Atomistry » Magnesium » PDB 7bdj-7bph » 7bm6
Atomistry »
  Magnesium »
    PDB 7bdj-7bph »
      7bm6 »

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

Last articles

Cl in 3RQB
Cl in 3RO8
Cl in 3RQ3
Cl in 3RQ1
Cl in 3RPL
Cl in 3RPS
Cl in 3ROI
Cl in 3RP8
Cl in 3ROV
Cl in 3ROH
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy