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

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

All present enzymatic activity of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, 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+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate, PDB code: 3amr 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) 23.95 / 1.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 90.129, 73.463, 52.810, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 17.8

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate (pdb code 3amr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate, PDB code: 3amr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 3amr

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Calcium binding site 1 out of 11 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, 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+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:13.4
occ:1.00
OD1 A:ASP313 2.2 17.4 1.0
O A:ILE312 2.3 14.3 1.0
OD1 A:ASP280 2.3 13.2 1.0
OE1 A:GLU15 2.4 14.0 1.0
O A:HOH855 2.4 17.9 1.0
OD1 A:ASN311 2.5 13.1 1.0
OE2 A:GLU15 2.5 20.2 1.0
CD A:GLU15 2.8 16.0 1.0
CG A:ASP280 3.3 12.3 1.0
C A:ILE312 3.4 15.8 1.0
CG A:ASP313 3.5 16.1 1.0
CG A:ASN311 3.6 13.1 1.0
NZ A:LYS323 3.9 12.9 1.0
OD2 A:ASP280 4.0 12.6 1.0
CA A:ASP313 4.0 15.2 1.0
N A:ASP313 4.0 14.6 1.0
ND2 A:ASN311 4.1 14.3 1.0
N A:ILE312 4.2 13.8 1.0
N A:ASP280 4.3 15.2 1.0
CB A:ASP313 4.3 15.7 1.0
CB A:ASP280 4.3 14.3 1.0
CG A:GLU15 4.3 14.9 1.0
OD2 A:ASP313 4.3 17.3 1.0
CA A:ILE312 4.4 14.7 1.0
O A:HOH895 4.4 22.2 1.0
ND2 A:ASN321 4.5 13.5 1.0
CE A:LYS323 4.5 13.0 1.0
O A:HOH629 4.6 37.8 1.0
O A:HOH1031 4.6 36.1 1.0
O A:HOH954 4.7 24.5 1.0
O A:HOH456 4.7 26.9 1.0
CB A:ASN311 4.9 13.9 1.0
C A:ASN311 4.9 13.8 1.0
CA A:ASP280 4.9 14.3 1.0

Calcium binding site 2 out of 11 in 3amr

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Calcium binding site 2 out of 11 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, 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+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:16.0
occ:1.00
O A:HOH847 1.9 32.6 1.0
O A:HOH848 2.0 21.3 1.0
OD1 A:ASP220 2.0 15.6 1.0
ND1 A:HIS226 2.1 24.6 1.0
O A:HOH846 2.2 17.0 1.0
OD2 A:ASP220 2.3 16.4 1.0
CG A:ASP220 2.5 14.2 1.0
CE1 A:HIS226 3.0 24.5 1.0
CG A:HIS226 3.2 16.2 1.0
CB A:HIS226 3.6 14.4 1.0
O A:HOH443 3.9 39.9 1.0
CB A:ASP220 4.0 13.4 1.0
O A:HOH718 4.1 51.4 1.0
N A:HIS226 4.1 13.2 1.0
OD2 A:ASP223 4.1 19.9 1.0
NE2 A:HIS226 4.1 22.3 1.0
CD2 A:HIS226 4.2 16.6 1.0
OD1 A:ASP223 4.3 15.1 1.0
O A:HOH747 4.3 52.3 1.0
O A:HOH561 4.4 98.9 1.0
CA A:HIS226 4.4 13.7 1.0
O A:ARG221 4.4 13.7 1.0
N A:ARG221 4.6 13.2 1.0
CG A:ASP223 4.6 16.6 1.0
CB A:ARG225 4.7 15.2 1.0
CA A:ASP220 4.8 14.5 1.0
OH A:TYR259 4.9 14.9 1.0
N A:LEU227 5.0 11.8 1.0

