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Calcium in PDB 1h6l: Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions

Enzymatic activity of Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions

All present enzymatic activity of Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions:
3.1.3.8;

Protein crystallography data

The structure of Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions, PDB code: 1h6l was solved by S.Shin, 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) 20 / 1.8
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.378, 65.644, 104.767, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions (pdb code 1h6l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions, PDB code: 1h6l:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 1h6l

Go back to Calcium Binding Sites List in 1h6l
Calcium binding site 1 out of 7 in the Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:14.8
occ:1.00
 OD2 A:ASP308 2.6 14.9 1.0
OD1 A:ASN339 2.6 12.2 1.0
O A:ILE340 2.6 18.9 1.0
OE2 A:GLU43 2.7 15.9 1.0
OD1 A:ASP341 2.7 24.8 1.0
O A:HOH2004 2.7 22.3 1.0
OE1 A:GLU43 2.8 21.6 1.0
CD A:GLU43 3.1 20.4 1.0
O A:HOH2131 3.2 31.3 1.0
CG A:ASP308 3.4 14.8 1.0
C A:ILE340 3.5 20.0 1.0
CG A:ASP341 3.6 24.4 1.0
CG A:ASN339 3.7 14.8 1.0
OD1 A:ASP308 3.8 15.1 1.0
NZ A:LYS351 3.9 11.2 1.0
CA A:ASP341 4.0 23.4 1.0
N A:ASP341 4.1 21.2 1.0
ND2 A:ASN339 4.1 14.9 1.0
N A:ILE340 4.2 16.6 1.0
CB A:ASP308 4.4 15.2 1.0
OD2 A:ASP341 4.4 23.2 1.0
CB A:ASP341 4.4 23.5 1.0
CA A:ILE340 4.5 19.6 1.0
N A:ASP308 4.5 16.1 1.0
CG A:GLU43 4.6 16.1 1.0
OD1 A:ASN349 4.6 13.8 1.0
O A:HOH2129 4.6 32.1 1.0
CE A:LYS351 4.7 12.0 1.0
CG2 A:THR307 4.8 26.8 1.0
C A:ASN339 4.9 16.6 1.0
CB A:ASN339 5.0 15.0 1.0

Calcium binding site 2 out of 7 in 1h6l

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Calcium binding site 2 out of 7 in the Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:17.0
occ:1.00
 O A:GLY309 2.5 16.3 1.0
O A:GLU338 2.5 15.5 1.0
OD1 A:ASN336 2.6 13.9 1.0
O A:HOH2112 2.7 28.8 1.0
OD1 A:ASP308 2.7 15.1 1.0
O A:HOH2111 2.9 49.9 1.0
ND2 A:ASN336 3.2 9.4 1.0
CG A:ASN336 3.3 13.1 1.0
C A:GLY309 3.5 15.6 1.0
C A:GLU338 3.6 15.8 1.0
CG A:ASP308 3.6 14.8 1.0
CA A:ASN339 4.1 15.7 1.0
CA A:THR310 4.2 13.7 1.0
N A:THR310 4.3 14.7 1.0
CB A:ASP308 4.3 15.2 1.0
N A:ASN339 4.3 15.0 1.0
N A:GLY309 4.3 14.4 1.0
N A:ILE340 4.4 16.6 1.0
CA A:GLY309 4.5 14.8 1.0
NZ A:LYS351 4.5 11.2 1.0
OD2 A:ASP308 4.5 14.9 1.0
C A:ASP308 4.6 15.5 1.0
OG A:SER311 4.6 19.2 1.0
N A:SER311 4.6 14.2 1.0
CA A:GLU338 4.6 17.6 1.0
C A:THR310 4.7 13.7 1.0
C A:ASN339 4.7 16.6 1.0
CE A:LYS351 4.8 12.0 1.0
CG1 A:ILE340 4.8 21.9 1.0
CB A:ASN336 4.8 9.5 1.0
CB A:GLU338 4.9 22.9 1.0
N A:GLU338 4.9 13.2 1.0
O A:ASP308 4.9 15.5 1.0

Calcium binding site 3 out of 7 in 1h6l

Go back to Calcium Binding Sites List in 1h6l
Calcium binding site 3 out of 7 in the Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:11.2
occ:1.00
 O A:VAL101 2.5 11.0 1.0
O A:PRO57 2.5 9.5 1.0
O A:HOH2116 2.5 11.0 1.0
O A:HOH2117 2.5 9.5 1.0
O A:HOH2055 2.6 13.2 1.0
OD2 A:ASP56 2.6 12.6 1.0
OD1 A:ASP56 2.8 9.9 1.0
CG A:ASP56 3.1 10.9 1.0
C A:VAL101 3.7 12.2 1.0
C A:PRO57 3.7 11.5 1.0
OD2 A:ASP317 4.2 12.4 1.0
N A:VAL101 4.3 12.1 1.0
O A:HOH2071 4.4 15.7 1.0
N A:PRO57 4.4 10.4 1.0
O A:HOH2013 4.5 14.1 1.0
CB A:ASP56 4.5 10.0 1.0
CA A:ASP102 4.6 12.9 1.0
N A:ALA58 4.6 10.9 1.0
O A:HOH2089 4.6 18.1 1.0
CB A:ALA58 4.6 11.2 1.0
N A:ASP102 4.6 12.4 1.0
CA A:ALA58 4.6 10.6 1.0
CA A:VAL101 4.6 10.7 1.0
CG1 A:VAL101 4.7 11.3 1.0
CA A:PRO57 4.7 11.5 1.0
OD1 A:ASP102 4.7 11.8 1.0
C A:ASP56 4.8 10.0 1.0
O A:ILE316 4.8 10.5 1.0
CG A:ASP317 4.8 12.4 1.0
CB A:ASP102 4.9 11.6 1.0
CD A:PRO57 4.9 11.0 1.0
CG A:ASP102 5.0 14.2 1.0

Calcium binding site 4 out of 7 in 1h6l

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Calcium binding site 4 out of 7 in the Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:10.4
occ:1.00
 O1 A:PO4501 2.5 14.9 1.0
O A:HOH2087 2.6 13.7 1.0
O A:HOH2026 2.7 20.7 1.0
OD1 A:ASP55 2.7 12.2 1.0
OE1 A:GLU211 2.7 12.7 1.0
OD2 A:ASP55 2.7 9.5 1.0
OE2 A:GLU211 2.8 14.6 1.0
CG A:ASP55 3.1 11.7 1.0
CD A:GLU211 3.1 14.6 1.0
OD2 A:ASP314 3.4 13.0 1.0
P A:PO4501 3.7 18.5 1.0
O3 A:PO4501 3.7 14.7 1.0
CA A:CA405 3.7 11.4 1.0
CG A:ASP314 3.9 12.5 1.0
OE2 A:GLU260 4.0 14.2 1.0
CB A:ASP314 4.1 10.9 1.0
OH A:TYR159 4.4 14.7 1.0
ND2 A:ASN99 4.5 13.6 1.0
O4 A:PO4501 4.5 16.0 1.0
OD1 A:ASN99 4.5 14.0 1.0
CG A:GLU211 4.5 12.0 1.0
CB A:ASP55 4.5 9.3 1.0
OD1 A:ASN100 4.6 13.1 1.0
CE2 A:TYR159 4.6 13.7 1.0
O A:HOH2027 4.7 20.0 1.0
CZ A:TYR159 4.7 16.7 1.0
OD1 A:ASP314 4.7 13.2 1.0
O A:HOH2012 4.7 18.4 1.0
O3 A:PO4502 4.8 17.6 1.0
CD A:GLU260 4.8 17.0 1.0
O2 A:PO4501 4.8 13.2 1.0
NZ A:LYS76 4.9 15.8 1.0
CG A:ASN99 4.9 13.1 1.0

Calcium binding site 5 out of 7 in 1h6l

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Calcium binding site 5 out of 7 in the Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:11.4
occ:1.00
 O1 A:PO4501 2.4 14.9 1.0
O A:HOH2078 2.5 12.6 1.0
OE1 A:GLU211 2.6 12.7 1.0
OH A:TYR159 2.6 14.7 1.0
OE2 A:GLU260 2.7 14.2 1.0
OE1 A:GLU260 2.7 15.3 1.0
OE2 A:GLU227 2.8 23.2 1.0
CD A:GLU260 3.1 17.0 1.0
CD A:GLU227 3.4 21.4 1.0
CZ A:TYR159 3.5 16.7 1.0
OE1 A:GLU227 3.5 21.0 1.0
P A:PO4501 3.6 18.5 1.0
CA A:CA404 3.7 10.4 1.0
CD A:GLU211 3.8 14.6 1.0
CA A:CA406 3.8 14.2 1.0
CE1 A:TYR159 3.9 15.2 1.0
O2 A:PO4501 3.9 13.2 1.0
O4 A:PO4501 4.0 16.0 1.0
OD2 A:ASP314 4.2 13.0 1.0
O4 A:PO4502 4.3 15.2 1.0
CB A:GLU211 4.3 12.9 1.0
O A:HOH2087 4.4 13.7 1.0
OE1 A:GLN209 4.4 27.0 1.0
O A:HOH2145 4.5 20.9 1.0
CG A:GLU227 4.5 19.9 1.0
CE2 A:TYR159 4.5 13.7 1.0
CG A:GLU260 4.6 12.5 1.0
CG A:GLU211 4.6 12.0 1.0
OE2 A:GLU211 4.7 14.6 1.0
O A:HOH2086 4.7 15.0 1.0
O3 A:PO4501 4.9 14.7 1.0

