Atomistry » Calcium » PDB 1gxr-1h71 » 1h6l
Atomistry »
  Calcium »
    PDB 1gxr-1h71 »
      1h6l »

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

Go back to Calcium Binding Sites List in 1h6l
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

Go back to Calcium Binding Sites List in 1h6l
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

Go back to Calcium Binding Sites List in 1h6l
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

Go back to Calcium Binding Sites List in 1h6l
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy