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Calcium in PDB 7bm6: 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: 7bm6 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) 45.00 / 2.16
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 164.132, 164.132, 168.37, 90, 90, 120
R / Rfree (%) 15.3 / 18.2

Other elements in 7bm6:

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 7bm6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 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: 7bm6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7bm6

Go back to Calcium Binding Sites List in 7bm6
Calcium binding site 1 out of 2 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:17.7
occ:1.00
 O A:HOH945 2.1 17.7 1.0
O A:HOH951 2.1 22.6 1.0
O A:HOH1205 2.1 22.6 1.0
OD1 A:ASP449 2.2 28.5 1.0
NE2 A:HIS480 2.2 27.6 1.0
ND1 A:HIS431 2.4 27.9 1.0
CD2 A:HIS480 3.1 25.9 1.0
CE1 A:HIS431 3.2 28.8 1.0
CG A:ASP449 3.2 29.6 1.0
CE1 A:HIS480 3.2 27.4 1.0
OD2 A:ASP449 3.5 30.6 1.0
CG A:HIS431 3.5 26.9 1.0
CB A:HIS431 3.9 25.8 1.0
O A:HOH907 3.9 32.5 1.0
N A:ASN327 4.1 26.6 1.0
O A:ALA474 4.2 27.4 1.0
OD2 A:ASP433 4.2 37.8 1.0
O A:ASN327 4.3 25.7 1.0
N A:GLY451 4.3 25.1 1.0
CG A:HIS480 4.3 26.4 1.0
ND1 A:HIS480 4.3 27.6 1.0
NE2 A:HIS431 4.3 27.6 1.0
N A:TYR450 4.5 22.9 1.0
CA A:ASN327 4.5 26.2 1.0
CD2 A:HIS431 4.5 26.6 1.0
O A:PRO325 4.5 27.0 1.0
CB A:ASP449 4.5 26.9 1.0
O A:GLY451 4.7 22.9 1.0
C A:ASN327 4.7 27.6 1.0
CA A:GLY451 4.9 23.7 1.0
CA A:ASP449 4.9 25.0 1.0
C A:ASP449 4.9 25.4 1.0

Calcium binding site 2 out of 2 in 7bm6

Go back to Calcium Binding Sites List in 7bm6
Calcium binding site 2 out of 2 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
B:Ca802

b:17.8
occ:1.00
 O B:HOH1209 2.1 27.5 1.0
O B:HOH913 2.1 20.7 1.0
O B:HOH997 2.2 24.4 1.0
NE2 B:HIS480 2.2 27.5 1.0
OD1 B:ASP449 2.2 31.2 1.0
ND1 B:HIS431 2.3 26.4 1.0
CE1 B:HIS431 3.0 26.8 1.0
CD2 B:HIS480 3.1 26.6 1.0
CE1 B:HIS480 3.1 27.7 1.0
CG B:ASP449 3.2 28.4 1.0
CG B:HIS431 3.4 26.2 1.0
OD2 B:ASP449 3.4 29.6 1.0
O B:HOH910 3.8 31.5 1.0
CB B:HIS431 3.9 25.5 1.0
OD2 B:ASP433 4.0 42.2 1.0
N B:ASN327 4.1 26.5 1.0
O B:ALA474 4.2 27.4 1.0
NE2 B:HIS431 4.2 26.3 1.0
ND1 B:HIS480 4.2 26.8 1.0
CG B:HIS480 4.3 25.6 1.0
O B:ASN327 4.3 27.2 1.0
N B:GLY451 4.3 26.0 1.0
CD2 B:HIS431 4.4 27.1 1.0
CA B:ASN327 4.5 26.8 1.0
CB B:ASP449 4.5 25.9 1.0
O B:PRO325 4.6 25.7 1.0
N B:TYR450 4.6 24.2 1.0
O B:GLY451 4.7 23.6 1.0
C B:ASN327 4.8 26.5 1.0
CG B:ASP433 4.8 35.8 1.0
CA B:ASP449 4.9 24.4 1.0
CA B:GLY451 4.9 26.3 1.0
C B:ASP449 5.0 24.9 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 23:19:48 2024

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