Magnesium in PDB 4gbf: Crystal Structure of the C-Terminal Domain of GP131 From Bacteriophage Phikz

The structure of Crystal Structure of the C-Terminal Domain of GP131 From Bacteriophage Phikz, PDB code: 4gbf was solved by L.V.Sycheva, M.M.Shneider, P.G.Leiman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.18 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.449, 86.353, 97.362, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.9

The structure of Crystal Structure of the C-Terminal Domain of GP131 From Bacteriophage Phikz also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of the C-Terminal Domain of GP131 From Bacteriophage Phikz (pdb code 4gbf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of the C-Terminal Domain of GP131 From Bacteriophage Phikz, PDB code: 4gbf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of the C-Terminal Domain of GP131 From Bacteriophage Phikz


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 the C-Terminal Domain of GP131 From Bacteriophage Phikz within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:48.1 occ:1.00 O A:HOH1117 2.0 43.4 1.0 O A:HOH1125 2.1 40.6 1.0 O A:HOH1078 2.1 35.1 1.0 O A:HOH1013 2.1 36.2 1.0 O A:HOH1041 2.1 46.0 1.0 O A:HIS717 2.2 30.9 1.0 C A:HIS717 3.3 29.4 1.0 O A:GLY719 3.6 32.4 1.0 CA A:ALA718 3.8 25.7 1.0 N A:ALA718 4.0 25.1 1.0 C A:ALA718 4.1 26.0 1.0 N A:GLY719 4.3 24.3 1.0 O A:HOH966 4.4 29.7 1.0 CA A:HIS717 4.5 30.5 1.0 O A:ALA718 4.6 27.2 1.0 C A:GLY719 4.7 30.4 1.0 O A:HOH1173 4.8 41.7 1.0 O A:HOH972 5.0 30.5 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the C-Terminal Domain of GP131 From Bacteriophage Phikz


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 the C-Terminal Domain of GP131 From Bacteriophage Phikz within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:51.3 occ:1.00 ND2 A:ASN754 1.9 37.9 1.0 O A:HOH1122 2.1 47.4 1.0 O A:HOH1097 2.1 50.4 1.0 O A:HOH1005 2.1 42.8 1.0 CG A:ASN754 3.1 38.7 1.0 OD1 A:ASN754 3.5 41.3 1.0 O A:ASN749 3.7 25.7 1.0 O A:HOH1112 3.9 39.2 1.0 O A:LEU752 4.2 23.6 1.0 CB A:ASN754 4.4 31.3 1.0 C A:ASN749 4.6 26.0 1.0 O A:SER750 4.7 27.1 1.0 CA A:SER750 4.7 26.4 1.0 NH2 A:ARG756 4.7 28.8 1.0 O A:HOH1022 4.8 27.3 1.0 C A:SER750 4.8 22.8 1.0 NH1 A:ARG756 5.0 33.6 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the C-Terminal Domain of GP131 From Bacteriophage Phikz


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 the C-Terminal Domain of GP131 From Bacteriophage Phikz within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg805 b:31.9 occ:1.00 O A:HOH1136 2.1 30.7 1.0 O A:HOH1103 2.1 33.9 1.0 O A:HOH1085 2.1 30.4 1.0 O A:HOH1077 2.1 29.2 1.0 O A:HOH1101 2.1 35.5 1.0 O A:HOH940 2.1 31.6 1.0 O A:ASP713 4.2 25.6 1.0 OD1 A:ASP715 4.2 29.3 1.0 OD2 A:ASP715 4.3 28.7 1.0 O A:HOH961 4.4 31.4 1.0 O A:HOH954 4.5 28.6 1.0 CB A:ASP713 4.5 24.4 1.0 O A:HOH1102 4.6 41.5 1.0 O A:HOH936 4.6 35.0 1.0 CG A:ASP715 4.7 31.1 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the C-Terminal Domain of GP131 From Bacteriophage Phikz


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 the C-Terminal Domain of GP131 From Bacteriophage Phikz within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg803 b:46.4 occ:1.00 O B:HOH1134 2.1 40.6 1.0 O B:HOH1038 2.1 33.3 1.0 O B:HOH1115 2.1 53.4 1.0 O B:HOH1133 2.1 54.6 1.0 O B:HOH1128 2.1 49.8 1.0 O B:HOH1094 2.1 38.6 1.0 O B:HOH1002 4.2 42.5 1.0 OE2 B:GLU532 4.2 48.3 1.0 O B:ALA551 4.3 18.4 1.0 CD B:GLU532 4.3 49.0 1.0 O B:HOH1005 4.3 33.6 1.0 O B:HIS533 4.4 26.1 1.0 CG B:GLU532 4.6 43.0 1.0 OE1 B:GLU532 4.6 52.0 1.0 C B:ALA551 5.0 23.5 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the C-Terminal Domain of GP131 From Bacteriophage Phikz


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 the C-Terminal Domain of GP131 From Bacteriophage Phikz within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg804 b:69.5 occ:1.00 O B:HOH1129 2.1 55.8 1.0 O B:HOH1105 2.1 43.5 1.0 OD1 B:ASP708 2.2 57.3 1.0 CG B:ASP708 3.1 52.6 1.0 OD2 B:ASP708 3.4 54.5 1.0 O B:ASP708 3.9 32.1 1.0 O A:ALA551 4.0 30.8 1.0 O A:HOH1099 4.2 41.4 1.0 O A:HIS533 4.2 29.6 1.0 O B:HOH1158 4.3 52.7 1.0 NZ A:LYS554 4.3 46.9 1.0 CG A:LYS554 4.4 35.2 1.0 CB B:ASP708 4.4 40.1 1.0 OE2 A:GLU532 4.6 63.0 1.0 CA B:ASP708 4.7 33.2 1.0 C B:ASP708 4.7 30.0 1.0 CG A:GLU532 4.8 52.9 1.0 C A:ALA551 4.9 31.6 1.0

L.V.Sycheva, M.M.Shneider, N.N.Sykilinda, M.A.Ivanova, K.A.Miroshnikov, P.G.Leiman. Crystal Structure and Location of GP131 in the Bacteriophage Phikz Virion. Virology V. 434 257 2012.
ISSN: ISSN 0042-6822
PubMed: 23031178
DOI: 10.1016/J.VIROL.2012.09.001