Atomistry » Barium » PDB 1djh-2x6b » 1djh
Atomistry »
  Barium »
    PDB 1djh-2x6b »
      1djh »

Barium in PDB 1djh: Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium

Enzymatic activity of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium

All present enzymatic activity of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium:
3.1.4.11;

Protein crystallography data

The structure of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium, PDB code: 1djh 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 / 2.50
Space group F 41 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 398.250, 398.250, 398.250, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 27

Barium Binding Sites:

The binding sites of Barium atom in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium (pdb code 1djh). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 6 binding sites of Barium where determined in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium, PDB code: 1djh:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6;

Barium binding site 1 out of 6 in 1djh

Go back to Barium Binding Sites List in 1djh
Barium binding site 1 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1

b:71.3
occ:0.50
 O A:HOH976 2.7 44.8 1.0
OE1 A:GLU390 2.8 78.4 1.0
OD1 A:ASN312 2.8 25.8 1.0
OD1 A:ASP343 2.9 42.6 1.0
OD2 A:ASP343 3.1 41.3 1.0
O A:HOH1080 3.3 56.2 1.0
CG A:ASP343 3.4 41.0 1.0
OE1 A:GLU341 3.5 37.1 1.0
CD A:GLU390 3.8 77.2 1.0
O A:HOH974 3.9 46.0 1.0
CG A:ASN312 4.0 30.1 1.0
O A:HOH973 4.3 35.1 1.0
CD A:GLU341 4.3 51.1 1.0
CG A:GLU390 4.5 47.3 1.0
OE2 A:GLU390 4.5 81.5 1.0
ND2 A:ASN312 4.6 21.2 1.0
CB A:GLU390 4.6 36.1 1.0
NH2 A:ARG549 4.7 38.7 1.0
CB A:GLU341 4.8 22.8 1.0
CB A:ASP343 4.9 28.2 1.0
CG A:GLU341 4.9 32.8 1.0
OH A:TYR314 5.0 24.1 1.0

Barium binding site 2 out of 6 in 1djh

Go back to Barium Binding Sites List in 1djh
Barium binding site 2 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba2

b:99.5
occ:0.40
 O A:ILE651 2.6 72.1 1.0
OD1 A:ASN677 2.7 87.1 1.0
OD2 A:ASP653 3.1 64.9 1.0
OD1 A:ASP653 3.2 47.7 1.0
OG A:SER650 3.2 0.2 1.0
CG A:ASP653 3.5 48.0 1.0
C A:ILE651 3.7 69.4 1.0
N A:ILE651 3.8 79.6 1.0
CG A:ASN677 3.8 88.7 1.0
CA A:ILE651 4.2 74.9 1.0
BA A:BA3 4.5 0.8 0.4
CB A:ILE651 4.5 78.7 1.0
CB A:SER650 4.5 0.9 1.0
ND2 A:ASN677 4.6 85.9 1.0
CA A:ASN677 4.6 42.2 1.0
N A:ASN677 4.6 41.0 1.0
CB A:ASN677 4.7 51.1 1.0
C A:SER650 4.8 94.6 1.0
N A:VAL652 4.8 56.2 1.0
O A:VAL652 4.8 41.9 1.0
C A:VAL652 4.8 43.8 1.0
CB A:ASP653 4.9 34.3 1.0
CA A:SER650 4.9 0.8 1.0

Barium binding site 3 out of 6 in 1djh

Go back to Barium Binding Sites List in 1djh
Barium binding site 3 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3

b:0.8
occ:0.40
 O A:TYR707 2.8 46.2 1.0
OD1 A:ASP706 3.0 47.0 1.0
OD2 A:ASP653 3.3 64.9 1.0
OD2 A:ASP706 3.5 54.0 1.0
CG A:ASP706 3.5 45.9 1.0
OD1 A:ASP708 3.9 0.5 1.0
C A:TYR707 3.9 50.4 1.0
CG A:ASP653 4.0 48.0 1.0
CB A:ASP653 4.2 34.3 1.0
N A:ASP653 4.5 33.7 1.0
BA A:BA2 4.5 99.5 0.4
O A:ILE651 4.5 72.1 1.0
NZ A:LYS646 4.5 0.0 0.0
C A:ASP706 4.6 37.8 1.0
N A:TYR707 4.7 40.1 1.0
O A:ASP706 4.7 37.8 1.0
CB A:ASP708 4.7 65.8 1.0
CG A:ASP708 4.7 99.8 1.0
N A:ASP708 4.7 56.7 1.0
CA A:ASP708 4.8 61.6 1.0
CB A:ASP706 4.8 34.3 1.0
CA A:TYR707 4.8 43.6 1.0
OD1 A:ASP653 4.9 47.7 1.0
CA A:ASP653 5.0 32.1 1.0

