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Calcium in PDB 5eyh: Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0

Enzymatic activity of Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0

All present enzymatic activity of Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0:
3.1.3.25;

Protein crystallography data

The structure of Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0, PDB code: 5eyh 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) 75.90 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.505, 60.331, 79.939, 90.00, 108.28, 90.00
R / Rfree (%) 18.1 / 24.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0 (pdb code 5eyh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0, PDB code: 5eyh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5eyh

Go back to Calcium Binding Sites List in 5eyh
Calcium binding site 1 out of 5 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0


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 Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:22.4
occ:1.00
 OE2 A:GLU70 2.1 35.3 1.0
O3X A:NAP306 2.2 14.1 0.2
OD1 A:ASP88 2.3 24.3 1.0
O A:ILE90 2.3 22.0 1.0
O3X A:NAP306 2.3 22.8 0.8
O A:HOH406 2.4 13.9 1.0
O A:HOH408 2.4 16.3 1.0
OD2 A:ASP88 3.0 23.7 1.0
CG A:ASP88 3.0 23.1 1.0
CD A:GLU70 3.3 33.6 1.0
C A:ILE90 3.4 22.3 1.0
P2B A:NAP306 3.4 25.2 0.8
P2B A:NAP306 3.5 14.2 0.2
CA A:CA305 3.7 43.2 1.0
O1X A:NAP306 3.8 24.4 0.8
OE1 A:GLU70 3.9 33.8 1.0
CA A:CA302 4.0 29.9 1.0
CA A:ASP91 4.0 22.9 1.0
OG1 A:THR93 4.0 28.8 1.0
O1X A:NAP306 4.1 14.2 0.2
N A:ASP91 4.1 22.5 1.0
O2X A:NAP306 4.1 14.1 0.2
O A:HOH409 4.2 26.9 1.0
O2X A:NAP306 4.2 23.8 0.8
OD2 A:ASP47 4.2 21.9 1.0
N A:ILE90 4.4 22.0 1.0
OE2 A:GLU71 4.4 34.8 1.0
CB A:ASP88 4.4 22.2 1.0
CA A:ILE90 4.5 22.0 1.0
O A:HOH414 4.5 21.2 1.0
CG A:GLU70 4.5 29.9 1.0
CB A:GLU70 4.5 27.1 1.0
O2B A:NAP306 4.6 27.2 0.8
O2B A:NAP306 4.6 13.9 0.2
CD1 A:TRP208 4.7 22.0 1.0
NE1 A:TRP208 4.9 22.1 1.0
CD A:PRO89 4.9 19.8 1.0
N A:GLY92 4.9 23.9 1.0
CA A:ASP88 5.0 20.6 1.0
CB A:ILE90 5.0 21.5 1.0
C A:ASP91 5.0 23.1 1.0
N A:PRO89 5.0 20.2 1.0
CB A:ASP91 5.0 22.6 1.0

Calcium binding site 2 out of 5 in 5eyh

Go back to Calcium Binding Sites List in 5eyh
Calcium binding site 2 out of 5 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0


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 Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:29.9
occ:1.00
 O1X A:NAP306 2.2 24.4 0.8
O A:HOH459 2.3 35.6 1.0
O A:HOH422 2.3 33.9 1.0
OE1 A:GLU70 2.3 33.8 1.0
O1X A:NAP306 2.4 14.2 0.2
O A:HOH408 2.4 16.3 1.0
O A:HOH426 2.5 18.8 1.0
O A:HOH409 2.9 26.9 1.0
CD A:GLU70 3.2 33.6 1.0
OE2 A:GLU70 3.3 35.3 1.0
P2B A:NAP306 3.4 25.2 0.8
P2B A:NAP306 3.5 14.2 0.2
O3X A:NAP306 3.8 14.1 0.2
O A:HOH414 3.8 21.2 1.0
NZ A:LYS36 3.9 41.0 1.0
CA A:CA301 4.0 22.4 1.0
O2X A:NAP306 4.0 23.8 0.8
O3X A:NAP306 4.0 22.8 0.8
O A:LEU42 4.0 31.9 1.0
O2X A:NAP306 4.2 14.1 0.2
OD1 A:ASP41 4.3 45.8 1.0
C8A A:NAP306 4.5 14.3 0.2
CE A:LYS36 4.6 38.6 1.0
OG1 A:THR93 4.6 28.8 1.0
CG A:GLU70 4.6 29.9 1.0
O2B A:NAP306 4.6 27.2 0.8
C8A A:NAP306 4.7 32.9 0.8
O2B A:NAP306 4.8 13.9 0.2
N7A A:NAP306 4.8 14.1 0.2
O A:HOH406 4.8 13.9 1.0
OE2 A:GLU71 4.9 34.8 1.0

Calcium binding site 3 out of 5 in 5eyh

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Calcium binding site 3 out of 5 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0


