Magnesium in PDB 4h2u: Crystal Structure of Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp

The structure of Crystal Structure of Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp, PDB code: 4h2u was solved by M.Luic, I.Weygand-Durasevic, N.Ivic, M.Mocibob, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.32 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.709, 100.904, 104.266, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.9

The structure of Crystal Structure of Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp (pdb code 4h2u). 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 Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp, PDB code: 4h2u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp


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 Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:45.1 occ:1.00 O2B A:ATP402 2.7 44.1 0.8 OE2 A:GLU161 2.8 37.1 1.0 NH1 A:ARG159 2.9 22.8 1.0 O A:HOH555 2.9 32.6 1.0 N7 A:ATP402 3.0 20.1 0.8 O3G A:ATP402 3.1 43.8 0.8 CD A:ARG159 3.6 25.6 1.0 NH1 A:ARG168 3.6 32.8 1.0 CD A:GLU161 3.7 44.1 1.0 OE1 A:GLU161 3.7 44.7 1.0 O3B A:ATP402 3.9 51.2 0.8 C8 A:ATP402 3.9 20.9 0.8 PB A:ATP402 3.9 49.3 0.8 CZ A:ARG159 4.0 29.0 1.0 C5 A:ATP402 4.1 17.1 0.8 PG A:ATP402 4.2 56.5 0.8 N6 A:ATP402 4.2 18.6 0.8 NE A:ARG159 4.2 25.4 1.0 O3A A:ATP402 4.3 37.4 0.8 O A:HOH654 4.3 41.9 1.0 C6 A:ATP402 4.6 20.6 0.8 CG A:ARG159 4.8 22.5 1.0 CZ A:ARG168 4.9 38.1 1.0 CB A:ARG159 4.9 18.6 1.0 CD1 A:LEU88 4.9 22.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp


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 Bradyrhizobium Japonicum Glycine:[Carrier Protein] Ligase Complexed with Cognate Carrier Protein and Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:48.7 occ:1.00 O2B B:ATP402 2.0 43.6 0.9 O B:HOH649 2.0 29.0 1.0 O B:HOH650 2.1 31.7 1.0 O2G B:ATP402 2.5 36.7 0.9 O3B B:ATP402 3.3 42.7 0.9 PB B:ATP402 3.4 45.1 0.9 PG B:ATP402 3.6 38.8 0.9 CG B:PRO216 3.7 52.4 1.0 NH1 B:ARG159 3.7 23.3 1.0 OE2 B:GLU161 4.1 33.9 1.0 NH1 B:ARG168 4.1 36.1 1.0 OE1 B:GLU161 4.2 38.8 1.0 CD B:PRO216 4.2 53.4 1.0 O3G B:ATP402 4.3 45.6 0.9 O3A B:ATP402 4.4 35.5 0.9 O1B B:ATP402 4.4 47.2 0.9 CD1 B:LEU88 4.5 25.8 1.0 CD B:GLU161 4.5 40.1 1.0 N7 B:ATP402 4.8 25.5 0.9 O1G B:ATP402 4.8 39.6 0.9 CD B:ARG159 4.9 26.4 1.0 CZ B:ARG159 4.9 27.8 1.0 CB B:PRO216 5.0 46.7 1.0

M.Mocibob, N.Ivic, M.Luic, I.Weygand-Durasevic. Adaptation of Aminoacyl-Trna Synthetase Catalytic Core to Carrier Protein Aminoacylation. Structure V. 21 614 2013.
ISSN: ISSN 0969-2126
PubMed: 23541895
DOI: 10.1016/J.STR.2013.02.017