Magnesium in PDB 8bv3: Bacillus Subtilis Dnaa Domain III Structure

The structure of Bacillus Subtilis Dnaa Domain III Structure, PDB code: 8bv3 was solved by S.Pintar, J.A.Hubbard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.40 / 2.38
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	81.578, 81.578, 223.196, 90, 90, 120
R / Rfree (%)	19.1 / 23.9

The structure of Bacillus Subtilis Dnaa Domain III Structure also contains other interesting chemical elements:

Potassium

(K)

9 atoms

The binding sites of Magnesium atom in the Bacillus Subtilis Dnaa Domain III Structure (pdb code 8bv3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Bacillus Subtilis Dnaa Domain III Structure, PDB code: 8bv3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:30.0 occ:1.00 OG1 A:THR55 2.2 33.1 1.0 O3G A:ANP301 2.2 48.3 1.0 O1B A:ANP301 2.3 43.0 1.0 O A:HOH405 2.4 32.6 1.0 PB A:ANP301 3.3 41.1 1.0 CB A:THR55 3.4 37.8 1.0 PG A:ANP301 3.4 58.4 1.0 N3B A:ANP301 3.5 49.1 1.0 OD1 A:ASP111 3.7 45.0 1.0 OD2 A:ASP111 3.8 43.0 1.0 OD2 A:ASP112 3.8 46.1 1.0 N A:THR55 4.1 40.7 1.0 CG A:ASP111 4.1 46.1 1.0 O1A A:ANP301 4.2 50.9 1.0 OD1 A:ASP112 4.2 46.6 1.0 CA A:THR55 4.3 37.3 1.0 O2B A:ANP301 4.4 43.1 1.0 O3A A:ANP301 4.4 43.0 1.0 CG2 A:THR55 4.4 39.4 1.0 CG A:ASP112 4.4 46.9 1.0 O2G A:ANP301 4.4 54.5 1.0 NZ A:LYS54 4.5 52.9 1.0 O1G A:ANP301 4.6 46.1 1.0 CB A:LYS54 4.6 36.9 1.0 NH2 A:ARG210 4.7 67.2 1.0 PA A:ANP301 4.7 39.9 1.0

Magnesium binding site 2 out of 5 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:30.0 occ:1.00 O3G B:ANP301 2.0 33.1 1.0 O B:HOH404 2.2 46.3 1.0 O1B B:ANP301 2.3 31.1 1.0 OG1 B:THR55 2.3 27.7 1.0 O B:HOH405 2.3 26.5 1.0 O B:HOH408 2.4 20.4 1.0 PG B:ANP301 3.4 43.4 1.0 PB B:ANP301 3.5 32.5 1.0 CB B:THR55 3.5 28.9 1.0 OD2 B:ASP112 3.6 45.8 1.0 N3B B:ANP301 3.6 34.1 1.0 OD2 B:ASP111 3.7 28.8 1.0 OD1 B:ASP111 3.8 37.2 1.0 OD1 B:ASP112 4.0 44.0 1.0 CG B:ASP111 4.0 37.2 1.0 N B:THR55 4.1 28.4 1.0 O C:HOH431 4.2 20.9 1.0 O2G B:ANP301 4.2 45.4 1.0 CG B:ASP112 4.2 37.3 1.0 O1A B:ANP301 4.3 26.2 1.0 CA B:THR55 4.3 30.6 1.0 O2B B:ANP301 4.4 27.6 1.0 CG2 B:THR55 4.5 29.3 1.0 O1G B:ANP301 4.5 35.6 1.0 NH2 C:ARG161 4.5 34.0 1.0 O3A B:ANP301 4.5 29.6 1.0 CE B:LYS54 4.7 31.5 1.0 CB B:LYS54 4.7 26.6 1.0 NH2 B:ARG210 4.8 32.5 1.0 PA B:ANP301 4.8 29.6 1.0

