Magnesium in PDB 8u9f: Crystal Structure of Bacteroides Thetaiotamicron BT1285 in Complex with Nai

The structure of Crystal Structure of Bacteroides Thetaiotamicron BT1285 in Complex with Nai, PDB code: 8u9f was solved by D.E.Sastre, M.V.A.S.Navarro, E.J.Sundberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.50 / 1.08
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.54, 70.005, 70.159, 90, 90, 90
R / Rfree (%)	11.1 / 12.7

The structure of Crystal Structure of Bacteroides Thetaiotamicron BT1285 in Complex with Nai also contains other interesting chemical elements:

Iodine

(I)

23 atoms

The binding sites of Magnesium atom in the Crystal Structure of Bacteroides Thetaiotamicron BT1285 in Complex with Nai (pdb code 8u9f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Bacteroides Thetaiotamicron BT1285 in Complex with Nai, PDB code: 8u9f:

Magnesium binding site 1 out of 1 in the Crystal Structure of Bacteroides Thetaiotamicron BT1285 in Complex with Nai


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Bacteroides Thetaiotamicron BT1285 in Complex with Nai within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg431 b:11.2 occ:1.00 H A:THR242 2.1 6.0 1.0 H A:SER224 2.7 7.4 0.6 H A:SER224 2.7 9.0 0.4 O A:SER224 2.7 8.1 0.4 O A:PHE221 2.8 6.2 1.0 HD2 A:TYR219 2.8 8.3 1.0 HA A:TYR241 2.8 6.5 1.0 O A:SER224 2.8 6.6 0.6 N A:THR242 2.9 5.0 1.0 HA A:PHE222 3.0 6.7 1.0 HD1 A:TYR241 3.0 8.3 1.0 H A:ASN223 3.0 6.7 1.0 HE2 A:TYR219 3.0 8.9 1.0 O A:THR242 3.2 6.0 1.0 N A:ASN223 3.3 5.6 1.0 N A:SER224 3.4 7.5 0.4 N A:SER224 3.4 6.2 0.6 C A:SER224 3.5 8.0 0.4 CD2 A:TYR219 3.5 7.0 1.0 C A:SER224 3.5 6.2 0.6 C A:PHE222 3.5 5.7 1.0 CE2 A:TYR219 3.6 7.5 1.0 HB A:THR242 3.6 6.5 1.0 CA A:PHE222 3.6 5.6 1.0 CA A:TYR241 3.7 5.4 1.0 C A:PHE221 3.7 5.4 1.0 HA A:PRO225 3.7 9.2 0.4 HA A:PRO225 3.7 8.5 0.6 CD1 A:TYR241 3.7 6.9 1.0 C A:TYR241 3.8 5.2 1.0 CA A:THR242 3.8 5.0 1.0 C A:THR242 3.9 4.7 1.0 N A:PHE222 4.0 5.3 1.0 CA A:SER224 4.1 9.3 0.4 CA A:SER224 4.1 6.7 0.6 CB A:THR242 4.2 5.4 1.0 C A:ASN223 4.2 6.3 1.0 CA A:ASN223 4.2 5.8 1.0 N A:PRO225 4.2 6.6 0.6 N A:PRO225 4.3 7.8 0.4 O A:PHE222 4.3 6.6 1.0 HE1 A:TYR241 4.3 7.9 1.0 HA A:ASN223 4.4 6.9 1.0 CA A:PRO225 4.4 7.6 0.4 CA A:PRO225 4.4 7.1 0.6 CE1 A:TYR241 4.5 6.6 1.0 O A:PRO240 4.5 6.8 1.0 CG A:TYR241 4.5 6.2 1.0 O A:HOH567 4.6 4.3 0.5 HD1 A:PHE222 4.6 9.8 1.0 CB A:TYR241 4.6 6.2 1.0 N A:TYR241 4.6 5.6 1.0 HB3 A:TYR219 4.6 7.3 1.0 H A:PHE222 4.7 6.4 1.0 HA A:THR242 4.7 6.0 1.0 CG A:TYR219 4.7 6.2 1.0 HA A:SER224 4.7 11.1 0.4 HA A:SER224 4.8 8.0 0.6 OG1 A:THR242 4.8 6.3 1.0 HB2 A:SER224 4.8 9.3 0.6 HB2 A:TYR241 4.9 7.4 1.0 CZ A:TYR219 4.9 7.2 1.0 HB2 A:PHE221 4.9 7.3 1.0 HB3 A:SER224 4.9 15.1 0.4 CB A:PHE222 5.0 6.8 1.0 C A:PRO240 5.0 5.6 1.0 CA A:PHE221 5.0 5.4 1.0

D.E.Sastre, N.Sultana, M.V.A.S.Navarro, M.Huliciak, J.Du, J.O.Cifuente, M.Flowers, X.Liu, P.Lollar, B.Trastoy, M.E.Guerin, E.J.Sundberg. Human Gut Microbes Express Functionally Distinct Endoglycosidases to Metabolize the Same N-Glycan Substrate Nat Commun 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-48802-3