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Calcium in PDB 7bjt: Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt

Enzymatic activity of Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt

All present enzymatic activity of Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt:
4.2.2.3;

Protein crystallography data

The structure of Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt, PDB code: 7bjt was solved by M.Czjzek, T.Roret, D.Jouanneau, N.Le Duff, A.Jeudy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.70 / 1.42
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 163.39, 163.39, 166.73, 90, 90, 120
R / Rfree (%) 16.1 / 17

Other elements in 7bjt:

The structure of Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt (pdb code 7bjt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt, PDB code: 7bjt:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7bjt

Go back to Calcium Binding Sites List in 7bjt
Calcium binding site 1 out of 3 in the Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:8.5
occ:1.00
 O A:HOH921 2.2 10.7 1.0
OD1 A:ASP449 2.2 12.3 1.0
NE2 A:HIS480 2.2 11.9 1.0
O A:HOH1225 2.2 12.8 1.0
O A:HOH925 2.2 11.5 1.0
ND1 A:HIS431 2.3 11.8 1.0
CE1 A:HIS431 3.1 12.0 1.0
CD2 A:HIS480 3.2 11.8 1.0
CG A:ASP449 3.2 12.2 1.0
CE1 A:HIS480 3.2 11.9 1.0
CG A:HIS431 3.4 12.0 1.0
OD2 A:ASP449 3.4 12.5 1.0
O A:HOH913 3.7 19.8 1.0
CB A:HIS431 3.8 12.3 1.0
OD2 A:ASP433 3.8 25.1 1.0
O A:ALA474 4.1 12.5 1.0
N A:ASN327 4.1 12.4 1.0
NE2 A:HIS431 4.2 12.0 1.0
ND1 A:HIS480 4.3 12.0 1.0
N A:GLY451 4.3 12.0 1.0
CG A:HIS480 4.3 11.9 1.0
O A:ASN327 4.3 12.2 1.0
CD2 A:HIS431 4.4 12.1 1.0
CA A:ASN327 4.4 12.4 1.0
O A:PRO325 4.5 12.5 1.0
CB A:ASP449 4.5 12.1 1.0
N A:TYR450 4.6 11.9 1.0
O A:GLY451 4.6 12.4 1.0
CG A:ASP433 4.6 20.7 1.0
C A:ASN327 4.7 12.3 1.0
CA A:GLY451 4.8 12.2 1.0
C A:ASP449 5.0 12.0 1.0
CA A:ASP449 5.0 12.0 1.0
C A:LEU326 5.0 12.5 1.0
OD1 A:ASP433 5.0 23.7 1.0

Calcium binding site 2 out of 3 in 7bjt

Go back to Calcium Binding Sites List in 7bjt
Calcium binding site 2 out of 3 in the Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca806

b:17.8
occ:1.00
 O A:HOH1256 3.0 16.4 1.0
N A:ALA319 3.3 14.5 1.0
N A:GLY443 3.3 15.4 1.0
O A:HOH1079 3.4 14.5 1.0
OG1 A:THR417 3.6 14.2 1.0
CB A:ASP318 3.6 13.8 1.0
CB A:TYR440 3.7 12.6 1.0
CA A:ASP318 3.8 13.8 1.0
CB A:ALA319 3.8 15.1 1.0
CA A:GLY443 3.9 15.4 1.0
N A:LYS442 3.9 14.9 1.0
CB A:THR417 4.0 13.8 1.0
C A:ASP318 4.0 14.2 1.0
CA A:ALA319 4.1 15.0 1.0
C A:LYS442 4.2 15.8 1.0
CA A:LYS442 4.2 15.9 1.0
C A:GLU441 4.6 14.0 1.0
C A:TYR440 4.6 12.9 1.0
CG A:TYR440 4.6 12.5 1.0
CG A:ASP318 4.7 13.9 1.0
CG2 A:THR417 4.8 14.0 1.0
N A:GLU441 4.8 13.1 1.0
OE2 A:GLU414 4.8 18.1 1.0
O A:TYR440 4.8 13.2 1.0
CA A:TYR440 4.8 12.7 1.0
O A:GLU414 4.8 19.6 1.0
CG A:GLU414 4.9 19.8 1.0
C A:GLY443 4.9 15.2 1.0

Calcium binding site 3 out of 3 in 7bjt

Go back to Calcium Binding Sites List in 7bjt
Calcium binding site 3 out of 3 in the Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:8.5
occ:1.00
 OD1 B:ASP449 2.2 12.8 1.0
O B:HOH930 2.2 12.6 1.0
O B:HOH1230 2.2 13.5 1.0
O B:HOH925 2.2 12.7 1.0
NE2 B:HIS480 2.3 12.5 1.0
ND1 B:HIS431 2.3 12.5 1.0
CE1 B:HIS431 3.1 12.7 1.0
CG B:ASP449 3.1 12.7 1.0
CD2 B:HIS480 3.2 12.4 1.0
CE1 B:HIS480 3.2 12.5 1.0
CG B:HIS431 3.4 12.7 1.0
OD2 B:ASP449 3.4 13.0 1.0
O B:HOH921 3.7 15.7 1.0
CB B:HIS431 3.8 12.8 1.0
O B:ALA474 4.1 12.7 1.0
N B:ASN327 4.1 12.8 1.0
NE2 B:HIS431 4.2 12.7 1.0
ND1 B:HIS480 4.3 12.5 1.0
CG B:HIS480 4.3 12.4 1.0
N B:GLY451 4.3 12.4 1.0
O B:ASN327 4.3 12.7 1.0
CD2 B:HIS431 4.4 12.8 1.0
OD2 B:ASP433 4.4 16.5 1.0
CA B:ASN327 4.5 12.9 1.0
O B:PRO325 4.5 13.2 1.0
CB B:ASP449 4.5 12.6 1.0
N B:TYR450 4.6 12.3 1.0
O B:GLY451 4.7 13.0 1.0
C B:ASN327 4.7 12.9 1.0
CA B:GLY451 4.8 12.6 1.0
C B:ASP449 4.9 12.4 1.0
CA B:ASP449 4.9 12.5 1.0

Reference:

D.Jouanneau, L.J.Klau, R.Larocque, A.Jaffrennou, G.Duval, N.Le Duff, T.Roret, A.Jeudy, F.L.Aachmann, M.Czjzek, F.Thomas. Structure-Function Analysis of A New PL17 Oligoalginate Lyase From the Marine Bacterium Zobellia Galactanivorans Dsijt. Glycobiology 2021.
ISSN: ESSN 1460-2423
PubMed: 34184062
DOI: 10.1093/GLYCOB/CWAB058
Page generated: Thu Jul 18 23:18:47 2024

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