Calcium binding site 3 out of 11 in 3amr

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Calcium binding site 3 out of 11 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, 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+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:8.2
occ:1.00
OD1 A:ASP230 2.0 12.0 1.0
O A:HOH849 2.1 13.8 1.0
O A:HOH850 2.1 16.2 1.0
O A:HOH852 2.1 15.3 1.0
O A:HOH851 2.1 14.4 1.0
OD1 A:ASP200 2.1 13.1 1.0
CG A:ASP230 3.0 10.7 1.0
CG A:ASP200 3.1 13.7 1.0
OD2 A:ASP230 3.3 11.9 1.0
OD2 A:ASP200 3.3 20.9 1.0
O A:HOH363 4.0 42.6 1.0
O A:HOH1000 4.0 19.8 1.0
OE1 A:GLU199 4.2 12.8 1.0
O A:HOH969 4.3 25.5 1.0
CB A:ASP230 4.3 9.9 1.0
O A:HOH1131 4.4 43.3 1.0
CB A:ASP200 4.4 12.8 1.0
CB A:GLU199 4.5 11.7 1.0
CD A:ARG229 4.6 16.6 1.0
CA A:ASP230 4.7 9.6 1.0
CA A:ASP200 4.8 11.6 1.0
N A:ASP200 4.8 10.6 1.0
CB A:ARG229 4.9 12.0 1.0
N A:ASP230 4.9 10.2 1.0
CG A:ARG229 4.9 13.5 1.0
C A:GLU199 5.0 9.9 1.0

Calcium binding site 4 out of 11 in 3amr

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Calcium binding site 4 out of 11 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, 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+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:12.5
occ:1.00
O A:HOH859 2.0 21.7 1.0
NE2 A:HIS121 2.1 16.2 1.0
O A:HOH860 2.1 18.6 1.0
O A:HOH861 2.1 21.7 1.0
CD2 A:HIS121 3.0 15.7 1.0
CE1 A:HIS121 3.1 15.0 1.0
O A:HOH499 4.0 98.7 1.0
O A:HOH1146 4.1 31.9 1.0
OD2 A:ASP118 4.2 18.6 1.0
CG A:HIS121 4.2 14.0 1.0
ND1 A:HIS121 4.2 16.0 1.0
O A:HOH527 4.3 31.7 1.0
O A:HOH1066 4.3 68.0 1.0
O A:HOH1024 4.4 26.8 1.0

Calcium binding site 5 out of 11 in 3amr

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Calcium binding site 5 out of 11 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, 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 5 of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:10.6
occ:1.00
O A:HOH856 2.3 12.1 1.0
O A:VAL73 2.4 10.7 1.0
O A:PRO29 2.4 11.1 1.0
O A:HOH857 2.4 12.1 1.0
O A:HOH858 2.4 12.4 1.0
OD2 A:ASP28 2.5 14.1 1.0
OD1 A:ASP28 2.7 13.9 1.0
CG A:ASP28 3.0 11.8 1.0
C A:VAL73 3.6 9.9 1.0
C A:PRO29 3.6 10.7 1.0
N A:VAL73 4.3 9.5 1.0
OD1 A:ASP289 4.3 15.2 1.0
CB A:ASP28 4.4 10.8 1.0
N A:PRO29 4.4 10.1 1.0
N A:ALA30 4.4 11.4 1.0
CA A:ASP74 4.4 9.8 1.0
N A:ASP74 4.4 9.3 1.0
CB A:ALA30 4.4 11.7 1.0
O A:HOH983 4.5 14.0 1.0
O A:HOH885 4.5 14.4 1.0
CA A:ALA30 4.5 11.0 1.0
CA A:VAL73 4.5 10.4 1.0
O A:HOH987 4.6 17.8 1.0
CA A:PRO29 4.6 10.6 1.0
CD A:PRO29 4.7 10.3 1.0
CG1 A:VAL73 4.7 11.8 1.0
CB A:ASP74 4.7 10.3 1.0
C A:ASP28 4.7 10.3 1.0
OD1 A:ASP74 4.7 11.5 1.0
O A:ILE288 4.7 10.1 1.0
CG A:ASP289 4.9 13.1 1.0
CG A:ASP74 5.0 11.4 1.0

Calcium binding site 6 out of 11 in 3amr

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Calcium binding site 6 out of 11 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, 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 6 of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:13.0
occ:1.00
O A:HOH461 2.4 14.9 1.0
OD1 A:ASP286 2.4 14.4 1.0
OD1 A:ASP27 2.4 15.1 1.0
O A:HOH606 2.5 13.0 1.0
OE1 A:GLU183 2.5 11.4 1.0
OD2 A:ASP27 2.5 18.4 1.0
OE2 A:GLU183 2.6 12.0 1.0
CG A:ASP27 2.8 15.0 1.0
O32 A:IHS900 2.9 11.9 1.0
CD A:GLU183 2.9 10.6 1.0
CG A:ASP286 3.2 13.1 1.0
O A:HOH745 3.4 38.9 1.0
CB A:ASP286 3.6 11.3 1.0
OE1 A:GLU232 3.8 12.4 1.0
O42 A:IHS900 3.8 12.1 1.0
CA A:CA908 3.9 10.2 1.0
S2 A:IHS900 3.9 11.5 1.0
OD2 A:ASP286 4.3 12.2 1.0
CB A:ASP27 4.3 14.9 1.0
ND2 A:ASN72 4.4 11.3 1.0
CG A:GLU183 4.4 10.7 1.0
OD1 A:ASN71 4.5 14.8 1.0
ND2 A:ASN71 4.5 12.7 1.0
OH A:TYR131 4.6 13.3 1.0
CA A:ASP286 4.6 10.2 1.0
O A:HOH512 4.6 0.9 1.0
CD A:GLU232 4.7 9.9 1.0
O22 A:IHS900 4.7 10.8 1.0
O A:HOH914 4.7 15.2 1.0
O A:HOH844 4.7 15.3 1.0
CE1 A:TYR131 4.8 12.2 1.0
O2 A:IHS900 4.9 16.2 1.0
NZ A:LYS48 4.9 23.5 1.0
CZ A:TYR131 4.9 11.8 1.0
CG A:ASN71 5.0 12.8 1.0

