Magnesium in PDB 1xef: Crystal Structure of the Atp/MG2+ Bound Composite Dimer of Hlyb-Nbd

The structure of Crystal Structure of the Atp/MG2+ Bound Composite Dimer of Hlyb-Nbd, PDB code: 1xef was solved by J.Zaitseva, S.Jenewein, I.B.Holland, L.Schmitt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.926, 194.917, 63.706, 90.00, 110.68, 90.00
R / Rfree (%)	21.9 / 26.4

The binding sites of Magnesium atom in the Crystal Structure of the Atp/MG2+ Bound Composite Dimer of Hlyb-Nbd (pdb code 1xef). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Atp/MG2+ Bound Composite Dimer of Hlyb-Nbd, PDB code: 1xef:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Atp/MG2+ Bound Composite Dimer of Hlyb-Nbd


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 Atp/MG2+ Bound Composite Dimer of Hlyb-Nbd within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:30.1 occ:1.00 O3G A:ATP800 1.9 30.9 1.0 O A:HOH171 2.0 38.1 1.0 O A:HOH165 2.0 21.3 1.0 O2B A:ATP800 2.1 31.7 1.0 O A:HOH160 2.1 32.4 1.0 OG A:SER509 2.3 44.8 1.0 PG A:ATP800 3.1 30.2 1.0 PB A:ATP800 3.2 31.8 1.0 CB A:SER509 3.3 45.0 1.0 O3B A:ATP800 3.3 31.4 1.0 O1A A:ATP800 3.7 33.3 1.0 O2G A:ATP800 3.9 30.6 1.0 O3A A:ATP800 4.3 32.8 1.0 N B:GLY608 4.3 42.3 1.0 O1G A:ATP800 4.3 30.3 1.0 N A:SER509 4.3 44.6 1.0 O A:HOH120 4.3 40.0 1.0 CA A:SER509 4.4 45.0 1.0 O1B A:ATP800 4.4 32.0 1.0 OD1 A:ASP630 4.4 49.6 1.0 OD2 A:ASP630 4.4 49.1 1.0 PA A:ATP800 4.5 33.5 1.0 CB B:SER607 4.7 42.3 1.0 CG A:ASP630 4.9 49.0 1.0 CA B:GLY608 4.9 42.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Atp/MG2+ Bound Composite Dimer of Hlyb-Nbd


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 Atp/MG2+ Bound Composite Dimer of Hlyb-Nbd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1801 b:42.6 occ:1.00 O3G B:ATP1800 1.9 36.7 1.0 O B:HOH36 2.1 36.3 1.0 O B:HOH169 2.1 32.2 1.0 O2B B:ATP1800 2.2 37.7 1.0 OG B:SER509 2.2 45.5 1.0 O B:HOH162 2.3 40.6 1.0 PG B:ATP1800 3.1 36.7 1.0 CB B:SER509 3.3 45.6 1.0 PB B:ATP1800 3.4 37.5 1.0 O3B B:ATP1800 3.6 37.7 1.0 O B:HOH90 3.6 40.9 1.0 O B:HOH109 3.6 42.9 1.0 O2G B:ATP1800 3.7 36.9 1.0 N B:SER509 4.0 45.0 1.0 O1A B:ATP1800 4.0 40.1 1.0 OD1 B:ASP630 4.0 49.0 1.0 OD2 B:ASP630 4.2 48.9 1.0 CA B:SER509 4.2 45.6 1.0 O1G B:ATP1800 4.4 36.6 1.0 O1B B:ATP1800 4.4 37.8 1.0 O3A B:ATP1800 4.4 39.1 1.0 N A:GLY608 4.5 51.0 1.0 CG B:ASP630 4.5 48.5 1.0 O B:HOH167 4.7 43.1 1.0 PA B:ATP1800 4.7 40.3 1.0 CB A:SER607 4.9 52.0 1.0 CB B:LYS508 5.0 44.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Atp/MG2+ Bound Composite Dimer of Hlyb-Nbd


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 the Atp/MG2+ Bound Composite Dimer of Hlyb-Nbd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2801 b:35.1 occ:1.00 O3G C:ATP2800 1.9 29.3 1.0 O C:HOH166 1.9 37.8 1.0 O C:HOH137 2.0 37.9 1.0 O2B C:ATP2800 2.1 30.9 1.0 O C:HOH148 2.1 33.2 1.0 OG C:SER509 2.2 46.4 1.0 PG C:ATP2800 3.2 28.9 1.0 CB C:SER509 3.3 46.2 1.0 PB C:ATP2800 3.4 30.7 1.0 O3B C:ATP2800 3.6 30.1 1.0 O1A C:ATP2800 3.9 33.4 1.0 O2G C:ATP2800 4.0 28.9 1.0 OD1 C:ASP630 4.0 50.9 1.0 OD2 C:ASP630 4.1 50.5 1.0 N C:SER509 4.1 45.8 1.0 CA C:SER509 4.3 46.2 1.0 O1G C:ATP2800 4.4 29.6 1.0 N D:GLY608 4.4 43.6 1.0 O1B C:ATP2800 4.4 30.8 1.0 O3A C:ATP2800 4.4 32.1 1.0 O D:HOH95 4.5 39.5 1.0 CG C:ASP630 4.5 50.2 1.0 PA C:ATP2800 4.7 33.4 1.0 CB D:SER607 4.9 43.9 1.0 CA D:GLY608 4.9 43.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Atp/MG2+ Bound Composite Dimer of Hlyb-Nbd


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Atp/MG2+ Bound Composite Dimer of Hlyb-Nbd within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg3801 b:38.1 occ:1.00 O3G D:ATP3800 1.8 34.9 1.0 O D:HOH147 2.0 34.8 1.0 O D:HOH150 2.1 30.8 1.0 O2B D:ATP3800 2.1 36.6 1.0 OG D:SER509 2.2 45.3 1.0 O D:HOH8 2.2 29.7 1.0 PG D:ATP3800 3.1 34.8 1.0 CB D:SER509 3.2 45.3 1.0 PB D:ATP3800 3.3 36.7 1.0 O3B D:ATP3800 3.6 36.1 1.0 O2G D:ATP3800 3.7 35.4 1.0 O1A D:ATP3800 3.8 39.6 1.0 N D:SER509 4.1 44.7 1.0 OD1 D:ASP630 4.2 51.3 1.0 OD2 D:ASP630 4.2 51.4 1.0 CA D:SER509 4.2 45.3 1.0 O3A D:ATP3800 4.3 38.3 1.0 O1G D:ATP3800 4.3 35.1 1.0 N C:GLY608 4.3 54.4 1.0 O C:HOH48 4.4 47.3 1.0 O1B D:ATP3800 4.5 36.6 1.0 PA D:ATP3800 4.5 39.8 1.0 O D:HOH116 4.6 58.9 1.0 CG D:ASP630 4.7 51.0 1.0 CB C:SER607 4.7 55.0 1.0 CA C:GLY608 4.9 54.1 1.0

J.Zaitseva, S.Jenewein, T.Jumpertz, I.B.Holland, L.Schmitt. H662 Is the Linchpin of Atp Hydrolysis in the Nucleotide-Binding Domain of the Abc Transporter Hlyb Embo J. V. 24 1901 2005.
ISSN: ISSN 0261-4189
PubMed: 15889153
DOI: 10.1038/SJ.EMBOJ.7600657