Barium binding site 4 out of 6 in 1djh

Go back to Barium Binding Sites List in 1djh
Barium binding site 4 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba1

b:61.7
occ:0.50
 OD2 B:ASP343 2.7 41.8 1.0
OD1 B:ASN312 2.7 27.1 1.0
OD1 B:ASP343 3.0 41.4 1.0
O B:HOH868 3.2 46.5 1.0
CG B:ASP343 3.3 40.2 1.0
O B:HOH870 3.5 57.8 1.0
OE1 B:GLU390 3.6 78.0 1.0
OE1 B:GLU341 3.8 37.1 1.0
CD B:GLU390 3.8 77.1 1.0
CG B:ASN312 3.8 30.3 1.0
OE2 B:GLU390 3.9 81.2 1.0
ND2 B:ASN312 4.3 21.8 1.0
O B:HOH869 4.3 40.1 1.0
O B:HOH866 4.5 66.4 1.0
CG B:GLU390 4.7 47.8 1.0
OH B:TYR314 4.7 23.4 1.0
CD B:GLU341 4.7 51.0 1.0
CB B:ASP343 4.7 28.1 1.0
CB B:GLU390 4.8 36.2 1.0
O B:HOH1118 4.9 43.0 1.0
O B:HOH867 4.9 80.1 1.0
NE2 B:HIS311 4.9 26.6 1.0
NH2 B:ARG549 4.9 39.3 1.0

Barium binding site 5 out of 6 in 1djh

Go back to Barium Binding Sites List in 1djh
Barium binding site 5 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba2

b:93.0
occ:0.40
 O B:HOH1079 2.7 61.5 1.0
O B:ILE651 2.7 55.6 1.0
OD1 B:ASN677 2.9 87.2 1.0
OD1 B:ASP653 2.9 57.3 1.0
CG B:ASP653 3.6 48.8 1.0
OD2 B:ASP653 3.7 55.1 1.0
C B:ILE651 3.8 56.3 1.0
CG B:ASN677 4.0 88.6 1.0
N B:ILE651 4.0 70.4 1.0
BA B:BA3 4.2 86.5 0.4
CB B:SER650 4.3 83.0 1.0
CA B:ILE651 4.4 63.7 1.0
CB B:ILE651 4.5 66.1 1.0
ND2 B:ASN677 4.6 85.5 1.0
OG B:SER650 4.8 92.3 1.0
CA B:ASN677 4.8 42.1 1.0
O B:VAL652 4.8 32.7 1.0
N B:ASN677 4.9 40.8 1.0
C B:VAL652 4.9 35.6 1.0
CB B:ASN677 4.9 51.1 1.0
N B:VAL652 5.0 45.7 1.0
CB B:ASP653 5.0 32.2 1.0

Barium binding site 6 out of 6 in 1djh

Go back to Barium Binding Sites List in 1djh
Barium binding site 6 out of 6 in the Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Phosphoinositide-Specific Phospholipase C-DELTA1 From Rat Complexed with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba3

b:86.5
occ:0.40
 O B:TYR707 2.9 40.5 1.0
OD1 B:ASP706 2.9 46.9 1.0
OD1 B:ASP708 3.2 92.3 1.0
OD2 B:ASP706 3.3 53.6 1.0
CG B:ASP706 3.4 46.0 1.0
CG B:ASP653 4.0 48.8 1.0
OD1 B:ASP653 4.0 57.3 1.0
C B:TYR707 4.1 43.6 1.0
CB B:ASP653 4.1 32.2 1.0
BA B:BA2 4.2 93.0 0.4
N B:ASP653 4.3 29.7 1.0
O B:ILE651 4.3 55.6 1.0
CG B:ASP708 4.4 87.4 1.0
OD2 B:ASP653 4.5 55.1 1.0
CB B:ASP706 4.7 34.6 1.0
N B:TYR707 4.7 34.0 1.0
C B:VAL652 4.8 35.6 1.0
C B:ASP706 4.8 36.9 1.0
CA B:ASP653 4.9 29.9 1.0
CA B:VAL652 4.9 42.1 1.0
N B:ASP708 4.9 46.7 1.0
CA B:ASP708 4.9 50.1 1.0
CA B:TYR707 5.0 34.0 1.0

Reference:

L.O.Essen, O.Perisic, D.E.Lynch, M.Katan, R.L.Williams. A Ternary Metal Binding Site in the C2 Domain of Phosphoinositide-Specific Phospholipase C-DELTA1. Biochemistry V. 36 2753 1997.
ISSN: ISSN 0006-2960
PubMed: 9062102
DOI: 10.1021/BI962466T
Page generated: Mon Jul 7 02:00:35 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy