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Calcium in PDB 2poo: Thermostable Phytase in Fully Calcium Loaded State

Enzymatic activity of Thermostable Phytase in Fully Calcium Loaded State

All present enzymatic activity of Thermostable Phytase in Fully Calcium Loaded State:
3.1.3.8;

Protein crystallography data

The structure of Thermostable Phytase in Fully Calcium Loaded State, PDB code: 2poo was solved by N.-C.Ha, B.-H.Oh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.980, 65.150, 105.680, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Thermostable Phytase in Fully Calcium Loaded State (pdb code 2poo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Thermostable Phytase in Fully Calcium Loaded State, PDB code: 2poo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2poo

Go back to Calcium Binding Sites List in 2poo
Calcium binding site 1 out of 6 in the Thermostable Phytase in Fully Calcium Loaded State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thermostable Phytase in Fully Calcium Loaded State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:22.9
occ:1.00
 OD1 A:ASP308 2.5 17.5 1.0
OD1 A:ASP341 2.6 38.9 1.0
OE1 A:GLU43 2.6 19.8 1.0
OE2 A:GLU43 2.7 24.6 1.0
O A:ILE340 2.7 27.6 1.0
OD1 A:ASN339 2.8 23.1 1.0
CD A:GLU43 3.0 16.2 1.0
O A:HOH529 3.1 28.8 1.0
CG A:ASP308 3.4 15.8 1.0
C A:ILE340 3.6 26.6 1.0
CG A:ASP341 3.6 33.3 1.0
CG A:ASN339 3.8 21.5 1.0
OD2 A:ASP308 4.0 18.4 1.0
CA A:ASP341 4.1 32.0 1.0
NZ A:LYS351 4.1 8.0 1.0
N A:ASP341 4.1 29.3 1.0
N A:ILE340 4.2 22.2 1.0
ND2 A:ASN339 4.2 20.3 1.0
OD2 A:ASP341 4.2 31.9 1.0
CB A:ASP308 4.3 19.6 1.0
CB A:ASP341 4.4 34.3 1.0
N A:ASP308 4.4 18.9 1.0
O A:HOH555 4.5 65.3 1.0
CG A:GLU43 4.5 19.9 1.0
CA A:ILE340 4.5 22.6 1.0
CE A:LYS351 4.6 8.5 1.0
OD1 A:ASN349 4.7 20.0 1.0
C A:ASN339 4.9 19.4 1.0

Calcium binding site 2 out of 6 in 2poo

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Calcium binding site 2 out of 6 in the Thermostable Phytase in Fully Calcium Loaded State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thermostable Phytase in Fully Calcium Loaded State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:28.0
occ:1.00
 O A:GLU338 2.3 25.3 1.0
O A:GLY309 2.4 19.4 1.0
OD1 A:ASP336 2.5 14.9 1.0
OD2 A:ASP308 2.6 18.4 1.0
O A:HOH507 2.7 36.9 1.0
O A:HOH554 2.9 46.8 1.0
OD2 A:ASP336 3.1 4.3 1.0
CG A:ASP336 3.2 7.3 1.0
C A:GLY309 3.5 18.2 1.0
C A:GLU338 3.5 22.8 1.0
CG A:ASP308 3.6 15.8 1.0
CA A:THR310 4.1 14.5 1.0
N A:THR310 4.2 18.0 1.0
CA A:ASN339 4.2 21.5 1.0
N A:ASN339 4.2 21.7 1.0
CB A:ASP308 4.3 19.6 1.0
N A:GLY309 4.3 17.3 1.0
OD1 A:ASP308 4.4 17.5 1.0
NZ A:LYS351 4.4 8.0 1.0
CA A:GLY309 4.4 15.9 1.0
CA A:GLU338 4.4 21.7 1.0
N A:ILE340 4.5 22.2 1.0
OG A:SER311 4.5 12.8 1.0
C A:ASP308 4.6 16.6 1.0
CB A:GLU338 4.6 28.2 1.0
CD1 A:ILE340 4.6 35.1 1.0
C A:THR310 4.6 12.8 1.0
CB A:ASP336 4.7 11.0 1.0
N A:SER311 4.7 16.0 1.0
N A:GLU338 4.7 18.6 1.0
C A:ASN339 4.8 19.4 1.0
CE A:LYS351 4.9 8.5 1.0
O A:ASP308 4.9 18.2 1.0

Calcium binding site 3 out of 6 in 2poo

Go back to Calcium Binding Sites List in 2poo
Calcium binding site 3 out of 6 in the Thermostable Phytase in Fully Calcium Loaded State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thermostable Phytase in Fully Calcium Loaded State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:39.9
occ:1.00
 OE1 A:GLU260 2.5 26.4 1.0
OE2 A:GLU227 2.6 27.1 1.0
OH A:TYR159 2.8 42.0 1.0
OE2 A:GLU260 2.9 28.4 1.0
CD A:GLU260 3.1 28.6 1.0
O A:HOH552 3.3 69.7 1.0
OE1 A:GLU211 3.4 37.1 1.0
CD A:GLU211 3.4 22.5 1.0
OE2 A:GLU211 3.4 31.5 1.0
CZ A:TYR159 3.5 34.4 1.0
CD A:GLU227 3.6 23.4 1.0
CE2 A:TYR159 3.7 32.8 1.0
OE1 A:GLU227 4.0 28.2 1.0
CB A:GLU211 4.1 25.1 1.0
CA A:CA806 4.1 57.4 1.0
OD1 A:ASP314 4.3 34.7 1.0
CG A:GLU211 4.3 28.4 1.0
CG A:GLU260 4.6 19.5 1.0
CE1 A:TYR159 4.6 33.3 1.0
CG A:GLU227 4.8 22.3 1.0
CD2 A:TYR159 4.9 25.9 1.0

