Manganese in PDB 5m7d: Blood Group Synthase Aaglyb in Complex with Udp-Gal and Cryoprotected with Glycerol

All present enzymatic activity of Blood Group Synthase Aaglyb in Complex with Udp-Gal and Cryoprotected with Glycerol:
2.4.1.37; 2.4.1.40;

The structure of Blood Group Synthase Aaglyb in Complex with Udp-Gal and Cryoprotected with Glycerol, PDB code: 5m7d was solved by J.Rocha, A.Royant, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	52.643, 148.796, 79.782, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 15.7

The binding sites of Manganese atom in the Blood Group Synthase Aaglyb in Complex with Udp-Gal and Cryoprotected with Glycerol (pdb code 5m7d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Blood Group Synthase Aaglyb in Complex with Udp-Gal and Cryoprotected with Glycerol, PDB code: 5m7d:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Blood Group Synthase Aaglyb in Complex with Udp-Gal and Cryoprotected with Glycerol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Blood Group Synthase Aaglyb in Complex with Udp-Gal and Cryoprotected with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:8.9 occ:0.75 MN A:MN401 0.0 8.9 0.8 MN A:MN401 2.1 9.7 0.2 O A:HOH752 2.1 14.6 1.0 O1B A:GDU402 2.1 16.5 1.0 OD2 A:ASP211 2.2 8.1 1.0 O1A A:GDU402 2.2 11.6 1.0 OD1 A:ASP213 2.3 10.4 1.0 OD2 A:ASP213 2.5 14.4 1.0 CG A:ASP213 2.7 10.2 1.0 CG A:ASP211 3.3 7.0 1.0 PB A:GDU402 3.4 12.9 1.0 PA A:GDU402 3.5 12.3 1.0 CB A:ASP211 3.6 5.7 1.0 O3D A:GDU402 3.8 8.7 1.0 O3A A:GDU402 3.8 14.3 1.0 O3B A:GDU402 3.8 12.9 1.0 O2' A:GDU402 3.9 14.1 1.0 O A:HOH556 4.0 30.6 1.0 CB A:ASP213 4.2 8.6 1.0 OD1 A:ASP211 4.4 7.0 1.0 NZ A:LYS346 4.4 23.5 0.5 C5D A:GDU402 4.4 8.7 1.0 O5D A:GDU402 4.5 10.3 1.0 C3D A:GDU402 4.6 7.1 1.0 O2A A:GDU402 4.6 15.4 1.0 O2B A:GDU402 4.7 17.6 1.0 O A:HOH546 4.7 23.3 1.0 C1' A:GDU402 4.8 12.2 1.0 C2' A:GDU402 4.8 12.0 1.0 SD A:MET214 4.8 9.6 1.0 O A:ASP213 4.9 8.6 1.0 N A:ASP213 5.0 6.9 1.0 C4D A:GDU402 5.0 7.6 1.0

Manganese binding site 2 out of 2 in the Blood Group Synthase Aaglyb in Complex with Udp-Gal and Cryoprotected with Glycerol


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Blood Group Synthase Aaglyb in Complex with Udp-Gal and Cryoprotected with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:9.7 occ:0.25 MN A:MN401 0.0 9.7 0.2 OD2 A:ASP213 2.0 14.4 1.0 O1A A:GDU402 2.0 11.6 1.0 O1B A:GDU402 2.0 16.5 1.0 MN A:MN401 2.1 8.9 0.8 NZ A:LYS346 2.3 23.5 0.5 PA A:GDU402 2.7 12.3 1.0 CG A:ASP213 2.9 10.2 1.0 PB A:GDU402 2.9 12.9 1.0 O3A A:GDU402 2.9 14.3 1.0 CE A:LYS346 3.2 15.7 0.5 OD1 A:ASP213 3.2 10.4 1.0 O2A A:GDU402 3.3 15.4 1.0 O A:HOH752 3.6 14.6 1.0 O2B A:GDU402 3.9 17.6 1.0 CD A:LYS346 4.0 15.1 0.5 OD2 A:ASP211 4.1 8.1 1.0 O3B A:GDU402 4.1 12.9 1.0 CB A:ASP213 4.1 8.6 1.0 O5D A:GDU402 4.2 10.3 1.0 O A:HOH546 4.3 23.3 1.0 O3D A:GDU402 4.6 8.7 1.0 NH2 A:ARG352 4.7 25.1 0.5 CE1 A:HIS348 4.7 33.1 0.5 C5D A:GDU402 4.8 8.7 1.0 OH A:TYR126 4.8 14.1 1.0 CE2 A:TYR126 4.8 10.4 1.0 ND1 A:HIS348 4.9 34.0 0.5 C3D A:GDU402 5.0 7.1 1.0

J.Rocha, A.Royant. Blood Group Synthase Aaglyb in Complex with Udp-Gal and Cryoprotected with Glycerol To Be Published.