Magnesium in PDB 4m32: Crystal Structure of Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis

The structure of Crystal Structure of Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis, PDB code: 4m32 was solved by S.M.Williams, A.V.Chandran, M.S.Vijayabaskar, S.Roy, H.Balaram, S.Vishveshwara, M.Vijayan, D.Chatterji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.86
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	89.650, 89.650, 421.071, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 20.8

The structure of Crystal Structure of Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis (pdb code 4m32). 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 Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis, PDB code: 4m32:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis


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 Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:10.4 occ:0.33 OD1 A:ASN48 2.1 7.9 1.0 OD2 A:ASP51 2.2 7.9 1.0 CG A:ASP51 3.1 8.3 1.0 CG A:ASN48 3.1 8.5 1.0 ND2 A:ASN48 3.6 7.7 1.0 CB A:ASP51 3.7 8.2 1.0 OD1 A:ASP51 4.0 8.5 1.0 CB A:ASN48 4.3 8.9 1.0 N A:ASP51 4.5 8.2 1.0 O A:HOH352 4.6 6.1 0.3 CA A:ASN48 4.6 9.1 1.0 CA A:ASP51 4.7 8.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis


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 Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:11.9 occ:1.00 OD1 C:ASN48 2.0 11.3 1.0 OD1 B:ASN48 2.1 10.7 1.0 OD2 B:ASP51 2.1 10.2 1.0 OD2 C:ASP51 2.1 12.3 1.0 CG C:ASP51 3.0 12.3 1.0 CG B:ASP51 3.0 10.8 1.0 CG C:ASN48 3.1 12.0 1.0 CG B:ASN48 3.1 10.8 1.0 CB C:ASP51 3.6 12.4 1.0 ND2 C:ASN48 3.7 11.6 1.0 ND2 B:ASN48 3.7 9.6 1.0 CB B:ASP51 3.7 11.2 1.0 OD1 C:ASP51 3.9 11.9 1.0 OD1 B:ASP51 3.9 10.7 1.0 O B:HOH364 4.3 7.9 1.0 CB C:ASN48 4.3 12.3 1.0 CB B:ASN48 4.4 11.3 1.0 N B:ASP51 4.5 11.2 1.0 N C:ASP51 4.5 12.2 1.0 CA C:ASN48 4.6 12.5 1.0 CA C:ASP51 4.6 12.4 1.0 CA B:ASP51 4.7 11.2 1.0 CA B:ASN48 4.7 11.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis


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 Gated-Pore Mutant D138N of Second Dna-Binding Protein Under Starvation From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:40.1 occ:0.33 O D:HOH389 1.9 36.9 1.0 O D:HOH392 3.3 24.3 1.0 ND1 D:HIS141 3.8 13.4 1.0 ND2 D:ASN138 3.9 18.3 1.0 CE1 D:HIS141 4.1 13.5 1.0 CB D:ASN138 4.3 14.8 1.0 CA D:ASN138 4.5 14.4 1.0 CG D:ASN138 4.6 16.5 1.0

S.M.Williams, A.V.Chandran, M.S.Vijayabaskar, S.Roy, H.Balaram, S.Vishveshwara, M.Vijayan, D.Chatterji. A Histidine Aspartate Ionic Lock Gates the Iron Passage in Miniferritins From Mycobacterium Smegmatis J.Biol.Chem. V. 289 11042 2014.
ISSN: ISSN 0021-9258
PubMed: 24573673
DOI: 10.1074/JBC.M113.524421