Manganese in PDB 7q4i: Crystal Structure of DMC1GALT1 in Complex with Udp-MN2+ and the Apd- Tgalnac-Rp

All present enzymatic activity of Crystal Structure of DMC1GALT1 in Complex with Udp-MN2+ and the Apd- Tgalnac-Rp:
2.4.1.122;

The structure of Crystal Structure of DMC1GALT1 in Complex with Udp-MN2+ and the Apd- Tgalnac-Rp, PDB code: 7q4i was solved by A.M.Gonzalez-Ramirez, H.Coelho, I.Companon, A.S.Grosso, Z.Yang, Y.Narimatsu, H.Clausen, F.Marcelo, F.Corzana, R.Hurtado-Guerrero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.241, 80.445, 71.949, 90, 93.19, 90
R / Rfree (%)	17.5 / 23.5

The binding sites of Manganese atom in the Crystal Structure of DMC1GALT1 in Complex with Udp-MN2+ and the Apd- Tgalnac-Rp (pdb code 7q4i). 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 DMC1GALT1 in Complex with Udp-MN2+ and the Apd- Tgalnac-Rp, PDB code: 7q4i:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of DMC1GALT1 in Complex with Udp-MN2+ and the Apd- Tgalnac-Rp


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 DMC1GALT1 in Complex with Udp-MN2+ and the Apd- Tgalnac-Rp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:22.9 occ:1.00 O1A A:UDP401 2.1 27.2 1.0 O2B A:UDP401 2.1 24.0 1.0 OD1 A:ASP183 2.2 21.3 1.0 NE2 A:HIS324 2.2 19.7 1.0 OD2 A:ASP181 2.2 26.0 1.0 OD2 A:ASP183 2.4 21.3 1.0 CG A:ASP183 2.6 21.9 1.0 CE1 A:HIS324 3.2 19.7 1.0 CD2 A:HIS324 3.2 16.5 1.0 CG A:ASP181 3.2 26.8 1.0 PA A:UDP401 3.3 26.4 1.0 PB A:UDP401 3.3 24.5 1.0 CB A:ASP181 3.5 24.6 1.0 O3A A:UDP401 3.6 26.0 1.0 C5' A:UDP401 4.0 28.7 1.0 O5' A:UDP401 4.1 26.4 1.0 CB A:ASP183 4.2 21.2 1.0 O1B A:UDP401 4.2 25.2 1.0 O A:HOH504 4.3 23.8 1.0 ND1 A:HIS324 4.3 17.6 1.0 CG A:HIS324 4.3 16.9 1.0 OD1 A:ASP181 4.4 23.8 1.0 O3B A:UDP401 4.4 23.7 1.0 O2A A:UDP401 4.6 24.3 1.0 CE1 A:TYR325 4.6 21.4 1.0 C3' A:UDP401 4.7 30.3 1.0 CA A:GLY222 4.7 22.6 1.0 C4' A:UDP401 4.8 30.1 1.0 N A:ASP183 4.8 22.3 1.0 CA A:ASP183 4.9 19.9 1.0 CD1 A:TYR325 4.9 22.9 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of DMC1GALT1 in Complex with Udp-MN2+ and the Apd- Tgalnac-Rp


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 DMC1GALT1 in Complex with Udp-MN2+ and the Apd- Tgalnac-Rp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:26.2 occ:1.00 O1B B:UDP401 2.0 26.3 1.0 O1A B:UDP401 2.1 30.2 1.0 OD2 B:ASP181 2.2 33.2 1.0 NE2 B:HIS324 2.2 23.7 1.0 OD1 B:ASP183 2.2 19.9 1.0 OD2 B:ASP183 2.4 21.6 1.0 CG B:ASP183 2.7 20.3 1.0 CE1 B:HIS324 3.2 23.1 1.0 CG B:ASP181 3.2 30.2 1.0 CD2 B:HIS324 3.2 22.4 1.0 PB B:UDP401 3.3 24.6 1.0 PA B:UDP401 3.4 25.8 1.0 CB B:ASP181 3.5 27.0 1.0 O3A B:UDP401 3.6 23.9 1.0 O B:HOH508 4.1 23.5 1.0 O2B B:UDP401 4.2 22.7 1.0 CB B:ASP183 4.2 21.5 1.0 O5' B:UDP401 4.2 29.4 1.0 C5' B:UDP401 4.2 28.7 1.0 ND1 B:HIS324 4.3 21.6 1.0 CG B:HIS324 4.3 23.4 1.0 O3B B:UDP401 4.3 25.6 1.0 OD1 B:ASP181 4.4 26.6 1.0 O2A B:UDP401 4.6 24.3 1.0 CE1 B:TYR325 4.6 31.3 1.0 C3' B:UDP401 4.6 30.6 1.0 CA B:GLY222 4.7 24.7 1.0 C4' B:UDP401 4.8 28.4 1.0 CD1 B:TYR325 4.8 29.4 1.0 N B:ASP183 4.9 24.1 1.0 CA B:ASP183 5.0 21.9 1.0

A.M.Gonzalez-Ramirez, A.S.Grosso, Z.Yang, I.Companon, H.Coelho, Y.Narimatsu, H.Clausen, F.Marcelo, F.Corzana, R.Hurtado-Guerrero. Structural Basis For the Synthesis of the Core 1 Structure By C1GALT1. Nat Commun V. 13 2398 2022.
ISSN: ESSN 2041-1723
PubMed: 35504880
DOI: 10.1038/S41467-022-29833-0