Magnesium in PDB 2dya: Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase

All present enzymatic activity of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase:
2.7.4.6;

The structure of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase, PDB code: 2dya was solved by M.Kato-Murayama, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.06 / 1.77
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	69.707, 69.707, 107.117, 90.00, 90.00, 120.00
R / Rfree (%)	11.4 / 16.9

The structure of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase (pdb code 2dya). 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 Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase, PDB code: 2dya:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase


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 Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:16.0 occ:1.00 O1A A:ADP501 2.1 14.0 1.0 O1B A:ADP501 2.3 13.5 1.0 O A:HOH720 2.4 15.0 1.0 O A:HOH721 2.5 11.8 1.0 O A:HOH718 2.6 14.3 1.0 PB A:ADP501 3.4 14.8 1.0 O A:HOH749 3.5 20.6 1.0 PA A:ADP501 3.5 14.7 1.0 O3B A:ADP501 3.8 16.0 1.0 O3A A:ADP501 3.9 15.4 1.0 NH1 A:ARG91 4.1 14.5 1.0 OE2 A:GLU57 4.1 22.6 1.0 NE2 A:HIS58 4.3 13.8 1.0 O A:HOH725 4.3 13.0 1.0 O A:HOH724 4.3 10.1 1.0 C5' A:ADP501 4.4 13.2 1.0 O5' A:ADP501 4.4 12.8 1.0 CE1 A:HIS124 4.4 13.2 1.0 O2A A:ADP501 4.5 14.1 1.0 OD2 A:ASP127 4.6 15.7 1.0 OE1 A:GLU57 4.6 19.7 1.0 CD A:GLU57 4.6 22.5 1.0 O A:HOH719 4.6 8.7 1.0 ND1 A:HIS124 4.7 12.4 1.0 O A:HOH747 4.8 10.1 1.0 O2B A:ADP501 4.8 12.6 1.0 O A:ALA125 4.9 12.5 1.0 CZ A:ARG91 4.9 15.8 1.0 CB A:ASP127 4.9 15.8 1.0 NH2 A:ARG91 5.0 14.6 1.0 O A:HOH803 5.0 19.7 1.0 CE1 A:HIS58 5.0 13.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase


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 Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:36.3 occ:1.00 O1A B:ADP502 2.2 24.7 1.0 O1B B:ADP502 2.2 24.9 1.0 O B:HOH752 2.3 21.7 1.0 O B:HOH743 2.5 16.0 1.0 O B:HOH738 2.6 16.3 1.0 PB B:ADP502 3.5 25.1 1.0 PA B:ADP502 3.6 25.0 1.0 OE2 B:GLU57 3.8 32.0 1.0 O B:HOH779 4.0 40.9 1.0 O3A B:ADP502 4.0 26.5 1.0 O3B B:ADP502 4.1 26.5 1.0 O B:HOH725 4.1 11.6 1.0 NH1 B:ARG91 4.2 18.9 1.0 OD2 B:ASP127 4.2 24.0 1.0 NE2 B:HIS58 4.2 30.5 1.0 C5' B:ADP502 4.4 23.2 1.0 CE1 B:HIS124 4.5 9.8 1.0 O5' B:ADP502 4.5 24.2 1.0 O B:HOH729 4.5 10.2 1.0 O2A B:ADP502 4.6 25.9 1.0 O B:HOH720 4.7 18.2 1.0 O B:HOH781 4.7 23.2 1.0 CD B:GLU57 4.8 30.4 1.0 O2B B:ADP502 4.8 25.3 1.0 ND1 B:HIS124 4.8 7.7 1.0 CB B:ASP127 4.8 18.8 1.0 CG B:ASP127 4.9 21.1 1.0 O B:HOH721 4.9 6.4 1.0 CE1 B:HIS58 5.0 30.1 1.0

M.Kato-Murayama, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama. Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase To Be Published.