Magnesium in PDB 3tva: Crystal Structure of Xylose Isomerase Domain Protein From Planctomyces Limnophilus

The structure of Crystal Structure of Xylose Isomerase Domain Protein From Planctomyces Limnophilus, PDB code: 3tva was solved by Y.Kim, R.Wu, J.Bearden, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.55 / 2.15
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	105.324, 105.324, 178.936, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19.3

The structure of Crystal Structure of Xylose Isomerase Domain Protein From Planctomyces Limnophilus also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Xylose Isomerase Domain Protein From Planctomyces Limnophilus (pdb code 3tva). 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 Xylose Isomerase Domain Protein From Planctomyces Limnophilus, PDB code: 3tva:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Xylose Isomerase Domain Protein From Planctomyces Limnophilus


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 Xylose Isomerase Domain Protein From Planctomyces Limnophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg291 b:7.9 occ:1.00 OD2 A:ASP181 2.4 19.6 1.0 OE2 A:GLU155 2.4 36.1 1.0 OE1 A:GLU256 2.5 26.3 1.0 ND1 A:HIS208 2.5 17.1 1.0 O2 A:GOL293 2.8 50.0 1.0 O3 A:GOL293 2.8 52.5 1.0 CD A:GLU155 3.3 32.2 1.0 CE1 A:HIS208 3.3 19.5 1.0 CD A:GLU256 3.3 31.2 1.0 CG A:ASP181 3.3 22.1 1.0 CG A:HIS208 3.5 21.7 1.0 OE1 A:GLU155 3.5 33.6 1.0 OE2 A:GLU256 3.6 31.4 1.0 C3 A:GOL293 3.6 57.8 1.0 CB A:ASP181 3.6 17.1 1.0 C2 A:GOL293 3.6 58.4 1.0 CB A:HIS208 3.8 17.8 1.0 NZ A:LYS210 3.9 24.6 1.0 ND2 A:ASN184 4.0 16.2 1.0 CE A:LYS210 4.3 29.4 1.0 OD1 A:ASN184 4.5 21.4 1.0 OD1 A:ASP181 4.5 19.8 1.0 NE2 A:HIS208 4.5 22.9 1.0 CG A:GLU155 4.6 26.9 1.0 ND2 A:ASN179 4.6 19.1 1.0 CG A:ASN184 4.6 20.7 1.0 CD2 A:HIS208 4.6 23.2 1.0 CG A:GLU256 4.7 26.0 1.0 CB A:GLU256 4.9 20.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Xylose Isomerase Domain Protein From Planctomyces Limnophilus


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 Xylose Isomerase Domain Protein From Planctomyces Limnophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg291 b:15.6 occ:1.00 OD2 B:ASP181 2.4 19.9 1.0 ND1 B:HIS208 2.4 14.1 1.0 OE2 B:GLU155 2.4 38.5 1.0 OE1 B:GLU256 2.5 40.1 1.0 O B:HOH347 2.9 44.5 1.0 CD B:GLU256 3.2 39.3 1.0 CD B:GLU155 3.2 35.5 1.0 CE1 B:HIS208 3.3 17.2 1.0 OE1 B:GLU155 3.3 34.8 1.0 OE2 B:GLU256 3.3 45.2 1.0 CG B:ASP181 3.3 23.2 1.0 CG B:HIS208 3.5 16.4 1.0 O B:HOH358 3.6 63.4 1.0 CB B:ASP181 3.6 15.4 1.0 NZ B:LYS210 3.7 23.5 1.0 CB B:HIS208 3.9 15.2 1.0 ND2 B:ASN184 3.9 19.0 1.0 OD1 B:ASN184 4.4 20.4 1.0 NE2 B:HIS208 4.4 17.2 1.0 CE B:LYS210 4.5 21.7 1.0 OD1 B:ASP181 4.5 22.4 1.0 CG B:GLU256 4.5 31.7 1.0 CG B:ASN184 4.5 21.1 1.0 CD2 B:HIS208 4.6 16.9 1.0 OD1 B:ASN179 4.6 25.8 1.0 CG B:GLU155 4.6 25.5 1.0 CB B:GLU256 4.7 26.2 1.0 CA B:ASP181 5.0 18.7 1.0

Y.Kim, R.Wu, J.Bearden, A.Joachimiak. Crystal Structure of Xylose Isomerase Domain Protein From Planctomyces Limnophilus To Be Published.