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Calcium in PDB 3azz: Crystal Structure of the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone

Enzymatic activity of Crystal Structure of the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone

All present enzymatic activity of Crystal Structure of the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone:
3.2.1.39;

Protein crystallography data

The structure of Crystal Structure of the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone, PDB code: 3azz was solved by W.Y.Jeng, N.C.Wang, A.H.J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.40 / 1.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.990, 120.232, 120.995, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone (pdb code 3azz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone, PDB code: 3azz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3azz

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Calcium binding site 1 out of 4 in the Crystal Structure of the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone


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 the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:30.6
occ:1.00
 O A:HOH779 2.3 28.6 1.0
O A:GLY61 2.3 27.6 1.0
O A:HOH790 2.4 47.3 1.0
O A:GLU17 2.4 28.2 1.0
O A:ASP249 2.4 25.2 1.0
OD1 A:ASP249 2.5 26.5 1.0
OD1 A:ASP19 2.8 39.2 1.0
C A:ASP249 3.4 24.9 1.0
C A:GLY61 3.4 28.7 1.0
C A:GLU17 3.5 28.2 1.0
CG A:ASP249 3.6 24.6 1.0
CG A:ASP19 3.8 37.7 1.0
CA A:ASP249 3.9 24.5 1.0
CA A:GLY61 4.0 29.1 1.0
OD2 A:ASP19 4.1 39.1 1.0
CA A:GLU17 4.2 28.3 1.0
CB A:ASP249 4.4 25.0 1.0
OD2 A:ASP249 4.5 26.7 1.0
O A:HOH930 4.5 69.1 1.0
CB A:GLU17 4.5 29.1 1.0
N A:TYR250 4.5 24.7 1.0
N A:CYS62 4.6 27.7 1.0
C A:PHE18 4.6 31.4 1.0
N A:PHE18 4.6 28.9 1.0
OE1 A:GLU17 4.6 32.5 1.0
O A:PHE18 4.6 30.6 1.0
CB A:PHE18 4.7 28.7 1.0
CB A:TYR250 4.8 24.9 1.0
CA A:PHE18 4.8 29.2 1.0
CA A:CYS62 4.9 27.6 1.0
N A:ASP19 4.9 32.5 1.0
CA A:TYR250 4.9 25.0 1.0

Calcium binding site 2 out of 4 in 3azz

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Calcium binding site 2 out of 4 in the Crystal Structure of the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone


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 the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:29.6
occ:1.00
 O B:GLY61 2.3 26.8 1.0
O B:GLU17 2.4 24.9 1.0
O B:HOH785 2.4 27.6 1.0
O B:ASP249 2.4 23.9 1.0
OD1 B:ASP249 2.4 25.6 1.0
O B:HOH782 2.5 34.7 1.0
OD1 B:ASP19 2.8 36.3 1.0
C B:ASP249 3.4 23.8 1.0
C B:GLY61 3.4 26.6 1.0
C B:GLU17 3.5 26.0 1.0
CG B:ASP249 3.6 25.3 1.0
CG B:ASP19 3.7 35.3 1.0
CA B:ASP249 3.9 23.6 1.0
CA B:GLY61 4.0 27.1 1.0
OD2 B:ASP19 4.0 38.4 1.0
CA B:GLU17 4.3 25.1 1.0
CB B:ASP249 4.3 23.4 1.0
O B:PHE18 4.4 27.5 1.0
C B:PHE18 4.5 28.8 1.0
N B:TYR250 4.5 23.8 1.0
OD2 B:ASP249 4.5 26.2 1.0
O B:HOH531 4.6 63.0 1.0
N B:PHE18 4.6 26.1 1.0
N B:CYS62 4.6 24.7 1.0
CB B:GLU17 4.6 25.7 1.0
OE1 B:GLU17 4.6 26.1 1.0
CB B:PHE18 4.7 27.4 1.0
CB B:TYR250 4.8 23.1 1.0
CA B:PHE18 4.8 27.4 1.0
N B:ASP19 4.8 30.3 1.0
CA B:TYR250 4.9 23.5 1.0
CA B:CYS62 4.9 24.3 1.0
CB B:ASP19 5.0 34.0 1.0

