Manganese in PDB 6nqt: Galnac-T2 Soaked with Udp-Sugar

All present enzymatic activity of Galnac-T2 Soaked with Udp-Sugar:
2.4.1.41;

The structure of Galnac-T2 Soaked with Udp-Sugar, PDB code: 6nqt was solved by D.Fernandez, C.R.Bertozzi, B.Schumann, A.Agbay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.70 / 3.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	116.575, 120.126, 247.389, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 28.6

The binding sites of Manganese atom in the Galnac-T2 Soaked with Udp-Sugar (pdb code 6nqt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Galnac-T2 Soaked with Udp-Sugar, PDB code: 6nqt:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Galnac-T2 Soaked with Udp-Sugar


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Galnac-T2 Soaked with Udp-Sugar within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:49.3 occ:1.00 O1A A:LR7702 1.8 47.2 1.0 NE2 A:HIS226 2.1 51.2 1.0 OD2 A:ASP224 2.3 39.1 1.0 NE2 A:HIS359 2.3 39.7 1.0 O1B A:LR7702 2.3 43.3 1.0 CE1 A:HIS226 3.0 51.6 1.0 PA A:LR7702 3.2 44.5 1.0 CD2 A:HIS226 3.2 52.5 1.0 CD2 A:HIS359 3.2 40.9 1.0 CE1 A:HIS359 3.3 37.9 1.0 CG A:ASP224 3.4 43.5 1.0 PB A:LR7702 3.4 43.6 1.0 O3A A:LR7702 3.7 43.2 1.0 CB A:ASP224 3.8 42.7 1.0 NH1 A:ARG362 3.8 53.6 1.0 O1' A:LR7702 4.0 57.8 1.0 O2A A:LR7702 4.1 41.7 1.0 ND1 A:HIS226 4.1 51.0 1.0 CG A:HIS226 4.3 50.6 1.0 O5B A:LR7702 4.3 46.0 1.0 N2' A:LR7702 4.3 54.8 1.0 C5B A:LR7702 4.4 48.3 1.0 ND1 A:HIS359 4.4 38.3 1.0 CG A:HIS359 4.4 40.6 1.0 O A:VAL360 4.4 45.3 1.0 OD1 A:ASP224 4.5 44.6 1.0 C3B A:LR7702 4.7 46.4 1.0 O2B A:LR7702 4.7 46.6 1.0 C8' A:LR7702 4.7 47.2 1.0 C4B A:LR7702 4.9 47.0 1.0

Manganese binding site 2 out of 6 in the Galnac-T2 Soaked with Udp-Sugar


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Galnac-T2 Soaked with Udp-Sugar within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:30.6 occ:1.00 O1A B:LR7702 2.0 50.8 1.0 NE2 B:HIS226 2.2 33.6 1.0 OD2 B:ASP224 2.2 37.8 1.0 NE2 B:HIS359 2.4 46.7 1.0 O2B B:LR7702 2.8 57.7 1.0 PA B:LR7702 3.0 48.5 1.0 O5B B:LR7702 3.0 51.2 1.0 CE1 B:HIS226 3.1 32.3 1.0 CD2 B:HIS226 3.2 33.2 1.0 CG B:ASP224 3.3 40.5 1.0 CD2 B:HIS359 3.3 46.7 1.0 CE1 B:HIS359 3.4 46.9 1.0 O3A B:LR7702 3.5 50.0 1.0 PB B:LR7702 3.5 57.1 1.0 O1' B:LR7702 3.6 68.7 1.0 CB B:ASP224 3.8 39.3 1.0 N2' B:LR7702 4.0 75.3 1.0 ND1 B:HIS226 4.2 31.1 1.0 OD1 B:ASP224 4.3 48.3 1.0 O2A B:LR7702 4.3 41.9 1.0 CG B:HIS226 4.3 33.2 1.0 C5B B:LR7702 4.4 54.0 1.0 C3' B:LR7702 4.5 87.3 1.0 ND1 B:HIS359 4.5 47.0 1.0 O B:VAL360 4.5 46.5 1.0 CG B:HIS359 4.5 47.4 1.0 C3B B:LR7702 4.5 58.7 1.0 C2' B:LR7702 4.5 81.1 1.0 O3' B:LR7702 4.6 88.0 1.0 O3B B:LR7702 4.6 65.3 1.0 C1' B:LR7702 4.7 81.7 1.0 C4B B:LR7702 4.8 56.9 1.0 O1B B:LR7702 5.0 67.6 1.0

