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Magnesium 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:

Calcium (Ca) 3 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 7bjt). 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: 7bjt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7bjt

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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:22.5
occ:1.00
 OG1 A:THR83 2.8 13.7 1.0
O A:LEU141 2.9 13.1 1.0
O A:HOH1063 2.9 13.0 1.0
NE2 A:HIS130 3.1 13.6 1.0
N A:HIS84 3.5 12.8 1.0
C A:THR83 3.6 13.1 1.0
O A:ASP77 3.7 14.0 1.0
CA A:HIS84 3.7 12.7 1.0
CB A:THR83 3.7 13.5 1.0
CD2 A:HIS130 3.8 13.6 1.0
O A:THR83 3.8 12.9 1.0
CB A:PRO75 3.8 13.8 1.0
CA A:PHE142 3.8 12.5 1.0
C A:LEU141 3.9 13.1 1.0
CA A:PRO75 4.1 14.1 1.0
N A:LYS76 4.1 15.0 1.0
N A:ASP77 4.2 14.5 1.0
CB A:HIS84 4.2 12.8 1.0
CE1 A:HIS130 4.2 13.6 1.0
CA A:THR83 4.3 13.4 1.0
N A:PHE142 4.3 12.7 1.0
CD1 A:PHE142 4.4 12.3 1.0
C A:PRO75 4.6 14.6 1.0
C A:PHE142 4.6 12.4 1.0
C A:ASP77 4.6 13.9 1.0
N A:TRP143 4.6 12.3 1.0
CB A:PHE142 4.7 12.4 1.0
CD2 A:HIS87 4.7 12.7 1.0
CG A:PRO75 4.7 13.8 1.0
CG A:PHE142 4.8 12.3 1.0
ND1 A:HIS84 4.8 12.8 1.0
CA A:ASP77 4.9 14.3 1.0
CG A:HIS84 5.0 12.7 1.0
C A:LYS76 5.0 15.0 1.0

Magnesium binding site 2 out of 4 in 7bjt

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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:Mg805

b:12.4
occ:1.00
 O A:HOH1415 3.0 17.7 1.0
O A:HOH990 3.1 13.9 1.0
O A:HOH1425 3.2 20.3 1.0
ND2 A:ASN240 3.4 16.7 1.0
N A:TYR136 3.6 13.4 1.0
CD1 A:TYR136 3.7 14.1 1.0
CA A:SER135 3.7 13.2 1.0
CB A:ASN240 3.8 15.9 1.0
CG A:ASN240 4.1 16.4 1.0
OG A:SER135 4.2 12.8 1.0
C A:SER135 4.2 13.3 1.0
O A:ARG134 4.2 13.9 1.0
C3 A:GOL804 4.3 17.3 1.0
CZ3 A:TRP143 4.3 12.2 1.0
CB A:SER135 4.4 13.0 1.0
CH2 A:TRP143 4.4 12.1 1.0
CE1 A:TYR136 4.4 14.0 1.0
CG A:TYR136 4.6 13.9 1.0
CB A:TYR136 4.6 13.8 1.0
N A:SER135 4.6 13.4 1.0
CA A:TYR136 4.7 13.6 1.0
C A:ARG134 4.7 14.1 1.0
C2 A:GOL804 4.7 16.8 1.0
N A:ASN240 4.9 15.2 1.0
CA A:ASN240 4.9 15.5 1.0
O2 A:GOL804 4.9 16.5 1.0
O A:HOH1130 4.9 20.9 1.0

Magnesium binding site 3 out of 4 in 7bjt

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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:34.4
occ:1.00
 OH B:TYR268 2.6 18.9 1.0
OG1 B:THR202 2.7 16.1 1.0
OD1 B:ASN257 3.0 19.9 1.0
C B:HIS198 3.4 18.3 1.0
O B:HIS198 3.4 17.9 1.0
O B:HOH1307 3.5 31.4 1.0
CZ B:TYR268 3.5 17.3 1.0
CE1 B:TYR268 3.5 17.1 1.0
N B:ASN199 3.6 17.9 1.0
CZ B:PHE282 3.6 15.7 1.0
CG B:ASN257 3.9 19.5 1.0
CA B:ASN199 3.9 17.3 1.0
CB B:THR202 3.9 15.6 1.0
CE2 B:PHE282 3.9 15.5 1.0
N B:HIS198 3.9 19.1 1.0
CG B:PRO261 4.0 16.5 1.0
CA B:HIS198 4.0 19.5 0.5
CB B:ASN257 4.1 19.1 1.0
CA B:HIS198 4.1 18.6 0.5
O B:ASN257 4.2 19.2 1.0
OE2 B:GLU270 4.6 24.6 1.0
CB B:PRO261 4.6 16.4 1.0
CG2 B:THR202 4.7 15.4 1.0
CA B:ASN257 4.7 18.8 1.0
CE1 B:PHE282 4.7 15.7 1.0
CB B:ASN199 4.8 17.6 1.0
CE2 B:TYR268 4.8 17.2 1.0
C B:VAL197 4.8 19.6 1.0
CD1 B:TYR268 4.9 16.7 1.0
C B:ASN257 4.9 19.0 1.0
N B:THR202 5.0 15.4 1.0
C B:ASN199 5.0 16.9 1.0
CA B:THR202 5.0 15.3 1.0

Magnesium binding site 4 out of 4 in 7bjt

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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:Mg806

b:11.7
occ:1.00
 O B:HOH1248 3.0 15.6 1.0
N B:GLY443 3.2 15.3 1.0
N B:ALA319 3.2 14.7 1.0
O B:HOH1116 3.4 15.2 1.0
CB B:ASP318 3.6 14.2 1.0
OG1 B:THR417 3.6 14.3 1.0
CB B:TYR440 3.7 12.8 1.0
CA B:GLY443 3.8 15.2 1.0
CB B:ALA319 3.8 15.5 1.0
CA B:ASP318 3.9 14.2 1.0
N B:LYS442 4.0 14.7 1.0
CB B:THR417 4.0 13.8 1.0
C B:ASP318 4.0 14.4 1.0
CA B:ALA319 4.1 15.4 1.0
C B:LYS442 4.2 15.3 1.0
CA B:LYS442 4.2 15.5 1.0
CG B:TYR440 4.6 12.9 1.0
C B:TYR440 4.6 12.9 1.0
C B:GLU441 4.6 14.0 1.0
CG B:ASP318 4.7 14.2 1.0
CG2 B:THR417 4.7 14.0 1.0
N B:GLU441 4.8 13.2 1.0
OE2 B:GLU414 4.8 17.7 1.0
O B:TYR440 4.8 13.0 1.0
CA B:TYR440 4.8 12.8 1.0
O B:GLU414 4.9 18.5 1.0
C B:GLY443 4.9 15.1 1.0
CG B:GLU414 4.9 19.1 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 10:27:28 2024

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