Atomistry » Calcium » PDB 2g8e-2gsm » 2gjp
Atomistry »
  Calcium »
    PDB 2g8e-2gsm »
      2gjp »

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

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