Manganese in PDB 6iwr: Crystal Structure of Galnac-T7 with Udp, Galnac and MN2+

The structure of Crystal Structure of Galnac-T7 with Udp, Galnac and MN2+, PDB code: 6iwr was solved by C.Yu, Y.X.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.25 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	137.435, 158.264, 251.484, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.8

The binding sites of Manganese atom in the Crystal Structure of Galnac-T7 with Udp, Galnac and MN2+ (pdb code 6iwr). 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-T7 with Udp, Galnac and MN2+, PDB code: 6iwr:
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-T7 with Udp, Galnac and MN2+


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-T7 with Udp, Galnac and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:0.0 occ:1.00 OD2 A:ASP301 2.9 36.5 1.0 NE2 A:HIS440 3.4 43.5 1.0 NE2 A:HIS303 3.4 40.8 1.0 CE1 A:HIS440 3.7 39.7 1.0 CE1 A:HIS303 4.0 43.9 1.0 CG A:ASP301 4.1 41.6 1.0 NH1 A:ARG443 4.3 45.6 1.0 OD1 A:ASP301 4.5 46.2 1.0 CD2 A:HIS303 4.6 35.2 1.0 CD2 A:HIS440 4.7 36.6 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of Galnac-T7 with Udp, Galnac and MN2+


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-T7 with Udp, Galnac and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn701 b:87.2 occ:1.00 OD2 B:ASP301 2.4 46.0 1.0 NE2 B:HIS440 3.0 42.8 1.0 NE2 B:HIS303 3.2 41.3 1.0 CE1 B:HIS440 3.4 43.7 1.0 CG B:ASP301 3.5 47.0 1.0 CE1 B:HIS303 3.9 39.6 1.0 OD1 B:ASP301 4.0 45.0 1.0 CD2 B:HIS440 4.2 37.5 1.0 CD2 B:HIS303 4.4 39.5 1.0 ND1 B:HIS440 4.7 37.1 1.0 NH1 B:ARG443 4.7 42.9 1.0 CB B:ASP301 4.8 34.3 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of Galnac-T7 with Udp, Galnac and MN2+


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-T7 with Udp, Galnac and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn701 b:93.6 occ:1.00 OD2 C:ASP301 2.3 39.1 1.0 NE2 C:HIS303 2.6 43.0 1.0 CE1 C:HIS303 3.0 38.7 1.0 NE2 C:HIS440 3.4 45.1 1.0 CG C:ASP301 3.4 47.3 1.0 CE1 C:HIS440 3.9 42.8 1.0 CD2 C:HIS303 4.0 40.0 1.0 OD1 C:ASP301 4.0 51.5 1.0 NH1 C:ARG443 4.0 51.5 1.0 ND1 C:HIS303 4.3 35.7 1.0 CD2 C:HIS440 4.6 38.0 1.0 CB C:ASP301 4.6 33.3 1.0 CG C:HIS303 4.8 33.7 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of Galnac-T7 with Udp, Galnac and MN2+


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-T7 with Udp, Galnac and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn703 b:56.3 occ:1.00 OD2 D:ASP301 2.0 59.8 1.0 O2A D:UDP702 2.4 68.6 1.0 NE2 D:HIS440 2.4 47.6 1.0 O3B D:UDP702 2.4 65.7 1.0 NE2 D:HIS303 2.4 55.1 1.0 CE1 D:HIS440 2.9 45.1 1.0 O2B D:UDP702 3.0 55.2 1.0 PB D:UDP702 3.2 63.6 1.0 CG D:ASP301 3.2 58.0 1.0 CE1 D:HIS303 3.4 56.8 1.0 PA D:UDP702 3.4 76.1 1.0 CD2 D:HIS303 3.4 50.9 1.0 O5' D:UDP702 3.6 65.5 1.0 CD2 D:HIS440 3.6 48.1 1.0 HN2 D:NAG701 3.8 69.7 1.0 O3A D:UDP702 3.8 73.5 1.0 H82 D:NAG701 4.0 71.9 1.0 OD1 D:ASP301 4.1 56.8 1.0 CB D:ASP301 4.1 50.8 1.0 ND1 D:HIS440 4.2 42.4 1.0 H3' D:UDP702 4.3 82.5 1.0 H81 D:NAG701 4.4 71.9 1.0 NH1 D:ARG443 4.4 59.2 1.0 ND1 D:HIS303 4.5 54.1 1.0 CG D:HIS440 4.6 44.3 1.0 CG D:HIS303 4.6 53.3 1.0 C8 D:NAG701 4.6 59.9 1.0 O D:ILE441 4.6 52.4 1.0 O1B D:UDP702 4.6 64.1 1.0 N2 D:NAG701 4.6 58.1 1.0 O1A D:UDP702 4.9 71.7 1.0 H3 D:NAG701 4.9 79.4 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of Galnac-T7 with Udp, Galnac and MN2+


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-T7 with Udp, Galnac and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn701 b:83.0 occ:1.00 NE2 E:HIS303 2.5 43.3 1.0 OD2 E:ASP301 2.6 45.0 1.0 NE2 E:HIS440 3.0 46.1 1.0 CE1 E:HIS303 3.2 42.0 1.0 CE1 E:HIS440 3.2 44.8 1.0 CD2 E:HIS303 3.7 38.3 1.0 NH1 E:ARG443 3.8 57.5 1.0 CG E:ASP301 3.9 48.3 1.0 CD2 E:HIS440 4.4 37.9 1.0 ND1 E:HIS303 4.4 34.1 1.0 ND1 E:HIS440 4.5 42.1 1.0 OD1 E:ASP301 4.6 45.6 1.0 CG E:HIS303 4.7 33.5 1.0 O E:ILE441 4.7 38.0 1.0 CB E:ASP301 4.9 38.4 1.0 CZ E:ARG443 4.9 60.5 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of Galnac-T7 with Udp, Galnac and MN2+


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-T7 with Udp, Galnac and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn701 b:91.3 occ:1.00 OD2 F:ASP301 2.8 51.0 1.0 NE2 F:HIS303 3.5 54.1 1.0 CG F:ASP301 3.8 62.1 1.0 NE2 F:HIS440 3.8 62.4 1.0 CE1 F:HIS303 3.9 59.9 1.0 OD1 F:ASP301 4.0 61.8 1.0 CE1 F:HIS440 4.2 64.6 1.0 NH1 F:ARG443 4.4 66.9 1.0 CD2 F:HIS303 4.8 55.7 1.0

C.Yu, L.Liang, Y.Yin. Structural Basis of Carbohydrate Transfer Activity of Udp-Galnac: Polypeptide N-Acetylgalactosaminyltransferase 7. Biochem. Biophys. Res. V. 510 266 2019COMMUN..
ISSN: ESSN 1090-2104
PubMed: 30685086
DOI: 10.1016/J.BBRC.2019.01.084