Manganese in PDB 2vfz: Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose

All present enzymatic activity of Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose:
2.4.1.151; 2.4.1.87;

The structure of Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose, PDB code: 2vfz was solved by H.Jamaluddin, P.Tumbale, S.G.Withers, K.R.Acharya, K.Brew, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.06 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.735, 64.759, 66.468, 83.34, 83.95, 70.14
R / Rfree (%)	17.8 / 23.3

The structure of Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose (pdb code 2vfz). 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 Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose, PDB code: 2vfz:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose


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 Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1361 b:41.3 occ:1.00 OD1 A:ASP227 2.4 23.7 1.0 O1A A:UPF1360 2.4 40.7 1.0 OD2 A:ASP227 2.5 26.1 1.0 O1B A:UPF1360 2.5 45.9 1.0 OD2 A:ASP225 2.6 20.6 1.0 CG A:ASP227 2.8 23.3 1.0 CG A:ASP225 3.4 21.3 1.0 PB A:UPF1360 3.4 44.3 1.0 O3B A:UPF1360 3.4 47.4 1.0 PA A:UPF1360 3.6 41.8 1.0 CB A:ASP225 3.6 18.5 1.0 O3A A:UPF1360 3.8 42.9 1.0 O3D A:UPF1360 3.9 32.7 1.0 NZ A:LYS359 4.1 58.6 1.0 O A:HOH2202 4.1 27.8 1.0 F2' A:UPF1360 4.2 50.3 1.0 C5D A:UPF1360 4.2 38.7 1.0 CB A:ASP227 4.3 21.9 1.0 OD1 A:ASP225 4.4 22.0 1.0 O5D A:UPF1360 4.4 41.0 1.0 O A:HOH2162 4.4 42.6 1.0 CE A:LYS359 4.5 59.6 1.0 C3D A:UPF1360 4.5 34.9 1.0 C1' A:UPF1360 4.7 49.1 1.0 O A:ASP227 4.8 20.3 1.0 C2' A:UPF1360 4.8 48.9 1.0 O2B A:UPF1360 4.8 46.7 1.0 O2A A:UPF1360 4.8 44.2 1.0 C4D A:UPF1360 4.9 36.4 1.0 C3' A:UPF1360 4.9 48.0 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose


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 Alpha-1,3 Galactosyltransferase (R365K) in Complex with Udp-2F-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2365 b:26.0 occ:1.00 O1A B:UPF2364 2.2 23.6 1.0 O1B B:UPF2364 2.3 29.6 1.0 OD1 B:ASP1227 2.4 22.1 1.0 OD2 B:ASP1225 2.4 22.7 1.0 O B:HOH2247 2.5 14.4 1.0 OD2 B:ASP1227 2.5 16.9 1.0 CG B:ASP1227 2.8 19.1 1.0 PB B:UPF2364 3.3 26.5 1.0 CG B:ASP1225 3.4 23.3 1.0 O3B B:UPF2364 3.4 30.8 1.0 PA B:UPF2364 3.4 22.9 1.0 O3A B:UPF2364 3.6 27.0 1.0 CB B:ASP1225 3.6 21.0 1.0 NZ B:LYS1359 3.9 28.0 1.0 O3D B:UPF2364 3.9 20.7 1.0 O B:HOH2199 4.0 30.9 1.0 CE B:LYS1359 4.1 26.8 1.0 O B:HOH2111 4.2 22.7 1.0 C5D B:UPF2364 4.3 20.9 1.0 CB B:ASP1227 4.3 18.7 1.0 F2' B:UPF2364 4.3 32.9 1.0 O5D B:UPF2364 4.4 22.7 1.0 O B:HOH2113 4.5 26.5 1.0 O2A B:UPF2364 4.5 26.1 1.0 OD1 B:ASP1225 4.6 24.7 1.0 C3D B:UPF2364 4.6 20.3 1.0 O2B B:UPF2364 4.7 27.8 1.0 C1' B:UPF2364 4.7 32.1 1.0 C2' B:UPF2364 4.9 32.5 1.0 O B:ASP1227 4.9 18.7 1.0 C3' B:UPF2364 4.9 32.3 1.0 CB B:ALA1282 4.9 16.2 1.0 C4D B:UPF2364 5.0 21.7 1.0

H.Jamaluddin, P.Tumbale, S.G.Withers, K.R.Acharya, K.Brew. Conformational Changes Induced By Binding Udp-2F- Galactose to Alpha-1,3 Galactosyltransferase- Implications For Catalysis J.Mol.Biol. V. 369 1270 2007.
ISSN: ISSN 0022-2836
PubMed: 17493636
DOI: 10.1016/J.JMB.2007.04.012