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Calcium in PDB 2d3l: Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose.

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

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

Protein crystallography data

The structure of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose., PDB code: 2d3l 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 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.450, 82.460, 126.910, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21.3

Other elements in 2d3l:

The structure of Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose. 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 Maltopentaose. (pdb code 2d3l). 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 Maltopentaose., PDB code: 2d3l:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 2d3l

Go back to Calcium Binding Sites List in 2d3l
Calcium binding site 1 out of 3 in the Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose.


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 Maltopentaose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:22.2
occ:1.00
 OD1 A:ASP188 2.3 18.4 1.0
OD1 A:ASP207 2.3 18.0 1.0
O A:ALA186 2.4 25.0 1.0
OD1 A:ASP163 2.5 19.4 1.0
OD2 A:ASP209 2.6 22.5 1.0
OD2 A:ASP163 2.6 23.2 1.0
O A:HOH793 2.9 30.7 1.0
CG A:ASP163 2.9 19.0 1.0
CG A:ASP207 3.2 16.9 1.0
CG A:ASP188 3.3 21.5 1.0
CG A:ASP209 3.4 22.7 1.0
C A:ALA186 3.6 23.9 1.0
CB A:ASP209 3.8 22.3 1.0
OD2 A:ASP207 3.8 17.7 1.0
N A:ASP188 3.8 22.6 1.0
C A:TRP187 3.9 24.2 1.0
OD2 A:ASP188 3.9 18.6 1.0
CA A:ASP188 4.1 21.2 1.0
CB A:ASP207 4.2 17.3 1.0
O A:TRP187 4.2 23.3 1.0
N A:ALA186 4.2 23.6 1.0
CB A:ASP188 4.3 21.1 1.0
N A:ASP209 4.3 22.6 1.0
CA A:ASP207 4.3 17.4 1.0
CB A:ASP163 4.4 18.3 1.0
OD1 A:ASP209 4.4 23.6 1.0
CA A:TRP187 4.5 22.8 1.0
N A:TRP187 4.5 23.4 1.0
NA A:NA504 4.5 27.7 1.0
N A:MET208 4.5 18.2 1.0
CA A:ALA186 4.6 23.5 1.0
CA A:ASP209 4.7 21.0 1.0
C A:ASP207 4.7 18.9 1.0
OD2 A:ASP199 4.9 20.4 1.0
O A:HOH762 4.9 31.3 1.0

Calcium binding site 2 out of 3 in 2d3l

Go back to Calcium Binding Sites List in 2d3l
Calcium binding site 2 out of 3 in the Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose.


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 Maltopentaose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:22.3
occ:1.00
 OD1 A:ASN106 2.3 21.2 1.0
OD1 A:ASP205 2.3 17.9 1.0
O A:HIS240 2.3 20.0 1.0
O A:HOH884 2.5 14.4 1.0
O A:ASP199 2.5 18.9 1.0
OD1 A:ASP199 2.5 19.7 1.0
CG A:ASP205 3.2 19.2 1.0
CG A:ASN106 3.4 19.0 1.0
OD2 A:ASP205 3.4 20.3 1.0
C A:ASP199 3.4 19.8 1.0
C A:HIS240 3.5 20.0 1.0
CG A:ASP199 3.5 18.8 1.0
O A:HOH724 3.7 23.5 1.0
NA A:NA504 3.9 27.7 1.0
CA A:ASP199 3.9 19.5 1.0
O A:ASN106 4.0 19.7 1.0
ND2 A:ASN106 4.0 17.8 1.0
CB A:HIS240 4.1 20.8 1.0
OD2 A:ASP199 4.3 20.4 1.0
CB A:ASP199 4.3 17.9 1.0
CA A:HIS240 4.4 20.2 1.0
N A:ILE241 4.4 17.5 1.0
O A:HOH713 4.4 17.2 1.0
N A:TYR200 4.5 19.1 1.0
O A:ILE206 4.5 18.8 1.0
CA A:ILE241 4.5 18.0 1.0
CB A:ASN106 4.5 18.5 1.0
CB A:ASP205 4.6 18.0 1.0
CA A:ASN106 4.7 19.0 1.0
CG1 A:ILE241 4.8 17.2 1.0
C A:ASN106 4.8 18.9 1.0
CA A:TYR200 4.8 20.3 1.0

Calcium binding site 3 out of 3 in 2d3l

Go back to Calcium Binding Sites List in 2d3l
Calcium binding site 3 out of 3 in the Crystal Structure of Maltohexaose-Producing Amylase From Bacillus Sp.707 Complexed with Maltopentaose.


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 Maltopentaose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:30.5
occ:1.00
 O A:TYR307 2.3 22.3 1.0
OD1 A:ASN409 2.4 23.4 1.0
O A:GLY305 2.4 20.6 1.0
O A:HIS408 2.6 26.3 1.0
OD2 A:ASP432 2.6 25.6 1.0
OD1 A:ASP432 2.6 20.3 1.0
CG A:ASP432 2.9 24.8 1.0
C A:GLY305 3.3 22.1 1.0
C A:TYR307 3.5 21.9 1.0
CG A:ASN409 3.5 25.3 1.0
C A:HIS408 3.6 24.8 1.0
N A:TYR307 3.7 21.6 1.0
CA A:ASN409 3.8 24.7 1.0
C A:ASN306 4.0 22.7 1.0
CG A:MET309 4.0 20.1 1.0
N A:ASN409 4.1 24.7 1.0
N A:ASN306 4.1 22.2 1.0
CB A:ASN409 4.1 24.5 1.0
CA A:GLY305 4.2 21.2 1.0
CA A:TYR307 4.2 21.6 1.0
CA A:ASN306 4.2 23.4 1.0
N A:MET309 4.4 21.5 1.0
CB A:ASP432 4.5 22.3 1.0
N A:ASP308 4.5 21.7 1.0
ND1 A:HIS408 4.6 27.6 1.0
ND2 A:ASN409 4.6 25.5 1.0
CA A:ASP308 4.6 20.1 1.0
O A:ASN306 4.6 23.2 1.0
O A:HOH761 4.7 23.0 1.0
CA A:HIS408 4.7 25.3 1.0
CB A:TYR307 4.8 22.4 1.0
CB A:HIS408 4.8 25.6 1.0
CB A:MET309 4.9 21.6 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 09:40:45 2024

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