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

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

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

Protein crystallography data

The structure of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-4,5-Bisphosphate, PDB code: 1djz 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 / 2.95
Space group F 41 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 396.490, 396.490, 396.490, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 27.4

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 1djz

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


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

b:59.2
occ:1.00
 O2 A:IP21 2.4 70.9 1.0
OD2 A:ASP343 2.4 28.9 1.0
OD1 A:ASP343 2.5 36.9 1.0
OE1 A:GLU341 2.7 34.4 1.0
OE1 A:GLU390 2.7 50.3 1.0
CG A:ASP343 2.8 30.7 1.0
ND2 A:ASN312 2.8 3.4 1.0
OD1 A:ASN312 3.3 51.7 1.0
CG A:ASN312 3.4 20.4 1.0
C2 A:IP21 3.5 72.9 1.0
CD A:GLU390 3.6 60.8 1.0
CD A:GLU341 3.9 69.2 1.0
OE2 A:GLU390 4.0 65.9 1.0
C3 A:IP21 4.1 76.8 1.0
C4 A:IP21 4.1 91.6 1.0
O3 A:IP21 4.3 71.7 1.0
CB A:ASP343 4.3 15.2 1.0
OH A:TYR314 4.6 15.6 1.0
CB A:ASN312 4.7 16.6 1.0
OE2 A:GLU341 4.7 57.1 1.0
C1 A:IP21 4.7 76.5 1.0
O A:HOH799 4.7 13.0 1.0
CA A:ASN312 4.7 10.7 1.0
CG A:GLU390 4.8 42.1 1.0
CB A:GLU390 4.8 28.2 1.0
O43 A:IP21 4.8 0.2 1.0
C6 A:IP21 4.8 85.6 1.0
C5 A:IP21 4.9 97.2 1.0
O1 A:IP21 4.9 75.5 1.0
CG A:GLU341 4.9 37.6 1.0
CE2 A:TYR314 5.0 5.6 1.0

Calcium binding site 2 out of 4 in 1djz

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


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

b:66.4
occ:1.00
 OD1 A:ASP653 2.4 40.3 1.0
OD1 A:ASN677 2.4 90.0 1.0
O A:ILE651 2.6 45.9 1.0
CG A:ASP653 3.2 41.7 1.0
OD2 A:ASP653 3.5 65.4 1.0
CG A:ASN677 3.5 86.2 1.0
C A:ILE651 3.6 45.0 1.0
OG A:SER650 3.8 0.7 1.0
N A:ILE651 3.9 62.8 1.0
CA A:ASN677 4.0 35.1 1.0
N A:ASN677 4.1 33.7 1.0
CB A:ILE651 4.1 64.9 1.0
O A:VAL652 4.1 31.6 1.0
CA A:ILE651 4.2 58.6 1.0
CB A:ASN677 4.2 43.2 1.0
C A:VAL652 4.3 31.8 1.0
CB A:ASP653 4.5 27.0 1.0
ND2 A:ASN677 4.5 85.6 1.0
N A:VAL652 4.6 30.6 1.0
N A:ASP653 4.7 28.0 1.0
CD1 A:ILE651 4.7 98.5 1.0
CA A:VAL652 4.8 28.1 1.0

Calcium binding site 3 out of 4 in 1djz

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Calcium binding site 3 out of 4 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Inositol-4,5-Bisphosphate


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

b:37.6
occ:1.00
 O2 B:IP21 1.9 59.2 1.0
OD2 B:ASP343 2.2 27.8 1.0
OD1 B:ASP343 2.7 35.2 1.0
CG B:ASP343 2.8 29.2 1.0
OE1 B:GLU390 2.8 51.0 1.0
OD1 B:ASN312 3.0 51.0 1.0
OE1 B:GLU341 3.0 34.0 1.0
ND2 B:ASN312 3.2 3.5 1.0
CG B:ASN312 3.3 20.8 1.0
C2 B:IP21 3.3 58.6 1.0
O3 B:IP21 3.4 54.2 1.0
O1 B:IP21 3.6 53.2 1.0
CD B:GLU390 3.7 61.0 1.0
C3 B:IP21 3.9 58.9 1.0
OE2 B:GLU390 4.0 65.2 1.0
C1 B:IP21 4.1 57.9 1.0
CD B:GLU341 4.2 69.1 1.0
CB B:ASP343 4.3 15.1 1.0
O B:HOH853 4.3 23.7 1.0
C4 B:IP21 4.4 68.5 1.0
OH B:TYR314 4.4 16.6 1.0
C6 B:IP21 4.5 64.4 1.0
CB B:ASN312 4.6 16.6 1.0
OE2 B:GLU341 4.9 58.0 1.0
CA B:ASN312 4.9 10.6 1.0
CG B:GLU390 4.9 42.4 1.0
CD2 B:HIS356 4.9 7.8 1.0
CE1 B:TYR314 5.0 3.0 1.0

Calcium binding site 4 out of 4 in 1djz

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


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

b:74.5
occ:1.00
 O B:ILE651 2.5 47.2 1.0
OD1 B:ASN677 2.6 89.6 1.0
OD1 B:ASP653 2.8 47.1 1.0
C B:ILE651 3.5 46.7 1.0
CG B:ASP653 3.6 47.9 1.0
OD2 B:ASP653 3.7 60.6 1.0
CG B:ASN677 3.8 86.1 1.0
N B:ILE651 3.8 61.0 1.0
O B:ASN649 3.9 86.6 1.0
CG2 B:ILE651 3.9 58.7 1.0
CA B:ILE651 3.9 54.2 1.0
CB B:ILE651 4.0 57.0 1.0
CB B:ASN649 4.3 86.3 0.0
OD1 B:ASN649 4.3 0.1 0.0
C B:ASN649 4.4 87.1 1.0
CG B:ASN649 4.5 0.0 0.0
ND2 B:ASN677 4.6 85.3 1.0
CA B:ASN677 4.7 34.9 1.0
N B:VAL652 4.7 33.5 1.0
O B:VAL652 4.7 24.8 1.0
CB B:ASN677 4.7 43.5 1.0
N B:ASN677 4.8 33.4 1.0
C B:VAL652 4.9 25.1 1.0
CA B:ASN649 5.0 85.0 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 07:34:31 2024

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