Calcium binding site 7 out of 11 in 3amr

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Calcium binding site 7 out of 11 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, 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 7 of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:11.7
occ:1.00
OD2 A:ASP286 2.3 12.2 1.0
O A:HOH844 2.3 15.3 1.0
O A:HOH842 2.3 14.6 1.0
OD2 A:ASP24 2.4 13.7 1.0
O A:HOH843 2.4 12.6 1.0
O42 A:IHS900 2.5 12.1 1.0
OD1 A:ASP24 2.5 13.6 1.0
CG A:ASP24 2.8 12.6 1.0
CG A:ASP286 3.3 13.1 1.0
S2 A:IHS900 3.6 11.5 1.0
O22 A:IHS900 3.7 10.8 1.0
OD1 A:ASP286 3.8 14.4 1.0
NZ A:LYS48 4.0 23.5 1.0
OD1 A:ASP27 4.2 15.1 1.0
CB A:ASP24 4.3 14.8 1.0
NE2 A:GLN307 4.3 12.1 1.0
O A:HOH898 4.3 18.2 1.0
NE2 A:GLN251 4.3 10.6 1.0
CB A:ASP286 4.4 11.3 1.0
C2 A:IHS900 4.5 16.1 1.0
O12 A:IHS900 4.6 12.9 1.0
O34 A:IHS900 4.6 34.8 1.0
O A:ASP284 4.7 11.1 1.0
O32 A:IHS900 4.7 11.9 1.0
NE2 A:GLN320 4.7 11.9 1.0
O13 A:IHS900 4.8 17.2 1.0
CE A:LYS48 4.8 21.2 1.0
O14 A:IHS900 4.8 28.9 1.0
O A:ALA26 4.9 12.5 1.0
O A:HOH1203 5.0 27.9 1.0

Calcium binding site 8 out of 11 in 3amr

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Calcium binding site 8 out of 11 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, 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 8 of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:10.2
occ:1.00
OE2 A:GLU183 2.3 12.0 1.0
OE2 A:GLU199 2.3 14.8 1.0
O32 A:IHS900 2.4 11.9 1.0
OE2 A:GLU232 2.4 11.6 1.0
O A:HOH845 2.5 12.1 1.0
OE1 A:GLU232 2.5 12.4 1.0
OH A:TYR131 2.5 13.3 1.0
CD A:GLU232 2.9 9.9 1.0
CD A:GLU199 3.2 12.1 1.0
CZ A:TYR131 3.5 11.8 1.0
CD A:GLU183 3.5 10.6 1.0
S2 A:IHS900 3.6 11.5 1.0
OE1 A:GLU199 3.6 12.8 1.0
O22 A:IHS900 3.8 10.8 1.0
CA A:CA909 3.8 15.0 1.0
CA A:CA906 3.9 13.0 1.0
OD1 A:ASP286 4.0 14.4 1.0
CE2 A:TYR131 4.0 12.4 1.0
CB A:GLU183 4.0 11.6 1.0
O12 A:IHS900 4.1 12.9 1.0
O A:HOH606 4.3 13.0 1.0
CG A:GLU183 4.3 10.7 1.0
OE1 A:GLN181 4.3 18.4 1.0
CG A:GLU232 4.4 10.1 1.0
OE1 A:GLU183 4.4 11.4 1.0
CG A:GLU199 4.4 12.6 1.0
CE1 A:TYR131 4.5 12.2 1.0
O A:HOH512 4.6 0.9 1.0
O4 A:IHS900 4.6 16.9 1.0
O A:HOH890 4.7 13.2 1.0
O A:HOH461 4.7 14.9 1.0
O42 A:IHS900 4.7 12.1 1.0
O A:HOH1092 4.7 25.9 1.0

