Magnesium in PDB 3vx4: Crystal Structure of the Nucleotide-Binding Domain of S. Mutans Coma, A Bifunctional Atp-Binding Cassette Transporter Involved in the Quorum-Sensing Pathway

The structure of Crystal Structure of the Nucleotide-Binding Domain of S. Mutans Coma, A Bifunctional Atp-Binding Cassette Transporter Involved in the Quorum-Sensing Pathway, PDB code: 3vx4 was solved by S.Ishii, T.Yano, A.Okamoto, T.Murakawa, H.Hayashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.43 / 2.69
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	129.611, 129.611, 72.425, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of the Nucleotide-Binding Domain of S. Mutans Coma, A Bifunctional Atp-Binding Cassette Transporter Involved in the Quorum-Sensing Pathway (pdb code 3vx4). 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 the Nucleotide-Binding Domain of S. Mutans Coma, A Bifunctional Atp-Binding Cassette Transporter Involved in the Quorum-Sensing Pathway, PDB code: 3vx4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Nucleotide-Binding Domain of S. Mutans Coma, A Bifunctional Atp-Binding Cassette Transporter Involved in the Quorum-Sensing Pathway


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 the Nucleotide-Binding Domain of S. Mutans Coma, A Bifunctional Atp-Binding Cassette Transporter Involved in the Quorum-Sensing Pathway within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:15.8 occ:1.00 OE1 A:GLN609 1.9 15.4 1.0 O2B A:ATP801 2.0 11.4 1.0 O A:HOH964 2.0 12.1 1.0 OG1 A:THR568 2.0 17.5 1.0 O3G A:ATP801 2.1 11.2 1.0 O A:HOH920 2.3 8.4 1.0 CD A:GLN609 3.0 15.8 1.0 CB A:THR568 3.1 15.8 1.0 PB A:ATP801 3.2 11.6 1.0 PG A:ATP801 3.2 11.3 1.0 O3B A:ATP801 3.4 11.7 1.0 NE2 A:GLN609 3.8 14.2 1.0 O2A A:ATP801 3.9 11.6 1.0 O1G A:ATP801 3.9 10.7 1.0 N A:THR568 4.0 14.7 1.0 CG A:GLN609 4.0 16.5 1.0 OD1 A:ASP689 4.1 13.2 1.0 CA A:THR568 4.1 15.1 1.0 OD2 A:ASP689 4.2 14.8 1.0 O A:HOH938 4.2 12.1 1.0 O3A A:ATP801 4.2 11.7 1.0 CG2 A:THR568 4.2 15.0 1.0 O1B A:ATP801 4.3 10.7 1.0 O A:HOH922 4.3 12.9 1.0 PA A:ATP801 4.4 12.6 1.0 N D:GLY667 4.4 13.1 1.0 O2G A:ATP801 4.4 11.8 1.0 CG A:ASP689 4.5 14.7 1.0 O1A A:ATP801 4.8 11.7 1.0 CB D:SER666 4.9 12.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Nucleotide-Binding Domain of S. Mutans Coma, A Bifunctional Atp-Binding Cassette Transporter Involved in the Quorum-Sensing Pathway


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 the Nucleotide-Binding Domain of S. Mutans Coma, A Bifunctional Atp-Binding Cassette Transporter Involved in the Quorum-Sensing Pathway within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg802 b:13.5 occ:1.00 OE1 D:GLN609 1.9 16.8 1.0 OG1 D:THR568 2.0 10.8 1.0 O3G D:ATP801 2.0 9.1 1.0 O2B D:ATP801 2.1 11.2 1.0 O D:HOH982 2.2 10.8 1.0 O D:HOH977 2.3 6.8 1.0 CD D:GLN609 3.1 15.4 1.0 CB D:THR568 3.2 10.5 1.0 PB D:ATP801 3.2 10.9 1.0 PG D:ATP801 3.3 9.6 1.0 O3B D:ATP801 3.4 10.3 1.0 O2A D:ATP801 3.7 14.1 1.0 NE2 D:GLN609 3.9 14.4 1.0 N A:GLY667 4.0 17.3 1.0 CG D:GLN609 4.1 15.4 1.0 CG2 D:THR568 4.1 9.9 1.0 N D:THR568 4.1 11.1 1.0 O D:HOH961 4.1 9.8 1.0 CA D:THR568 4.2 10.7 1.0 O1G D:ATP801 4.2 9.5 1.0 OD2 D:ASP689 4.2 9.9 1.0 O3A D:ATP801 4.3 12.0 1.0 OD1 D:ASP689 4.3 9.5 1.0 O2G D:ATP801 4.3 9.6 1.0 O1B D:ATP801 4.3 10.6 1.0 PA D:ATP801 4.4 14.4 1.0 CB A:SER666 4.5 17.4 1.0 CA A:GLY667 4.6 16.8 1.0 CG D:ASP689 4.7 10.0 1.0 O1A D:ATP801 4.8 13.6 1.0 CA A:SER666 4.9 17.9 1.0 C A:SER666 5.0 17.5 1.0

S.Ishii, T.Yano, A.Okamoto, T.Murakawa, H.Hayashi. Boundary of the Nucleotide-Binding Domain of Streptococcus Coma Based on Functional and Structural Analysis Biochemistry V. 52 2545 2013.
ISSN: ISSN 0006-2960
PubMed: 23534432
DOI: 10.1021/BI3017069