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Cadmium 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:

Calcium (Ca) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 7 binding sites of Cadmium 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 Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 3ams

Go back to Cadmium Binding Sites List in 3ams
Cadmium binding site 1 out of 7 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 Cadmium with other atoms in the Cd 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:Cd904

b:34.8
occ:1.00
O A:HOH451 2.1 32.4 1.0
OD1 A:ASP286 2.3 35.9 1.0
OE1 A:GLU183 2.4 24.1 1.0
OD1 A:ASP27 2.5 29.5 1.0
O A:HOH547 2.6 30.1 1.0
OD2 A:ASP27 2.6 29.8 1.0
OE2 A:GLU183 2.6 19.6 1.0
CD A:GLU183 2.9 23.9 1.0
CG A:ASP27 2.9 29.1 1.0
O4 A:IHS4000 3.1 35.0 1.0
CG A:ASP286 3.4 29.8 1.0
CB A:ASP286 3.7 29.0 1.0
OE1 A:GLU232 3.9 27.9 1.0
CD A:CD905 4.0 35.9 1.0
O3 A:IHS4000 4.0 33.2 1.0
S1 A:IHS4000 4.1 36.7 1.0
ND2 A:ASN71 4.2 29.9 1.0
OD1 A:ASN71 4.3 28.0 1.0
CG A:GLU183 4.4 26.5 1.0
ND2 A:ASN72 4.4 27.6 1.0
CB A:ASP27 4.4 26.2 1.0
OD2 A:ASP286 4.5 28.3 1.0
NZ A:LYS48 4.5 34.4 1.0
O A:HOH491 4.5 34.9 1.0
OH A:TYR131 4.6 27.0 1.0
CG A:ASN71 4.7 28.8 1.0
O A:HOH529 4.7 38.3 1.0
CE1 A:TYR131 4.8 25.4 1.0
CA A:ASP286 4.8 26.1 1.0
O2 A:IHS4000 4.8 33.8 1.0
CD A:GLU232 4.9 25.0 1.0
CZ A:TYR131 4.9 27.8 1.0
O46 A:IHS4000 5.0 43.3 1.0

Cadmium binding site 2 out of 7 in 3ams

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Cadmium binding site 2 out of 7 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 Cadmium with other atoms in the Cd 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:Cd905

b:35.9
occ:1.00
OE2 A:GLU183 2.3 19.6 1.0
O4 A:IHS4000 2.4 35.0 1.0
OE2 A:GLU199 2.4 28.5 1.0
OE1 A:GLU232 2.4 27.9 1.0
OH A:TYR131 2.5 27.0 1.0
O A:HOH527 2.6 21.9 1.0
OE2 A:GLU232 2.6 24.5 1.0
CD A:GLU232 2.9 25.0 1.0
CD A:GLU199 3.2 29.6 1.0
OE1 A:GLU199 3.4 28.6 1.0
CZ A:TYR131 3.5 27.8 1.0
S1 A:IHS4000 3.5 36.7 1.0
CD A:GLU183 3.6 23.9 1.0
CD A:CD906 3.7 73.2 1.0
O2 A:IHS4000 3.8 33.8 1.0
CE2 A:TYR131 4.0 27.4 1.0
CD A:CD904 4.0 34.8 1.0
CB A:GLU183 4.0 23.4 1.0
O1 A:IHS4000 4.0 40.5 1.0
CG A:GLU183 4.3 26.5 1.0
O A:HOH547 4.3 30.1 1.0
OD1 A:ASP286 4.3 35.9 1.0
CG A:GLU232 4.4 24.8 1.0
OE1 A:GLN181 4.4 35.0 1.0
CE1 A:TYR131 4.4 25.4 1.0
OE1 A:GLU183 4.5 24.1 1.0
O26 A:IHS4000 4.5 40.3 1.0
CG A:GLU199 4.6 28.8 1.0
O A:HOH451 4.7 32.4 1.0
O3 A:IHS4000 4.7 33.2 1.0
O A:HOH494 4.8 31.3 1.0

Cadmium binding site 3 out of 7 in 3ams

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Cadmium binding site 3 out of 7 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 Cadmium with other atoms in the Cd 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:Cd906

b:73.2
occ:1.00
OE1 A:GLN251 2.3 27.3 1.0
OE2 A:GLU232 2.4 24.5 1.0
O2 A:IHS4000 2.4 33.8 1.0
OD2 A:ASP230 2.5 23.4 1.0
O32 A:IHS4000 2.6 48.0 1.0
O A:HOH527 2.6 21.9 1.0
CD A:GLN251 3.3 27.7 1.0
CG A:ASP230 3.4 29.4 1.0
CD A:GLU232 3.5 25.0 1.0
S1 A:IHS4000 3.5 36.7 1.0
S2 A:IHS4000 3.5 51.1 1.0
O42 A:IHS4000 3.6 50.2 1.0
NE2 A:GLN251 3.7 25.2 1.0
O1 A:IHS4000 3.7 40.5 1.0
CD A:CD905 3.7 35.9 1.0
CB A:ASP230 3.8 33.8 1.0
O4 A:IHS4000 3.9 35.0 1.0
O12 A:IHS4000 4.0 50.0 1.0
OE1 A:GLU199 4.0 28.6 1.0
CG A:GLU232 4.2 24.8 1.0
O A:HOH406 4.2 26.5 1.0
OE1 A:GLU232 4.3 27.9 1.0
O A:HOH448 4.3 23.0 1.0
OD1 A:ASP230 4.6 28.6 1.0
C2 A:IHS4000 4.7 48.6 1.0
CG A:GLN251 4.7 24.4 1.0
CD A:GLU199 4.7 29.6 1.0
C1 A:IHS4000 4.7 45.8 1.0
O3 A:IHS4000 4.7 33.2 1.0
O A:HOH405 4.8 28.5 1.0
O22 A:IHS4000 4.8 49.3 1.0
OE2 A:GLU199 4.9 28.5 1.0

Cadmium binding site 4 out of 7 in 3ams

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Cadmium binding site 4 out of 7 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 Cadmium with other atoms in the Cd 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:Cd907

b:38.0
occ:1.00
O A:HOH405 2.4 28.5 1.0
OD2 A:ASP286 2.4 28.3 1.0
O A:HOH529 2.5 38.3 1.0
OD2 A:ASP24 2.5 35.2 1.0
O3 A:IHS4000 2.6 33.2 1.0
O A:HOH530 2.6 32.0 1.0
OD1 A:ASP24 2.6 38.1 1.0
CG A:ASP24 2.9 35.6 1.0
CG A:ASP286 3.1 29.8 1.0
OD1 A:ASP286 3.3 35.9 1.0
O2 A:IHS4000 3.6 33.8 1.0
S1 A:IHS4000 3.7 36.7 1.0
NZ A:LYS48 3.8 34.4 1.0
NE2 A:GLN251 4.3 25.2 1.0
OD1 A:ASP27 4.3 29.5 1.0
CB A:ASP286 4.3 29.0 1.0
NE2 A:GLN307 4.3 26.1 1.0
C1 A:IHS4000 4.4 45.8 1.0
CB A:ASP24 4.4 33.5 1.0
O12 A:IHS4000 4.6 50.0 1.0
O1 A:IHS4000 4.6 40.5 1.0
CE A:LYS48 4.6 32.8 1.0
O A:ASP284 4.6 28.8 1.0
O13 A:IHS4000 4.6 57.9 1.0
O4 A:IHS4000 4.7 35.0 1.0
O33 A:IHS4000 4.7 58.6 1.0
NE2 A:GLN320 4.8 26.3 1.0
O A:ALA26 5.0 24.4 1.0

Cadmium binding site 5 out of 7 in 3ams

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Cadmium binding site 5 out of 7 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 Cadmium with other atoms in the Cd binding site number 5 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:Cd908

b:46.0
occ:1.00
OD1 A:ASP230 2.2 28.6 1.0
OD1 A:ASP200 2.2 28.7 1.0
O A:HOH449 2.2 29.2 1.0
O A:HOH448 2.3 23.0 1.0
O A:HOH528 2.3 24.8 1.0
O A:HOH450 2.4 44.9 1.0
CG A:ASP230 3.0 29.4 1.0
CG A:ASP200 3.0 30.4 1.0
OD2 A:ASP230 3.1 23.4 1.0
OD2 A:ASP200 3.2 27.8 1.0
OE1 A:GLU199 4.3 28.6 1.0
CB A:ASP230 4.4 33.8 1.0
CG A:ARG229 4.4 35.9 1.0
CB A:ASP200 4.5 28.6 1.0
CB A:GLU199 4.6 27.4 1.0
O A:HOH755 4.7 51.1 1.0
N A:ASP200 4.7 28.5 1.0
CA A:ASP230 4.8 31.9 1.0
O A:HOH407 4.8 50.6 1.0
CA A:ASP200 4.8 29.9 1.0
CD A:ARG229 4.9 34.0 1.0
N A:ASP230 5.0 36.5 1.0

Cadmium binding site 6 out of 7 in 3ams

Go back to Cadmium Binding Sites List in 3ams
Cadmium binding site 6 out of 7 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 Cadmium with other atoms in the Cd binding site number 6 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:Cd909

b:43.9
occ:1.00
ND1 A:HIS226 2.1 39.7 1.0
O A:HOH502 2.2 35.9 1.0
OD1 A:ASP220 2.2 28.5 1.0
O A:HOH501 2.5 34.6 1.0
OD2 A:ASP220 2.6 28.2 1.0
O A:HOH500 2.6 39.7 1.0
CG A:ASP220 2.8 30.5 1.0
CE1 A:HIS226 2.9 38.5 1.0
CG A:HIS226 3.2 38.1 1.0
CB A:HIS226 3.7 35.9 1.0
NE2 A:HIS226 4.1 39.1 1.0
OD2 A:ASP223 4.2 38.3 1.0
N A:HIS226 4.2 36.2 1.0
CD2 A:HIS226 4.3 38.6 1.0
CB A:ASP220 4.3 30.2 1.0
OD1 A:ASP223 4.4 36.2 1.0
O A:ARG221 4.6 33.6 1.0
CA A:HIS226 4.6 34.9 1.0
CB A:ARG225 4.6 41.1 1.0
N A:ARG221 4.7 31.4 1.0
CG A:ASP223 4.7 35.3 1.0
CA A:ASP220 4.9 31.4 1.0
NE A:ARG225 4.9 56.3 1.0

Cadmium binding site 7 out of 7 in 3ams

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Cadmium binding site 7 out of 7 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 Cadmium with other atoms in the Cd binding site number 7 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:Cd911

b:42.8
occ:0.50
O A:HOH443 2.3 31.1 1.0
O A:HOH442 2.3 29.5 1.0
NE2 A:HIS314 2.3 29.0 1.0
CE1 A:HIS314 3.3 25.8 1.0
CD2 A:HIS314 3.3 27.5 1.0
OD2 A:ASP313 4.2 30.3 1.0
ND1 A:HIS314 4.4 27.4 1.0
CG A:HIS314 4.5 29.8 1.0
CB A:ASP313 4.5 27.8 1.0
CG A:ASP313 4.7 29.2 1.0
O A:HOH564 5.0 50.9 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 Dec 12 08:19:03 2020

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