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Calcium in PDB 5eyg: Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+

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

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

Protein crystallography data

The structure of Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+, PDB code: 5eyg 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) 19.59 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.089, 78.880, 112.409, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.7

Other elements in 5eyg:

The structure of Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+ (pdb code 5eyg). 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 Impase/Nadp Phosphatase Complexed with Nadp and CA2+, PDB code: 5eyg:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5eyg

Go back to Calcium Binding Sites List in 5eyg
Calcium binding site 1 out of 4 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+


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+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:16.8
occ:1.00
 OD1 A:ASP209 2.1 18.7 1.0
OD2 A:ASP88 2.2 15.0 1.0
OD1 A:ASP91 2.3 12.5 1.0
O2B A:NAP308 2.4 16.2 1.0
O2X A:NAP308 2.4 15.6 1.0
O A:HOH458 2.6 14.6 1.0
P2B A:NAP308 3.0 18.0 1.0
CG A:ASP209 3.3 17.0 1.0
CG A:ASP91 3.4 12.8 1.0
CG A:ASP88 3.4 13.1 1.0
C2B A:NAP308 3.7 17.5 1.0
O3B A:NAP308 3.7 14.2 1.0
CA A:CA302 3.8 13.2 1.0
CB A:ASP91 3.9 12.5 1.0
CA A:ASP91 4.0 12.6 1.0
O3X A:NAP308 4.0 18.3 1.0
O1X A:NAP308 4.0 15.9 1.0
OD1 A:ASP88 4.1 13.9 1.0
OD2 A:ASP209 4.1 16.1 1.0
OE2 A:GLU70 4.2 20.3 1.0
CD1 A:TRP208 4.2 13.7 1.0
C1B A:NAP308 4.2 19.1 1.0
C3B A:NAP308 4.3 17.4 1.0
CB A:ASP209 4.3 15.1 1.0
CA A:ASP209 4.3 14.4 1.0
OD2 A:ASP91 4.4 11.9 1.0
CB A:ASP88 4.5 11.8 1.0
O A:HOH479 4.6 25.6 1.0
NE1 A:TRP208 4.6 14.9 1.0
N A:GLY92 4.7 13.5 1.0
N A:ASP209 4.7 13.6 1.0
C A:ASP91 4.8 12.9 1.0
O A:ILE90 4.8 13.4 1.0
N9A A:NAP308 5.0 20.4 1.0

Calcium binding site 2 out of 4 in 5eyg

Go back to Calcium Binding Sites List in 5eyg
Calcium binding site 2 out of 4 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+


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+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:13.2
occ:1.00
 O2X A:NAP308 2.2 15.6 1.0
OD1 A:ASP88 2.3 13.9 1.0
O A:HOH468 2.3 12.9 1.0
OE2 A:GLU70 2.3 20.3 1.0
O A:ILE90 2.3 13.4 1.0
O A:HOH411 2.4 12.8 1.0
CG A:ASP88 3.1 13.1 1.0
OD2 A:ASP88 3.2 15.0 1.0
CD A:GLU70 3.4 20.5 1.0
C A:ILE90 3.4 12.7 1.0
P2B A:NAP308 3.5 18.0 1.0
OG1 A:THR93 3.7 16.2 1.0
CA A:CA301 3.8 16.8 1.0
OE1 A:GLU70 4.0 24.6 1.0
CA A:ASP91 4.1 12.6 1.0
O3X A:NAP308 4.1 18.3 1.0
N A:ASP91 4.1 12.5 1.0
O A:HOH458 4.2 14.6 1.0
OD2 A:ASP47 4.2 20.1 1.0
O1X A:NAP308 4.3 15.9 1.0
O A:HOH443 4.4 21.1 1.0
N A:ILE90 4.4 12.4 1.0
CG A:GLU70 4.4 18.2 1.0
CA A:ILE90 4.4 12.3 1.0
OE2 A:GLU71 4.5 16.7 1.0
CB A:ASP88 4.6 11.8 1.0
CB A:GLU70 4.6 16.3 1.0
O2B A:NAP308 4.7 16.2 1.0
O A:HOH409 4.7 19.3 1.0
CB A:ILE90 4.9 12.0 1.0
CD A:PRO89 4.9 12.1 1.0
CB A:THR93 5.0 14.9 1.0

