Magnesium in PDB 4znl: Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride

The structure of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride, PDB code: 4znl was solved by B.J.Hilbert, J.A.Hayes, N.P.Stone, C.M.Duffy, B.A.Kelch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.46 / 2.07
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	76.920, 76.920, 131.120, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 23.8

The structure of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride also contains other interesting chemical elements:

Fluorine

(F)

9 atoms

The binding sites of Magnesium atom in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride (pdb code 4znl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride, PDB code: 4znl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:15.1 occ:1.00 F3 A:BEF302 1.9 22.4 1.0 OG A:SER44 2.0 17.7 1.0 O A:HOH509 2.0 16.5 1.0 O3B A:ADP303 2.1 15.8 1.0 O A:HOH411 2.1 12.0 1.0 O A:HOH549 2.3 20.6 1.0 CB A:SER44 3.0 17.5 1.0 BE A:BEF302 3.3 40.8 1.0 O A:HOH583 3.3 40.6 1.0 PB A:ADP303 3.4 19.9 1.0 O1B A:ADP303 3.8 15.6 1.0 N A:SER44 3.9 15.5 1.0 OD2 A:ASP149 4.0 19.8 1.0 CA A:SER44 4.0 16.2 1.0 OE2 A:GLU150 4.1 28.5 1.0 O A:HOH526 4.1 24.8 1.0 O3A A:ADP303 4.2 20.8 1.0 F1 A:BEF302 4.2 40.4 1.0 O A:HOH533 4.2 35.0 1.0 O A:HOH496 4.2 33.0 1.0 OD1 A:ASP149 4.3 22.3 1.0 O1A A:ADP303 4.3 20.1 1.0 F2 A:BEF302 4.4 30.0 1.0 O2B A:ADP303 4.5 16.9 1.0 CG A:ASP149 4.5 20.2 1.0 O2A A:ADP303 4.5 18.6 1.0 PA A:ADP303 4.5 19.4 1.0 CB A:LYS43 4.9 17.5 1.0 C A:LYS43 4.9 15.1 1.0 NH1 A:ARG79 5.0 31.6 1.0

Magnesium binding site 2 out of 3 in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:30.9 occ:1.00 F2 B:BEF302 2.0 43.0 1.0 OG B:SER44 2.0 24.1 1.0 O1B B:ADP303 2.1 25.6 1.0 O B:HOH509 2.1 36.6 1.0 O B:HOH452 2.2 29.6 1.0 O B:HOH414 2.2 39.3 1.0 CB B:SER44 3.0 26.1 1.0 BE B:BEF302 3.4 46.5 1.0 PB B:ADP303 3.4 27.6 1.0 O B:HOH535 3.6 72.7 1.0 OD2 B:ASP149 3.8 21.4 1.0 O3B B:ADP303 3.8 29.0 1.0 N B:SER44 3.8 29.6 1.0 CA B:SER44 3.9 27.8 1.0 O2A B:ADP303 4.1 26.1 1.0 O3A B:ADP303 4.2 29.8 1.0 O B:HOH507 4.2 32.2 1.0 O B:HOH516 4.2 33.2 1.0 OD1 B:ASP149 4.3 23.1 1.0 O B:HOH502 4.3 34.1 1.0 OE2 B:GLU150 4.3 36.6 1.0 F1 B:BEF302 4.4 60.7 1.0 O1A B:ADP303 4.4 26.8 1.0 PA B:ADP303 4.4 26.7 1.0 CG B:ASP149 4.4 22.3 1.0 F3 B:BEF302 4.5 61.3 1.0 O2B B:ADP303 4.5 26.1 1.0 NH1 B:ARG79 4.7 50.4 1.0 O B:HOH476 4.8 23.9 1.0 CB B:LYS43 4.9 34.4 1.0 C B:LYS43 4.9 29.8 1.0 O B:HOH530 4.9 46.6 1.0 NZ B:LYS43 5.0 39.1 1.0

Magnesium binding site 3 out of 3 in the Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Phage P74-26 Large Terminase Atpase Domain Bound to Adp Beryllium Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:17.5 occ:1.00 F3 C:BEF302 2.0 22.1 1.0 O C:HOH414 2.0 20.1 1.0 O1B C:ADP303 2.0 19.7 1.0 O C:HOH418 2.0 21.3 1.0 OG C:SER44 2.1 18.2 1.0 O C:HOH523 2.3 29.8 1.0 CB C:SER44 3.2 18.9 1.0 PB C:ADP303 3.3 40.9 1.0 BE C:BEF302 3.3 25.7 1.0 O3B C:ADP303 3.7 16.3 1.0 OD2 C:ASP149 3.9 25.4 1.0 N C:SER44 3.9 20.1 1.0 O C:HOH526 3.9 44.6 1.0 O C:HOH538 4.0 32.8 1.0 O2A C:ADP303 4.1 21.1 1.0 CA C:SER44 4.1 19.1 1.0 OE2 C:GLU150 4.2 30.4 1.0 O C:HOH452 4.2 29.7 1.0 O C:HOH505 4.2 26.0 1.0 O3A C:ADP303 4.3 80.3 1.0 OD1 C:ASP149 4.3 27.5 1.0 O2B C:ADP303 4.3 20.2 1.0 F1 C:BEF302 4.4 27.4 1.0 F2 C:BEF302 4.5 24.9 1.0 CG C:ASP149 4.5 25.5 1.0 PA C:ADP303 4.5 20.2 1.0 O1A C:ADP303 4.5 18.4 1.0 CB C:LYS43 4.7 23.9 1.0 CE C:LYS43 4.9 29.0 1.0 NZ C:LYS43 5.0 30.3 1.0 C C:LYS43 5.0 21.0 1.0

B.J.Hilbert, J.A.Hayes, N.P.Stone, C.M.Duffy, B.Sankaran, B.A.Kelch. Structure and Mechanism of the Atpase That Powers Viral Genome Packaging. Proc.Natl.Acad.Sci.Usa V. 112 E3792 2015.
ISSN: ESSN 1091-6490
PubMed: 26150523
DOI: 10.1073/PNAS.1506951112