Magnesium in PDB 5oiu: Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus

The structure of Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus, PDB code: 5oiu was solved by V.Karuppiah, J.P.Derrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.11 / 2.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	220.390, 107.660, 137.830, 90.00, 112.95, 90.00
R / Rfree (%)	19 / 24.6

The structure of Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus also contains other interesting chemical elements:

Zinc	(Zn)	6 atoms
Chlorine	(Cl)	12 atoms

The binding sites of Magnesium atom in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus (pdb code 5oiu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus, PDB code: 5oiu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus


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 Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:33.7 occ:1.00 O3G A:ATP501 1.9 42.1 1.0 O A:HOH634 2.0 39.3 1.0 O A:HOH601 2.1 36.4 1.0 OG A:SER166 2.2 33.1 1.0 O2B A:ATP501 2.4 30.1 1.0 OE2 A:GLU191 3.3 52.3 1.0 PG A:ATP501 3.4 44.5 1.0 CB A:SER166 3.4 34.1 1.0 PB A:ATP501 3.6 33.5 1.0 O A:HOH644 3.8 39.9 1.0 O3B A:ATP501 3.8 39.2 1.0 O A:HOH604 3.9 45.9 1.0 O A:HOH636 4.1 40.4 1.0 O A:HOH649 4.1 45.6 1.0 N A:SER166 4.2 31.9 1.0 O2G A:ATP501 4.2 40.3 1.0 CA A:SER166 4.3 32.1 1.0 CD A:GLU191 4.3 48.5 1.0 O1G A:ATP501 4.3 37.7 1.0 OE1 A:GLU191 4.4 42.5 1.0 O2A A:ATP501 4.5 29.4 1.0 O1B A:ATP501 4.5 30.0 1.0 O3A A:ATP501 4.9 30.8 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus


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 Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:34.8 occ:1.00 O B:HOH606 2.0 35.8 1.0 O B:HOH629 2.0 37.5 1.0 O2G B:ATP501 2.0 34.5 1.0 O2B B:ATP501 2.0 32.4 1.0 O B:HOH604 2.1 37.4 1.0 OG B:SER166 2.2 37.0 1.0 CB B:SER166 3.2 34.1 1.0 PB B:ATP501 3.3 34.7 1.0 PG B:ATP501 3.3 43.6 1.0 O3B B:ATP501 3.6 40.6 1.0 OE2 B:GLU191 3.8 61.6 1.0 N B:SER166 3.9 29.8 1.0 CA B:SER166 4.1 28.7 1.0 O1G B:ATP501 4.2 39.5 1.0 O B:HOH650 4.2 36.2 1.0 O B:HOH633 4.3 42.4 1.0 O2A B:ATP501 4.3 31.4 1.0 O1B B:ATP501 4.3 31.7 1.0 O B:HOH637 4.3 32.8 1.0 O3G B:ATP501 4.4 43.9 1.0 O3A B:ATP501 4.5 35.5 1.0 CD B:GLU191 4.7 51.4 1.0 PA B:ATP501 4.7 34.9 1.0 O1A B:ATP501 4.8 30.6 1.0 CB B:LYS165 4.8 31.9 1.0 OE1 B:GLU191 4.9 53.0 1.0 NZ B:LYS165 4.9 41.0 1.0 C B:LYS165 4.9 31.3 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus


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 Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:47.2 occ:1.00 O C:HOH605 1.9 45.1 1.0 O C:HOH609 2.0 44.5 1.0 O2B C:ATP501 2.0 44.6 1.0 O2G C:ATP501 2.1 51.4 1.0 O C:HOH617 2.1 34.6 1.0 OG C:SER166 2.2 43.5 1.0 CB C:SER166 3.0 34.1 1.0 PB C:ATP501 3.2 43.6 1.0 PG C:ATP501 3.3 47.2 1.0 O3B C:ATP501 3.3 37.2 1.0 N C:SER166 3.7 39.2 1.0 OE2 C:GLU191 3.9 53.2 1.0 CA C:SER166 3.9 37.3 1.0 O3G C:ATP501 4.1 50.2 1.0 O2A C:ATP501 4.1 52.2 1.0 O1B C:ATP501 4.1 38.4 1.0 O3A C:ATP501 4.4 36.6 1.0 O1G C:ATP501 4.4 43.1 1.0 O C:HOH619 4.5 36.1 1.0 PA C:ATP501 4.6 44.5 1.0 NZ C:LYS165 4.7 47.7 1.0 CB C:LYS165 4.8 36.0 1.0 C C:LYS165 4.8 39.8 1.0 CD C:GLU191 4.8 54.5 1.0 O1A C:ATP501 4.8 44.1 1.0 OE1 C:GLU191 4.9 63.2 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus


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 Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:34.7 occ:1.00 O1G D:ATP501 2.0 42.4 1.0 O D:HOH618 2.0 42.9 1.0 OG D:SER166 2.1 42.1 1.0 O D:HOH610 2.1 28.9 1.0 O2B D:ATP501 2.2 37.8 1.0 O D:HOH601 2.3 34.8 1.0 CB D:SER166 3.3 37.4 1.0 PB D:ATP501 3.4 38.9 1.0 PG D:ATP501 3.4 43.5 1.0 O3B D:ATP501 3.6 39.0 1.0 N D:SER166 3.9 42.3 1.0 CA D:SER166 4.1 38.2 1.0 OE2 D:GLU191 4.2 60.2 1.0 O1B D:ATP501 4.2 37.0 1.0 O2G D:ATP501 4.3 44.0 1.0 O3G D:ATP501 4.3 35.6 1.0 O2A D:ATP501 4.5 43.6 1.0 CE D:LYS165 4.6 43.1 1.0 O3A D:ATP501 4.6 39.2 1.0 PA D:ATP501 4.9 41.0 1.0 NZ D:LYS165 4.9 42.4 1.0 C D:LYS165 4.9 40.7 1.0 CB D:LYS165 5.0 33.9 1.0 O1A D:ATP501 5.0 43.3 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:46.3 occ:1.00 OG E:SER166 2.3 35.8 1.0 O E:HOH601 2.4 27.2 1.0 O1G E:ATP501 2.5 45.9 1.0 O2B E:ATP501 2.6 37.0 1.0 O2A E:ATP501 3.1 36.2 1.0 PG E:ATP501 3.2 50.7 1.0 CB E:SER166 3.2 34.0 1.0 OE1 E:GLU191 3.2 57.5 1.0 OE2 E:GLU191 3.3 56.6 1.0 O2G E:ATP501 3.3 46.8 1.0 O3B E:ATP501 3.4 43.6 1.0 PB E:ATP501 3.5 35.9 1.0 CD E:GLU191 3.6 55.7 1.0 O E:HOH621 3.8 52.4 1.0 PA E:ATP501 4.1 34.7 1.0 O3A E:ATP501 4.2 38.0 1.0 CA E:SER166 4.4 34.8 1.0 N E:SER166 4.4 32.5 1.0 O E:HOH659 4.5 47.9 1.0 O1A E:ATP501 4.6 39.3 1.0 O3G E:ATP501 4.6 41.2 1.0 OH E:TYR192 4.8 51.0 1.0 O1B E:ATP501 4.9 38.3 1.0 O E:HOH667 5.0 52.6 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Pilf Type IV Pilus Assembly Atpase From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:37.8 occ:1.00 O F:HOH621 1.8 33.7 1.0 O F:HOH604 1.9 32.7 1.0 O2G F:ATP501 2.0 36.2 1.0 OG F:SER166 2.0 33.5 1.0 O2B F:ATP501 2.3 32.0 1.0 O F:HOH603 2.4 33.2 1.0 CB F:SER166 3.2 34.0 1.0 PG F:ATP501 3.4 49.9 1.0 PB F:ATP501 3.6 34.9 1.0 O3B F:ATP501 3.9 41.3 1.0 OE1 F:GLU191 3.9 54.8 1.0 OE2 F:GLU191 4.0 63.4 1.0 O F:HOH623 4.0 33.7 1.0 N F:SER166 4.1 30.2 1.0 CA F:SER166 4.2 36.7 1.0 O1G F:ATP501 4.2 46.5 1.0 O2A F:ATP501 4.3 31.4 1.0 CD F:GLU191 4.3 58.3 1.0 O3G F:ATP501 4.4 40.3 1.0 O1B F:ATP501 4.6 35.0 1.0 O F:HOH652 4.7 44.4 1.0 O3A F:ATP501 4.7 33.5 1.0 PA F:ATP501 4.8 34.6 1.0 O1A F:ATP501 4.9 36.6 1.0

R.Collins, V.Karuppiah, C.A.Siebert, R.Dajani, A.Thistlethwaite, J.P.Derrick. Structural Cycle of the Thermus Thermophilus Pilf Atpase: the Powering of Type Iva Pilus Assembly. Sci Rep V. 8 14022 2018.
ISSN: ESSN 2045-2322
PubMed: 30232337
DOI: 10.1038/S41598-018-32218-3