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 Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:43.2
occ:1.00
 O3X A:NAP306 2.1 14.1 0.2
OD1 A:ASP209 2.1 27.0 1.0
O3X A:NAP306 2.2 22.8 0.8
OD2 A:ASP88 2.2 23.7 1.0
OD1 A:ASP91 2.3 24.9 1.0
O2B A:NAP306 2.4 13.9 0.2
O2B A:NAP306 2.6 27.2 0.8
P2B A:NAP306 2.9 14.2 0.2
P2B A:NAP306 3.0 25.2 0.8
O A:HOH414 3.2 21.2 1.0
CG A:ASP91 3.3 24.3 1.0
CG A:ASP209 3.4 24.4 1.0
CG A:ASP88 3.4 23.1 1.0
CB A:ASP91 3.7 22.6 1.0
O3B A:NAP306 3.7 13.2 0.2
O3B A:NAP306 3.7 25.9 0.8
CA A:ASP91 3.7 22.9 1.0
CA A:CA301 3.7 22.4 1.0
C2B A:NAP306 3.7 13.8 0.2
C2B A:NAP306 3.8 29.6 0.8
O1X A:NAP306 3.8 24.4 0.8
O1X A:NAP306 3.9 14.2 0.2
O2X A:NAP306 4.0 14.1 0.2
OD1 A:ASP88 4.1 24.3 1.0
CA A:ASP209 4.1 22.0 1.0
CD1 A:TRP208 4.2 22.0 1.0
OD2 A:ASP209 4.2 25.1 1.0
CB A:ASP209 4.2 24.0 1.0
C3B A:NAP306 4.2 13.7 0.2
O2X A:NAP306 4.3 23.8 0.8
C3B A:NAP306 4.3 30.7 0.8
C1B A:NAP306 4.3 13.8 0.2
OD2 A:ASP91 4.3 25.4 1.0
C1B A:NAP306 4.4 30.9 0.8
CB A:ASP88 4.4 22.2 1.0
N A:GLY92 4.5 23.9 1.0
OE2 A:GLU70 4.5 35.3 1.0
C A:ASP91 4.6 23.1 1.0
N A:ASP209 4.6 23.4 1.0
NE1 A:TRP208 4.6 22.1 1.0
O A:ILE90 4.7 22.0 1.0
N A:ASP91 4.8 22.5 1.0

Calcium binding site 4 out of 5 in 5eyh

Go back to Calcium Binding Sites List in 5eyh
Calcium binding site 4 out of 5 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0


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 Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:30.4
occ:1.00
 OD1 B:ASP209 2.0 40.1 1.0
O2X B:NAP303 2.3 24.9 1.0
OD2 B:ASP88 2.3 28.4 1.0
O2B B:NAP303 2.5 26.3 1.0
OD1 B:ASP91 2.5 25.8 1.0
O B:HOH439 2.7 32.3 1.0
P2B B:NAP303 3.1 26.8 1.0
CG B:ASP209 3.2 36.5 1.0
CG B:ASP91 3.5 27.1 1.0
CG B:ASP88 3.5 31.6 1.0
O3B B:NAP303 3.7 28.6 1.0
C2B B:NAP303 3.7 29.0 1.0
CA B:CA302 3.9 28.6 1.0
OD2 B:ASP209 3.9 36.2 1.0
CB B:ASP91 4.0 27.6 1.0
CA B:ASP91 4.1 26.9 1.0
CD1 B:TRP208 4.1 38.1 1.0
O1X B:NAP303 4.2 26.1 1.0
C1B B:NAP303 4.2 30.5 1.0
CA B:ASP209 4.2 36.6 1.0
CB B:ASP209 4.2 35.9 1.0
OD1 B:ASP88 4.2 32.9 1.0
C3B B:NAP303 4.3 28.8 1.0
O3X B:NAP303 4.3 24.2 1.0
OE1 B:GLU70 4.5 36.3 1.0
O B:HOH403 4.5 38.4 1.0
NE1 B:TRP208 4.5 37.1 1.0
OD2 B:ASP91 4.6 24.3 1.0
CB B:ASP88 4.6 32.9 1.0
N B:ASP209 4.7 34.4 1.0
N B:GLY92 4.8 26.2 1.0
O B:HOH423 4.9 25.9 1.0
O B:ILE90 4.9 28.9 1.0
C B:ASP91 4.9 25.3 1.0
N9A B:NAP303 5.0 34.1 1.0

Calcium binding site 5 out of 5 in 5eyh

Go back to Calcium Binding Sites List in 5eyh
Calcium binding site 5 out of 5 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:28.6
occ:1.00
 O B:HOH423 2.1 25.9 1.0
OD1 B:ASP88 2.2 32.9 1.0
O B:HOH418 2.3 26.5 1.0
O2X B:NAP303 2.4 24.9 1.0
O B:ILE90 2.4 28.9 1.0
OE1 B:GLU70 2.4 36.3 1.0
CG B:ASP88 3.0 31.6 1.0
OD2 B:ASP88 3.0 28.4 1.0
C B:ILE90 3.5 28.1 1.0
CD B:GLU70 3.6 42.9 1.0
P2B B:NAP303 3.7 26.8 1.0
CA B:CA301 3.9 30.4 1.0
O B:HOH401 4.0 42.5 1.0
O B:HOH403 4.0 38.4 1.0
OG1 B:THR93 4.1 26.7 1.0
CA B:ASP91 4.1 26.9 1.0
OD2 B:ASP47 4.2 35.3 1.0
N B:ASP91 4.2 27.6 1.0
O3X B:NAP303 4.3 24.2 1.0
O B:HOH439 4.3 32.3 1.0
OE2 B:GLU71 4.3 43.2 1.0
N B:ILE90 4.4 27.3 1.0
OE2 B:GLU70 4.4 44.3 1.0
O1X B:NAP303 4.4 26.1 1.0
CB B:GLU70 4.4 43.3 1.0
CB B:ASP88 4.5 32.9 1.0
CA B:ILE90 4.5 28.2 1.0
CG B:GLU70 4.5 41.9 1.0
O2B B:NAP303 4.7 26.3 1.0
CD1 B:TRP208 4.8 38.1 1.0
CD B:PRO89 4.8 30.5 1.0
NE1 B:TRP208 4.9 37.1 1.0
N B:PRO89 4.9 29.6 1.0
CA B:ASP88 5.0 34.2 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: Sun Jul 14 19:00:59 2024

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