Manganese in PDB 7xpt: Crystal Structrue of Mtdl:Gdp:Mn Soaked with Gdp-Glc

The structure of Crystal Structrue of Mtdl:Gdp:Mn Soaked with Gdp-Glc, PDB code: 7xpt was solved by F.D.Li, C.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.70 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.275, 98.825, 58.102, 90, 96.77, 90
R / Rfree (%)	21.5 / 25.9

The binding sites of Manganese atom in the Crystal Structrue of Mtdl:Gdp:Mn Soaked with Gdp-Glc (pdb code 7xpt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structrue of Mtdl:Gdp:Mn Soaked with Gdp-Glc, PDB code: 7xpt:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structrue of Mtdl:Gdp:Mn Soaked with Gdp-Glc


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structrue of Mtdl:Gdp:Mn Soaked with Gdp-Glc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:38.7 occ:1.00 O14 A:GDG401 2.1 31.8 1.0 OD2 A:ASP111 2.3 35.8 1.0 O A:HOH510 2.3 32.4 1.0 O19 A:GDG401 2.3 33.4 1.0 NE2 A:HIS287 2.3 32.1 1.0 OD1 A:ASP111 2.4 33.6 1.0 CG A:ASP111 2.7 37.8 1.0 CD2 A:HIS287 3.3 40.6 1.0 CE1 A:HIS287 3.3 34.6 1.0 P13 A:GDG401 3.4 41.0 1.0 P17 A:GDG401 3.4 36.4 1.0 O16 A:GDG401 3.8 39.1 1.0 O20 A:GDG401 3.9 39.6 1.0 ND2 A:ASN112 4.0 40.6 1.0 O15 A:GDG401 4.0 43.7 1.0 OD2 A:ASP109 4.1 31.4 1.0 CB A:ASP111 4.1 35.9 1.0 CG A:ARG289 4.2 40.9 1.0 CB A:ASP109 4.3 34.1 1.0 ND1 A:HIS287 4.4 41.2 1.0 CG A:HIS287 4.5 36.1 1.0 O31 A:GDG401 4.5 41.9 1.0 CA A:ARG289 4.6 39.4 1.0 O12 A:GDG401 4.6 37.6 1.0 CG A:ASP109 4.7 40.1 1.0 O18 A:GDG401 4.7 35.0 1.0 ND2 A:ASN290 4.7 46.7 1.0 N A:ASN290 4.7 34.2 1.0 C11 A:GDG401 4.8 38.2 1.0 CB A:ARG289 4.8 38.3 1.0 CD A:ARG289 4.9 39.4 1.0 CA A:ASP111 5.0 42.7 1.0 NE A:ARG289 5.0 43.7 1.0 NE2 A:GLN229 5.0 34.0 1.0

Manganese binding site 2 out of 2 in the Crystal Structrue of Mtdl:Gdp:Mn Soaked with Gdp-Glc


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structrue of Mtdl:Gdp:Mn Soaked with Gdp-Glc within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:45.2 occ:1.00 O14 B:GDG401 2.2 44.8 1.0 O B:HOH520 2.3 40.3 1.0 NE2 B:HIS287 2.3 37.2 1.0 O19 B:GDG401 2.3 35.8 1.0 OD2 B:ASP111 2.3 42.9 1.0 OD1 B:ASP111 2.5 40.5 1.0 CG B:ASP111 2.7 43.3 1.0 CD2 B:HIS287 3.2 43.1 1.0 CE1 B:HIS287 3.3 42.6 1.0 P17 B:GDG401 3.5 43.6 1.0 P13 B:GDG401 3.5 51.3 1.0 CG B:ARG289 3.7 48.4 1.0 O16 B:GDG401 3.8 51.2 1.0 O20 B:GDG401 4.0 44.3 1.0 O15 B:GDG401 4.1 54.2 1.0 CB B:ASP111 4.2 49.2 1.0 ND2 B:ASN112 4.2 45.3 1.0 OD2 B:ASP109 4.3 42.1 1.0 ND1 B:HIS287 4.4 44.8 1.0 CG B:HIS287 4.4 42.5 1.0 CD B:ARG289 4.4 50.8 1.0 CB B:ASP109 4.5 39.5 1.0 CB B:ARG289 4.5 42.6 1.0 O31 B:GDG401 4.5 49.6 1.0 CA B:ARG289 4.5 46.1 1.0 O18 B:GDG401 4.7 46.1 1.0 N B:ASN290 4.8 47.0 1.0 O12 B:GDG401 4.8 42.3 1.0 CG B:ASP109 4.8 47.4 1.0 O B:ASP111 4.9 43.8 1.0 C11 B:GDG401 4.9 46.2 1.0 NE2 B:GLN229 4.9 38.9 1.0

X.Du, X.Chu, N.Liu, X.Jia, H.Peng, Y.Xiao, L.Liu, H.Yu, F.Li, C.He. Structures of the Ndp-Pyranose Mutase Belonging to Glycosyltransferase Family 75 Reveal Residues Important For Mn 2+ Coordination and Substrate Binding. J.Biol.Chem. V. 299 02903 2023.
ISSN: ESSN 1083-351X
PubMed: 36642179
DOI: 10.1016/J.JBC.2023.102903