Magnesium in PDB 5bq5: Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3

The structure of Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3, PDB code: 5bq5 was solved by E.Arias-Palomo, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.80 / 2.10
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	133.806, 133.806, 70.950, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 20.3

The structure of Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3 also contains other interesting chemical elements:

Fluorine

(F)

9 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3 (pdb code 5bq5). 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 the Istb Aaa+ Domain Bound to Adp-BEF3, PDB code: 5bq5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3


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 Istb Aaa+ Domain Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:23.3 occ:1.00 F3 A:BEF303 1.8 22.7 1.0 O1B A:ADP301 2.0 16.1 1.0 O A:HOH416 2.1 21.3 1.0 O A:HOH457 2.1 16.3 1.0 O A:HOH499 2.1 19.5 1.0 OG1 A:THR112 2.1 17.8 1.0 BE A:BEF303 3.0 22.0 1.0 PB A:ADP301 3.1 19.3 1.0 HB A:THR112 3.2 20.7 1.0 O2B A:ADP301 3.2 20.3 1.0 CB A:THR112 3.2 17.3 1.0 H A:THR112 3.5 21.3 1.0 HG3 A:GLU167 3.7 36.8 1.0 F1 A:BEF303 3.8 22.7 1.0 HH22 A:ARG237 3.8 25.2 1.0 OD1 A:ASP166 4.0 24.7 1.0 HG21 A:THR112 4.0 20.1 1.0 O3A A:ADP301 4.0 23.8 1.0 OD2 A:ASP166 4.1 23.3 1.0 N A:THR112 4.1 17.8 1.0 HB2 A:LYS111 4.1 22.2 1.0 O1A A:ADP301 4.1 19.8 1.0 O A:HOH575 4.2 49.1 1.0 F2 A:BEF303 4.2 23.8 1.0 CG2 A:THR112 4.2 16.8 1.0 CA A:THR112 4.2 17.1 1.0 HE2 A:LYS111 4.2 26.5 1.0 O3B A:ADP301 4.2 20.0 1.0 O A:HOH562 4.3 32.9 1.0 HZ3 A:LYS111 4.4 26.9 1.0 OE2 A:GLU167 4.4 32.0 1.0 OG1 A:THR197 4.4 23.6 1.0 CG A:ASP166 4.5 23.4 1.0 HA A:THR112 4.5 20.5 1.0 PA A:ADP301 4.6 20.8 1.0 HG23 A:THR112 4.6 20.1 1.0 HE2 A:TYR170 4.6 60.4 1.0 NH2 A:ARG237 4.6 21.0 1.0 CG A:GLU167 4.6 30.6 1.0 HZ2 A:LYS111 4.6 26.9 1.0 HH21 A:ARG237 4.8 25.2 1.0 HB A:THR197 4.8 27.1 1.0 HA A:GLU167 4.8 30.8 1.0 O2A A:ADP301 4.8 21.8 1.0 NZ A:LYS111 4.9 22.4 1.0 H A:GLU167 4.9 27.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3


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 Istb Aaa+ Domain Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:28.0 occ:1.00 F3 B:BEF303 1.8 32.0 1.0 O B:HOH436 2.1 21.7 1.0 O B:HOH465 2.1 25.4 1.0 OG1 B:THR112 2.1 23.7 1.0 O2B B:ADP301 2.1 23.9 1.0 O B:HOH426 2.1 32.2 1.0 BE B:BEF303 3.0 29.3 1.0 HB B:THR112 3.2 29.0 1.0 PB B:ADP301 3.2 25.0 1.0 CB B:THR112 3.2 24.1 1.0 O3B B:ADP301 3.3 27.4 1.0 H B:THR112 3.5 28.4 1.0 HG3 B:GLU167 3.5 48.0 1.0 HG1 B:THR197 3.7 33.2 1.0 F1 B:BEF303 3.7 29.7 1.0 HH22 B:ARG237 3.9 33.0 1.0 OD1 B:ASP166 4.0 28.8 1.0 OD2 B:ASP166 4.0 30.0 1.0 HB2 B:LYS111 4.0 28.4 1.0 N B:THR112 4.1 23.7 1.0 HG21 B:THR112 4.1 29.1 1.0 O2A B:ADP301 4.1 25.0 1.0 HE2 B:LYS111 4.1 31.9 1.0 O3A B:ADP301 4.1 26.2 1.0 F2 B:BEF303 4.2 31.8 1.0 CA B:THR112 4.2 23.9 1.0 CG2 B:THR112 4.2 24.2 1.0 O1B B:ADP301 4.3 25.4 1.0 CG B:ASP166 4.4 29.1 1.0 OG1 B:THR197 4.4 27.7 1.0 O B:HOH525 4.4 37.8 1.0 CG B:GLU167 4.4 40.0 1.0 HZ3 B:LYS111 4.5 31.1 1.0 HA B:THR112 4.5 28.8 1.0 OE2 B:GLU167 4.5 40.8 1.0 O B:HOH520 4.6 49.8 1.0 HG23 B:THR112 4.6 29.1 1.0 PA B:ADP301 4.6 26.3 1.0 NH2 B:ARG237 4.6 27.5 1.0 HE2 B:TYR170 4.6 72.5 1.0 HZ2 B:LYS111 4.7 31.1 1.0 HG2 B:GLU167 4.7 48.0 1.0 HB B:THR197 4.7 32.0 1.0 HH21 B:ARG237 4.7 33.0 1.0 H B:GLU167 4.8 38.8 1.0 O1A B:ADP301 4.9 26.3 1.0 NZ B:LYS111 4.9 25.9 1.0 HA B:GLU167 4.9 43.7 1.0 CE B:LYS111 4.9 26.6 1.0 CB B:LYS111 5.0 23.7 1.0 HG21 B:THR197 5.0 30.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Istb Aaa+ Domain Bound to Adp-BEF3


