Manganese in PDB 8y2l: The Crystal Structure of Glucosyltransferase Tcdb From Clostridioides Difficile

The structure of The Crystal Structure of Glucosyltransferase Tcdb From Clostridioides Difficile, PDB code: 8y2l was solved by S.Fan, X.Wei, R.Lv, C.Wang, M.Tang, Y.Jin, Z.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.15 / 3.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	155.166, 268.755, 194.862, 90, 90, 90
R / Rfree (%)	24.4 / 30

The binding sites of Manganese atom in the The Crystal Structure of Glucosyltransferase Tcdb From Clostridioides Difficile (pdb code 8y2l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the The Crystal Structure of Glucosyltransferase Tcdb From Clostridioides Difficile, PDB code: 8y2l:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the The Crystal Structure of Glucosyltransferase Tcdb From Clostridioides Difficile


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Glucosyltransferase Tcdb From Clostridioides Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:186.3 occ:1.00 O A:HOH701 1.7 147.6 1.0 OE1 A:GLU515 1.7 154.2 1.0 O3B A:UDP602 1.7 221.3 1.0 OD2 A:ASP288 1.7 160.2 1.0 O1A A:UDP602 1.8 204.6 1.0 OG A:SER518 1.8 218.2 1.0 CB A:SER518 2.6 216.6 1.0 CD A:GLU515 2.8 144.4 1.0 CG A:ASP288 3.0 148.4 1.0 PB A:UDP602 3.1 242.6 1.0 PA A:UDP602 3.1 207.2 1.0 O3A A:UDP602 3.4 223.1 1.0 OE2 A:GLU515 3.4 138.8 1.0 OD1 A:ASP288 3.6 152.4 1.0 O2B A:UDP602 3.8 243.3 1.0 CA A:GLU515 4.0 152.4 1.0 CG A:GLU515 4.1 145.3 1.0 O5' A:UDP602 4.1 200.8 1.0 CA A:SER518 4.1 207.5 1.0 CB A:ASP288 4.1 143.0 1.0 O2A A:UDP602 4.1 199.9 1.0 O1B A:UDP602 4.2 248.8 1.0 CB A:GLU515 4.3 147.6 1.0 O A:GLU515 4.4 169.1 1.0 O A:GLN514 4.5 150.3 1.0 C A:SER518 4.6 209.2 1.0 OE1 A:GLN385 4.6 116.6 1.0 C A:GLU515 4.7 160.9 1.0 N A:SER518 4.7 199.0 1.0 OD2 A:ASP286 4.8 141.7 1.0 N A:GLU515 4.9 149.6 1.0 O A:SER518 5.0 201.6 1.0

Manganese binding site 2 out of 3 in the The Crystal Structure of Glucosyltransferase Tcdb From Clostridioides Difficile


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Glucosyltransferase Tcdb From Clostridioides Difficile within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:186.3 occ:1.00 OD2 B:ASP288 1.7 156.3 1.0 O B:HOH701 1.7 138.2 1.0 O3B B:UDP602 1.8 214.9 1.0 O1A B:UDP602 1.8 207.5 1.0 OE1 B:GLU515 1.8 142.9 1.0 OG B:SER518 1.8 218.6 1.0 CB B:SER518 2.2 215.7 1.0 CD B:GLU515 2.9 130.8 1.0 CG B:ASP288 3.0 145.5 1.0 PB B:UDP602 3.1 234.9 1.0 PA B:UDP602 3.1 209.4 1.0 O3A B:UDP602 3.3 221.2 1.0 OE2 B:GLU515 3.5 123.6 1.0 OD1 B:ASP288 3.7 151.2 1.0 CA B:SER518 3.7 200.4 1.0 CA B:GLU515 3.8 140.7 1.0 O2B B:UDP602 3.8 228.1 1.0 CB B:ASP288 4.0 140.2 1.0 CG B:GLU515 4.0 132.1 1.0 O2A B:UDP602 4.1 197.8 1.0 O5' B:UDP602 4.1 200.3 1.0 O B:GLN514 4.2 144.9 1.0 O1B B:UDP602 4.2 243.9 1.0 CB B:GLU515 4.2 135.8 1.0 O B:GLU515 4.3 159.5 1.0 N B:SER518 4.4 186.8 1.0 C B:SER518 4.5 197.8 1.0 C B:GLU515 4.5 149.5 1.0 N B:GLU515 4.6 139.3 1.0 C B:GLN514 4.8 140.6 1.0 OE1 B:GLN385 4.8 120.7 1.0 O B:SER518 4.9 193.6 1.0 CD1 B:LEU519 5.0 195.4 1.0

Manganese binding site 3 out of 3 in the The Crystal Structure of Glucosyltransferase Tcdb From Clostridioides Difficile


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of Glucosyltransferase Tcdb From Clostridioides Difficile within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn601 b:179.5 occ:1.00 O C:HOH701 1.7 144.6 1.0 O3B C:UDP602 1.7 213.9 1.0 OD2 C:ASP288 1.7 156.6 1.0 OE1 C:GLU515 1.7 150.8 1.0 O1A C:UDP602 1.8 200.7 1.0 OG C:SER518 1.8 209.6 1.0 CB C:SER518 2.7 208.6 1.0 CD C:GLU515 2.8 141.0 1.0 CG C:ASP288 3.0 147.6 1.0 PA C:UDP602 3.1 206.0 1.0 PB C:UDP602 3.1 234.0 1.0 O3A C:UDP602 3.4 216.4 1.0 OE2 C:GLU515 3.4 132.6 1.0 OD1 C:ASP288 3.7 152.0 1.0 O2B C:UDP602 3.9 236.2 1.0 CA C:GLU515 4.0 152.4 1.0 CG C:GLU515 4.1 142.8 1.0 CA C:SER518 4.1 200.8 1.0 CB C:ASP288 4.1 142.5 1.0 O2A C:UDP602 4.1 198.8 1.0 O5' C:UDP602 4.1 200.1 1.0 O1B C:UDP602 4.2 238.7 1.0 CB C:GLU515 4.3 146.8 1.0 O C:GLU515 4.4 176.0 1.0 O C:GLN514 4.5 152.3 1.0 C C:SER518 4.6 199.9 1.0 OE1 C:GLN385 4.6 123.2 1.0 C C:GLU515 4.7 162.2 1.0 N C:SER518 4.7 194.7 1.0 OD2 C:ASP286 4.8 135.6 1.0 N C:GLU515 4.9 148.5 1.0 O C:SER518 5.0 194.7 1.0

S.Fan, X.Wei, R.Lv, C.Wang, M.Tang, Y.Jin, Z.Yang. The Crystal Structure of Glucosyltransferase Tcdb From Clostridioides Difficile To Be Published.