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Sodium in PDB 1ud4: Crystal Structure of Calcium Free Alpha Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38, in Calcium Containing Solution)

Enzymatic activity of Crystal Structure of Calcium Free Alpha Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38, in Calcium Containing Solution)

All present enzymatic activity of Crystal Structure of Calcium Free Alpha Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38, in Calcium Containing Solution):
3.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Calcium Free Alpha Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38, in Calcium Containing Solution), PDB code: 1ud4 was solved by T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.21 / 2.15
Space group P 2 3
Cell size a, b, c (Å), α, β, γ (°) 133.731, 133.731, 133.731, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Calcium Free Alpha Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38, in Calcium Containing Solution) (pdb code 1ud4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Calcium Free Alpha Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38, in Calcium Containing Solution), PDB code: 1ud4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1ud4

Go back to Sodium Binding Sites List in 1ud4
Sodium binding site 1 out of 3 in the Crystal Structure of Calcium Free Alpha Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38, in Calcium Containing Solution)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Calcium Free Alpha Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38, in Calcium Containing Solution) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1001

b:10.7
occ:1.00
 OD1 A:ASN104 2.3 9.9 1.0
O A:HOH2063 2.3 10.7 1.0
O A:HIS235 2.3 8.9 1.0
O A:ASP194 2.4 11.4 1.0
OD1 A:ASP194 2.4 12.3 1.0
OD1 A:ASN200 2.5 14.3 1.0
C A:HIS235 3.3 12.0 1.0
C A:ASP194 3.3 14.8 1.0
CG A:ASN200 3.4 13.7 1.0
CG A:ASN104 3.4 10.5 1.0
ND2 A:ASN200 3.5 11.8 1.0
CG A:ASP194 3.6 15.8 1.0
CB A:HIS235 3.8 9.8 1.0
CA A:ASP194 3.8 13.3 1.0
ND2 A:ASN104 4.0 8.5 1.0
O A:ASN104 4.0 9.4 1.0
CA A:HIS235 4.1 11.3 1.0
N A:ILE236 4.2 13.0 1.0
CB A:ASP194 4.3 14.3 1.0
ND2 A:ASN183 4.4 11.8 1.0
O A:HOH2011 4.4 8.8 1.0
CA A:ILE236 4.4 9.9 1.0
N A:TYR195 4.4 12.7 1.0
OD2 A:ASP194 4.5 12.3 1.0
CB A:ASN104 4.6 9.6 1.0
CG1 A:ILE236 4.8 8.2 1.0
O A:ILE201 4.8 12.4 1.0
C A:ASN104 4.8 11.9 1.0
CB A:ASN200 4.8 11.3 1.0
CA A:TYR195 4.8 12.9 1.0
CA A:ASN104 4.8 11.0 1.0

Sodium binding site 2 out of 3 in 1ud4

Go back to Sodium Binding Sites List in 1ud4
Sodium binding site 2 out of 3 in the Crystal Structure of Calcium Free Alpha Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38, in Calcium Containing Solution)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Calcium Free Alpha Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38, in Calcium Containing Solution) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1002

b:15.1
occ:1.00
 OD1 A:ASP404 2.3 16.1 1.0
O A:GLY300 2.3 17.4 1.0
O A:HOH2040 2.5 17.0 1.0
O A:TYR302 2.5 13.8 1.0
O A:TRP403 2.5 15.0 1.0
OD1 A:ASN427 2.5 14.9 1.0
CG A:ASN427 3.2 14.4 1.0
ND2 A:ASN427 3.2 13.4 1.0
C A:TRP403 3.4 16.2 1.0
CG A:ASP404 3.5 16.7 1.0
C A:GLY300 3.5 17.9 1.0
C A:TYR302 3.5 12.0 1.0
CA A:ASP404 3.7 14.8 1.0
N A:ASP404 3.9 14.2 1.0
C A:SER301 4.0 16.8 1.0
O A:HOH2235 4.1 24.1 1.0
N A:TYR302 4.1 12.6 1.0
CB A:ASP404 4.1 14.3 1.0
O A:SER301 4.3 17.2 1.0
CA A:GLY300 4.4 15.2 1.0
N A:ASP303 4.4 12.5 1.0
CD1 A:TRP403 4.4 22.9 1.0
N A:SER301 4.4 17.1 1.0
N A:MET304 4.4 11.2 1.0
CA A:TYR302 4.4 13.1 1.0
CA A:ASP303 4.5 12.2 1.0
CA A:SER301 4.5 16.6 1.0
CA A:TRP403 4.5 16.0 1.0
CB A:TRP403 4.5 16.3 1.0
OD2 A:ASP404 4.5 21.2 1.0
CG A:MET304 4.5 13.1 1.0
CB A:ASN427 4.7 13.2 1.0
C A:ASN427 4.9 14.3 1.0
N A:GLY428 4.9 13.9 1.0
CG A:TRP403 4.9 21.6 1.0
C A:ASP404 4.9 14.4 1.0
C A:ASP303 5.0 12.8 1.0

Sodium binding site 3 out of 3 in 1ud4

Go back to Sodium Binding Sites List in 1ud4
Sodium binding site 3 out of 3 in the Crystal Structure of Calcium Free Alpha Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38, in Calcium Containing Solution)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Calcium Free Alpha Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38, in Calcium Containing Solution) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1003

b:11.6
occ:1.00
 OD1 A:ASP325 2.2 11.5 1.0
O A:SER337 2.3 10.8 1.0
OD1 A:ASN289 2.3 8.9 1.0
O A:VAL324 2.4 9.4 1.0
CG A:ASP325 3.0 10.9 1.0
CG A:ASN289 3.4 10.1 1.0
C A:SER337 3.4 10.9 1.0
OD2 A:ASP325 3.6 11.4 1.0
C A:VAL324 3.6 8.6 1.0
OG1 A:THR329 3.8 8.0 1.0
CG2 A:VAL339 3.8 12.8 1.0
CA A:ASP325 3.9 8.6 1.0
ND2 A:ASN289 3.9 7.8 1.0
OG A:SER337 4.0 8.3 1.0
CB A:THR329 4.0 9.5 1.0
CB A:ASP325 4.0 9.5 1.0
O A:ASN289 4.2 11.8 1.0
N A:VAL339 4.2 10.9 1.0
N A:ASP325 4.2 7.5 1.0
CA A:TRP338 4.2 9.4 1.0
N A:TRP338 4.2 10.7 1.0
CB A:SER337 4.3 13.0 1.0
CG2 A:THR329 4.4 9.0 1.0
C A:TRP338 4.5 10.8 1.0
CA A:SER337 4.5 11.7 1.0
CB A:ASN289 4.6 10.8 1.0
CB A:VAL339 4.8 14.1 1.0
C A:ASN289 4.8 10.3 1.0
CA A:VAL324 4.8 9.1 1.0
CA A:ASN289 4.9 10.4 1.0
CB A:TYR293 4.9 12.2 1.0

Reference:

T.Nonaka, M.Fujihashi, A.Kita, H.Hagihara, K.Ozaki, S.Ito, K.Miki. Crystal Structure of Calcium-Free Alpha-Amylase From Bacillus Sp. Strain Ksm-K38 (AMYK38) and Its Sodium Ion Binding Sites J.Biol.Chem. V. 278 24818 2003.
ISSN: ISSN 0021-9258
PubMed: 12719434
DOI: 10.1074/JBC.M212763200
Page generated: Sun Oct 6 22:45:03 2024

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