Magnesium in PDB 7ckf: The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer

The structure of The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer, PDB code: 7ckf was solved by W.Cui, H.T.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.79 / 2.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.326, 79.329, 140.192, 90, 90, 90
R / Rfree (%)	21.2 / 25.9

The structure of The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer also contains other interesting chemical elements:

Aluminium	(Al)	2 atoms
Fluorine	(F)	6 atoms

The binding sites of Magnesium atom in the The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer (pdb code 7ckf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer, PDB code: 7ckf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:40.5 occ:1.00 O2B A:GDP402 2.0 39.8 1.0 OG1 A:THR75 2.1 36.2 1.0 F1 A:AF3403 2.4 39.5 1.0 OG A:SER52 2.4 30.6 1.0 CB A:THR75 3.1 33.6 1.0 CB A:SER52 3.1 30.9 1.0 PB A:GDP402 3.2 35.2 1.0 O1B A:GDP402 3.5 31.9 1.0 AL A:AF3403 3.8 52.2 1.0 N A:SER52 3.8 37.8 1.0 O1A A:GDP402 3.9 35.4 1.0 CG2 A:THR75 4.0 26.0 1.0 CA A:SER52 4.0 35.2 1.0 OD2 A:ASP97 4.1 32.4 1.0 N A:THR75 4.2 34.9 1.0 O3B A:GDP402 4.2 37.3 1.0 O A:HOH543 4.2 27.1 1.0 CA A:THR75 4.2 33.0 1.0 OD1 A:ASP97 4.3 33.6 1.0 F2 A:AF3403 4.3 40.0 1.0 O3A A:GDP402 4.3 37.2 1.0 O A:THR98 4.4 31.3 1.0 PA A:GDP402 4.5 38.2 1.0 O2A A:GDP402 4.5 42.2 1.0 O A:SER66 4.5 29.7 1.0 CG A:ASP97 4.6 36.2 1.0 CB A:LYS51 4.8 28.6 1.0 CE A:LYS51 4.9 33.8 1.0 C A:LYS51 5.0 37.7 1.0

Magnesium binding site 2 out of 2 in the The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The N-Terminus of Interferon-Inducible Antiviral Protein-Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:37.8 occ:1.00 F1 B:AF3403 2.1 46.8 1.0 O2B B:GDP402 2.1 39.8 1.0 OG1 B:THR75 2.3 38.4 1.0 OG B:SER52 2.6 38.6 1.0 CB B:THR75 2.9 38.9 1.0 PB B:GDP402 3.3 32.8 1.0 AL B:AF3403 3.3 49.9 1.0 O3B B:GDP402 3.5 38.6 1.0 CB B:SER52 3.6 35.3 1.0 F2 B:AF3403 3.7 37.5 1.0 CG2 B:THR75 3.8 38.3 1.0 O B:THR98 4.0 43.9 1.0 N B:SER52 4.0 37.2 1.0 N B:THR75 4.0 36.9 1.0 CA B:THR75 4.1 41.6 1.0 O1B B:GDP402 4.2 36.3 1.0 OD1 B:ASP97 4.2 43.6 1.0 O B:HOH505 4.2 40.2 1.0 OD2 B:ASP97 4.3 41.5 1.0 CA B:SER52 4.4 36.5 1.0 O2A B:GDP402 4.5 36.3 1.0 O3A B:GDP402 4.5 40.1 1.0 CG B:ASP97 4.6 41.3 1.0 F3 B:AF3403 4.6 42.3 1.0 NZ B:LYS51 4.7 32.1 1.0 CE B:LYS51 4.7 34.2 1.0 CB B:LYS51 4.8 31.1 1.0 PA B:GDP402 4.8 38.2 1.0 O B:SER66 4.9 42.9 1.0 O1A B:GDP402 4.9 42.2 1.0 C B:THR98 5.0 42.0 1.0

W.Cui, E.Braun, W.Wang, J.Tang, Y.Zheng, B.Slater, N.Li, C.Chen, Q.Liu, B.Wang, X.Li, Y.Duan, Y.Xiao, R.Ti, D.Hotter, X.Ji, L.Zhang, J.Cui, Y.Xiong, D.Sauter, Z.Wang, F.Kirchhoff, H.Yang. Structural Basis For Gtp-Induced Dimerization and Antiviral Function of Guanylate-Binding Proteins. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33876762
DOI: 10.1073/PNAS.2022269118