Magnesium in PDB 1lnz: Structure of the Obg Gtp-Binding Protein

The structure of Structure of the Obg Gtp-Binding Protein, PDB code: 1lnz was solved by J.Buglino, V.Shen, P.Hakimian, C.D.Lima, S.K.Burley, New Yorksgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.580, 105.006, 124.098, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 29.3

The binding sites of Magnesium atom in the Structure of the Obg Gtp-Binding Protein (pdb code 1lnz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Structure of the Obg Gtp-Binding Protein, PDB code: 1lnz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Structure of the Obg Gtp-Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Obg Gtp-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:28.0 occ:1.00 O A:GLN222 2.9 19.8 1.0 O A:HOH995 3.0 8.3 1.0 N A:GLY227 3.3 30.4 1.0 CA A:GLY225 3.3 27.3 1.0 N A:GLY225 3.4 27.1 1.0 C A:GLY225 3.5 28.3 1.0 N A:LEU226 3.5 27.8 1.0 O A:GLY223 3.8 26.5 1.0 C A:GLY223 3.9 26.1 1.0 CA A:GLY227 3.9 30.4 1.0 C A:GLN222 4.0 22.5 1.0 CA A:GLY223 4.0 24.9 1.0 O A:GLY225 4.2 29.1 1.0 C A:LEU226 4.3 30.1 1.0 CA A:LEU226 4.4 29.2 1.0 C A:VAL224 4.5 26.0 1.0 N A:VAL224 4.5 25.8 1.0 N A:GLY223 4.5 22.9 1.0 N A:HIS228 4.5 31.2 1.0 C A:GLY227 4.8 29.6 1.0

Magnesium binding site 2 out of 7 in the Structure of the Obg Gtp-Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Obg Gtp-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg906 b:42.4 occ:1.00 OD1 A:ASP203 2.5 56.5 1.0 O A:ASP203 2.8 49.9 1.0 CA A:ASP203 2.9 50.4 1.0 C A:ASP203 3.1 49.6 1.0 CG A:ASP203 3.3 55.3 1.0 CB A:ASP203 3.4 52.5 1.0 O A:THR202 3.8 48.2 1.0 N A:ASP203 4.1 49.6 1.0 N A:ASP204 4.3 49.5 1.0 OD2 A:ASP203 4.4 56.4 1.0 C A:THR202 4.4 48.1 1.0

Magnesium binding site 3 out of 7 in the Structure of the Obg Gtp-Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Obg Gtp-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:42.3 occ:1.00 OG B:SER172 2.2 34.2 1.0 O3B B:G4P600 2.5 41.5 1.0 CB B:SER172 3.4 30.3 1.0 PB B:G4P600 3.6 41.0 1.0 O1B B:G4P600 3.8 40.4 1.0 O2A B:G4P600 4.2 45.1 1.0 OD2 B:ASP212 4.4 53.2 1.0 N B:SER172 4.4 29.6 1.0 CA B:SER172 4.5 29.1 1.0 MG B:MG902 4.6 51.0 1.0 O2B B:G4P600 4.6 40.3 1.0 O3A B:G4P600 4.7 42.1 1.0 O B:HOH915 4.7 46.7 1.0 PA B:G4P600 4.9 43.3 1.0

Magnesium binding site 4 out of 7 in the Structure of the Obg Gtp-Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Obg Gtp-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:51.0 occ:1.00 O1B B:G4P600 2.4 40.4 1.0 O2A B:G4P600 3.7 45.1 1.0 N B:SER168 3.8 41.9 1.0 PB B:G4P600 3.8 41.0 1.0 CA B:SER168 3.9 41.9 1.0 CB B:SER168 4.1 42.6 1.0 OG B:SER168 4.2 47.2 1.0 O3B B:G4P600 4.5 41.5 1.0 MG B:MG901 4.6 42.3 1.0 PA B:G4P600 4.6 43.3 1.0 O3A B:G4P600 4.6 42.1 1.0 C5' B:G4P600 4.8 51.9 1.0 C B:PRO167 4.8 40.8 1.0 O2B B:G4P600 4.9 40.3 1.0

Magnesium binding site 5 out of 7 in the Structure of the Obg Gtp-Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Obg Gtp-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:28.2 occ:1.00 O B:HOH1077 2.3 30.2 1.0 O B:HOH1019 2.6 11.3 1.0 O B:HOH1024 2.9 22.1 1.0 OD1 B:ASN142 3.0 18.2 1.0 OG B:SER140 3.8 17.1 1.0 O B:HOH1075 3.8 42.0 1.0 CB B:SER140 4.1 16.2 1.0 CG B:ASN142 4.2 17.6 1.0 O B:GLY18 4.5 18.2 1.0 O B:SER140 4.5 12.6 1.0 C B:SER140 4.7 13.7 1.0 ND2 B:ASN142 4.8 16.8 1.0 O B:HOH1058 5.0 21.1 1.0 CG2 B:VAL20 5.0 23.0 1.0

Magnesium binding site 6 out of 7 in the Structure of the Obg Gtp-Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Obg Gtp-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg905 b:27.1 occ:1.00 O B:HOH1014 3.0 23.0 1.0 CG B:GLN138 3.8 22.9 1.0 OE1 B:GLN138 4.5 22.3 1.0 CD B:GLN138 4.6 22.1 1.0 O B:ALA136 4.8 30.4 1.0 CB B:GLN138 5.0 21.2 1.0

Magnesium binding site 7 out of 7 in the Structure of the Obg Gtp-Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Obg Gtp-Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg907 b:46.9 occ:1.00 ND2 B:ASN17 2.7 19.4 1.0 CG B:ASN17 3.9 21.1 1.0 ND2 B:ASN142 4.3 16.8 1.0 O B:HOH1058 4.3 21.1 1.0 OE1 A:GLU319 4.3 63.3 1.0 OD1 B:ASN17 4.3 22.0 1.0 O B:HOH958 4.5 9.6 1.0 O B:HOH1075 4.7 42.0 1.0 O B:HOH990 4.7 31.3 1.0 O B:HOH1083 4.7 31.1 1.0 CD A:GLU319 4.8 62.9 1.0 OE2 A:GLU319 4.8 63.5 1.0 CE1 B:HIS71 5.0 15.2 1.0 O B:HOH925 5.0 6.8 1.0

J.Buglino, V.Shen, P.Hakimian, C.D.Lima. Structural and Biochemical Analysis of the Obg Gtp Binding Protein Structure V. 10 1581 2002.
ISSN: ISSN 0969-2126
PubMed: 12429099
DOI: 10.1016/S0969-2126(02)00882-1