Magnesium in PDB 6joq: Crystal Structures of Phage Nrs-1 N300-Dntps-MG2+ Complex Provide Molecular Mechanisms For Substrate Specificity

The structure of Crystal Structures of Phage Nrs-1 N300-Dntps-MG2+ Complex Provide Molecular Mechanisms For Substrate Specificity, PDB code: 6joq was solved by H.J.Guo, M.J.Li, H.Wu, F.Yu, J.H.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.59 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.360, 55.388, 50.774, 90.00, 95.48, 90.00
R / Rfree (%)	19.3 / 23.2

The binding sites of Magnesium atom in the Crystal Structures of Phage Nrs-1 N300-Dntps-MG2+ Complex Provide Molecular Mechanisms For Substrate Specificity (pdb code 6joq). 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 Structures of Phage Nrs-1 N300-Dntps-MG2+ Complex Provide Molecular Mechanisms For Substrate Specificity, PDB code: 6joq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structures of Phage Nrs-1 N300-Dntps-MG2+ Complex Provide Molecular Mechanisms For Substrate Specificity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structures of Phage Nrs-1 N300-Dntps-MG2+ Complex Provide Molecular Mechanisms For Substrate Specificity within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:22.7 occ:1.00 O A:HOH523 1.9 22.4 1.0 O1A A:DGT401 2.0 31.8 1.0 OD1 A:ASP80 2.0 36.9 1.0 OD1 A:ASP78 2.1 30.5 1.0 O1B A:DGT401 2.2 35.7 1.0 O1G A:DGT401 2.3 38.8 1.0 CG A:ASP78 2.9 24.9 1.0 CG A:ASP80 3.1 34.0 1.0 OD2 A:ASP78 3.1 26.8 1.0 PA A:DGT401 3.2 33.1 1.0 PB A:DGT401 3.2 35.4 1.0 OD2 A:ASP80 3.5 35.5 1.0 PG A:DGT401 3.5 41.7 1.0 O3A A:DGT401 3.6 29.7 1.0 O3B A:DGT401 3.8 42.2 1.0 NE2 A:HIS115 3.9 25.2 1.0 O2A A:DGT401 4.1 27.1 1.0 C5' A:DGT401 4.2 37.2 1.0 O2G A:DGT401 4.2 29.1 1.0 O5' A:DGT401 4.3 34.0 1.0 CB A:ASP78 4.3 16.9 1.0 CB A:ASP80 4.4 32.3 1.0 O A:LEU79 4.4 32.8 1.0 O2B A:DGT401 4.4 38.5 1.0 CD2 A:HIS115 4.5 24.9 1.0 O3G A:DGT401 4.5 41.5 1.0 CA A:ASP80 4.6 35.4 1.0 O A:HOH502 4.6 23.3 1.0 C A:LEU79 4.7 29.5 1.0 CB A:SER108 4.7 31.3 1.0 O A:HOH560 4.7 31.0 1.0 OG A:SER108 4.8 26.5 1.0 N A:ASP80 4.8 29.5 1.0 CA A:ASP78 4.9 20.9 1.0 N A:LEU79 5.0 27.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structures of Phage Nrs-1 N300-Dntps-MG2+ Complex Provide Molecular Mechanisms For Substrate Specificity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structures of Phage Nrs-1 N300-Dntps-MG2+ Complex Provide Molecular Mechanisms For Substrate Specificity within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:29.7 occ:1.00 O A:GLU142 2.5 26.7 1.0 OD1 A:ASP72 2.5 27.7 1.0 O A:THR69 2.5 21.0 1.0 O A:PHE74 2.8 17.8 1.0 O A:ASP72 2.9 18.5 1.0 CG A:ASP72 3.3 31.6 1.0 C A:GLU142 3.6 23.4 1.0 N A:PHE74 3.6 23.9 1.0 C A:THR69 3.7 17.4 1.0 C A:ASP72 3.7 20.0 1.0 OD2 A:ASP72 3.8 35.0 1.0 C A:PHE74 3.8 22.1 1.0 CB A:GLU142 4.1 22.0 1.0 CA A:GLU142 4.1 21.8 1.0 O A:LYS70 4.2 32.1 1.0 CA A:PHE74 4.2 21.0 1.0 N A:THR69 4.3 24.8 1.0 C A:PRO73 4.3 26.8 1.0 C A:LYS70 4.4 25.2 1.0 CA A:ASP72 4.4 19.6 1.0 N A:ASP72 4.4 21.6 1.0 CB A:ASP72 4.4 25.1 1.0 CA A:LYS70 4.5 20.8 1.0 N A:PRO73 4.5 20.2 1.0 O A:HOH529 4.5 21.7 1.0 N A:LYS70 4.6 17.7 1.0 CA A:THR69 4.6 20.1 1.0 N A:SER143 4.7 21.5 1.0 CA A:PRO73 4.7 22.8 1.0 CB A:PHE74 4.7 16.0 1.0 CD2 A:LEU68 4.7 25.1 1.0 CB A:LEU68 4.8 27.8 1.0 C A:LEU68 5.0 27.9 1.0

H.Guo, M.Li, H.Wu, W.Wang, F.Yu, J.He. Crystal Structures of Phage Nrs-1 N300-Dntps-MG2+Complex Provide Molecular Mechanisms For Substrate Specificity. Biochem.Biophys.Res.Commun. V. 515 551 2019.
ISSN: ESSN 1090-2104
PubMed: 31176489
DOI: 10.1016/J.BBRC.2019.05.162