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Sodium in PDB 1wky: Crystal Structure of Alkaline Mannanase From Bacillus Sp. Strain Jamb- 602: Catalytic Domain and Its Carbohydrate Binding Module

Enzymatic activity of Crystal Structure of Alkaline Mannanase From Bacillus Sp. Strain Jamb- 602: Catalytic Domain and Its Carbohydrate Binding Module

All present enzymatic activity of Crystal Structure of Alkaline Mannanase From Bacillus Sp. Strain Jamb- 602: Catalytic Domain and Its Carbohydrate Binding Module:
3.2.1.78;

Protein crystallography data

The structure of Crystal Structure of Alkaline Mannanase From Bacillus Sp. Strain Jamb- 602: Catalytic Domain and Its Carbohydrate Binding Module, PDB code: 1wky was solved by M.Akita, N.Takeda, K.Hirasawa, H.Sakai, M.Kawamoto, M.Yamamoto, W.D.Grant, Y.Hatada, S.Ito, K.Horikoshi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.15 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.682, 79.480, 80.418, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20

Other elements in 1wky:

The structure of Crystal Structure of Alkaline Mannanase From Bacillus Sp. Strain Jamb- 602: Catalytic Domain and Its Carbohydrate Binding Module also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Alkaline Mannanase From Bacillus Sp. Strain Jamb- 602: Catalytic Domain and Its Carbohydrate Binding Module (pdb code 1wky). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Alkaline Mannanase From Bacillus Sp. Strain Jamb- 602: Catalytic Domain and Its Carbohydrate Binding Module, PDB code: 1wky:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1wky

Go back to Sodium Binding Sites List in 1wky
Sodium binding site 1 out of 2 in the Crystal Structure of Alkaline Mannanase From Bacillus Sp. Strain Jamb- 602: Catalytic Domain and Its Carbohydrate Binding Module


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 Alkaline Mannanase From Bacillus Sp. Strain Jamb- 602: Catalytic Domain and Its Carbohydrate Binding Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:15.2
occ:1.00
 O A:VAL263 2.3 17.7 1.0
O A:HIS256 2.3 16.2 1.0
OE1 A:GLU265 2.4 19.1 1.0
O A:HOH730 2.4 26.2 1.0
O A:HOH645 2.4 19.5 1.0
OD1 A:ASP262 2.4 18.6 1.0
C A:HIS256 3.4 15.6 1.0
CG A:ASP262 3.4 20.2 1.0
CD A:GLU265 3.4 20.9 1.0
C A:VAL263 3.4 15.8 1.0
OD2 A:ASP262 3.6 23.7 1.0
OE2 A:GLU265 3.8 24.6 1.0
N A:VAL263 3.8 15.8 1.0
CA A:HIS256 3.8 14.4 1.0
O A:HOH920 4.0 33.9 1.0
O A:HOH819 4.1 26.9 1.0
O A:HOH945 4.1 42.5 1.0
CB A:HIS256 4.2 14.1 1.0
O A:HOH659 4.2 21.9 1.0
CA A:VAL263 4.2 15.9 1.0
N A:GLU265 4.3 15.3 1.0
N A:ASP264 4.4 14.7 1.0
N A:ARG257 4.5 16.6 1.0
CA A:ASP264 4.5 15.6 1.0
CB A:ASP262 4.7 19.9 1.0
CB A:VAL263 4.7 13.7 1.0
CG A:GLU265 4.7 18.9 1.0
C A:ASP262 4.8 18.3 1.0
CA A:ASP262 5.0 18.9 1.0
CA A:ARG257 5.0 17.3 1.0
C A:ASP264 5.0 15.6 1.0

Sodium binding site 2 out of 2 in 1wky

Go back to Sodium Binding Sites List in 1wky
Sodium binding site 2 out of 2 in the Crystal Structure of Alkaline Mannanase From Bacillus Sp. Strain Jamb- 602: Catalytic Domain and Its Carbohydrate Binding Module


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 Alkaline Mannanase From Bacillus Sp. Strain Jamb- 602: Catalytic Domain and Its Carbohydrate Binding Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:20.4
occ:1.00
 O A:HOH824 2.3 25.2 1.0
O A:HOH854 2.4 21.0 1.0
OE1 A:GLU253 2.4 13.2 1.0
O A:HOH678 2.5 24.6 1.0
O A:HOH687 2.5 24.8 1.0
OE2 A:GLU158 2.6 15.3 1.0
CD A:GLU253 3.3 14.2 1.0
CD A:GLU158 3.4 16.8 1.0
OE2 A:GLU253 3.5 14.0 1.0
OE1 A:GLU158 3.7 17.1 1.0
N A:GLY27 3.9 42.9 1.0
CE2 A:TYR225 3.9 14.6 1.0
OH A:TYR225 3.9 14.2 1.0
O A:HOH670 4.1 22.0 1.0
ND1 A:HIS223 4.2 13.2 1.0
O A:HOH703 4.2 28.0 1.0
CZ A:TYR225 4.3 15.2 1.0
O A:HOH866 4.4 39.5 1.0
CA A:GLY27 4.6 42.7 1.0
O A:HOH679 4.7 25.8 1.0
CG A:GLU158 4.7 14.9 1.0
CG A:GLU253 4.7 13.0 1.0
OD1 A:ASN157 4.8 15.2 1.0
CE1 A:HIS223 4.8 14.6 1.0
CD2 A:TYR225 4.9 14.9 1.0

Reference:

M.Akita, N.Takeda, K.Hirasawa, H.Sakai, M.Kawamoto, M.Yamamoto, W.D.Grant, Y.Hatada, S.Ito, K.Horikoshi. Crystallization and Preliminary X-Ray Study of Alkaline Mannanase From An Alkaliphilic Bacillus Isolate. Acta Crystallogr.,Sect.D V. 60 1490 2004.
ISSN: ISSN 0907-4449
PubMed: 15272186
DOI: 10.1107/S0907444904014313
Page generated: Tue Dec 15 05:41:10 2020

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