Atomistry » Calcium » PDB 2cn6-2dbx » 2d3n
Atomistry »
  Calcium »
    PDB 2cn6-2dbx »
      2d3n »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy