Magnesium in PDB 3r0u: Crystal Structure of Nysgrc Enolase Target 200555, A Putative Dipeptide Epimerase From Francisella Philomiragia : Tartrate and Mg Complex

The structure of Crystal Structure of Nysgrc Enolase Target 200555, A Putative Dipeptide Epimerase From Francisella Philomiragia : Tartrate and Mg Complex, PDB code: 3r0u was solved by M.W.Vetting, B.Hillerich, R.D.Seidel, W.D.Zencheck, R.Toro, H.J.Imker, J.A.Gerlt, S.C.Almo, New York Structural Genomics Research Consortium(Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.61 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	121.070, 121.070, 149.040, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.5

The binding sites of Magnesium atom in the Crystal Structure of Nysgrc Enolase Target 200555, A Putative Dipeptide Epimerase From Francisella Philomiragia : Tartrate and Mg Complex (pdb code 3r0u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Nysgrc Enolase Target 200555, A Putative Dipeptide Epimerase From Francisella Philomiragia : Tartrate and Mg Complex, PDB code: 3r0u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Nysgrc Enolase Target 200555, A Putative Dipeptide Epimerase From Francisella Philomiragia : Tartrate and Mg 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 Nysgrc Enolase Target 200555, A Putative Dipeptide Epimerase From Francisella Philomiragia : Tartrate and Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg380 b:30.6 occ:1.00 O A:HOH625 2.0 24.5 1.0 OD2 A:ASP245 2.2 22.9 1.0 OE2 A:GLU220 2.2 26.0 1.0 O A:HOH427 2.2 26.4 1.0 O A:HOH497 2.3 28.6 1.0 OD2 A:ASP192 2.4 29.6 1.0 CD A:GLU220 3.1 26.7 1.0 CG A:ASP245 3.2 22.7 1.0 CG A:ASP192 3.2 25.7 1.0 OD1 A:ASP192 3.6 26.2 1.0 CB A:ASP245 3.6 20.8 1.0 CG A:GLU220 3.8 27.8 1.0 O A:HOH426 3.8 38.5 1.0 OE1 A:GLU220 3.9 29.9 1.0 O A:HOH579 4.0 37.3 1.0 NZ A:LYS269 4.1 22.0 1.0 ND2 A:ASN267 4.1 20.1 1.0 OE1 A:GLU246 4.2 24.3 1.0 OD1 A:ASN194 4.2 42.2 1.0 OE2 A:GLU246 4.2 30.7 1.0 O1 A:TAR384 4.3 54.5 1.0 OD1 A:ASP245 4.3 19.8 1.0 CB A:ASP192 4.5 27.5 1.0 CE A:LYS269 4.6 18.3 1.0 CD A:GLU246 4.6 28.7 1.0 O A:HOH416 4.8 19.3 1.0 O11 A:TAR384 4.9 59.2 1.0 C1 A:TAR384 4.9 57.3 1.0 CB A:GLU220 5.0 25.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Nysgrc Enolase Target 200555, A Putative Dipeptide Epimerase From Francisella Philomiragia : Tartrate and Mg 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 Nysgrc Enolase Target 200555, A Putative Dipeptide Epimerase From Francisella Philomiragia : Tartrate and Mg Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg386 b:51.3 occ:1.00 O A:HOH677 2.3 39.0 1.0 O A:THR235 2.3 42.6 1.0 O A:HOH679 2.5 43.8 1.0 O A:HOH678 2.5 49.8 1.0 O A:SER238 2.5 42.2 1.0 O A:HOH622 2.8 50.9 1.0 C A:THR235 3.6 44.3 1.0 C A:SER238 3.6 40.3 1.0 O A:LYS236 4.1 45.7 1.0 O A:HOH591 4.1 53.2 1.0 N A:SER238 4.3 37.3 1.0 OD1 A:ASN264 4.3 30.2 1.0 CA A:SER238 4.3 37.2 1.0 ND2 A:ASN264 4.4 30.2 1.0 C A:LYS236 4.4 45.0 1.0 N A:LYS236 4.4 45.0 1.0 CA A:LYS236 4.5 47.0 1.0 CG2 A:THR235 4.5 34.6 1.0 CA A:THR235 4.5 33.0 1.0 CB A:SER238 4.5 34.7 1.0 N A:ASN239 4.7 40.8 1.0 CG A:ASN264 4.8 29.2 1.0 O A:ILE240 4.8 35.6 1.0 CA A:ASN239 4.8 43.8 1.0 O A:HOH474 4.9 43.9 1.0

T.Lukk, A.Sakai, C.Kalyanaraman, S.D.Brown, H.J.Imker, L.Song, A.A.Fedorov, E.V.Fedorov, R.Toro, B.Hillerich, R.Seidel, Y.Patskovsky, M.W.Vetting, S.K.Nair, P.C.Babbitt, S.C.Almo, J.A.Gerlt, M.P.Jacobson. Homology Models Guide Discovery of Diverse Enzyme Specificities Among Dipeptide Epimerases in the Enolase Superfamily. Proc.Natl.Acad.Sci.Usa V. 109 4122 2012.
ISSN: ISSN 0027-8424
PubMed: 22392983
DOI: 10.1073/PNAS.1112081109