Manganese in PDB 7xps: Crystal Structrue of Mtdl:Gdp:Mn

The structure of Crystal Structrue of Mtdl:Gdp:Mn, PDB code: 7xps 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)	19.85 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	98.694, 162.243, 116.496, 90, 90, 90
R / Rfree (%)	22.4 / 26.7

The binding sites of Manganese atom in the Crystal Structrue of Mtdl:Gdp:Mn (pdb code 7xps). 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, PDB code: 7xps:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structrue of Mtdl:Gdp:Mn


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:66.8 occ:1.00 O A:HOH501 2.2 45.9 1.0 OD2 A:ASP111 2.3 35.2 1.0 O2A A:GDP401 2.3 78.0 1.0 NE2 A:HIS287 2.4 56.2 1.0 O3B A:GDP401 2.4 59.6 1.0 OD1 A:ASP111 2.6 31.6 1.0 CG A:ASP111 2.8 37.0 1.0 CE1 A:HIS287 3.2 37.1 1.0 CD2 A:HIS287 3.3 45.1 1.0 PA A:GDP401 3.6 92.4 1.0 PB A:GDP401 3.7 80.9 1.0 O3A A:GDP401 3.9 91.0 1.0 CG A:ARG289 4.2 53.3 0.5 ND2 A:ASN112 4.2 46.5 1.0 OD2 A:ASP109 4.2 50.0 1.0 CB A:ASP111 4.3 32.3 1.0 O1A A:GDP401 4.3 83.1 1.0 ND1 A:HIS287 4.3 53.1 1.0 CG A:HIS287 4.4 44.2 1.0 O1B A:GDP401 4.5 72.9 1.0 CA A:ARG289 4.5 42.4 0.5 CB A:ASP109 4.5 35.7 1.0 ND2 A:ASN290 4.6 44.6 0.5 N A:ASN290 4.7 48.3 0.5 CB A:ARG289 4.7 44.6 0.5 CG A:ASP109 4.8 47.5 1.0 O2B A:GDP401 4.8 72.0 1.0 O5' A:GDP401 4.8 84.4 1.0 CD A:ARG289 4.9 48.7 0.5 C5' A:GDP401 5.0 64.6 1.0

Manganese binding site 2 out of 2 in the Crystal Structrue of Mtdl:Gdp:Mn


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:58.4 occ:1.00 O1B B:GDP401 2.2 69.5 1.0 O1A B:GDP401 2.3 73.2 1.0 NE2 B:HIS287 2.5 50.8 1.0 OD2 B:ASP111 2.5 43.6 1.0 OD1 B:ASP111 2.8 34.4 1.0 CG B:ASP111 3.0 45.1 1.0 CE1 B:HIS287 3.3 45.9 1.0 CD2 B:HIS287 3.4 47.1 1.0 PB B:GDP401 3.5 70.1 1.0 PA B:GDP401 3.5 76.4 1.0 O3A B:GDP401 3.8 75.0 1.0 OD2 B:ASP109 3.9 52.6 1.0 ND2 B:ASN112 4.1 46.4 1.0 CG B:ARG289 4.1 47.9 0.5 O2A B:GDP401 4.2 71.8 1.0 O2B B:GDP401 4.3 73.1 1.0 CB B:ASP109 4.3 43.9 1.0 ND1 B:HIS287 4.5 59.3 1.0 O3B B:GDP401 4.5 76.2 1.0 CB B:ASP111 4.5 33.5 1.0 CA B:ARG289 4.5 41.4 0.5 CG B:HIS287 4.5 45.1 1.0 CG B:ASP109 4.5 46.1 1.0 CB B:ARG289 4.6 41.0 0.5 CD B:ARG289 4.7 45.1 0.5 O5' B:GDP401 4.7 73.3 1.0 N B:ASN290 4.8 45.7 0.5 C5' B:GDP401 4.9 49.5 1.0 CD B:GLN229 4.9 37.7 1.0 OE1 B:GLN229 5.0 42.8 1.0 NE2 B:GLN229 5.0 27.4 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