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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

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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

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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

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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

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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

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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

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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: Wed Jul 10 14:58:12 2024

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