Calcium binding site 4 out of 6 in 2poo

Go back to Calcium Binding Sites List in 2poo
Calcium binding site 4 out of 6 in the Thermostable Phytase in Fully Calcium Loaded State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thermostable Phytase in Fully Calcium Loaded State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca804

b:71.1
occ:1.00
 O A:HOH552 2.6 69.7 1.0
OD1 A:ASN100 2.7 27.2 1.0
OD2 A:ASP55 2.7 40.6 1.0
OE2 A:GLU211 2.8 31.5 1.0
OD1 A:ASP55 2.9 40.7 1.0
OE1 A:GLU211 3.1 37.1 1.0
CD A:GLU211 3.1 22.5 1.0
CG A:ASP55 3.2 33.7 1.0
OD1 A:ASN99 3.4 40.6 1.0
O A:HOH522 3.4 44.8 1.0
ND2 A:ASN99 3.6 30.5 1.0
CG A:ASN100 3.7 19.7 1.0
CG A:ASN99 3.8 37.8 1.0
ND2 A:ASN100 4.0 22.0 1.0
O A:ASN99 4.3 36.9 1.0
CG A:GLU211 4.4 28.4 1.0
CB A:ASP314 4.6 20.2 1.0
CB A:ASP55 4.6 26.6 1.0
C A:ASN99 4.7 35.2 1.0
CB A:ASP56 4.8 12.4 1.0
CG A:ASP314 4.9 27.5 1.0
OD1 A:ASP314 5.0 34.7 1.0

Calcium binding site 5 out of 6 in 2poo

Go back to Calcium Binding Sites List in 2poo
Calcium binding site 5 out of 6 in the Thermostable Phytase in Fully Calcium Loaded State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Thermostable Phytase in Fully Calcium Loaded State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca805

b:19.4
occ:1.00
 OD2 A:ASP56 2.3 18.2 1.0
O A:VAL101 2.5 21.2 1.0
O A:HOH533 2.5 16.9 1.0
O A:HOH526 2.5 13.0 1.0
O A:HOH515 2.6 14.2 1.0
O A:PRO57 2.7 8.9 1.0
CG A:ASP56 3.4 15.0 1.0
C A:VAL101 3.6 15.1 1.0
OD1 A:ASP56 3.8 22.0 1.0
C A:PRO57 3.9 5.4 1.0
CA A:ASP102 4.2 7.4 1.0
N A:ASP102 4.3 11.9 1.0
O A:HOH504 4.4 20.4 1.0
O A:HOH558 4.4 26.2 1.0
CB A:ASP102 4.5 11.1 1.0
O A:HOH534 4.5 7.0 1.0
N A:VAL101 4.5 12.7 1.0
OD2 A:ASP317 4.5 14.6 1.0
CB A:ALA58 4.5 11.3 1.0
CA A:ALA58 4.5 8.7 1.0
N A:ALA58 4.6 4.9 1.0
OD1 A:ASP102 4.6 17.7 1.0
CG A:ASP317 4.7 5.1 1.0
N A:PRO57 4.7 9.8 1.0
CG A:ASP102 4.7 12.1 1.0
CB A:ASP56 4.7 12.4 1.0
CA A:VAL101 4.7 10.8 1.0
O A:ILE316 4.8 19.0 1.0
CA A:PRO57 4.9 6.7 1.0
CB A:ASP317 5.0 11.2 1.0
CG1 A:VAL101 5.0 12.3 1.0

Calcium binding site 6 out of 6 in 2poo

Go back to Calcium Binding Sites List in 2poo
Calcium binding site 6 out of 6 in the Thermostable Phytase in Fully Calcium Loaded State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Thermostable Phytase in Fully Calcium Loaded State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca806

b:57.4
occ:1.00
 OD2 A:ASP258 2.7 31.3 1.0
OE2 A:GLU260 2.8 28.4 1.0
OE1 A:GLN279 3.1 33.6 1.0
CG A:ASP258 3.7 33.2 1.0
CD A:GLU260 3.9 28.6 1.0
CD A:GLN279 3.9 23.1 1.0
NE2 A:GLN279 4.0 20.4 1.0
CB A:ASP258 4.1 30.1 1.0
CA A:CA803 4.1 39.9 1.0
OD1 A:ASP314 4.6 34.7 1.0
OE1 A:GLU227 4.6 28.2 1.0
CG A:GLU260 4.7 19.5 1.0
OE1 A:GLU260 4.7 26.4 1.0
OD1 A:ASP258 4.9 34.0 1.0

Reference:

N.C.Ha, B.C.Oh, S.Shin, H.J.Kim, T.K.Oh, Y.O.Kim, K.Y.Choi, B.H.Oh. Crystal Structures of A Novel, Thermostable Phytase in Partially and Fully Calcium-Loaded States. Nat.Struct.Biol. V. 7 147 2000.
ISSN: ISSN 1072-8368
PubMed: 10655618
DOI: 10.1038/72421
Page generated: Tue Jul 8 07:44:57 2025

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