Calcium binding site 3 out of 4 in 5eyg

Go back to Calcium Binding Sites List in 5eyg
Calcium binding site 3 out of 4 in the Crystal Structure of Impase/Nadp Phosphatase Complexed with Nadp and CA2+


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+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:27.4
occ:1.00
 OD1 B:ASP209 2.0 23.0 1.0
OD2 B:ASP88 2.2 20.9 1.0
O1X B:NAP304 2.2 30.9 1.0
OD1 B:ASP91 2.2 16.6 1.0
O2B B:NAP304 2.5 31.2 1.0
O B:HOH420 2.6 26.7 1.0
P2B B:NAP304 3.1 32.4 1.0
CG B:ASP209 3.2 21.0 1.0
CG B:ASP91 3.2 14.9 1.0
CG B:ASP88 3.4 15.9 1.0
CB B:ASP91 3.7 14.3 1.0
C2B B:NAP304 3.8 35.2 1.0
O3B B:NAP304 3.8 21.0 1.0
CA B:ASP91 3.9 13.4 1.0
CA B:CA302 4.0 29.1 1.0
OD1 B:ASP88 4.0 15.6 1.0
O3X B:NAP304 4.1 23.8 1.0
CA B:ASP209 4.1 16.2 1.0
CB B:ASP209 4.1 19.1 1.0
OD2 B:ASP209 4.1 21.3 1.0
O2X B:NAP304 4.2 29.5 1.0
CD1 B:TRP208 4.3 17.7 1.0
OD2 B:ASP91 4.3 15.1 1.0
C3B B:NAP304 4.4 32.1 1.0
C1B B:NAP304 4.4 36.9 1.0
CB B:ASP88 4.4 14.8 1.0
N B:ASP209 4.5 15.2 1.0
N B:GLY92 4.7 15.1 1.0
O B:ILE90 4.8 11.8 1.0
C B:ASP91 4.8 13.9 1.0
NE1 B:TRP208 4.8 17.8 1.0
N B:ASP91 4.9 13.3 1.0
O B:HOH416 5.0 9.2 1.0

Calcium binding site 4 out of 4 in 5eyg

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


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+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:29.1
occ:1.00
 O B:HOH403 1.7 8.2 1.0
OD1 B:ASP88 2.5 15.6 1.0
O1X B:NAP304 2.5 30.9 1.0
O B:ILE90 2.5 11.8 1.0
O B:HOH416 2.6 9.2 1.0
O B:HOH425 2.7 24.9 1.0
CG B:ASP88 3.3 15.9 1.0
OD2 B:ASP88 3.4 20.9 1.0
O B:HOH433 3.6 48.4 1.0
C B:ILE90 3.6 13.5 1.0
P2B B:NAP304 3.7 32.4 1.0
OD2 B:ASP47 3.9 15.5 0.5
CA B:CA301 4.0 27.4 1.0
OE1 B:GLU70 4.0 25.3 1.0
O B:HOH420 4.1 26.7 1.0
OG1 B:THR93 4.1 16.1 1.0
O3X B:NAP304 4.2 23.8 1.0
CA B:ASP91 4.3 13.4 1.0
N B:ASP91 4.4 13.3 1.0
O2X B:NAP304 4.4 29.5 1.0
N B:ILE90 4.5 13.1 1.0
CA B:ILE90 4.5 14.1 1.0
CG B:ASP47 4.6 16.7 0.5
OD2 B:ASP47 4.7 26.1 0.5
CB B:ASP88 4.7 14.8 1.0
O2B B:NAP304 4.9 31.2 1.0
CB B:ILE90 4.9 16.7 1.0
OD1 B:ASP47 4.9 15.3 0.5
O B:HOH514 4.9 6.9 1.0
CD1 B:TRP208 4.9 17.7 1.0
CG B:ASP47 5.0 22.3 0.5

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 18:54:56 2024

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