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Magnesium 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:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7bm6

Go back to Magnesium Binding Sites List in 7bm6
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg802

b:37.0
occ:1.00
 OG1 A:THR83 2.8 24.9 1.0
O A:LEU141 2.9 23.5 1.0
O A:HOH1023 3.0 22.7 1.0
NE2 A:HIS130 3.1 26.1 1.0
N A:HIS84 3.4 24.0 1.0
C A:THR83 3.5 25.9 1.0
CB A:THR83 3.6 26.2 1.0
CA A:HIS84 3.6 23.7 1.0
CB A:PRO75 3.7 26.5 1.0
O A:THR83 3.7 25.9 1.0
O A:ASP77 3.7 27.8 1.0
CD2 A:HIS130 3.8 26.0 1.0
CA A:PHE142 3.9 24.1 1.0
C A:LEU141 3.9 25.4 1.0
CA A:PRO75 4.0 27.2 1.0
CB A:HIS84 4.1 23.8 1.0
N A:LYS76 4.2 27.6 1.0
CA A:THR83 4.2 25.6 1.0
N A:ASP77 4.2 25.8 1.0
CE1 A:HIS130 4.2 26.4 1.0
N A:PHE142 4.4 24.8 1.0
CD1 A:PHE142 4.5 23.8 1.0
C A:PRO75 4.5 27.6 1.0
C A:ASP77 4.7 26.7 1.0
CG A:PRO75 4.7 27.6 1.0
CD2 A:HIS87 4.7 23.0 1.0
C A:PHE142 4.7 23.8 1.0
CB A:PHE142 4.8 24.4 1.0
N A:TRP143 4.8 24.9 1.0
CG A:PHE142 4.8 23.9 1.0
CA A:ASP77 4.8 27.6 1.0
ND1 A:HIS84 4.9 24.7 1.0
CG A:HIS84 4.9 24.0 1.0
CG2 A:THR83 5.0 26.7 1.0
C A:LYS76 5.0 27.0 1.0

Magnesium binding site 2 out of 4 in 7bm6

Go back to Magnesium Binding Sites List in 7bm6
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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:Mg803

b:45.3
occ:1.00
 O A:HOH1315 2.1 38.8 1.0
O A:GLY443 2.3 27.8 1.0
O A:HOH1275 2.4 33.3 1.0
O A:HOH1031 2.5 32.9 1.0
O A:HOH982 2.6 34.0 1.0
O A:HOH903 3.2 45.9 1.0
C A:GLY443 3.5 27.4 1.0
OD2 A:ASP318 3.9 26.4 1.0
CA A:THR444 4.0 26.1 1.0
N A:GLU445 4.0 26.2 1.0
OE1 A:GLU322 4.1 40.2 1.0
N A:THR444 4.1 27.2 1.0
O A:HOH1167 4.4 42.2 1.0
C A:THR444 4.4 26.5 1.0
CA A:GLY443 4.5 26.9 1.0
CB A:GLU445 4.6 29.8 1.0
OD2 A:ASP320 4.7 41.2 1.0
CA A:GLU445 5.0 27.0 1.0

Magnesium binding site 3 out of 4 in 7bm6

Go back to Magnesium Binding Sites List in 7bm6
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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:Mg801

b:42.4
occ:1.00
 OH B:TYR268 2.8 31.9 1.0
OD1 B:ASN257 2.8 30.5 1.0
OG1 B:THR202 2.8 29.3 1.0
C B:HIS198 3.4 32.6 1.0
O B:HIS198 3.4 30.6 1.0
N B:ASN199 3.5 32.1 1.0
CE1 B:TYR268 3.6 28.6 1.0
CZ B:TYR268 3.7 30.8 1.0
CZ B:PHE282 3.7 25.5 1.0
CG B:ASN257 3.7 30.2 1.0
CG B:PRO261 3.8 27.5 1.0
N B:HIS198 3.8 33.6 1.0
CB B:ASN257 3.9 30.1 1.0
CA B:ASN199 3.9 33.8 1.0
CA B:HIS198 4.0 35.0 1.0
O B:ASN257 4.0 32.4 1.0
CB B:THR202 4.1 30.0 1.0
CE2 B:PHE282 4.1 25.2 1.0
CB B:PRO261 4.5 27.2 1.0
CA B:ASN257 4.5 29.9 1.0
C B:VAL197 4.7 35.0 1.0
C B:ASN257 4.7 31.2 1.0
CE1 B:PHE282 4.7 26.2 1.0
ND2 B:ASN257 4.8 30.8 1.0
CG2 B:THR202 4.8 30.0 1.0
OE2 B:GLU270 4.8 39.5 1.0
CB B:ASN199 4.8 36.8 1.0
CD B:PRO261 4.9 28.1 1.0
CD1 B:TYR268 5.0 28.8 1.0
N B:THR202 5.0 27.9 1.0

Magnesium binding site 4 out of 4 in 7bm6

Go back to Magnesium Binding Sites List in 7bm6
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg803

b:28.9
occ:1.00
 O B:HOH908 2.9 36.6 1.0
N B:ALA319 3.2 27.2 1.0
N B:GLY443 3.4 28.8 1.0
O B:HOH972 3.4 28.1 1.0
CB B:ASP318 3.6 27.5 1.0
OG1 B:THR417 3.6 28.1 1.0
CB B:TYR440 3.7 25.5 1.0
CA B:ASP318 3.8 27.6 1.0
N B:LYS442 4.0 28.4 1.0
CB B:ALA319 4.0 27.1 1.0
C B:ASP318 4.0 27.1 1.0
CB B:THR417 4.1 27.8 1.0
CA B:GLY443 4.1 29.5 1.0
CA B:ALA319 4.2 29.1 1.0
CA B:LYS442 4.2 30.6 1.0
C B:LYS442 4.3 28.5 1.0
O B:GLU414 4.4 37.1 1.0
C B:GLU441 4.5 27.5 1.0
C B:TYR440 4.6 26.2 1.0
CG B:TYR440 4.7 24.4 1.0
CG B:ASP318 4.7 29.6 1.0
N B:GLU441 4.7 26.3 1.0
OE2 B:GLU414 4.8 34.6 1.0
CA B:TYR440 4.8 25.8 1.0
CG2 B:THR417 4.8 28.1 1.0
O B:TYR440 4.8 26.0 1.0
CA B:GLU441 4.9 27.4 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: Wed Oct 2 10:28:29 2024

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