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Calcium in PDB 2d3n: Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose

Enzymatic activity of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose

All present enzymatic activity of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose:
3.2.1.98;

Protein crystallography data

The structure of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose, PDB code: 2d3n was solved by R.Kanai, K.Haga, T.Akiba, K.Yamane, K.Harata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.630, 82.690, 126.970, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.4

Other elements in 2d3n:

The structure of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose (pdb code 2d3n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose, PDB code: 2d3n:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2d3n

Go back to Calcium Binding Sites List in 2d3n
Calcium binding site 1 out of 3 in the Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:14.1
occ:1.00
 OD1 A:ASP188 2.3 17.4 1.0
O A:ALA186 2.3 15.8 1.0
OD1 A:ASP207 2.4 14.6 1.0
OD2 A:ASP209 2.5 19.4 1.0
OD1 A:ASP163 2.5 14.2 1.0
OD2 A:ASP163 2.5 12.9 1.0
O A:HOH771 2.6 15.1 1.0
CG A:ASP163 2.8 13.6 1.0
CG A:ASP207 3.2 14.1 1.0
CG A:ASP209 3.4 20.1 1.0
CG A:ASP188 3.4 16.7 1.0
C A:ALA186 3.5 15.9 1.0
OD2 A:ASP207 3.7 14.7 1.0
CB A:ASP209 3.8 18.9 1.0
N A:ASP188 3.8 14.9 1.0
C A:TRP187 4.0 16.2 1.0
OD2 A:ASP188 4.0 15.6 1.0
CB A:ASP207 4.1 13.0 1.0
CA A:ASP188 4.2 15.4 1.0
N A:ALA186 4.2 17.1 1.0
CB A:ASP163 4.3 13.3 1.0
CA A:ASP207 4.3 13.3 1.0
N A:ASP209 4.3 16.9 1.0
OD1 A:ASP209 4.4 19.2 1.0
CB A:ASP188 4.4 14.8 1.0
O A:TRP187 4.4 15.5 1.0
CA A:TRP187 4.4 14.2 1.0
N A:TRP187 4.4 13.8 1.0
NA A:NA504 4.4 15.6 1.0
CA A:ALA186 4.5 16.9 1.0
N A:MET208 4.6 13.9 1.0
CA A:ASP209 4.7 17.6 1.0
C A:ASP207 4.7 14.0 1.0
O A:HOH848 4.7 22.2 1.0
OD2 A:ASP199 4.9 15.0 1.0
O A:HOH856 4.9 22.0 1.0

Calcium binding site 2 out of 3 in 2d3n

Go back to Calcium Binding Sites List in 2d3n
Calcium binding site 2 out of 3 in the Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:14.3
occ:1.00
 OD1 A:ASN106 2.3 12.3 1.0
O A:ASP199 2.3 12.3 1.0
OD1 A:ASP205 2.3 12.1 1.0
OD1 A:ASP199 2.4 15.0 1.0
O A:HIS240 2.4 11.9 1.0
O A:HOH721 2.4 13.7 1.0
CG A:ASP205 3.1 13.7 1.0
OD2 A:ASP205 3.2 16.7 1.0
C A:ASP199 3.3 12.7 1.0
CG A:ASN106 3.4 13.4 1.0
CG A:ASP199 3.4 14.3 1.0
C A:HIS240 3.5 12.3 1.0
CA A:ASP199 3.8 13.8 1.0
O A:HOH738 3.9 13.9 1.0
NA A:NA504 4.0 15.6 1.0
CB A:HIS240 4.0 11.4 1.0
O A:ASN106 4.1 12.2 1.0
ND2 A:ASN106 4.1 14.9 1.0
CB A:ASP199 4.2 14.5 1.0
OD2 A:ASP199 4.3 15.0 1.0
O A:HOH717 4.3 13.7 1.0
CA A:HIS240 4.3 11.7 1.0
N A:TYR200 4.4 13.4 1.0
N A:ILE241 4.5 12.1 1.0
CB A:ASP205 4.5 12.9 1.0
CB A:ASN106 4.6 12.5 1.0
CA A:ILE241 4.6 12.8 1.0
O A:ILE206 4.6 14.1 1.0
CA A:TYR200 4.7 12.2 1.0
CA A:ASN106 4.8 13.0 1.0
C A:ASN106 4.8 13.2 1.0
CG1 A:ILE241 4.9 12.4 1.0

Calcium binding site 3 out of 3 in 2d3n

Go back to Calcium Binding Sites List in 2d3n
Calcium binding site 3 out of 3 in the Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:21.1
occ:1.00
 O A:TYR307 2.3 17.3 1.0
O A:HIS408 2.4 16.0 1.0
OD1 A:ASN409 2.5 17.1 1.0
O A:GLY305 2.5 17.3 1.0
OD1 A:ASP432 2.5 14.2 1.0
OD2 A:ASP432 2.6 14.6 1.0
O A:HOH804 2.7 19.6 1.0
CG A:ASP432 2.9 16.9 1.0
C A:HIS408 3.4 15.8 1.0
C A:GLY305 3.4 17.4 1.0
C A:TYR307 3.5 16.8 1.0
CG A:ASN409 3.6 17.2 1.0
CA A:ASN409 3.7 15.5 1.0
N A:TYR307 3.7 16.5 1.0
N A:ASN409 4.0 15.3 1.0
C A:ASN306 4.1 17.9 1.0
CG A:MET309 4.1 15.1 1.0
CB A:ASN409 4.2 16.2 1.0
N A:ASN306 4.2 16.8 1.0
CA A:TYR307 4.2 17.0 1.0
CA A:GLY305 4.3 15.9 1.0
CA A:ASN306 4.3 17.3 1.0
N A:MET309 4.3 13.4 1.0
CB A:ASP432 4.4 13.6 1.0
N A:ASP308 4.5 16.4 1.0
ND1 A:HIS408 4.6 23.0 1.0
CA A:HIS408 4.6 17.4 1.0
O A:HOH776 4.6 19.8 1.0
CA A:ASP308 4.6 14.7 1.0
CB A:HIS408 4.6 18.8 1.0
ND2 A:ASN409 4.7 17.4 1.0
O A:HOH714 4.7 12.9 1.0
O A:HOH796 4.7 23.7 1.0
O A:ASN306 4.8 17.0 1.0
CB A:TYR307 4.8 16.8 1.0
O A:HOH953 4.8 29.6 1.0
CB A:MET309 4.9 15.7 1.0
C A:ASN409 4.9 16.1 1.0
C A:ASP308 5.0 13.8 1.0

Reference:

R.Kanai, K.Haga, T.Akiba, K.Yamane, K.Harata. Role of TRP140 at Subsite -6 on the Maltohexaose Production of Maltohexaose-Producing Amylase From Alkalophilic Bacillus Sp.707 Protein Sci. V. 15 468 2006.
ISSN: ISSN 0961-8368
PubMed: 16452622
DOI: 10.1110/PS.051877006
Page generated: Fri Jul 12 09:40:46 2024

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