Manganese binding site 3 out of 6 in the Galnac-T2 Soaked with Udp-Sugar


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Galnac-T2 Soaked with Udp-Sugar within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn701 b:48.7 occ:1.00 O2A C:LR7702 2.0 51.9 1.0 O2B C:LR7702 2.2 55.5 1.0 NE2 C:HIS226 2.3 45.5 1.0 OD2 C:ASP224 2.4 61.3 1.0 NE2 C:HIS359 2.4 49.7 1.0 CE1 C:HIS226 3.2 44.8 1.0 PB C:LR7702 3.2 53.3 1.0 PA C:LR7702 3.2 52.6 1.0 CE1 C:HIS359 3.3 50.2 1.0 CD2 C:HIS226 3.4 49.0 1.0 O3A C:LR7702 3.4 54.7 1.0 CD2 C:HIS359 3.4 47.1 1.0 CG C:ASP224 3.5 57.1 1.0 O1' C:LR7702 3.5 57.2 1.0 CB C:ASP224 4.0 50.9 1.0 C5B C:LR7702 4.1 54.7 1.0 N2' C:LR7702 4.2 67.6 1.0 O5B C:LR7702 4.2 52.7 1.0 ND1 C:HIS226 4.3 47.5 1.0 O1A C:LR7702 4.4 53.7 1.0 O C:VAL360 4.4 48.2 1.0 ND1 C:HIS359 4.4 47.2 1.0 CG C:HIS226 4.5 45.7 1.0 OD1 C:ASP224 4.5 57.0 1.0 CG C:HIS359 4.6 44.9 1.0 O1B C:LR7702 4.6 55.9 1.0 C1' C:LR7702 4.7 65.8 1.0 C2' C:LR7702 4.8 67.8 1.0 C3B C:LR7702 4.8 50.0 1.0 C3' C:LR7702 4.9 68.7 1.0 C4B C:LR7702 4.9 53.1 1.0 NH2 C:ARG362 4.9 87.9 1.0

Manganese binding site 4 out of 6 in the Galnac-T2 Soaked with Udp-Sugar


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Galnac-T2 Soaked with Udp-Sugar within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn701 b:50.8 occ:1.00 O2A D:LR7702 2.1 52.8 1.0 NE2 D:HIS226 2.2 46.2 1.0 O2B D:LR7702 2.3 47.5 1.0 OD2 D:ASP224 2.3 72.9 1.0 NE2 D:HIS359 2.4 53.7 1.0 CE1 D:HIS226 3.0 48.9 1.0 PA D:LR7702 3.1 52.4 1.0 O5B D:LR7702 3.3 54.6 1.0 PB D:LR7702 3.3 45.0 1.0 CD2 D:HIS226 3.3 43.1 1.0 CE1 D:HIS359 3.4 51.8 1.0 CD2 D:HIS359 3.4 50.3 1.0 CG D:ASP224 3.4 65.2 1.0 O3A D:LR7702 3.6 44.3 1.0 O1' D:LR7702 3.7 71.9 1.0 CB D:ASP224 3.9 58.8 1.0 ND1 D:HIS226 4.2 45.0 1.0 C40 D:LR7702 4.3 64.9 1.0 CG D:HIS226 4.4 42.8 1.0 O1A D:LR7702 4.5 48.3 1.0 OD1 D:ASP224 4.5 74.4 1.0 ND1 D:HIS359 4.5 47.9 1.0 O D:VAL360 4.5 44.3 1.0 CG D:HIS359 4.5 49.7 1.0 C3B D:LR7702 4.6 48.4 1.0 C5B D:LR7702 4.7 50.2 1.0 O1B D:LR7702 4.7 41.6 1.0 O7' D:LR7702 4.7 56.4 1.0 O3B D:LR7702 4.9 49.4 1.0 C7' D:LR7702 4.9 71.3 1.0

Manganese binding site 5 out of 6 in the Galnac-T2 Soaked with Udp-Sugar


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Galnac-T2 Soaked with Udp-Sugar within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn701 b:47.7 occ:1.00 O2B E:LR7702 1.9 55.8 1.0 NE2 E:HIS226 2.2 67.1 1.0 OD2 E:ASP224 2.2 55.4 1.0 NE2 E:HIS359 2.4 61.4 1.0 CE1 E:HIS226 3.0 69.3 1.0 O5B E:LR7702 3.1 63.9 1.0 PB E:LR7702 3.1 62.1 1.0 O2A E:LR7702 3.2 59.1 1.0 CD2 E:HIS226 3.3 67.9 1.0 CG E:ASP224 3.3 57.0 1.0 CD2 E:HIS359 3.4 56.5 1.0 CE1 E:HIS359 3.4 58.9 1.0 O3A E:LR7702 3.5 62.4 1.0 PA E:LR7702 3.5 62.8 1.0 O1B E:LR7702 3.7 60.5 1.0 CB E:ASP224 3.8 55.7 1.0 C5B E:LR7702 4.0 66.0 1.0 N2' E:LR7702 4.0 79.6 1.0 ND1 E:HIS226 4.2 69.5 1.0 NH1 E:ARG362 4.2 81.0 1.0 CG E:HIS226 4.3 63.4 1.0 OD1 E:ASP224 4.4 60.1 1.0 O1' E:LR7702 4.5 69.2 1.0 O E:VAL360 4.5 62.6 1.0 C8' E:LR7702 4.5 66.5 1.0 CG E:HIS359 4.6 54.9 1.0 ND1 E:HIS359 4.6 52.4 1.0 C3B E:LR7702 4.7 78.1 1.0 C4B E:LR7702 4.7 73.1 1.0 C2' E:LR7702 4.8 73.3 1.0 C7' E:LR7702 4.9 71.8 1.0

Manganese binding site 6 out of 6 in the Galnac-T2 Soaked with Udp-Sugar


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Galnac-T2 Soaked with Udp-Sugar within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn701 b:73.2 occ:1.00 OD2 F:ASP224 1.9 70.1 1.0 NE2 F:HIS226 2.1 70.8 1.0 O2A F:LR7702 2.2 72.9 1.0 O2B F:LR7702 2.2 72.0 1.0 NE2 F:HIS359 2.3 62.5 1.0 CE1 F:HIS226 2.9 70.9 1.0 CG F:ASP224 3.1 68.5 1.0 CD2 F:HIS226 3.1 70.6 1.0 CD2 F:HIS359 3.2 57.9 1.0 CE1 F:HIS359 3.4 64.2 1.0 PB F:LR7702 3.5 70.8 1.0 PA F:LR7702 3.5 69.7 1.0 CB F:ASP224 3.8 69.6 1.0 O3A F:LR7702 3.8 65.2 1.0 C5B F:LR7702 3.9 70.7 1.0 ND1 F:HIS226 4.0 71.3 1.0 N2' F:LR7702 4.0 83.5 1.0 O1B F:LR7702 4.1 65.1 1.0 CG F:HIS226 4.2 70.6 1.0 OD1 F:ASP224 4.2 62.3 1.0 O5B F:LR7702 4.2 64.5 1.0 CG F:HIS359 4.4 60.3 1.0 ND1 F:HIS359 4.5 60.4 1.0 O F:VAL360 4.6 60.8 1.0 O3' F:LR7702 4.7 79.8 1.0 C8' F:LR7702 4.7 71.8 1.0 O1A F:LR7702 4.7 70.1 1.0 C3' F:LR7702 4.7 80.8 1.0 C2' F:LR7702 4.8 83.0 1.0 O1' F:LR7702 4.8 86.1 1.0 C4B F:LR7702 4.8 73.3 1.0 C3B F:LR7702 4.8 76.0 1.0 C7' F:LR7702 4.9 76.6 1.0 NH2 F:ARG362 5.0 97.7 1.0

D.Fernandez, C.R.Bertozzi, B.Schumann, A.Agbay. Galnac-T2 Soaked with Udp-Sugar To Be Published.