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Calcium in PDB 5f24: Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate

Enzymatic activity of Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate

All present enzymatic activity of Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate:
3.1.3.25;

Protein crystallography data

The structure of Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate, PDB code: 5f24 was solved by S.Bhattacharyya, D.Dutta, A.K.Ghosh, A.K.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.40 / 2.50
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.567, 67.835, 137.297, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 23.3

Other elements in 5f24:

The structure of Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate (pdb code 5f24). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate, PDB code: 5f24:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5f24

Go back to Calcium Binding Sites List in 5f24
Calcium binding site 1 out of 4 in the Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:13.8
occ:1.00
 O1 A:IPD306 2.3 21.9 1.0
OD1 A:ASP209 2.3 18.8 1.0
OD2 A:ASP88 2.3 18.8 1.0
OD1 A:ASP91 2.3 17.0 1.0
O A:HOH469 2.3 13.3 1.0
O8 A:IPD306 2.4 19.4 1.0
P1 A:IPD306 3.0 20.9 1.0
CG A:ASP91 3.4 17.3 1.0
C1 A:IPD306 3.5 23.8 1.0
CG A:ASP209 3.5 20.8 1.0
CG A:ASP88 3.5 18.8 1.0
O2 A:IPD306 3.6 25.2 1.0
C6 A:IPD306 3.8 25.5 1.0
CB A:ASP91 3.9 17.2 1.0
O7 A:IPD306 4.0 20.2 1.0
CA A:CA302 4.0 19.5 1.0
CA A:ASP91 4.0 18.0 1.0
C2 A:IPD306 4.0 23.9 1.0
O9 A:IPD306 4.1 20.2 1.0
O6 A:IPD306 4.1 26.0 1.0
O A:HOH404 4.1 20.1 1.0
OD1 A:ASP88 4.2 20.8 1.0
OD2 A:ASP209 4.2 22.2 1.0
OE2 A:GLU70 4.3 38.5 1.0
CD1 A:TRP208 4.5 18.1 1.0
OD2 A:ASP91 4.5 16.8 1.0
CA A:ASP209 4.5 20.8 1.0
CB A:ASP209 4.5 20.8 1.0
CB A:ASP88 4.6 18.7 1.0
N A:GLY92 4.7 18.8 1.0
O A:ILE90 4.7 18.9 1.0
C A:ASP91 4.9 18.1 1.0
NE1 A:TRP208 4.9 18.2 1.0
N A:ASP209 4.9 19.8 1.0
O A:HOH417 4.9 18.8 1.0

Calcium binding site 2 out of 4 in 5f24

Go back to Calcium Binding Sites List in 5f24
Calcium binding site 2 out of 4 in the Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:19.5
occ:1.00
 O A:HOH402 2.3 23.6 1.0
OE2 A:GLU70 2.3 38.5 1.0
O A:ILE90 2.3 18.9 1.0
O8 A:IPD306 2.3 19.4 1.0
O A:HOH417 2.3 18.8 1.0
OD1 A:ASP88 2.3 20.8 1.0
CG A:ASP88 3.1 18.8 1.0
OD2 A:ASP88 3.2 18.8 1.0
CD A:GLU70 3.3 50.6 1.0
C A:ILE90 3.4 18.5 1.0
P1 A:IPD306 3.6 20.9 1.0
OD2 A:ASP47 3.8 42.1 1.0
OE1 A:GLU70 3.8 56.5 1.0
OG1 A:THR93 3.9 20.4 1.0
O A:HOH469 3.9 13.3 1.0
CA A:CA301 4.0 13.8 1.0
O9 A:IPD306 4.2 20.2 1.0
OE2 A:GLU71 4.2 50.0 1.0
N A:ILE90 4.2 18.6 1.0
N A:ASP91 4.2 18.3 1.0
CA A:ASP91 4.3 18.0 1.0
CA A:ILE90 4.4 18.5 1.0
O7 A:IPD306 4.4 20.2 1.0
CG A:GLU70 4.4 52.9 1.0
CB A:ASP88 4.5 18.7 1.0
CB A:GLU70 4.6 54.3 1.0
O1 A:IPD306 4.7 21.9 1.0
CD A:PRO89 4.7 18.7 1.0
CB A:ILE90 4.8 18.6 1.0
N A:PRO89 4.9 18.3 1.0

