Magnesium in PDB 6rb7: Ruminococcus Gnavus Sialic Acid Aldolase Catalytic Lysine Mutant

The structure of Ruminococcus Gnavus Sialic Acid Aldolase Catalytic Lysine Mutant, PDB code: 6rb7 was solved by C.D.Owen, A.Bell, N.Juge, M.A.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.99 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.181, 121.390, 86.980, 90.00, 109.49, 90.00
R / Rfree (%)	12.9 / 15.1

The binding sites of Magnesium atom in the Ruminococcus Gnavus Sialic Acid Aldolase Catalytic Lysine Mutant (pdb code 6rb7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ruminococcus Gnavus Sialic Acid Aldolase Catalytic Lysine Mutant, PDB code: 6rb7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Ruminococcus Gnavus Sialic Acid Aldolase Catalytic Lysine Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ruminococcus Gnavus Sialic Acid Aldolase Catalytic Lysine Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:18.4 occ:1.00 O B:HOH769 2.7 33.3 1.0 O A:HOH677 3.0 24.0 1.0 ND2 A:ASN255 3.1 14.1 1.0 O A:HOH697 3.4 20.2 1.0 CD B:PRO116 3.6 14.0 1.0 CG A:PRO280 3.6 14.3 1.0 O B:HOH910 3.7 43.2 1.0 O A:HOH779 3.7 42.8 1.0 CD A:PRO280 3.7 14.0 1.0 CA A:ASN255 3.8 12.7 1.0 CB A:ASN255 3.9 11.7 1.0 CG A:ASN255 4.0 14.6 1.0 CG B:PRO116 4.0 17.8 1.0 CD2 B:LEU115 4.1 16.2 1.0 N A:ASN255 4.5 13.0 1.0 C3 A:GOL402 4.5 39.0 1.0 O A:HOH789 4.6 34.1 1.0 O B:HOH836 4.9 64.6 1.0 N B:PRO116 5.0 14.0 1.0 C A:ASN255 5.0 11.0 1.0

Magnesium binding site 2 out of 4 in the Ruminococcus Gnavus Sialic Acid Aldolase Catalytic Lysine Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ruminococcus Gnavus Sialic Acid Aldolase Catalytic Lysine Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:18.2 occ:1.00 O A:HOH768 2.7 38.0 1.0 O B:HOH701 3.1 22.8 1.0 ND2 B:ASN255 3.1 16.0 1.0 O B:HOH716 3.4 20.8 1.0 CD A:PRO116 3.6 15.0 1.0 O A:HOH922 3.6 47.2 1.0 CG B:PRO280 3.6 13.2 1.0 CD B:PRO280 3.7 12.3 1.0 CA B:ASN255 3.8 12.8 1.0 CB B:ASN255 3.9 13.2 1.0 CG B:ASN255 4.0 14.9 1.0 CD2 A:LEU115 4.0 16.9 1.0 CG A:PRO116 4.1 19.5 1.0 O A:HOH766 4.4 79.2 1.0 N B:ASN255 4.4 12.5 1.0 C3 B:GOL402 4.6 34.6 1.0 O B:HOH785 4.7 39.1 1.0 N A:PRO116 4.9 13.0 1.0 CA A:LEU115 5.0 11.5 1.0 C B:ASN255 5.0 14.1 1.0

Magnesium binding site 3 out of 4 in the Ruminococcus Gnavus Sialic Acid Aldolase Catalytic Lysine Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ruminococcus Gnavus Sialic Acid Aldolase Catalytic Lysine Mutant within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg403 b:19.2 occ:1.00 O E:HOH736 2.6 35.5 1.0 O E:HOH693 3.0 23.8 1.0 ND2 E:ASN255 3.1 17.1 1.0 O F:HOH938 3.3 46.8 1.0 O E:HOH718 3.3 19.8 1.0 CD F:PRO116 3.6 14.7 1.0 CG E:PRO280 3.6 13.2 1.0 CD E:PRO280 3.7 13.2 1.0 CA E:ASN255 3.8 13.9 1.0 CB E:ASN255 3.9 13.3 1.0 O3 E:GOL402 3.9 56.9 1.0 CG E:ASN255 4.0 14.5 1.0 CG F:PRO116 4.1 18.5 1.0 CD2 F:LEU115 4.2 19.9 1.0 N E:ASN255 4.4 13.7 1.0 O E:HOH802 4.7 35.7 1.0 C3 E:GOL402 4.8 32.7 1.0 C E:ASN255 5.0 13.9 1.0 N F:PRO116 5.0 13.3 1.0 N E:MET256 5.0 12.9 1.0

Magnesium binding site 4 out of 4 in the Ruminococcus Gnavus Sialic Acid Aldolase Catalytic Lysine Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ruminococcus Gnavus Sialic Acid Aldolase Catalytic Lysine Mutant within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg405 b:19.4 occ:1.00 O E:HOH764 2.7 35.1 1.0 O F:HOH647 2.9 25.1 1.0 ND2 F:ASN255 3.1 17.7 1.0 O F:HOH732 3.4 20.9 1.0 CG F:PRO280 3.6 12.8 1.0 CD E:PRO116 3.7 14.6 1.0 CD F:PRO280 3.7 12.8 1.0 CA F:ASN255 3.8 13.2 1.0 CB F:ASN255 3.8 11.8 1.0 CG F:ASN255 3.9 15.1 1.0 CG E:PRO116 4.1 19.8 1.0 CD2 E:LEU115 4.2 15.4 1.0 C1 F:GOL402 4.4 33.6 1.0 N F:ASN255 4.4 12.3 1.0 O F:HOH783 4.7 36.2 1.0 C F:ASN255 5.0 12.6 1.0 N F:MET256 5.0 12.3 1.0

A.Bell, J.Brunt, E.Crost, L.Vaux, R.Nepravishta, C.D.Owen, D.Latousakis, A.Xiao, W.Li, X.Chen, M.A.Walsh, J.Claesen, J.Angulo, G.H.Thomas, N.Juge. Elucidation of A Sialic Acid Metabolism Pathway in Mucus-Foraging Ruminococcus Gnavus Unravels Mechanisms of Bacterial Adaptation to the Gut. Nat Microbiol V. 4 2393 2019.
ISSN: ESSN 2058-5276
PubMed: 31636419
DOI: 10.1038/S41564-019-0590-7