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Calcium in PDB 2gjp: Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose

Enzymatic activity of Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose

All present enzymatic activity of Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose:
3.2.1.1;

Protein crystallography data

The structure of Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose, PDB code: 2gjp was solved by L.Lyhne-Iversen, T.J.Hobley, S.G.Kaasgaard, P.Harris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.84 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.993, 73.497, 151.094, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.4

Other elements in 2gjp:

The structure of Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose (pdb code 2gjp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose, PDB code: 2gjp:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2gjp

Go back to Calcium Binding Sites List in 2gjp
Calcium binding site 1 out of 3 in the Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1486

b:12.3
occ:1.00
 O A:ASP199 2.2 10.3 1.0
O A:HIS240 2.3 8.6 1.0
OD1 A:ASP199 2.3 12.3 1.0
OD1 A:ASP205 2.3 12.8 1.0
OD1 A:ASN106 2.4 13.9 1.0
O A:HOH1563 2.4 12.0 1.0
CG A:ASP205 3.0 13.8 1.0
OD2 A:ASP205 3.0 14.7 1.0
C A:ASP199 3.2 8.7 1.0
CG A:ASP199 3.4 12.7 1.0
C A:HIS240 3.5 8.0 1.0
CG A:ASN106 3.5 13.0 1.0
O A:HOH1499 3.7 16.7 1.0
CA A:ASP199 3.7 9.7 1.0
CB A:HIS240 3.9 10.7 1.0
NA A:NA1489 4.0 8.9 1.0
O A:ASN106 4.0 13.0 1.0
ND2 A:ASN106 4.1 14.5 1.0
CB A:ASP199 4.2 10.2 1.0
CA A:HIS240 4.2 9.3 1.0
O A:HOH1497 4.2 8.7 1.0
N A:TYR200 4.3 10.2 1.0
OD2 A:ASP199 4.4 13.1 1.0
CB A:ASP205 4.5 12.8 1.0
N A:ILE241 4.5 8.7 1.0
CA A:TYR200 4.6 9.0 1.0
CB A:ASN106 4.6 12.9 1.0
CA A:ILE241 4.6 10.6 1.0
O A:VAL206 4.7 11.7 1.0
CA A:ASN106 4.8 13.5 1.0
C A:ASN106 4.8 12.0 1.0
O A:TYR198 5.0 9.3 1.0

Calcium binding site 2 out of 3 in 2gjp

Go back to Calcium Binding Sites List in 2gjp
Calcium binding site 2 out of 3 in the Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1487

b:13.0
occ:1.00
 OD1 A:ASP207 2.2 13.1 1.0
OD1 A:ASP188 2.3 12.7 1.0
OD2 A:ASP209 2.3 22.5 1.0
O A:ALA186 2.3 11.2 1.0
O A:HOH1510 2.4 13.4 1.0
OD1 A:ASP163 2.4 12.6 1.0
OD2 A:ASP163 2.5 14.5 1.0
CG A:ASP163 2.8 12.0 1.0
CG A:ASP207 3.1 12.4 1.0
CG A:ASP209 3.3 20.9 1.0
CG A:ASP188 3.4 11.7 1.0
C A:ALA186 3.5 12.1 1.0
OD2 A:ASP207 3.7 12.0 1.0
N A:ASP188 3.8 11.2 1.0
CB A:ASP209 3.9 18.3 1.0
C A:TRP187 4.0 10.9 1.0
OD2 A:ASP188 4.1 12.1 1.0
N A:ALA186 4.1 14.7 1.0
CB A:ASP207 4.1 11.1 1.0
CA A:ASP188 4.2 10.8 1.0
CA A:ASP207 4.2 11.4 1.0
OD1 A:ASP209 4.3 20.4 1.0
CB A:ASP163 4.3 12.2 1.0
CB A:ASP188 4.4 10.6 1.0
NA A:NA1489 4.4 8.9 1.0
CA A:TRP187 4.4 11.2 1.0
N A:ASP209 4.4 16.1 1.0
N A:TRP187 4.4 11.7 1.0
CA A:ALA186 4.4 14.1 1.0
O A:TRP187 4.4 13.6 1.0
N A:MET208 4.6 10.7 1.0
C A:ASP207 4.7 11.1 1.0
OD2 A:ASP199 4.8 13.1 1.0
CA A:ASP209 4.8 17.1 1.0
O A:HOH1577 4.8 33.8 1.0
O A:HOH1594 4.9 24.6 1.0

Calcium binding site 3 out of 3 in 2gjp

Go back to Calcium Binding Sites List in 2gjp
Calcium binding site 3 out of 3 in the Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Bacillus Halmapalus Alpha-Amylase, Crystallized with the Substrate Analogue Acarbose and Maltose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1488

b:15.5
occ:1.00
 OD1 A:ASN409 2.3 16.8 1.0
O A:TYR307 2.3 15.8 1.0
O A:GLY305 2.3 17.2 1.0
O A:HOH1548 2.4 19.6 1.0
OD2 A:ASP432 2.4 14.0 1.0
OD1 A:ASP432 2.5 13.0 1.0
O A:HIS408 2.5 13.7 1.0
CG A:ASP432 2.8 12.9 1.0
C A:GLY305 3.4 17.1 1.0
C A:TYR307 3.5 17.4 1.0
CG A:ASN409 3.5 15.8 1.0
C A:HIS408 3.5 14.5 1.0
N A:TYR307 3.6 17.0 1.0
CA A:ASN409 3.7 13.7 1.0
C A:ASN306 3.9 19.7 1.0
N A:ASN409 4.0 13.6 1.0
CG A:MET309 4.1 15.8 1.0
CA A:ASN306 4.1 19.2 1.0
N A:ASN306 4.1 17.1 1.0
CB A:ASN409 4.1 15.5 1.0
CA A:TYR307 4.2 17.4 1.0
O A:HOH1704 4.3 37.6 1.0
CA A:GLY305 4.3 16.8 1.0
CB A:ASP432 4.4 14.7 1.0
N A:MET309 4.4 15.7 1.0
N A:ASP308 4.5 17.1 1.0
ND2 A:ASN409 4.5 17.9 1.0
O A:HOH1606 4.5 18.1 1.0
O A:ASN306 4.5 19.3 1.0
CA A:HIS408 4.6 15.2 1.0
CA A:ASP308 4.6 17.0 1.0
CB A:HIS408 4.6 16.6 1.0
O A:HOH1501 4.7 14.7 1.0
ND1 A:HIS408 4.7 21.4 1.0
CB A:TYR307 4.7 19.1 1.0
O A:HOH1655 4.9 22.4 1.0
CB A:MET309 4.9 14.0 1.0
C A:ASP432 5.0 14.9 1.0
C A:ASN409 5.0 15.9 1.0

Reference:

L.Lyhne-Iversen, T.J.Hobley, S.G.Kaasgaard, P.Harris. Structure of Bacillus Halmapalus Alpha-Amylase Crystallized with and Without the Substrate Analogue Acarbose and Maltose. Acta Crystallogr.,Sect.F V. 62 849 2006.
ISSN: ESSN 1744-3091
PubMed: 16946462
DOI: 10.1107/S174430910603096X
Page generated: Fri Jul 12 10:47:57 2024

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