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Calcium in PDB 3ams: Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate

Enzymatic activity of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate

All present enzymatic activity of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate:
3.1.3.8;

Protein crystallography data

The structure of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate, PDB code: 3ams was solved by Y.F.Zeng, T.P.Ko, H.L.Lai, Y.S.Cheng, T.H.Wu, Y.Ma, C.S.Yang, K.J.Cheng, C.H.Huang, R.T.Guo, J.R.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.08
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 89.897, 73.544, 52.533, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.9

Other elements in 3ams:

The structure of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate also contains other interesting chemical elements:

Cadmium (Cd) 7 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate (pdb code 3ams). 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 Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate, PDB code: 3ams:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3ams

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Calcium binding site 1 out of 4 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:24.1
occ:1.00
 OD1 A:ASP313 2.2 24.9 1.0
O A:ILE312 2.4 27.2 1.0
OD1 A:ASP280 2.4 24.7 1.0
O A:HOH401 2.4 28.3 1.0
OD1 A:ASN311 2.5 27.0 1.0
OE1 A:GLU15 2.5 30.3 1.0
OE2 A:GLU15 2.7 32.4 1.0
CD A:GLU15 2.9 32.5 1.0
CG A:ASP280 3.3 26.3 1.0
C A:ILE312 3.3 26.9 1.0
CG A:ASP313 3.4 29.2 1.0
CG A:ASN311 3.6 28.6 1.0
NZ A:LYS323 3.8 25.0 1.0
OD2 A:ASP280 3.8 24.4 1.0
CA A:ASP313 4.0 28.9 1.0
N A:ASP313 4.0 26.7 1.0
N A:ILE312 4.0 25.7 1.0
ND2 A:ASN311 4.0 25.5 1.0
CB A:ASP313 4.3 27.8 1.0
CB A:ASP280 4.3 24.7 1.0
OD2 A:ASP313 4.3 30.3 1.0
N A:ASP280 4.3 23.5 1.0
CA A:ILE312 4.4 25.8 1.0
CE A:LYS323 4.4 22.1 1.0
ND2 A:ASN321 4.4 24.1 1.0
CG A:GLU15 4.5 29.5 1.0
O A:HOH564 4.6 50.9 1.0
O A:HOH568 4.6 43.9 1.0
C A:ASN311 4.8 27.0 1.0
CB A:ASN311 4.9 27.3 1.0
CA A:ASP280 5.0 25.0 1.0
CB A:THR279 5.0 28.1 1.0

Calcium binding site 2 out of 4 in 3ams

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Calcium binding site 2 out of 4 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:20.8
occ:1.00
 O A:GLY281 2.3 24.1 1.0
O A:GLU310 2.4 25.6 1.0
OD2 A:ASP280 2.4 24.4 1.0
OD2 A:ASP308 2.4 22.5 1.0
O A:HOH402 2.6 30.1 1.0
O A:HOH445 2.7 32.2 1.0
OD1 A:ASP308 3.1 22.3 1.0
CG A:ASP308 3.1 24.2 1.0
C A:GLU310 3.4 27.3 1.0
C A:GLY281 3.4 25.2 1.0
CG A:ASP280 3.5 26.3 1.0
CA A:THR282 4.0 24.1 1.0
CA A:ASN311 4.0 27.7 1.0
CB A:ASP280 4.1 24.7 1.0
N A:ASN311 4.1 26.8 1.0
N A:THR282 4.1 25.9 1.0
NZ A:LYS323 4.2 25.0 1.0
O A:HOH446 4.3 64.3 1.0
N A:ILE312 4.3 25.7 1.0
N A:GLY281 4.4 27.1 1.0
OD1 A:ASP280 4.4 24.7 1.0
CA A:GLU310 4.5 29.0 1.0
C A:THR282 4.5 25.8 1.0
CB A:GLU310 4.5 31.7 1.0
CA A:GLY281 4.5 26.3 1.0
C A:ASP280 4.5 25.8 1.0
CB A:ASP308 4.6 22.7 1.0
C A:ASN311 4.6 27.0 1.0
CE A:LYS323 4.7 22.1 1.0
N A:SER283 4.7 26.1 1.0
O A:HOH447 4.7 41.2 1.0
OG A:SER283 4.7 31.2 1.0
CG1 A:ILE312 4.8 27.4 1.0
N A:GLU310 4.8 28.5 1.0
O A:ASP280 4.9 25.2 1.0

Calcium binding site 3 out of 4 in 3ams

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Calcium binding site 3 out of 4 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:29.6
occ:1.00
 O A:HOH409 2.2 25.2 1.0
O A:HOH488 2.4 30.4 1.0
O A:HOH410 2.4 25.8 1.0
O A:PRO29 2.4 22.8 1.0
OD2 A:ASP28 2.4 25.1 1.0
O A:VAL73 2.5 20.5 1.0
OD1 A:ASP28 2.7 27.6 1.0
CG A:ASP28 2.9 26.1 1.0
C A:PRO29 3.6 23.5 1.0
C A:VAL73 3.7 23.0 1.0
O A:HOH548 4.2 29.1 1.0
N A:PRO29 4.3 22.1 1.0
N A:VAL73 4.3 24.3 1.0
CB A:ASP28 4.4 23.8 1.0
CG1 A:VAL73 4.4 21.0 1.0
N A:ALA30 4.4 22.8 1.0
CA A:ASP74 4.5 24.6 1.0
O A:HOH490 4.5 35.9 1.0
CA A:ALA30 4.5 22.2 1.0
CB A:ALA30 4.5 22.6 1.0
N A:ASP74 4.5 22.5 1.0
OD1 A:ASP289 4.5 31.9 1.0
O A:HOH489 4.6 40.6 1.0
CA A:PRO29 4.6 22.8 1.0
CA A:VAL73 4.6 22.3 1.0
CD A:PRO29 4.7 21.7 1.0
OD1 A:ASP74 4.7 32.0 1.0
C A:ASP28 4.7 23.7 1.0
O A:ILE288 4.7 23.4 1.0
CB A:ASP74 4.8 27.0 1.0
CG A:ASP289 4.9 28.9 1.0

Calcium binding site 4 out of 4 in 3ams

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Calcium binding site 4 out of 4 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CD2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca910

b:32.0
occ:1.00
 O A:HOH522 1.9 25.8 1.0
NE2 A:HIS121 2.0 38.3 1.0
O A:HOH524 2.1 33.8 1.0
O A:HOH523 2.5 45.5 1.0
CD2 A:HIS121 3.0 38.9 1.0
O A:HOH702 3.1 66.4 1.0
CE1 A:HIS121 3.1 39.5 1.0
CG A:HIS121 4.1 36.6 1.0
ND1 A:HIS121 4.2 38.7 1.0
OD2 A:ASP118 4.3 35.5 1.0

Reference:

Y.F.Zeng, T.P.Ko, H.L.Lai, Y.S.Cheng, T.H.Wu, Y.Ma, C.C.Chen, C.S.Yang, K.J.Cheng, C.H.Huang, R.T.Guo, J.R.Liu. Crystal Structures of Bacillus Alkaline Phytase in Complex with Divalent Metal Ions and Inositol Hexasulfate J.Mol.Biol. V. 409 214 2011.
ISSN: ISSN 0022-2836
PubMed: 21463636
DOI: 10.1016/J.JMB.2011.03.063
Page generated: Tue Jul 8 10:52:56 2025

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