Manganese in PDB 5fv9: Crystal Structure of Galnac-T2 in Complex with Compound 16D

The structure of Crystal Structure of Galnac-T2 in Complex with Compound 16D, PDB code: 5fv9 was solved by M.Ghirardello, M.Rivas, A.Lacetera, I.Delso, E.Lira-Navarrete, T.Tejero, S.Martin-Santamaria, R.Hurtado-Guerrero, P.Merino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	250.15 / 2.07
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	116.493, 121.748, 250.155, 90.00, 90.00, 90.00
R / Rfree (%)	18.958 / 24.685

The binding sites of Manganese atom in the Crystal Structure of Galnac-T2 in Complex with Compound 16D (pdb code 5fv9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Galnac-T2 in Complex with Compound 16D, PDB code: 5fv9:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of Galnac-T2 in Complex with Compound 16D


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 Galnac-T2 in Complex with Compound 16D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1571 b:28.0 occ:1.00 OD2 A:ASP224 1.8 35.1 1.0 O2B A:UDP1570 2.0 41.8 1.0 NE2 A:HIS359 2.0 29.5 1.0 NE2 A:HIS226 2.0 24.6 1.0 CE1 A:HIS359 2.9 28.8 1.0 CG A:ASP224 3.0 35.1 1.0 PB A:UDP1570 3.0 44.3 1.0 CD2 A:HIS226 3.0 24.4 1.0 CE1 A:HIS226 3.0 24.6 1.0 O3A A:UDP1570 3.0 45.3 1.0 CD2 A:HIS359 3.1 28.4 1.0 O1B A:UDP1570 3.4 48.0 1.0 CB A:ASP224 3.5 29.1 1.0 O A:HOH2166 3.7 51.9 1.0 PA A:UDP1570 4.0 44.3 1.0 ND1 A:HIS359 4.1 28.2 1.0 ND1 A:HIS226 4.1 25.7 1.0 OD1 A:ASP224 4.1 37.1 1.0 CG A:HIS226 4.1 25.4 1.0 CG A:HIS359 4.2 27.4 1.0 O A:HOH2164 4.2 51.3 1.0 O2A A:UDP1570 4.2 49.6 1.0 O3B A:UDP1570 4.3 50.8 1.0 O1A A:UDP1570 4.3 42.7 1.0 O A:VAL360 4.6 31.5 1.0 CA A:ASP224 5.0 26.4 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of Galnac-T2 in Complex with Compound 16D


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 Galnac-T2 in Complex with Compound 16D within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1571 b:35.1 occ:1.00 NE2 B:HIS226 1.8 31.9 1.0 OD2 B:ASP224 1.8 46.7 1.0 O2B B:UDP1572 2.0 35.1 0.5 NE2 B:HIS359 2.0 35.1 1.0 CAK B:Y6W1570 2.5 53.7 0.5 CE1 B:HIS226 2.7 33.1 1.0 CD2 B:HIS226 2.9 35.3 1.0 O3A B:UDP1572 2.9 44.5 0.5 CE1 B:HIS359 2.9 35.4 1.0 CG B:ASP224 2.9 45.0 1.0 PB B:UDP1572 3.0 40.1 0.5 CAM B:Y6W1570 3.0 52.4 0.5 CD2 B:HIS359 3.1 37.0 1.0 CAL B:Y6W1570 3.2 53.1 0.5 CB B:ASP224 3.5 39.8 1.0 O1B B:UDP1572 3.6 36.2 0.5 O2 B:Y6W1570 3.7 56.8 0.5 ND1 B:HIS226 3.8 32.8 1.0 OAO B:Y6W1570 3.8 50.0 0.5 C1 B:Y6W1570 3.9 57.5 0.5 CG B:HIS226 3.9 34.5 1.0 PAN B:Y6W1570 4.1 54.1 0.5 OD1 B:ASP224 4.1 55.7 1.0 ND1 B:HIS359 4.1 39.1 1.0 CG B:HIS359 4.2 36.3 1.0 O3B B:UDP1572 4.2 42.8 0.5 C2 B:Y6W1570 4.2 57.7 0.5 PA B:UDP1572 4.4 51.2 0.5 C3 B:Y6W1570 4.4 55.6 0.5 NH2 B:ARG362 4.6 73.6 1.0 O B:VAL360 4.7 48.0 1.0 O2A B:UDP1572 4.7 53.9 0.5 OBH B:Y6W1570 4.8 50.9 0.5 O5 B:Y6W1570 4.9 58.8 0.5 O1A B:UDP1572 5.0 53.4 0.5

