Magnesium in PDB 3gkr: Crystal Structure of Weissella Viridescens Femx:Udp-Murnac-Hexapeptide Complex

All present enzymatic activity of Crystal Structure of Weissella Viridescens Femx:Udp-Murnac-Hexapeptide Complex:
2.3.2.10;

The structure of Crystal Structure of Weissella Viridescens Femx:Udp-Murnac-Hexapeptide Complex, PDB code: 3gkr was solved by V.Delfosse, J.Piton, R.Villet, M.Lecerf, M.Arthur, C.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.20 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.324, 101.836, 46.847, 90.00, 102.85, 90.00
R / Rfree (%)	17.3 / 21.6

The binding sites of Magnesium atom in the Crystal Structure of Weissella Viridescens Femx:Udp-Murnac-Hexapeptide Complex (pdb code 3gkr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Weissella Viridescens Femx:Udp-Murnac-Hexapeptide Complex, PDB code: 3gkr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Weissella Viridescens Femx:Udp-Murnac-Hexapeptide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Weissella Viridescens Femx:Udp-Murnac-Hexapeptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:20.6 occ:1.00 O A:HOH803 2.1 19.5 1.0 O A:THR66 2.3 13.4 1.0 O A:HOH607 2.4 23.8 1.0 O A:THR64 2.5 12.9 1.0 O A:HOH554 2.5 14.8 1.0 C A:THR66 3.5 10.9 1.0 C A:THR64 3.6 9.9 1.0 N A:THR66 3.8 10.6 1.0 N A:THR64 4.0 10.1 1.0 C A:PRO65 4.1 10.5 1.0 CA A:THR66 4.2 12.0 1.0 OG1 A:THR64 4.3 9.7 1.0 CA A:PRO65 4.3 8.3 1.0 O A:HOH816 4.3 41.2 1.0 N A:PRO65 4.4 8.6 1.0 CA A:THR64 4.5 8.7 1.0 N A:ASP67 4.5 12.8 1.0 CA A:ASP67 4.6 15.5 1.0 OD1 A:ASP63 4.6 21.1 1.0 CB A:ASP63 4.8 13.6 1.0 O A:PRO65 4.8 13.6 1.0 O A:LYS68 4.8 13.2 1.0 C A:ASP67 5.0 14.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Weissella Viridescens Femx:Udp-Murnac-Hexapeptide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Weissella Viridescens Femx:Udp-Murnac-Hexapeptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:23.8 occ:1.00 O A:HOH781 2.1 32.2 1.0 O A:HOH587 2.1 19.3 1.0 O A:LEU280 2.3 10.3 1.0 O A:HOH665 2.4 19.5 1.0 OD1 A:ASN283 2.4 23.3 1.0 O A:HOH850 2.5 32.1 1.0 O A:HOH862 3.3 22.4 1.0 C A:LEU280 3.5 9.4 1.0 CG A:ASN283 3.5 18.5 1.0 CA A:ASN283 3.9 12.2 1.0 N A:ASN283 4.0 10.1 1.0 O A:HOH626 4.1 20.7 1.0 O A:HOH625 4.1 16.6 1.0 CA A:LEU280 4.3 8.5 1.0 CB A:ASN283 4.3 13.4 1.0 N A:ASP281 4.4 8.2 1.0 ND2 A:ASN283 4.4 23.9 1.0 CA A:ASP281 4.5 9.4 1.0 C A:ASP281 4.6 11.6 1.0 O A:HOH553 4.6 14.2 1.0 CB A:LEU280 4.8 6.9 1.0 O A:ASP281 4.8 14.3 1.0 O A:ALA158 4.9 14.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Weissella Viridescens Femx:Udp-Murnac-Hexapeptide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Weissella Viridescens Femx:Udp-Murnac-Hexapeptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:23.6 occ:1.00 O A:HOH662 2.7 18.9 1.0 O A:PHE308 2.8 14.0 1.0 O A:HOH829 3.0 23.7 1.0 N A:LYS310 3.2 17.0 1.0 CD1 A:LEU150 3.5 19.5 1.0 CA A:VAL309 3.5 13.8 1.0 C A:PHE308 3.6 11.2 1.0 O A:HOH860 3.7 24.9 1.0 CE2 A:TYR165 3.8 12.2 1.0 C A:VAL309 3.9 15.9 1.0 CB A:LYS310 3.9 21.2 1.0 N A:VAL309 3.9 14.1 1.0 CG A:LYS310 4.0 27.2 1.0 CA A:LYS310 4.1 18.7 1.0 OH A:TYR165 4.4 12.6 1.0 CZ A:TYR165 4.5 8.1 1.0 CD2 A:TYR165 4.5 11.6 1.0 CG A:LEU150 4.6 11.9 1.0 N A:ASP311 4.8 19.8 1.0 CB A:VAL309 4.8 13.1 1.0 CA A:PHE308 4.8 14.1 1.0 O A:LEU164 4.9 10.2 1.0 CD2 A:LEU150 4.9 15.0 1.0

V.Delfosse, J.Piton, R.Villet, M.Lecerf, M.Arthur, C.Mayer. Structure of Weissella Viridescens Femx with the Udp-Murnac-Hexapeptide Product of the Alanine Transfer Reaction To Be Published.