Magnesium in PDB 6jon: 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: 6jon 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)	36.58 / 2.34
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.820, 55.290, 50.550, 90.00, 96.06, 90.00
R / Rfree (%)	22.3 / 23.3

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 6jon). 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: 6jon:
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:41.0 occ:1.00 OD1 A:ASP80 2.0 97.1 1.0 O A:HOH506 2.2 44.5 1.0 O2A A:DTP401 2.2 69.0 1.0 O2G A:DTP401 2.2 76.7 1.0 OD1 A:ASP78 2.2 84.6 1.0 O2B A:DTP401 2.5 73.8 1.0 CG A:ASP78 3.0 78.9 1.0 CG A:ASP80 3.1 95.9 1.0 OD2 A:ASP78 3.2 84.5 1.0 PB A:DTP401 3.5 72.3 1.0 PA A:DTP401 3.5 68.9 1.0 PG A:DTP401 3.5 75.4 1.0 OD2 A:ASP80 3.6 98.8 1.0 O3B A:DTP401 3.8 76.5 1.0 O3A A:DTP401 3.9 72.1 1.0 NE2 A:HIS115 4.0 61.3 1.0 C5' A:DTP401 4.3 68.3 1.0 O3G A:DTP401 4.3 78.5 1.0 CB A:ASP80 4.3 91.9 1.0 O A:LEU79 4.3 74.2 1.0 CB A:SER108 4.4 65.5 1.0 CD2 A:HIS115 4.4 60.7 1.0 O5' A:DTP401 4.5 69.0 1.0 OG A:SER108 4.5 67.2 1.0 CB A:ASP78 4.5 71.0 1.0 CA A:ASP80 4.5 84.7 1.0 O A:HOH505 4.6 72.0 1.0 C A:LEU79 4.6 74.4 1.0 O1G A:DTP401 4.6 76.4 1.0 O1A A:DTP401 4.7 69.4 1.0 N A:ASP80 4.7 79.0 1.0 N A:LEU79 4.8 67.8 1.0 O1B A:DTP401 4.9 74.3 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:1.0 occ:1.00 O A:GLU142 2.2 70.3 1.0 O A:THR69 2.4 60.1 1.0 OD1 A:ASP72 2.7 62.3 1.0 O A:PHE74 2.7 57.8 1.0 O A:ASP72 2.9 64.8 1.0 C A:GLU142 3.4 69.3 1.0 CG A:ASP72 3.4 62.0 1.0 C A:THR69 3.6 59.9 1.0 OD2 A:ASP72 3.8 61.9 1.0 C A:PHE74 3.8 58.3 1.0 N A:PHE74 3.8 61.1 1.0 C A:ASP72 3.9 64.1 1.0 CA A:GLU142 4.0 67.7 1.0 CB A:GLU142 4.0 70.6 1.0 N A:THR69 4.2 57.5 1.0 CA A:LYS70 4.3 65.7 1.0 O A:LYS70 4.3 66.8 1.0 CA A:PHE74 4.3 59.5 1.0 C A:LYS70 4.4 65.9 1.0 N A:LYS70 4.4 62.8 1.0 N A:SER143 4.5 70.3 1.0 CD2 A:LEU68 4.5 61.5 1.0 C A:PRO73 4.5 63.8 1.0 CA A:THR69 4.6 57.9 1.0 CA A:ASP72 4.6 63.8 1.0 CB A:ASP72 4.6 62.6 1.0 N A:ASP72 4.6 63.7 1.0 CB A:LEU68 4.7 58.9 1.0 N A:PRO73 4.7 63.9 1.0 CA A:SER143 4.8 72.7 1.0 CB A:SER143 4.8 73.7 1.0 CB A:PHE74 4.8 58.2 1.0 C A:LEU68 4.9 58.0 1.0 CA A:PRO73 4.9 64.7 1.0 N A:VAL75 5.0 57.9 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