Calcium binding site 3 out of 4 in 3azz

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Calcium binding site 3 out of 4 in the Crystal Structure of the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone


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 the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:32.0
occ:1.00
 O C:GLU17 2.3 27.1 1.0
O C:GLY61 2.3 26.4 1.0
O C:ASP249 2.3 26.1 1.0
O C:HOH797 2.4 30.2 1.0
OD1 C:ASP249 2.4 26.2 1.0
O C:HOH440 2.6 31.7 1.0
OD1 C:ASP19 2.8 37.6 1.0
C C:ASP249 3.3 25.2 1.0
C C:GLU17 3.4 27.4 1.0
C C:GLY61 3.4 27.6 1.0
CG C:ASP249 3.6 25.8 1.0
CG C:ASP19 3.8 35.0 1.0
CA C:ASP249 3.8 25.5 1.0
CA C:GLY61 4.0 28.8 1.0
OD2 C:ASP19 4.1 34.4 1.0
CA C:GLU17 4.2 27.2 1.0
CB C:ASP249 4.3 25.7 1.0
C C:PHE18 4.4 30.2 1.0
N C:TYR250 4.5 24.6 1.0
N C:PHE18 4.5 27.7 1.0
OD2 C:ASP249 4.5 28.8 1.0
O C:PHE18 4.5 30.4 1.0
N C:CYS62 4.6 27.0 1.0
CB C:GLU17 4.6 27.1 1.0
CB C:PHE18 4.6 27.7 1.0
OE1 C:GLU17 4.6 30.6 1.0
CA C:PHE18 4.7 28.3 1.0
CB C:TYR250 4.7 22.9 1.0
O C:HOH842 4.7 56.5 1.0
N C:ASP19 4.8 31.4 1.0
CA C:TYR250 4.9 23.7 1.0
CA C:CYS62 4.9 27.3 1.0

Calcium binding site 4 out of 4 in 3azz

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Calcium binding site 4 out of 4 in the Crystal Structure of the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Gluconolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:29.1
occ:1.00
 O D:GLY61 2.2 26.8 1.0
OD1 D:ASP249 2.3 26.8 1.0
O D:ASP249 2.4 24.7 1.0
O D:HOH775 2.4 30.6 1.0
O D:GLU17 2.4 26.9 1.0
O D:HOH665 2.4 37.6 1.0
OD1 D:ASP19 2.8 36.7 1.0
C D:ASP249 3.3 24.9 1.0
C D:GLY61 3.4 27.1 1.0
CG D:ASP249 3.5 25.4 1.0
C D:GLU17 3.6 27.6 1.0
CG D:ASP19 3.7 37.7 1.0
CA D:ASP249 3.8 24.9 1.0
CA D:GLY61 3.9 27.8 1.0
OD2 D:ASP19 4.0 41.1 1.0
CB D:ASP249 4.3 24.7 1.0
CA D:GLU17 4.3 27.4 1.0
OD2 D:ASP249 4.5 27.8 1.0
N D:TYR250 4.5 25.6 1.0
C D:PHE18 4.5 30.1 1.0
N D:CYS62 4.5 25.6 1.0
O D:PHE18 4.5 29.5 1.0
N D:PHE18 4.6 28.4 1.0
O D:HOH780 4.6 50.9 1.0
CB D:PHE18 4.6 28.5 1.0
OE1 D:GLU17 4.7 31.1 1.0
CB D:GLU17 4.7 27.9 1.0
CB D:TYR250 4.7 25.0 1.0
CA D:PHE18 4.8 28.9 1.0
N D:ASP19 4.8 32.1 1.0
CA D:CYS62 4.8 26.1 1.0
CA D:TYR250 4.9 24.3 1.0

Reference:

W.Y.Jeng, N.C.Wang, C.T.Lin, L.F.Shyur, A.H.Wang. Crystal Structures of the Laminarinase Catalytic Domain From Thermotoga Maritima MSB8 in Complex with Inhibitors: Essential Residues For Beta-1,3 and Beta-1,4 Glucan Selection. J.Biol.Chem. V. 286 45030 2011.
ISSN: ISSN 0021-9258
PubMed: 22065588
DOI: 10.1074/JBC.M111.271213
Page generated: Sat Jul 13 08:04:14 2024

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