Manganese in PDB 7xpu: Crystal Structure of Mtdl-S228A-His Soaked Gdp-Fucp and Mn

The structure of Crystal Structure of Mtdl-S228A-His Soaked Gdp-Fucp and Mn, PDB code: 7xpu 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)	47.12 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	98.189, 162.548, 115.662, 90, 90, 90
R / Rfree (%)	23.8 / 28

The binding sites of Manganese atom in the Crystal Structure of Mtdl-S228A-His Soaked Gdp-Fucp and Mn (pdb code 7xpu). 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 Structure of Mtdl-S228A-His Soaked Gdp-Fucp and Mn, PDB code: 7xpu:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Mtdl-S228A-His Soaked Gdp-Fucp and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Mtdl-S228A-His Soaked Gdp-Fucp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:23.7 occ:1.00 OD2 A:ASP111 1.9 27.5 1.0 O3P A:GFB401 2.1 31.4 1.0 O1X A:GFB401 2.3 26.5 1.0 O A:HOH508 2.3 25.8 1.0 NE2 A:HIS287 2.3 28.9 1.0 OD1 A:ASP111 2.5 24.2 1.0 CG A:ASP111 2.5 30.4 1.0 P A:GFB401 3.2 33.5 1.0 CE1 A:HIS287 3.3 23.8 1.0 CD2 A:HIS287 3.3 24.3 1.0 P1 A:GFB401 3.3 26.1 1.0 O2P A:GFB401 3.6 28.6 1.0 O1 A:GFB401 3.7 41.5 1.0 O1P A:GFB401 3.8 33.9 1.0 CB A:ASP111 4.0 30.9 1.0 CG A:ARG289 4.1 27.1 1.0 ND2 A:ASN112 4.1 26.7 1.0 OD2 A:ASP109 4.2 33.7 1.0 ND1 A:HIS287 4.4 29.9 1.0 CG A:HIS287 4.5 26.5 1.0 CB A:ASP109 4.5 25.3 1.0 O5' A:GFB401 4.5 28.4 1.0 CA A:ARG289 4.5 30.9 1.0 NE2 A:GLN229 4.6 27.5 1.0 C1 A:GFB401 4.6 41.9 1.0 CB A:ARG289 4.7 24.2 1.0 N A:ASN290 4.7 35.4 1.0 O2X A:GFB401 4.7 27.9 1.0 ND2 A:ASN290 4.8 30.2 1.0 CD A:ARG289 4.8 30.1 1.0 CG A:ASP109 4.8 35.7 1.0 C5' A:GFB401 4.8 27.1 1.0 NE A:ARG289 4.9 35.0 1.0 CA A:ASP111 4.9 27.7 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Mtdl-S228A-His Soaked Gdp-Fucp and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Mtdl-S228A-His Soaked Gdp-Fucp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:20.6 occ:1.00 OD2 B:ASP111 1.9 27.5 1.0 O3P B:GFB401 2.1 27.4 1.0 O1X B:GFB401 2.3 24.7 1.0 O B:HOH535 2.4 21.2 1.0 NE2 B:HIS287 2.4 22.1 1.0 OD1 B:ASP111 2.5 25.2 1.0 CG B:ASP111 2.5 26.3 1.0 P B:GFB401 3.2 26.2 1.0 CE1 B:HIS287 3.3 23.8 1.0 P1 B:GFB401 3.3 26.9 1.0 CD2 B:HIS287 3.4 22.6 1.0 O2P B:GFB401 3.6 23.3 1.0 O1 B:GFB401 3.6 35.6 1.0 O1P B:GFB401 3.9 29.9 1.0 CB B:ASP111 4.0 26.7 1.0 ND2 B:ASN112 4.1 21.1 1.0 CG B:ARG289 4.1 25.3 1.0 OD2 B:ASP109 4.2 33.8 1.0 ND1 B:HIS287 4.4 27.1 1.0 CB B:ASP109 4.5 23.7 1.0 CG B:HIS287 4.5 21.9 1.0 CA B:ARG289 4.5 30.5 1.0 O5' B:GFB401 4.6 29.2 1.0 C1 B:GFB401 4.6 40.3 1.0 N B:ASN290 4.7 28.5 1.0 CB B:ARG289 4.7 23.0 1.0 O B:HOH713 4.7 33.5 1.0 O2X B:GFB401 4.7 29.7 1.0 ND2 B:ASN290 4.7 23.2 1.0 CD B:ARG289 4.8 26.9 1.0 NE B:ARG289 4.9 31.7 1.0 CG B:ASP109 4.9 33.3 1.0 C5' B:GFB401 4.9 20.9 1.0 NE2 B:GLN229 4.9 24.9 1.0 CA B:ASP111 4.9 22.7 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