Manganese binding site 3 out of 6 in the Crystal Structure of Galnac-T2 in Complex with Compound 16D


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Galnac-T2 in Complex with Compound 16D within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1571 b:30.5 occ:1.00 OD2 C:ASP224 1.8 36.5 1.0 O2B C:UDP1570 2.0 47.5 1.0 NE2 C:HIS359 2.0 29.6 1.0 NE2 C:HIS226 2.0 32.8 1.0 O3A C:UDP1570 2.9 47.6 1.0 CD2 C:HIS226 2.9 31.1 1.0 CE1 C:HIS359 2.9 31.5 1.0 CD2 C:HIS359 3.0 29.2 1.0 CG C:ASP224 3.0 38.6 1.0 PB C:UDP1570 3.0 48.4 1.0 CE1 C:HIS226 3.0 32.0 1.0 O1B C:UDP1570 3.4 49.3 1.0 CB C:ASP224 3.5 33.0 1.0 O C:HOH2132 3.9 48.3 1.0 ND1 C:HIS359 4.0 28.9 1.0 OD1 C:ASP224 4.1 43.5 1.0 CG C:HIS226 4.1 29.6 1.0 CG C:HIS359 4.1 28.6 1.0 ND1 C:HIS226 4.1 29.8 1.0 PA C:UDP1570 4.2 47.9 1.0 O3B C:UDP1570 4.2 55.3 1.0 O C:VAL360 4.5 38.2 1.0 O1A C:UDP1570 4.6 41.7 1.0 O2A C:UDP1570 4.6 45.8 1.0 O C:HOH2213 4.9 55.0 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of Galnac-T2 in Complex with Compound 16D


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Galnac-T2 in Complex with Compound 16D within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1556 b:41.3 occ:1.00 OD2 D:ASP224 1.7 50.3 1.0 O2B D:UDP1555 1.8 59.4 1.0 NE2 D:HIS359 1.9 40.4 1.0 NE2 D:HIS226 1.9 43.2 1.0 CE1 D:HIS359 2.8 37.2 1.0 CG D:ASP224 2.9 54.7 1.0 CE1 D:HIS226 2.9 38.9 1.0 PB D:UDP1555 2.9 61.1 1.0 O3A D:UDP1555 2.9 51.1 1.0 CD2 D:HIS226 3.0 40.5 1.0 CD2 D:HIS359 3.0 37.7 1.0 O1B D:UDP1555 3.5 56.8 1.0 CB D:ASP224 3.5 45.7 1.0 OD1 D:ASP224 3.9 63.1 1.0 ND1 D:HIS359 4.0 37.7 1.0 ND1 D:HIS226 4.0 38.8 1.0 CG D:HIS226 4.1 37.7 1.0 CG D:HIS359 4.1 37.5 1.0 O3B D:UDP1555 4.1 64.2 1.0 O D:VAL360 4.2 46.6 1.0 PA D:UDP1555 4.3 53.9 1.0 O2A D:UDP1555 4.6 55.7 1.0 O D:HOH2147 4.6 54.3 1.0 NH2 D:ARG362 4.7 61.8 1.0 O1A D:UDP1555 4.8 57.3 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of Galnac-T2 in Complex with Compound 16D


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Galnac-T2 in Complex with Compound 16D within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1571 b:29.9 occ:1.00 NE2 E:HIS226 1.9 28.8 1.0 O2B E:UDP1570 1.9 29.2 0.5 NE2 E:HIS359 2.0 34.2 1.0 OD2 E:ASP224 2.0 41.1 1.0 CD2 E:HIS226 2.8 31.1 1.0 CE1 E:HIS359 2.9 32.2 1.0 O3A E:UDP1570 2.9 38.2 0.5 CE1 E:HIS226 2.9 31.3 1.0 PB E:UDP1570 3.0 33.2 0.5 CAK E:Y6W1572 3.0 54.4 0.5 CAM E:Y6W1572 3.0 63.2 0.5 CD2 E:HIS359 3.1 34.6 1.0 CG E:ASP224 3.1 40.4 1.0 O1B E:UDP1570 3.4 34.6 0.5 CB E:ASP224 3.6 34.2 1.0 CAL E:Y6W1572 3.6 56.7 0.5 O E:HOH2121 3.6 46.4 1.0 O2 E:Y6W1572 3.7 51.9 0.5 CG E:HIS226 4.0 30.8 1.0 ND1 E:HIS359 4.0 36.3 1.0 ND1 E:HIS226 4.0 29.5 1.0 PA E:UDP1570 4.1 36.1 0.5 CG E:HIS359 4.1 31.9 1.0 PAN E:Y6W1572 4.2 69.8 0.5 OD1 E:ASP224 4.2 39.1 1.0 O3B E:UDP1570 4.3 37.5 0.5 OAO E:Y6W1572 4.3 73.7 0.5 C1 E:Y6W1572 4.3 54.8 0.5 O2A E:UDP1570 4.4 34.9 0.5 C2 E:Y6W1572 4.5 55.2 0.5 O1A E:UDP1570 4.6 35.0 0.5 O E:VAL360 4.6 40.3 1.0 OBH E:Y6W1572 4.7 71.6 0.5 C3 E:Y6W1572 4.8 55.0 0.5 NH2 E:ARG362 4.9 50.3 1.0 O E:HOH2181 5.0 55.9 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of Galnac-T2 in Complex with Compound 16D


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Galnac-T2 in Complex with Compound 16D within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1571 b:34.2 occ:1.00 OD2 F:ASP224 1.5 40.6 1.0 NE2 F:HIS226 1.8 37.9 1.0 NE2 F:HIS359 2.1 38.1 1.0 O2B F:UDP1570 2.4 37.9 0.5 CG F:ASP224 2.8 47.8 1.0 CE1 F:HIS226 2.8 40.9 1.0 CD2 F:HIS226 2.8 36.1 1.0 O3A F:UDP1570 2.8 41.3 0.5 CD2 F:HIS359 2.9 37.4 1.0 PB F:UDP1570 3.0 38.6 0.5 CAM F:Y6W1572 3.0 70.1 0.5 CE1 F:HIS359 3.1 40.0 1.0 O1B F:UDP1570 3.3 37.8 0.5 CAK F:Y6W1572 3.3 62.6 0.5 CB F:ASP224 3.5 42.9 1.0 CAL F:Y6W1572 3.8 64.8 0.5 OD1 F:ASP224 3.8 56.5 1.0 ND1 F:HIS226 3.9 37.1 1.0 CG F:HIS226 3.9 34.6 1.0 O2 F:Y6W1572 4.0 63.5 0.5 CG F:HIS359 4.1 38.9 1.0 ND1 F:HIS359 4.2 40.3 1.0 PAN F:Y6W1572 4.2 77.3 0.5 PA F:UDP1570 4.2 42.7 0.5 C3 F:Y6W1572 4.3 65.7 0.5 OAO F:Y6W1572 4.4 78.8 0.5 O3B F:UDP1570 4.4 43.1 0.5 O F:VAL360 4.5 34.8 1.0 C2 F:Y6W1572 4.5 63.3 0.5 C1 F:Y6W1572 4.6 63.3 0.5 O2A F:UDP1570 4.6 45.8 0.5 OBH F:Y6W1572 4.7 74.6 0.5 O1A F:UDP1570 4.9 42.4 0.5 O3 F:Y6W1572 4.9 64.0 0.5

M.Ghirardello, M.De Las Rivas, A.Lacetera, I.Delso, E.Lira-Navarrete, T.Tejero, S.Martin-Santamaria, R.Hurtado-Guerrero, P.Merino. Glycomimetics Targeting Glycosyltransferases: Synthetic, Computational and Structural Studies of Less-Polar Conjugates. Chemistry V. 22 7215 2016.
ISSN: ISSN 0947-6539
PubMed: 27071848
DOI: 10.1002/CHEM.201600467