Calcium binding site 3 out of 4 in 5f24

Go back to Calcium Binding Sites List in 5f24
Calcium binding site 3 out of 4 in the Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:16.4
occ:1.00
 OE2 B:GLU70 2.3 30.1 1.0
O B:ILE90 2.3 23.7 1.0
OD1 B:ASP88 2.3 25.1 1.0
O B:HOH465 2.3 18.2 1.0
O B:HOH408 2.3 13.4 1.0
O8 B:IPD308 2.3 19.7 1.0
OD2 B:ASP88 2.5 24.8 1.0
CG B:ASP88 2.8 24.4 1.0
CD B:GLU70 3.4 32.8 1.0
C B:ILE90 3.4 23.7 1.0
CA B:CA302 3.6 20.3 1.0
P1 B:IPD308 3.7 24.8 1.0
O B:HOH463 3.8 16.9 1.0
OE1 B:GLU70 3.8 34.8 1.0
CA B:ASP91 4.0 22.8 1.0
N B:ASP91 4.1 23.5 1.0
OG1 B:THR93 4.1 24.6 1.0
OD2 B:ASP47 4.2 40.3 1.0
O B:HOH402 4.2 17.6 1.0
CB B:ASP88 4.3 23.5 1.0
N B:ILE90 4.3 23.8 1.0
O9 B:IPD308 4.3 21.9 1.0
O7 B:IPD308 4.4 20.7 1.0
CA B:ILE90 4.4 24.0 1.0
CG B:GLU70 4.6 32.7 1.0
O1 B:IPD308 4.6 24.1 1.0
OE2 B:GLU71 4.6 34.5 1.0
CB B:GLU70 4.7 32.5 1.0
O B:HOH424 4.8 28.1 1.0
CD B:PRO89 4.9 23.5 1.0
CB B:ASP91 4.9 23.0 1.0
CA B:ASP88 4.9 22.7 1.0
N B:PRO89 4.9 22.5 1.0
CB B:ILE90 4.9 25.2 1.0
OD1 B:ASP91 5.0 24.5 1.0
C B:ASP88 5.0 21.9 1.0
C B:ASP91 5.0 22.1 1.0
N B:GLY92 5.0 21.9 1.0

Calcium binding site 4 out of 4 in 5f24

Go back to Calcium Binding Sites List in 5f24
Calcium binding site 4 out of 4 in the Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Dual Specific Impase/Nadp Phosphatase Bound with D-Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:20.3
occ:1.00
 O8 B:IPD308 2.2 19.7 1.0
OD1 B:ASP209 2.3 27.0 1.0
OD2 B:ASP88 2.3 24.8 1.0
OD1 B:ASP91 2.3 24.5 1.0
O B:HOH463 2.4 16.9 1.0
O1 B:IPD308 2.4 24.1 1.0
P1 B:IPD308 3.1 24.8 1.0
CG B:ASP91 3.4 22.6 1.0
CG B:ASP209 3.5 24.9 1.0
CG B:ASP88 3.6 24.4 1.0
CA B:CA301 3.6 16.4 1.0
C1 B:IPD308 3.6 23.8 1.0
O2 B:IPD308 3.8 24.4 1.0
CB B:ASP91 3.9 23.0 1.0
CA B:ASP91 3.9 22.8 1.0
C6 B:IPD308 4.0 25.6 1.0
O7 B:IPD308 4.1 20.7 1.0
O6 B:IPD308 4.1 27.9 1.0
O9 B:IPD308 4.1 21.9 1.0
C2 B:IPD308 4.2 24.2 1.0
OD2 B:ASP209 4.3 24.6 1.0
O B:HOH407 4.3 18.9 1.0
OE2 B:GLU70 4.3 30.1 1.0
OD1 B:ASP88 4.4 25.1 1.0
CD1 B:TRP208 4.4 23.8 1.0
OD2 B:ASP91 4.4 21.1 1.0
CA B:ASP209 4.5 23.7 1.0
CB B:ASP209 4.5 23.8 1.0
O B:HOH402 4.5 17.6 1.0
CB B:ASP88 4.5 23.5 1.0
N B:GLY92 4.7 21.9 1.0
O B:ILE90 4.7 23.7 1.0
C B:ASP91 4.8 22.1 1.0
NE1 B:TRP208 4.9 24.3 1.0
N B:ASP209 4.9 24.1 1.0

Reference:

S.Bhattacharyya, A.Dutta, D.Dutta, A.K.Ghosh, A.K.Das. Structural Elucidation of the Nadp(H) Phosphatase Activity of Staphylococcal Dual-Specific Impase/Nadp(H) Phosphatase Acta Crystallogr D Struct V. 72 281 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26894675
DOI: 10.1107/S2059798316000620
Page generated: Wed Jul 9 05:48:20 2025

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