Manganese in PDB 7xpv: Crysteal Structure of Mtdl-S228A-His Soaked with Gdp-Fucf and Mn

The structure of Crysteal Structure of Mtdl-S228A-His Soaked with Gdp-Fucf and Mn, PDB code: 7xpv 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)	46.93 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	98.135, 162.67, 114.927, 90, 90, 90
R / Rfree (%)	25.8 / 29.3

The binding sites of Manganese atom in the Crysteal Structure of Mtdl-S228A-His Soaked with Gdp-Fucf and Mn (pdb code 7xpv). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crysteal Structure of Mtdl-S228A-His Soaked with Gdp-Fucf and Mn, PDB code: 7xpv:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crysteal Structure of Mtdl-S228A-His Soaked with Gdp-Fucf and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crysteal Structure of Mtdl-S228A-His Soaked with Gdp-Fucf and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:54.0 occ:1.00 O6 A:GRJ401 1.9 54.6 1.0 OD2 A:ASP111 2.0 60.8 1.0 NE2 A:HIS287 2.5 47.3 1.0 O2 A:GRJ401 2.6 48.6 1.0 CG A:ASP111 2.7 53.3 1.0 OD1 A:ASP111 2.8 50.8 1.0 P1 A:GRJ401 3.2 60.2 1.0 CD2 A:HIS287 3.4 50.4 1.0 CE1 A:HIS287 3.5 55.9 1.0 P A:GRJ401 3.5 60.0 1.0 O5 A:GRJ401 3.5 61.5 1.0 O4 A:GRJ401 3.8 54.5 1.0 O1 A:GRJ401 3.8 64.6 1.0 CG A:ARG289 4.0 57.8 1.0 CB A:ASP111 4.2 58.1 1.0 OD2 A:ASP109 4.3 51.4 1.0 ND2 A:ASN112 4.3 48.9 1.0 O7 A:GRJ401 4.5 51.0 1.0 CA A:ARG289 4.5 64.5 1.0 CG A:HIS287 4.6 49.6 1.0 ND1 A:HIS287 4.6 60.3 1.0 CB A:ARG289 4.6 57.5 1.0 CB A:ASP109 4.6 46.6 1.0 N A:ASN290 4.8 58.8 1.0 CG A:ASP109 4.9 50.1 1.0 ND2 A:ASN290 4.9 44.0 1.0 C6 A:GRJ401 5.0 42.9 1.0 O3 A:GRJ401 5.0 61.4 1.0

Manganese binding site 2 out of 2 in the Crysteal Structure of Mtdl-S228A-His Soaked with Gdp-Fucf and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crysteal Structure of Mtdl-S228A-His Soaked with Gdp-Fucf and Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:51.6 occ:1.00 O6 B:GRJ401 2.0 55.5 1.0 OD2 B:ASP111 2.0 49.4 1.0 NE2 B:HIS287 2.4 38.9 1.0 O2 B:GRJ401 2.5 40.3 1.0 CG B:ASP111 2.7 48.4 1.0 OD1 B:ASP111 2.7 52.1 1.0 P1 B:GRJ401 3.2 53.9 1.0 CE1 B:HIS287 3.3 47.1 1.0 CD2 B:HIS287 3.4 48.1 1.0 P B:GRJ401 3.5 50.3 1.0 O5 B:GRJ401 3.6 55.8 1.0 CG B:ARG289 3.7 47.7 1.0 O1 B:GRJ401 3.8 64.3 1.0 O4 B:GRJ401 3.8 51.8 1.0 ND2 B:ASN112 4.2 44.0 1.0 CB B:ASP111 4.2 47.5 1.0 OD2 B:ASP109 4.2 46.6 1.0 CD B:ARG289 4.3 54.8 1.0 ND1 B:HIS287 4.4 51.5 1.0 CB B:ARG289 4.5 41.6 1.0 CG B:HIS287 4.5 43.9 1.0 CA B:ARG289 4.5 47.8 1.0 CB B:ASP109 4.5 40.0 1.0 O7 B:GRJ401 4.6 48.1 1.0 CG B:ASP109 4.8 48.1 1.0 N B:ASN290 4.8 51.1 1.0 OE1 B:GLN229 4.9 44.5 1.0 O3 B:GRJ401 4.9 55.9 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