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 Istb Aaa+ Domain Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:33.2 occ:1.00 F3 C:BEF303 1.8 34.7 1.0 O3B C:ADP301 2.0 29.9 1.0 O C:HOH430 2.1 26.6 1.0 O C:HOH497 2.1 23.7 1.0 O C:HOH437 2.1 30.3 1.0 OG1 C:THR112 2.1 26.7 1.0 BE C:BEF303 2.9 34.0 1.0 PB C:ADP301 3.1 30.9 1.0 HB C:THR112 3.1 31.9 1.0 CB C:THR112 3.2 26.6 1.0 O2B C:ADP301 3.2 32.2 1.0 H C:THR112 3.5 33.5 1.0 HG3 C:GLU167 3.6 48.9 1.0 F1 C:BEF303 3.7 35.3 1.0 HG1 C:THR197 3.7 35.0 1.0 HH22 B:ARG221 3.8 56.0 1.0 HH22 C:ARG237 3.9 36.4 1.0 OD1 C:ASP166 4.0 34.2 1.0 HB2 C:LYS111 4.0 33.6 1.0 O3A C:ADP301 4.0 32.4 1.0 N C:THR112 4.0 27.9 1.0 HG21 C:THR112 4.1 30.1 1.0 OD2 C:ASP166 4.1 36.3 1.0 O2A C:ADP301 4.1 29.7 1.0 O C:HOH533 4.1 46.5 1.0 HE2 C:LYS111 4.1 38.4 1.0 F2 C:BEF303 4.1 33.9 1.0 CA C:THR112 4.2 27.4 1.0 CG2 C:THR112 4.2 25.1 1.0 HH21 B:ARG221 4.2 56.0 1.0 O1B C:ADP301 4.2 31.5 1.0 NH2 B:ARG221 4.3 46.7 1.0 HE1 C:TYR170 4.3 87.3 1.0 HZ3 C:LYS111 4.4 40.3 1.0 OG1 C:THR197 4.4 29.2 1.0 CG C:ASP166 4.4 35.7 1.0 CG C:GLU167 4.5 40.7 1.0 HA C:THR112 4.5 32.9 1.0 PA C:ADP301 4.5 30.5 1.0 HG23 C:THR112 4.6 30.1 1.0 O C:HOH540 4.6 44.4 1.0 HZ2 C:LYS111 4.6 40.3 1.0 HG2 C:GLU167 4.6 48.9 1.0 OE2 C:GLU167 4.6 44.5 1.0 HB C:THR197 4.6 32.9 1.0 NH2 C:ARG237 4.7 30.3 1.0 O1A C:ADP301 4.8 31.0 1.0 NZ C:LYS111 4.8 33.6 1.0 HH C:TYR170 4.8 0.7 1.0 HH21 C:ARG237 4.8 36.4 1.0 HG21 C:THR197 4.9 30.4 1.0 H C:GLU167 4.9 39.4 1.0 CE C:LYS111 4.9 32.0 1.0 CB C:LYS111 4.9 28.0 1.0 HA C:GLU167 5.0 42.5 1.0 HG22 C:THR112 5.0 30.1 1.0

E.Arias-Palomo, J.M.Berger. An Atypical Aaa+ Atpase Assembly Controls Efficient Transposition Through Dna Remodeling and Transposase Recruitment. Cell V. 162 860 2015.
ISSN: ISSN 1097-4172
PubMed: 26276634
DOI: 10.1016/J.CELL.2015.07.037