Magnesium in PDB 3wxm: Crystal Structure of Archaeal Pelota and Gtp-Bound EF1 Alpha Complex

The structure of Crystal Structure of Archaeal Pelota and Gtp-Bound EF1 Alpha Complex, PDB code: 3wxm was solved by K.Kobayashi, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.43 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	148.926, 158.944, 427.236, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 26.1

The binding sites of Magnesium atom in the Crystal Structure of Archaeal Pelota and Gtp-Bound EF1 Alpha Complex (pdb code 3wxm). 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 Archaeal Pelota and Gtp-Bound EF1 Alpha Complex, PDB code: 3wxm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Archaeal Pelota and Gtp-Bound EF1 Alpha Complex


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 Archaeal Pelota and Gtp-Bound EF1 Alpha Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:33.2 occ:1.00 OG A:SER20 2.0 38.1 1.0 O A:HOH606 2.0 35.3 1.0 O2G A:GTP501 2.0 36.0 1.0 O A:HOH822 2.1 29.5 1.0 OG1 A:THR71 2.1 36.4 1.0 O2B A:GTP501 2.3 33.8 1.0 CB A:SER20 3.1 37.9 1.0 CB A:THR71 3.2 35.9 1.0 PG A:GTP501 3.3 35.5 1.0 PB A:GTP501 3.4 32.4 1.0 O3B A:GTP501 3.4 34.7 1.0 N A:SER20 3.7 37.4 1.0 OD2 A:ASP90 3.9 37.9 1.0 CA A:SER20 4.0 36.6 1.0 OD2 A:ASP60 4.0 40.7 1.0 OD1 A:ASP90 4.1 35.2 1.0 O3G A:GTP501 4.1 32.6 1.0 OD1 A:ASP60 4.1 40.0 1.0 CG2 A:THR71 4.2 36.0 1.0 N A:THR71 4.2 34.9 1.0 CA A:THR71 4.2 35.2 1.0 O1A A:GTP501 4.3 36.8 1.0 O A:ALA91 4.3 33.9 1.0 O1B A:GTP501 4.3 31.2 1.0 O1G A:GTP501 4.4 26.7 1.0 CG A:ASP90 4.4 38.0 1.0 CG A:ASP60 4.5 38.2 1.0 CB A:LYS19 4.5 35.4 1.0 O3A A:GTP501 4.5 40.3 1.0 O2A A:GTP501 4.6 33.2 1.0 O A:HOH604 4.6 33.1 1.0 NZ A:LYS19 4.6 31.1 1.0 PA A:GTP501 4.7 36.9 1.0 C A:LYS19 4.7 36.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Archaeal Pelota and Gtp-Bound EF1 Alpha Complex


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 Archaeal Pelota and Gtp-Bound EF1 Alpha Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:37.5 occ:1.00 O C:HOH712 1.9 34.1 1.0 O2B C:GTP501 2.0 40.0 1.0 O2G C:GTP501 2.0 40.9 1.0 O C:HOH792 2.0 35.7 1.0 OG C:SER20 2.1 45.6 1.0 OG1 C:THR71 2.1 40.7 1.0 CB C:SER20 3.1 44.0 1.0 PG C:GTP501 3.1 38.7 1.0 PB C:GTP501 3.1 41.7 1.0 O3B C:GTP501 3.2 41.0 1.0 CB C:THR71 3.2 39.1 1.0 O1A C:GTP501 3.7 44.2 1.0 N C:THR71 3.9 44.2 1.0 N C:SER20 3.9 43.2 1.0 O3G C:GTP501 3.9 42.3 1.0 OD1 C:ASP60 4.0 39.9 1.0 CA C:SER20 4.0 41.2 1.0 CA C:THR71 4.1 40.0 1.0 OD2 C:ASP60 4.1 44.5 1.0 O3A C:GTP501 4.1 40.0 1.0 O1B C:GTP501 4.2 38.9 1.0 O1G C:GTP501 4.2 32.8 1.0 OD2 C:ASP90 4.3 46.9 1.0 CG2 C:THR71 4.3 41.0 1.0 CG C:LYS19 4.3 39.1 1.0 OD1 C:ASP90 4.3 47.8 1.0 PA C:GTP501 4.3 41.2 1.0 CG C:ASP60 4.5 39.2 1.0 O C:HOH605 4.5 40.0 1.0 O C:ALA91 4.6 39.3 1.0 CG C:ASP90 4.7 46.6 1.0 O2A C:GTP501 4.7 43.1 1.0 CE C:LYS19 4.8 36.0 1.0 C C:ILE70 4.8 45.6 1.0 NZ C:LYS19 4.8 31.0 1.0 C C:LYS19 4.9 42.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Archaeal Pelota and Gtp-Bound EF1 Alpha Complex


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 Archaeal Pelota and Gtp-Bound EF1 Alpha Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:38.2 occ:1.00 O E:HOH778 1.9 37.7 1.0 OG1 E:THR71 1.9 40.9 1.0 O2G E:GTP501 2.0 35.5 1.0 OG E:SER20 2.1 39.0 1.0 O2B E:GTP501 2.3 34.2 1.0 O E:HOH603 2.4 32.4 1.0 CB E:SER20 3.0 37.0 1.0 CB E:THR71 3.1 39.4 1.0 PG E:GTP501 3.3 36.5 1.0 PB E:GTP501 3.4 32.6 1.0 N E:SER20 3.5 36.5 1.0 O3B E:GTP501 3.6 42.1 1.0 CA E:SER20 3.8 36.8 1.0 OD1 E:ASP90 3.9 43.3 1.0 OD2 E:ASP90 3.9 44.5 1.0 OD1 E:ASP60 4.0 41.0 1.0 CG2 E:THR71 4.1 35.2 1.0 N E:THR71 4.1 39.6 1.0 OD2 E:ASP60 4.1 38.9 1.0 O1B E:GTP501 4.2 33.2 1.0 O3G E:GTP501 4.2 41.2 1.0 CA E:THR71 4.2 40.1 1.0 O1G E:GTP501 4.3 31.1 1.0 O1A E:GTP501 4.3 35.6 1.0 CG E:ASP90 4.3 40.2 1.0 CB E:LYS19 4.4 34.8 1.0 O E:ALA91 4.4 36.8 1.0 C E:LYS19 4.5 35.5 1.0 CG E:ASP60 4.5 42.8 1.0 O3A E:GTP501 4.5 36.2 1.0 CE E:LYS19 4.6 34.1 1.0 O E:HOH601 4.7 30.6 1.0 PA E:GTP501 4.7 39.1 1.0 O2A E:GTP501 4.7 35.2 1.0 CA E:LYS19 4.9 38.5 1.0 NZ E:LYS19 5.0 32.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Archaeal Pelota and Gtp-Bound EF1 Alpha Complex


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 Archaeal Pelota and Gtp-Bound EF1 Alpha Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg502 b:50.6 occ:1.00 O G:HOH724 1.9 40.2 1.0 O2B G:GTP501 2.0 55.1 1.0 O G:HOH601 2.0 50.5 1.0 OG G:SER20 2.1 50.7 1.0 O2G G:GTP501 2.2 53.8 1.0 OG1 G:THR71 2.4 51.8 1.0 CB G:SER20 2.6 55.3 1.0 PB G:GTP501 3.1 51.1 1.0 PG G:GTP501 3.3 48.6 1.0 CB G:THR71 3.3 45.7 1.0 O3B G:GTP501 3.3 56.3 1.0 N G:SER20 3.5 53.0 1.0 CA G:SER20 3.6 57.0 1.0 NZ G:LYS19 3.8 48.8 1.0 OD2 G:ASP60 3.9 52.6 1.0 OD2 G:ASP90 3.9 52.7 1.0 O1A G:GTP501 4.0 58.6 1.0 OD1 G:ASP60 4.0 51.5 1.0 O3A G:GTP501 4.1 54.6 1.0 OD1 G:ASP90 4.1 49.1 1.0 N G:THR71 4.1 46.5 1.0 O3G G:GTP501 4.1 48.7 1.0 O1B G:GTP501 4.3 51.1 1.0 CA G:THR71 4.3 47.2 1.0 O1G G:GTP501 4.4 41.2 1.0 O2A G:GTP501 4.4 58.0 1.0 PA G:GTP501 4.4 56.1 1.0 CG2 G:THR71 4.4 43.4 1.0 CG G:ASP60 4.4 51.5 1.0 O G:HOH602 4.4 46.7 1.0 CG G:ASP90 4.5 50.8 1.0 C G:LYS19 4.6 55.7 1.0 CB G:LYS19 4.6 50.4 1.0 O G:ALA91 4.8 41.0 1.0 C G:SER20 4.9 58.0 1.0 N G:LYS19 5.0 57.1 1.0 CA G:LYS19 5.0 51.8 1.0

K.Kobayashi, I.Kikuno, K.Kuroha, K.Saito, K.Ito, R.Ishitani, T.Inada, O.Nureki. Structural Basis For Mrna Surveillance By Archaeal Pelota and Gtp-Bound EF1 Alpha Complex Proc.Natl.Acad.Sci.Usa V. 107 17575 2010.
ISSN: ISSN 0027-8424
PubMed: 20876129
DOI: 10.1073/PNAS.1009598107