Magnesium in PDB 3tcs: Crystal Structure of A Putative Racemase From Roseobacter Denitrificans

The structure of Crystal Structure of A Putative Racemase From Roseobacter Denitrificans, PDB code: 3tcs was solved by S.Eswaramoorthy, S.Chamala, B.Evans, R.Foti, A.Gizzi, B.Hillerich, A.Kar, J.Lafleur, R.Seidel, G.Villigas, W.Zencheck, S.C.Almo, S.Swaminathan, Newyork Structural Genomics Research Consortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.45 / 1.88
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	182.492, 64.745, 76.449, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 21.6

The structure of Crystal Structure of A Putative Racemase From Roseobacter Denitrificans also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of A Putative Racemase From Roseobacter Denitrificans (pdb code 3tcs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Putative Racemase From Roseobacter Denitrificans, PDB code: 3tcs:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A Putative Racemase From Roseobacter Denitrificans


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 A Putative Racemase From Roseobacter Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg368 b:18.7 occ:1.00 O A:DAL370 1.9 24.5 1.0 OE2 A:GLU209 1.9 20.6 1.0 OE1 A:GLU235 2.1 20.6 1.0 OD2 A:ASP183 2.1 22.2 1.0 O A:HOH402 2.2 18.2 1.0 N A:DAL370 2.2 17.5 1.0 C A:DAL370 2.6 20.9 1.0 CA A:DAL370 2.8 20.7 1.0 CD A:GLU209 3.0 23.6 1.0 CD A:GLU235 3.0 20.0 1.0 CG A:ASP183 3.2 23.2 1.0 OE2 A:GLU235 3.4 21.0 1.0 OD1 A:ASP183 3.6 21.5 1.0 CG A:GLU209 3.7 22.1 1.0 O A:HOH438 3.8 20.6 1.0 OE1 A:GLU209 3.9 21.6 1.0 O A:HOH422 3.9 22.3 1.0 NZ A:LYS145 4.1 21.6 1.0 CB A:DAL370 4.2 17.3 1.0 CD2 A:HIS285 4.2 14.4 1.0 OD1 A:ASN185 4.2 22.4 1.0 CG A:GLU235 4.3 20.8 1.0 NH1 A:ARG147 4.4 21.7 1.0 CB A:ASP183 4.5 22.4 1.0 OE1 A:GLU210 4.7 25.7 1.0 CB A:GLU209 4.7 23.4 1.0 NE2 A:HIS285 4.9 14.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of A Putative Racemase From Roseobacter Denitrificans


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 A Putative Racemase From Roseobacter Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg369 b:35.2 occ:1.00 O A:HOH420 2.0 27.0 1.0 O A:HOH419 2.1 28.4 1.0 O A:HOH418 2.1 25.7 1.0 O A:HOH421 2.2 31.4 1.0 O A:THR224 2.3 34.8 1.0 O A:LEU227 2.3 32.4 1.0 C A:LEU227 3.5 32.0 1.0 C A:THR224 3.5 34.5 1.0 CA A:ASP228 4.2 32.6 1.0 OD1 A:ASP253 4.2 31.7 1.0 OD2 A:ASP253 4.2 30.1 1.0 N A:ASP228 4.3 32.4 1.0 O A:ASP228 4.3 32.1 1.0 CG2 A:THR224 4.3 32.8 1.0 O A:ILE229 4.3 28.4 1.0 CA A:ASP225 4.4 35.8 1.0 C A:ASP228 4.4 31.8 1.0 N A:ASP225 4.4 34.1 1.0 CA A:THR224 4.4 33.1 1.0 N A:LEU227 4.5 32.6 1.0 CA A:LEU227 4.5 32.3 1.0 CG A:ASP253 4.6 28.3 1.0 C A:ASP225 4.7 34.9 1.0 O A:ASP225 5.0 35.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of A Putative Racemase From Roseobacter Denitrificans


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 A Putative Racemase From Roseobacter Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg368 b:11.0 occ:1.00 O B:DAL370 2.0 20.3 1.0 OE2 B:GLU209 2.0 9.8 1.0 OE1 B:GLU235 2.0 11.1 1.0 OD2 B:ASP183 2.1 9.2 1.0 O B:HOH379 2.1 10.8 1.0 N B:DAL370 2.4 11.0 1.0 C B:DAL370 2.6 13.4 1.0 CA B:DAL370 2.9 13.7 1.0 CD B:GLU209 3.0 11.7 1.0 CD B:GLU235 3.0 13.3 1.0 CG B:ASP183 3.1 9.1 1.0 OE2 B:GLU235 3.3 13.8 1.0 OD1 B:ASP183 3.5 8.6 1.0 CG B:GLU209 3.7 11.0 1.0 O B:HOH422 3.8 11.7 1.0 OE1 B:GLU209 3.9 11.8 1.0 O B:HOH424 3.9 14.2 1.0 OD1 B:ASN185 4.1 14.7 1.0 NZ B:LYS145 4.1 7.9 1.0 CD2 B:HIS285 4.2 10.0 1.0 CG B:GLU235 4.3 11.6 1.0 NH1 B:ARG147 4.3 9.7 1.0 CB B:DAL370 4.3 9.3 1.0 CB B:ASP183 4.4 8.4 1.0 OE1 B:GLU210 4.5 12.2 1.0 CB B:GLU209 4.7 7.5 1.0 CG B:ASN185 4.9 13.8 1.0 CB B:GLU235 4.9 8.3 1.0 CE B:LYS145 5.0 9.5 1.0 NE2 B:HIS285 5.0 9.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of A Putative Racemase From Roseobacter Denitrificans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Putative Racemase From Roseobacter Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg369 b:14.6 occ:1.00 O B:HOH412 2.0 11.6 1.0 O B:THR224 2.0 11.4 1.0 O B:LEU227 2.0 12.9 1.0 O B:HOH398 2.1 12.9 1.0 O B:HOH406 2.2 13.2 1.0 O B:HOH416 2.3 15.4 1.0 C B:THR224 3.2 12.3 1.0 C B:LEU227 3.3 13.6 1.0 CA B:THR224 4.1 11.3 1.0 CG2 B:THR224 4.1 11.7 1.0 N B:LEU227 4.2 11.7 1.0 N B:ASP228 4.2 14.1 1.0 N B:ASP225 4.2 12.8 1.0 CA B:LEU227 4.2 13.1 1.0 OD2 B:ASP253 4.3 11.8 1.0 CA B:ASP228 4.3 14.6 1.0 CA B:ASP225 4.3 14.3 1.0 C B:ASP225 4.4 14.2 1.0 O B:ASP228 4.4 13.2 1.0 O B:ASP225 4.4 14.8 1.0 O B:ILE229 4.4 10.5 1.0 C B:ASP228 4.5 14.0 1.0 OD1 B:ASP253 4.5 11.8 1.0 CB B:THR224 4.8 12.3 1.0 CB B:LEU227 4.8 11.7 1.0 CG B:ASP253 4.8 13.3 1.0 O B:HOH510 4.8 23.2 1.0 O B:VAL223 4.8 9.9 1.0 N B:ALA226 4.9 14.1 1.0

S.Eswaramoorthy, S.C.Almo, S.Swaminathan. Crystal Structure of A Putative Racemase From Roseobacter Denitrificans To Be Published.