Magnesium binding site 3 out of 5 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg305 b:30.0 occ:1.00 O3G C:ANP301 2.0 45.4 1.0 OG1 C:THR55 2.2 32.9 1.0 O1B C:ANP301 2.3 34.8 1.0 O C:HOH406 2.4 28.8 1.0 CB C:THR55 3.4 32.0 1.0 PG C:ANP301 3.4 47.3 1.0 PB C:ANP301 3.4 34.4 1.0 N3B C:ANP301 3.6 36.3 1.0 OD2 C:ASP111 3.7 39.0 1.0 OD2 C:ASP112 3.8 42.5 1.0 OD1 C:ASP112 3.9 43.8 1.0 N C:THR55 4.1 31.6 1.0 OD1 C:ASP111 4.1 44.5 1.0 CG C:ASP111 4.2 38.5 1.0 O D:HOH421 4.2 26.9 1.0 O2G C:ANP301 4.3 43.9 1.0 CA C:THR55 4.3 30.7 1.0 CG C:ASP112 4.3 38.6 1.0 O1A C:ANP301 4.3 32.4 1.0 NH2 D:ARG161 4.4 43.6 1.0 CG2 C:THR55 4.4 30.7 1.0 O3A C:ANP301 4.4 35.9 1.0 O1G C:ANP301 4.4 43.1 1.0 O2B C:ANP301 4.5 35.4 1.0 NH2 C:ARG210 4.5 44.0 1.0 NZ C:LYS54 4.7 49.9 1.0 PA C:ANP301 4.8 35.7 1.0 CB C:LYS54 4.9 29.5 1.0

Magnesium binding site 4 out of 5 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg304 b:30.0 occ:1.00 O D:HOH411 1.9 37.8 1.0 OG1 D:THR55 2.0 38.0 1.0 O3G D:ANP301 2.4 49.5 1.0 O1B D:ANP301 2.4 40.9 1.0 O D:HOH420 2.4 29.7 1.0 O D:HOH403 2.5 35.6 1.0 CB D:THR55 3.2 39.5 1.0 PG D:ANP301 3.6 54.9 1.0 PB D:ANP301 3.6 34.4 1.0 N3B D:ANP301 3.8 38.8 1.0 O E:HOH409 3.8 23.9 1.0 OD2 D:ASP111 3.9 33.4 1.0 OD1 D:ASP111 4.0 36.1 1.0 OD2 D:ASP112 4.0 50.8 1.0 O1A D:ANP301 4.0 30.1 1.0 N D:THR55 4.1 32.0 1.0 CG2 D:THR55 4.1 40.4 1.0 CG D:ASP111 4.1 37.5 1.0 OD1 D:ASP112 4.2 45.3 1.0 CA D:THR55 4.2 34.6 1.0 NH2 E:ARG161 4.4 37.1 1.0 O3A D:ANP301 4.5 38.9 1.0 CG D:ASP112 4.5 45.5 1.0 O2G D:ANP301 4.6 56.7 1.0 O1G D:ANP301 4.6 47.1 1.0 NH2 D:ARG210 4.6 41.3 1.0 PA D:ANP301 4.7 36.4 1.0 O2B D:ANP301 4.7 32.8 1.0

Magnesium binding site 5 out of 5 in the Bacillus Subtilis Dnaa Domain III Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bacillus Subtilis Dnaa Domain III Structure within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg303 b:30.0 occ:1.00 OG1 E:THR55 2.1 36.6 1.0 O3G E:ANP301 2.2 58.5 1.0 O1B E:ANP301 2.5 47.0 1.0 O E:HOH407 2.8 32.5 1.0 CB E:THR55 3.5 41.3 1.0 OD1 E:ASP112 3.5 56.6 1.0 PG E:ANP301 3.5 68.8 1.0 OD1 E:ASP111 3.6 46.4 1.0 PB E:ANP301 3.6 42.1 1.0 OD2 E:ASP111 3.6 37.2 1.0 N3B E:ANP301 3.8 54.4 1.0 CG E:ASP111 3.9 41.1 1.0 OD2 E:ASP112 3.9 48.9 1.0 N E:THR55 4.0 44.7 1.0 CG E:ASP112 4.1 48.0 1.0 O2G E:ANP301 4.2 52.4 1.0 CA E:THR55 4.2 44.6 1.0 O2B E:ANP301 4.4 41.0 1.0 O1A E:ANP301 4.4 42.6 1.0 CG2 E:THR55 4.5 38.0 1.0 NZ E:LYS54 4.5 38.3 1.0 CB E:LYS54 4.6 37.9 1.0 O3A E:ANP301 4.8 40.0 1.0 O1G E:ANP301 4.8 57.3 1.0 NH2 E:ARG210 4.9 45.4 1.0 PA E:ANP301 5.0 41.7 1.0

S.Pintar, A.Basle, J.A.Hubbard. Bacillus Subtilis Dnaa Domain III_IV Structure To Be Published.