677 4.2 40.5 1.0
CA A:ASN677 4.2 42.2 1.0
CB A:ILE651 4.3 76.1 1.0
C A:VAL652 4.4 47.8 1.0
ND2 A:ASN677 4.5 78.5 1.0
CB A:ASP653 4.5 37.8 1.0
CB A:ASN677 4.5 53.5 1.0
N A:VAL652 4.5 53.0 1.0
O A:VAL652 4.6 48.7 1.0
N A:ASP653 4.7 37.8 1.0
CA A:VAL652 4.8 49.8 1.0

Calcium binding site 3 out of 6 in 1djw

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Calcium binding site 3 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2-Methylene-1,2-Cyclic- Monophosphonate


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-Methylene-1,2-Cyclic- Monophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:58.8
occ:0.40
 O A:TYR707 1.6 49.6 1.0
C A:TYR707 2.5 55.5 1.0
OD1 A:ASP706 2.7 43.9 1.0
OD2 A:ASP653 3.1 62.7 1.0
CA A:TYR707 3.4 49.4 1.0
N A:TYR707 3.4 45.8 1.0
N A:ASP708 3.4 62.5 1.0
CG A:ASP706 3.6 44.7 1.0
C A:ASP706 3.6 41.3 1.0
O A:HOH1043 3.6 60.2 1.0
CA A:ASP708 3.7 67.2 1.0
O A:ASP706 3.7 40.8 1.0
CB A:ASP653 3.7 37.8 1.0
CG A:ASP653 3.8 52.5 1.0
CB A:TYR707 4.1 53.2 1.0
OD2 A:ASP706 4.2 49.2 1.0
CB A:ASP708 4.3 71.5 1.0
O A:ASP653 4.4 37.1 1.0
CB A:ASP706 4.5 35.7 1.0
N A:ASP653 4.5 37.8 1.0
CA A:ASP706 4.5 34.2 1.0
CA A:ASP653 4.6 35.4 1.0
CD2 A:TYR707 4.6 60.8 1.0
CG A:ASP708 4.6 97.2 1.0
CG A:TYR707 4.7 59.2 1.0
OD1 A:ASP708 4.8 95.5 1.0
C A:ASP653 4.9 37.4 1.0
C A:ASP708 4.9 75.8 1.0

Calcium binding site 4 out of 6 in 1djw

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Calcium binding site 4 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2-Methylene-1,2-Cyclic- Monophosphonate


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-Methylene-1,2-Cyclic- Monophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:46.0
occ:1.00
 OD2 B:ASP343 2.2 34.4 1.0
O2P B:CIP1 2.3 54.6 0.7
P B:CIP1 2.4 55.4 0.7
OD1 B:ASP343 2.4 30.6 1.0
O1P B:CIP1 2.5 55.9 0.7
CG B:ASP343 2.6 33.3 1.0
OD1 B:ASN312 2.6 24.0 1.0
C7 B:CIP1 2.6 53.1 0.7
OE1 B:GLU341 2.8 52.1 1.0
OE1 B:GLU390 2.9 55.2 1.0
CD B:GLU390 3.6 60.2 1.0
CG B:ASN312 3.7 38.9 1.0
OE2 B:GLU390 3.8 55.4 1.0
O1 B:CIP1 4.0 55.2 0.7
C2 B:CIP1 4.0 53.2 0.7
OH B:TYR314 4.0 25.0 1.0
CD B:GLU341 4.1 65.9 1.0
CB B:ASP343 4.1 27.5 1.0
O3 B:CIP1 4.1 45.6 0.7
ND2 B:ASN312 4.2 23.9 1.0
O B:HOH1032 4.3 38.0 1.0
O B:HOH1008 4.5 40.0 1.0
C1 B:CIP1 4.5 54.4 0.7
C3 B:CIP1 4.5 47.5 0.7
CB B:GLU390 4.6 37.4 1.0
O B:HOH774 4.6 42.8 1.0
CG B:GLU390 4.7 48.5 1.0
CE1 B:TYR314 4.7 16.4 1.0
OE2 B:GLU341 4.8 58.4 1.0
C6 B:CIP1 4.8 49.9 0.7
C4 B:CIP1 4.8 45.1 0.7
CZ B:TYR314 4.9 21.0 1.0
CB B:ASN312 4.9 21.4 1.0
CA B:ASP343 4.9 26.3 1.0

Calcium binding site 5 out of 6 in 1djw

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Calcium binding site 5 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2-Methylene-1,2-Cyclic- Monophosphonate


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-Methylene-1,2-Cyclic- Monophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:54.4
occ:0.60
 OD1 B:ASN677 2.5 76.5 1.0
O B:ILE651 2.7 60.4 1.0
OD1 B:ASP653 2.8 55.1 1.0
O B:HOH998 3.6 57.4 1.0
O B:ASN649 3.6 82.4 1.0
CG B:ASP653 3.6 51.2 1.0
OD2 B:ASP653 3.7 62.0 1.0
CG B:ASN677 3.7 82.0 1.0
CG2 B:ILE651 3.8 69.5 1.0
C B:ILE651 3.8 58.1 1.0
N B:ILE651 4.2 71.4 1.0
CB B:ILE651 4.4 66.8 1.0
CA B:ILE651 4.4 64.7 1.0
OD1 B:ASN649 4.4 0.0 1.0
ND2 B:ASN677 4.5 78.4 1.0
CG B:ASN649 4.5 0.0 1.0
C B:ASN649 4.5 85.7 1.0
CB B:ASN649 4.6 94.2 1.0
CA B:ASN677 4.6 41.7 1.0
CB B:ASN677 4.8 53.8 1.0
N B:ASN677 4.8 40.3 1.0
O B:VAL652 4.9 31.9 1.0
C B:VAL652 4.9 33.8 1.0
N B:VAL652 4.9 44.5 1.0
ND2 B:ASN649 5.0 0.2 1.0

Calcium binding site 6 out of 6 in 1djw

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Calcium binding site 6 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-2-Methylene-1,2-Cyclic- Monophosphonate


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-Methylene-1,2-Cyclic- Monophosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4

b:59.8
occ:0.60
 O B:TYR707 1.9 41.2 1.0
O B:HOH998 2.5 57.4 1.0
OD1 B:ASP708 2.7 72.6 1.0
OD1 B:ASP706 2.7 43.5 1.0
C B:TYR707 3.1 45.4 1.0
CG B:ASP706 3.5 44.2 1.0
CG B:ASP708 3.6 70.1 1.0
CA B:ASP708 3.8 51.5 1.0
N B:ASP708 3.8 49.1 1.0
OD2 B:ASP706 3.9 48.3 1.0
N B:TYR707 4.0 36.0 1.0
CG B:ASP653 4.1 51.2 1.0
CB B:ASP653 4.1 31.4 1.0
CA B:TYR707 4.1 36.5 1.0
O B:HOH897 4.2 77.1 1.0
C B:ASP706 4.2 39.6 1.0
OD2 B:ASP653 4.2 62.0 1.0
OD2 B:ASP708 4.3 65.8 1.0
CB B:ASP708 4.3 54.3 1.0
OD1 B:ASP653 4.4 55.1 1.0
O B:ASP706 4.4 40.0 1.0
CB B:ASP706 4.6 35.1 1.0
N B:ASP653 4.7 27.4 1.0
CA B:ASP706 4.9 33.4 1.0
CB B:TYR707 4.9 36.7 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: Mon Jul 7 14:25:52 2025

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