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Samarium in PDB 1qat: 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride

Enzymatic activity of 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride

All present enzymatic activity of 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride:
3.1.4.11;

Protein crystallography data

The structure of 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride, PDB code: 1qat was solved by J.A.Grobler, J.H.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.600, 75.100, 86.400, 66.40, 85.60, 89.80
R / Rfree (%) 19.4 / 26.1

Samarium Binding Sites:

The binding sites of Samarium atom in the 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride (pdb code 1qat). This binding sites where shown within 5.0 Angstroms radius around Samarium atom.
In total 5 binding sites of Samarium where determined in the 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride, PDB code: 1qat:
Jump to Samarium binding site number: 1; 2; 3; 4; 5;

Samarium binding site 1 out of 5 in 1qat

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Samarium binding site 1 out of 5 in the 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 1 of 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm1001

b:39.0
occ:1.00
 OD1 A:ASN677 2.5 66.9 1.0
O A:ILE651 2.6 63.8 1.0
OD2 A:ASP653 3.0 54.2 1.0
OD1 A:ASP653 3.1 38.4 1.0
CG A:ASN677 3.2 62.7 1.0
CG A:ASP653 3.2 45.0 1.0
ND2 A:ASN677 3.3 66.2 1.0
C A:ILE651 3.6 59.2 1.0
C A:VAL652 4.1 40.9 1.0
O A:VAL652 4.3 43.7 1.0
N A:VAL652 4.3 51.2 1.0
N A:ASP653 4.4 38.2 1.0
CA A:VAL652 4.4 43.7 1.0
CB A:ASN677 4.5 55.2 1.0
CB A:ASP653 4.5 39.7 1.0
CA A:ILE651 4.5 66.1 1.0
CA A:ASN677 4.7 47.7 1.0
CB A:ILE651 4.7 69.5 1.0
N A:ILE651 4.8 66.4 1.0
CA A:ASP653 4.9 37.9 1.0
N A:ASN677 4.9 45.5 1.0

Samarium binding site 2 out of 5 in 1qat

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Samarium binding site 2 out of 5 in the 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 2 of 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sm1002

b:49.0
occ:1.00
 OD2 B:ASP653 2.6 53.7 1.0
O B:ILE651 2.8 63.4 1.0
OD1 B:ASP653 2.9 38.3 1.0
CG B:ASP653 2.9 44.6 1.0
OD1 B:ASN677 3.0 65.5 1.0
SM B:SM1003 3.3 57.7 1.0
ND2 B:ASN677 3.4 65.0 1.0
CG B:ASN677 3.5 62.4 1.0
O B:VAL652 3.7 44.6 1.0
C B:ILE651 3.9 58.6 1.0
C B:VAL652 3.9 41.5 1.0
CB B:ASP653 4.2 39.5 1.0
OD1 B:ASP708 4.2 84.3 1.0
N B:ASP653 4.3 38.2 1.0
CA B:VAL652 4.4 44.2 1.0
N B:VAL652 4.5 52.1 1.0
CA B:ASP653 4.7 37.7 1.0
CB B:ASN677 4.8 53.9 1.0
O B:TYR707 4.8 41.9 1.0
CA B:ASN677 4.9 47.3 1.0
CA B:ILE651 5.0 63.3 1.0

Samarium binding site 3 out of 5 in 1qat

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Samarium binding site 3 out of 5 in the 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 3 of 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sm1003

b:57.7
occ:1.00
 OD2 B:ASP653 2.8 53.7 1.0
O B:TYR707 2.9 41.9 1.0
OD1 B:ASP708 3.0 84.3 1.0
OD1 B:ASP706 3.0 39.4 1.0
SM B:SM1002 3.3 49.0 1.0
CG B:ASP653 3.4 44.6 1.0
OD2 B:ASP706 3.5 37.9 1.0
C B:TYR707 3.5 46.8 1.0
CG B:ASP706 3.5 36.3 1.0
CG B:ASP708 3.6 81.7 1.0
CB B:ASP653 3.7 39.5 1.0
N B:TYR707 3.9 40.9 1.0
N B:ASP653 4.1 38.2 1.0
CB B:ASP708 4.1 76.2 1.0
CA B:TYR707 4.2 42.6 1.0
N B:ASP708 4.2 57.3 1.0
OD2 B:ASP708 4.4 85.1 1.0
OD1 B:ASP653 4.4 38.3 1.0
CA B:ASP708 4.5 71.0 1.0
C B:VAL652 4.5 41.5 1.0
CA B:ASP653 4.5 37.7 1.0
O B:ILE651 4.6 63.4 1.0
CA B:VAL652 4.7 44.2 1.0
CB B:ASP706 4.9 34.6 1.0

Samarium binding site 4 out of 5 in 1qat

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Samarium binding site 4 out of 5 in the 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 4 of 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sm1004

b:23.5
occ:1.00
 OD2 A:ASP343 2.6 19.0 1.0
OE2 A:GLU341 2.7 13.3 1.0
OD1 A:ASP343 2.7 17.1 1.0
OD1 A:ASN312 3.0 12.1 1.0
CG A:ASP343 3.0 13.8 1.0
OE2 A:GLU390 3.2 38.0 1.0
CD A:GLU390 3.6 32.3 1.0
CD A:GLU341 3.8 15.8 1.0
OE1 A:GLU390 3.9 35.4 1.0
CG A:ASN312 4.1 2.8 1.0
OH A:TYR314 4.3 2.6 1.0
CB A:ASP343 4.5 10.3 1.0
CG A:GLU390 4.5 21.7 1.0
CG A:GLU341 4.5 12.0 1.0
ND2 A:ASN312 4.6 3.1 1.0
CB A:GLU390 4.6 10.0 1.0
OE1 A:GLU341 4.8 25.4 1.0
NE2 A:HIS311 5.0 10.5 1.0

Samarium binding site 5 out of 5 in 1qat

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Samarium binding site 5 out of 5 in the 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride


Mono view


Stereo pair view

A full contact list of Samarium with other atoms in the Sm binding site number 5 of 1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Delta Complex with Samarium (III) Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sm1005

b:23.6
occ:1.00
 OE2 B:GLU341 2.6 11.9 1.0
OD2 B:ASP343 2.6 19.7 1.0
OD1 B:ASP343 2.7 21.4 1.0
OD1 B:ASN312 2.8 16.6 1.0
CG B:ASP343 3.0 19.7 1.0
OE2 B:GLU390 3.3 39.1 1.0
CD B:GLU390 3.8 34.0 1.0
CD B:GLU341 3.8 17.3 1.0
CG B:ASN312 3.9 4.6 1.0
OE1 B:GLU390 4.1 35.8 1.0
OH B:TYR314 4.3 2.7 1.0
ND2 B:ASN312 4.4 6.5 1.0
CG B:GLU341 4.5 12.7 1.0
CB B:ASP343 4.5 13.6 1.0
CG B:GLU390 4.7 23.1 1.0
OE1 B:GLU341 4.7 17.4 1.0
CB B:GLU390 4.8 14.2 1.0
NE2 B:HIS311 4.9 6.9 1.0

Reference:

J.A.Grobler, L.O.Essen, R.L.Williams, J.H.Hurley. C2 Domain Conformational Changes in Phospholipase C-Delta 1. Nat.Struct.Biol. V. 3 788 1996.
ISSN: ISSN 1072-8368
PubMed: 8784353
DOI: 10.1038/NSB0996-788
Page generated: Thu Oct 10 13:47:51 2024

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