Magnesium in PDB 2yzj: Crystal Structure of Dctp Deaminase From Sulfolobus Tokodaii

The structure of Crystal Structure of Dctp Deaminase From Sulfolobus Tokodaii, PDB code: 2yzj was solved by M.Kanagawa, S.Baba, S.Kuramitsu, S.Yokoyama, G.Kawai, G.Sampei, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.65 / 1.66
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.770, 53.757, 53.757, 107.47, 107.52, 107.50
R / Rfree (%)	20.8 / 22.7

The binding sites of Magnesium atom in the Crystal Structure of Dctp Deaminase From Sulfolobus Tokodaii (pdb code 2yzj). 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 Dctp Deaminase From Sulfolobus Tokodaii, PDB code: 2yzj:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Dctp Deaminase From Sulfolobus Tokodaii


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 Dctp Deaminase From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg310 b:66.5 occ:1.00 MG B:MG240 2.1 62.5 1.0 CB C:PRO112 2.4 14.1 1.0 CB B:PRO112 2.6 14.3 1.0 CG B:PRO112 3.1 15.9 1.0 CA C:PRO112 3.4 13.6 1.0 MG B:MG290 3.5 71.0 1.0 CG C:PRO112 3.6 15.4 1.0 CD1 C:LEU96 3.7 17.4 1.0 CB A:PRO112 4.0 13.2 1.0 CD B:PRO112 4.0 13.9 1.0 CA B:PRO112 4.0 13.1 1.0 O C:ILE97 4.0 14.4 1.0 CG C:LEU96 4.1 16.3 1.0 CD2 C:LEU96 4.1 17.6 1.0 CG2 C:THR98 4.1 13.5 1.0 N C:PRO112 4.3 13.6 1.0 CD C:PRO112 4.3 15.3 1.0 CG A:PRO112 4.4 14.8 1.0 C C:PRO112 4.5 13.5 1.0 N B:PRO112 4.5 13.7 1.0 CD1 B:LEU96 4.6 17.9 1.0 CA C:THR98 4.7 13.6 1.0 CB C:THR98 4.7 13.6 1.0 C C:ILE97 4.9 14.0 1.0 C B:PRO112 4.9 13.1 1.0 N C:THR113 5.0 13.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Dctp Deaminase From Sulfolobus Tokodaii


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 Dctp Deaminase From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg290 b:71.0 occ:1.00 CG B:LEU96 2.6 17.6 1.0 CD2 B:LEU96 2.7 18.0 1.0 CD1 B:LEU96 2.7 17.9 1.0 CG2 B:THR98 3.0 13.9 1.0 CB A:PRO112 3.5 13.2 1.0 MG B:MG310 3.5 66.5 1.0 MG B:MG240 3.5 62.5 1.0 O B:ILE97 3.7 14.5 1.0 CG A:PRO112 3.8 14.8 1.0 CB B:PRO112 3.9 14.3 1.0 CB B:THR98 4.0 14.1 1.0 CD1 A:LEU96 4.1 18.2 1.0 CB B:LEU96 4.1 17.0 1.0 C B:ILE97 4.2 14.5 1.0 CA B:THR98 4.2 14.0 1.0 CA B:PRO112 4.4 13.1 1.0 N B:THR98 4.4 13.9 1.0 CD2 A:LEU96 4.6 18.3 1.0 C B:LEU96 4.7 15.0 1.0 N B:ILE97 4.7 14.7 1.0 CD2 C:LEU96 4.7 17.6 1.0 CA B:LEU96 4.9 16.0 1.0 CA A:PRO112 4.9 13.3 1.0 CG A:LEU96 5.0 17.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Dctp Deaminase From Sulfolobus Tokodaii


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 Dctp Deaminase From Sulfolobus Tokodaii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg240 b:62.5 occ:1.00 MG B:MG310 2.1 66.5 1.0 CB A:PRO112 2.4 13.2 1.0 CB B:PRO112 2.5 14.3 1.0 CG A:PRO112 2.5 14.8 1.0 CB C:PRO112 2.6 14.1 1.0 CG C:PRO112 3.0 15.4 1.0 CD B:PRO112 3.0 13.9 1.0 CG B:PRO112 3.0 15.9 1.0 CD A:PRO112 3.0 14.0 1.0 CA B:PRO112 3.3 13.1 1.0 CD C:PRO112 3.3 15.3 1.0 N B:PRO112 3.4 13.7 1.0 MG B:MG290 3.5 71.0 1.0 CA A:PRO112 3.5 13.3 1.0 CA C:PRO112 3.7 13.6 1.0 N A:PRO112 3.7 12.1 1.0 N C:PRO112 3.9 13.6 1.0 C B:PRO111 4.6 13.4 1.0 C B:PRO112 4.6 13.1 1.0 C A:PRO112 4.8 13.7 1.0 C A:PRO111 4.8 14.5 1.0 C C:PRO111 5.0 14.8 1.0

M.Kanagawa, S.Baba, S.Kuramitsu, S.Yokoyama, G.Kawai, G.Sampei. Crystal Structure of Dctp Deaminase From Sulfolobus Tokodaii To Be Published.