Calcium binding site 9 out of 11 in 3amr

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Calcium binding site 9 out of 11 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, 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 9 of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:15.0
occ:1.00
O43 A:IHS900 2.3 22.8 1.0
OD2 A:ASP230 2.3 11.9 1.0
OE2 A:GLU232 2.4 11.6 1.0
OE1 A:GLN251 2.4 10.7 1.0
O22 A:IHS900 2.4 10.8 1.0
O A:HOH845 2.6 12.1 1.0
O33 A:IHS900 3.1 26.3 1.0
S3 A:IHS900 3.2 19.6 1.0
CG A:ASP230 3.3 10.7 1.0
CD A:GLN251 3.4 9.9 1.0
CD A:GLU232 3.5 9.9 1.0
S2 A:IHS900 3.5 11.5 1.0
CB A:ASP230 3.6 9.9 1.0
NE2 A:GLN251 3.6 10.6 1.0
O13 A:IHS900 3.8 17.2 1.0
CA A:CA908 3.8 10.2 1.0
O12 A:IHS900 3.8 12.9 1.0
O32 A:IHS900 3.9 11.9 1.0
O A:HOH607 4.1 12.4 1.0
CG A:GLU232 4.1 10.1 1.0
OE1 A:GLU199 4.2 12.8 1.0
O A:HOH851 4.4 14.4 1.0
OE1 A:GLU232 4.4 12.4 1.0
OD1 A:ASP230 4.5 12.0 1.0
O23 A:IHS900 4.5 24.1 1.0
C3 A:IHS900 4.6 18.1 1.0
CD A:GLU199 4.7 12.1 1.0
CG A:GLN251 4.7 10.9 1.0
O42 A:IHS900 4.8 12.1 1.0
OD1 A:ASP286 4.8 14.4 1.0
C2 A:IHS900 4.8 16.1 1.0
O A:HOH842 4.8 14.6 1.0
OE2 A:GLU199 4.8 14.8 1.0
O A:HOH1092 4.8 25.9 1.0
O A:HOH1043 5.0 31.4 1.0

Calcium binding site 10 out of 11 in 3amr

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Calcium binding site 10 out of 11 in the Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, 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 10 of Crystal Structures of Bacillus Subtilis Alkaline Phytase in Complex with CA2+, CO2+, NI2+, MG2+ and Myo-Inositol Hexasulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca910

b:12.2
occ:1.00
O A:GLU310 2.3 12.8 1.0
O A:GLY281 2.3 13.9 1.0
O A:HOH853 2.4 15.2 1.0
OD2 A:ASP280 2.4 12.6 1.0
OD2 A:ASP308 2.4 12.4 1.0
O A:HOH854 2.4 14.5 1.0
CG A:ASP308 3.1 11.7 1.0
OD1 A:ASP308 3.2 11.3 1.0
C A:GLU310 3.4 12.1 1.0
CG A:ASP280 3.5 12.3 1.0
C A:GLY281 3.5 11.9 1.0
CA A:ASN311 3.9 12.6 1.0
CB A:ASP280 4.0 14.3 1.0
CA A:THR282 4.1 12.0 1.0
N A:ASN311 4.1 12.6 1.0
N A:ILE312 4.2 13.8 1.0
N A:THR282 4.2 12.5 1.0
O A:HOH642 4.2 0.7 1.0
NZ A:LYS323 4.3 12.9 1.0
OD1 A:ASP280 4.4 13.2 1.0
O A:HOH989 4.4 20.7 1.0
CA A:GLU310 4.5 12.3 1.0
N A:GLY281 4.5 13.3 1.0
C A:THR282 4.5 10.9 1.0
C A:ASN311 4.5 13.8 1.0
CA A:GLY281 4.6 14.7 1.0
CB A:GLU310 4.6 13.8 1.0
CB A:ASP308 4.6 11.9 1.0
C A:ASP280 4.6 13.5 1.0
O A:HOH1096 4.6 34.5 1.0
N A:SER283 4.7 12.5 1.0
OG A:SER283 4.7 15.7 1.0
O A:HOH929 4.8 21.2 1.0
N A:GLU310 4.8 11.7 1.0
CE A:LYS323 4.9 13.0 1.0
O A:ASP280 4.9 13.5 1.0
CA A:ASP280 5.0 14.3 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: Sat Jul 13 07:53:59 2024

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