Atomistry » Calcium » PDB 1de4-1dv8 » 1djw
Atomistry »
  Calcium »
    PDB 1de4-1dv8 »
      1djw »

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

Go back to Calcium Binding Sites List in 1djw
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

Go back to Calcium Binding Sites List in 1djw
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

Go back to Calcium Binding Sites List in 1djw
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

Go back to Calcium Binding Sites List in 1djw
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

Go back to Calcium Binding Sites List in 1djw
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

Go back to Calcium Binding Sites List in 1djw
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: Thu Jul 11 07:33:58 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy