Magnesium in PDB 1o87: A New Mggdp Complex of the Ffh Ng Domain

The structure of A New Mggdp Complex of the Ffh Ng Domain, PDB code: 1o87 was solved by D.M.Freymann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.80 / 2.1
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.415, 113.631, 61.382, 90.00, 111.76, 90.00
R / Rfree (%)	19.5 / 23.7

The structure of A New Mggdp Complex of the Ffh Ng Domain also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the A New Mggdp Complex of the Ffh Ng Domain (pdb code 1o87). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the A New Mggdp Complex of the Ffh Ng Domain, PDB code: 1o87:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the A New Mggdp Complex of the Ffh Ng Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A New Mggdp Complex of the Ffh Ng Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1300 b:21.6 occ:1.00 O A:HOH2128 2.1 18.1 1.0 O A:HOH2055 2.1 19.9 1.0 OG1 A:THR112 2.1 17.8 1.0 O1B A:GDP1299 2.1 17.0 1.0 O A:HOH2127 2.1 17.2 1.0 O A:HOH2074 2.1 21.4 1.0 CB A:THR112 3.2 18.5 1.0 PB A:GDP1299 3.3 18.1 1.0 O3B A:GDP1299 3.5 18.2 1.0 N A:THR112 3.9 18.9 1.0 O1A A:GDP1299 4.0 18.0 1.0 OD1 A:ASP135 4.0 37.1 1.0 OD1 A:ASP187 4.0 23.4 1.0 CA A:THR112 4.1 18.2 1.0 OD2 A:ASP187 4.2 18.9 1.0 CG2 A:THR112 4.2 19.2 1.0 OE1 A:GLN144 4.3 22.0 1.0 O A:HOH2075 4.3 19.5 1.0 O2B A:GDP1299 4.3 17.1 1.0 O3A A:GDP1299 4.4 16.5 1.0 O A:HOH2078 4.5 40.2 1.0 PA A:GDP1299 4.5 16.7 1.0 CG A:ASP187 4.6 20.5 1.0 CG A:ARG138 4.7 47.4 1.0 O2A A:GDP1299 4.7 16.9 1.0 CB A:LYS111 4.8 19.9 1.0 CE A:LYS111 4.9 25.2 1.0 C A:LYS111 5.0 19.0 1.0

Magnesium binding site 2 out of 4 in the A New Mggdp Complex of the Ffh Ng Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A New Mggdp Complex of the Ffh Ng Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1301 b:22.4 occ:1.00 O A:ASP212 2.2 19.1 1.0 O A:HOH2090 2.2 23.8 1.0 O A:HOH2091 2.2 29.6 1.0 O A:HOH2092 2.2 22.7 1.0 O A:HOH2032 3.1 32.3 1.0 C A:ASP212 3.3 17.2 1.0 CA A:ASP212 3.9 17.5 1.0 OE2 A:GLU213 4.1 20.8 1.0 CD A:GLU213 4.3 18.3 1.0 CB A:ASP212 4.3 18.1 1.0 O A:HOH2033 4.4 33.0 1.0 N A:GLU213 4.5 17.0 1.0 O A:HOH2089 4.5 26.9 1.0 O A:HOH2047 4.5 28.5 1.0 OE1 A:GLU213 4.6 21.6 1.0 CG A:GLU213 4.8 16.9 1.0 CG2 A:THR240 4.9 18.8 1.0 CA A:GLU213 4.9 16.1 1.0

Magnesium binding site 3 out of 4 in the A New Mggdp Complex of the Ffh Ng Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A New Mggdp Complex of the Ffh Ng Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1300 b:26.1 occ:1.00 OG1 B:THR112 2.0 15.2 1.0 O1B B:GDP1299 2.1 18.8 1.0 O B:HOH2143 2.1 22.6 1.0 O B:HOH2098 2.1 27.8 1.0 O B:HOH2067 2.1 22.2 1.0 CB B:THR112 3.2 19.6 1.0 PB B:GDP1299 3.3 21.1 1.0 O3B B:GDP1299 3.5 26.0 1.0 OD1 B:ASP187 3.8 21.7 1.0 N B:THR112 3.9 19.0 1.0 CA B:THR112 4.1 19.3 1.0 CG2 B:THR112 4.1 21.1 1.0 O1A B:GDP1299 4.2 22.5 1.0 NZ B:LYS111 4.2 24.8 1.0 OD2 B:ASP187 4.3 17.1 1.0 O2B B:GDP1299 4.3 21.9 1.0 O3A B:GDP1299 4.4 24.0 1.0 CG B:GLN144 4.5 33.9 1.0 CG B:ASP187 4.6 20.5 1.0 PA B:GDP1299 4.6 22.1 1.0 O2A B:GDP1299 4.6 20.9 1.0 O B:HOH2099 4.7 28.0 1.0 O B:ALA141 4.8 34.4 1.0 CB B:LYS111 4.8 19.9 1.0 C B:LYS111 5.0 19.4 1.0

Magnesium binding site 4 out of 4 in the A New Mggdp Complex of the Ffh Ng Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A New Mggdp Complex of the Ffh Ng Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1301 b:21.1 occ:1.00 O B:ASP212 2.2 16.7 1.0 O B:HOH2116 2.2 27.8 1.0 O B:HOH2117 2.2 26.4 1.0 C B:ASP212 3.3 14.6 1.0 CA B:ASP212 3.9 15.1 1.0 CB B:ASP212 4.3 15.7 1.0 O B:HOH2049 4.3 23.8 1.0 OE1 B:GLU213 4.3 14.6 1.0 O B:HOH2114 4.4 23.5 1.0 CD B:GLU213 4.4 14.5 1.0 N B:GLU213 4.5 14.9 1.0 O B:HOH2036 4.6 29.5 1.0 OE2 B:GLU213 4.8 16.2 1.0 CG B:GLU213 4.8 15.8 1.0 CA B:GLU213 4.9 14.6 1.0 CG2 B:THR240 5.0 19.2 1.0

P.J.Focia, H.Alam, T.Lu, U.D.Ramirez, D.M.Freymann. Novel Protein and MG2+ Configurations in the MG2+Gdp Complex of the Srp Gtpase Ffh Proteins: Struct.,Funct., V. 54 222 2004GENET..
ISSN: ISSN 0887-3585
PubMed: 14696184
DOI: 10.1002/PROT.10598