Calcium binding site 6 out of 7 in 1h6l

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Calcium binding site 6 out of 7 in the Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:14.2
occ:1.00
 O A:HOH2143 2.5 59.3 1.0
OE1 A:GLN279 2.6 14.6 1.0
O4 A:PO4501 2.6 16.0 1.0
OD2 A:ASP258 2.7 14.9 1.0
OE1 A:GLU260 2.7 15.3 1.0
O A:HOH2078 2.7 12.6 1.0
O A:HOH2098 2.9 28.6 1.0
O2 A:PO4501 3.5 13.2 1.0
CD A:GLN279 3.5 15.7 1.0
P A:PO4501 3.5 18.5 1.0
CG A:ASP258 3.7 17.8 1.0
CD A:GLU260 3.8 17.0 1.0
NE2 A:GLN279 3.8 15.5 1.0
CA A:CA405 3.8 11.4 1.0
CB A:ASP258 3.9 15.6 1.0
O1 A:PO4501 3.9 14.9 1.0
OD2 A:ASP314 4.3 13.0 1.0
OE1 A:GLU227 4.3 21.0 1.0
O A:HOH2099 4.3 23.3 1.0
O A:HOH2144 4.3 37.8 1.0
CG A:GLU260 4.5 12.5 1.0
OE2 A:GLU260 4.6 14.2 1.0
O A:HOH2145 4.6 20.9 1.0
O A:HOH2114 4.7 28.9 1.0
OD1 A:ASP258 4.8 20.3 1.0
CG A:GLN279 4.9 13.4 1.0
O3 A:PO4501 4.9 14.7 1.0
CD A:GLU227 5.0 21.4 1.0

Calcium binding site 7 out of 7 in 1h6l

Go back to Calcium Binding Sites List in 1h6l
Calcium binding site 7 out of 7 in the Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Beta-Propeller Phytase in Complex with Phosphate and Calcium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:12.2
occ:1.00
 OD1 A:ASP314 2.5 13.2 1.0
O A:HOH2144 2.5 37.8 1.0
O3 A:PO4501 2.6 14.7 1.0
O A:HOH2012 2.6 18.4 1.0
OD1 A:ASP52 2.6 19.5 1.0
O A:HOH2113 2.7 13.0 1.0
OD2 A:ASP52 2.8 19.0 1.0
CG A:ASP52 3.1 20.9 1.0
O4 A:PO4501 3.4 16.0 1.0
CG A:ASP314 3.5 12.5 1.0
P A:PO4501 3.5 18.5 1.0
NZ A:LYS76 3.9 15.8 1.0
OD2 A:ASP314 3.9 13.0 1.0
O A:HOH2010 4.2 26.7 1.0
OD1 A:ASP55 4.2 12.2 1.0
NE2 A:GLN279 4.4 15.5 1.0
NE2 A:GLN335 4.4 12.9 1.0
O2 A:PO4501 4.5 13.2 1.0
CB A:ASP52 4.6 18.7 1.0
CB A:ASP314 4.6 10.9 1.0
CE A:LYS76 4.6 18.5 1.0
O1 A:PO4501 4.6 14.9 1.0
O A:ALA54 4.7 10.7 1.0
O A:ASP312 4.9 14.2 1.0
NE2 A:GLN348 4.9 13.5 1.0
OE1 A:GLN335 4.9 14.6 1.0
CD A:GLN335 5.0 12.2 1.0

Reference:

S.Shin, N.C.Ha, B.H.Oh, T.Oh, B.H.Oh. Enzyme Mechanism and Catalytic Property of Beta Propeller Phytase Structure V. 9 851 2001.
ISSN: ISSN 0969-2126
PubMed: 11566134
DOI: 10.1016/S0969-2126(01)00637-2
Page generated: Thu Jul 11 09:56:53 2024

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