Magnesium in PDB 7ed6: Crystal Structure of Thermus Thermophilus Faka Atp-Binding Domain

The structure of Crystal Structure of Thermus Thermophilus Faka Atp-Binding Domain, PDB code: 7ed6 was solved by M.Nakatani, S.Nakahara, K.Fukui, T.Murakawa, R.Masui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.10 / 1.93
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.19, 90.19, 111.62, 90, 90, 90
R / Rfree (%)	20.8 / 23.6

The binding sites of Magnesium atom in the Crystal Structure of Thermus Thermophilus Faka Atp-Binding Domain (pdb code 7ed6). 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 Thermus Thermophilus Faka Atp-Binding Domain, PDB code: 7ed6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus Faka Atp-Binding Domain


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 Thermus Thermophilus Faka Atp-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:27.6 occ:1.00 O2A A:ADP203 2.0 26.3 1.0 OD1 A:ASP40 2.0 28.3 1.0 O3B A:ADP203 2.0 24.6 1.0 O A:HOH325 2.1 23.9 1.0 OD1 A:ASN32 2.2 23.1 1.0 OD1 A:ASP38 2.2 30.5 1.0 CG A:ASP40 3.1 27.7 1.0 PA A:ADP203 3.1 26.4 1.0 PB A:ADP203 3.1 30.7 1.0 CG A:ASN32 3.2 25.7 1.0 CG A:ASP38 3.2 34.3 1.0 O3A A:ADP203 3.3 29.5 1.0 MG A:MG202 3.4 30.6 1.0 OD2 A:ASP38 3.5 37.3 1.0 OD2 A:ASP40 3.5 32.4 1.0 ND2 A:ASN32 3.6 24.5 1.0 O2B A:ADP203 3.6 26.7 1.0 OG1 A:THR41 4.0 30.6 1.0 O1A A:ADP203 4.0 29.7 1.0 O A:VAL36 4.0 31.1 1.0 N A:ASP40 4.2 28.6 1.0 N A:THR41 4.3 23.3 1.0 O5' A:ADP203 4.3 25.1 1.0 CB A:ASP40 4.4 28.7 1.0 O1B A:ADP203 4.4 29.7 1.0 CB A:ASN32 4.5 27.6 1.0 O A:HOH322 4.5 28.0 1.0 CB A:ASP38 4.5 34.9 1.0 C A:ASP40 4.6 23.0 1.0 C5' A:ADP203 4.6 24.6 1.0 N A:ASP38 4.6 36.6 1.0 CA A:ASP40 4.6 25.8 1.0 ND2 A:ASN44 4.6 26.3 1.0 C A:ASP38 4.7 33.9 1.0 N A:GLY39 4.7 33.6 1.0 O A:HOH347 4.8 35.1 1.0 CA A:ASP38 4.8 35.5 1.0 CG2 A:VAL36 4.8 33.5 1.0 CA A:THR41 4.8 27.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus Faka Atp-Binding Domain


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 Thermus Thermophilus Faka Atp-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:30.6 occ:1.00 O A:HOH322 2.0 28.0 1.0 O A:HOH347 2.0 35.1 1.0 OD2 A:ASP38 2.0 37.3 1.0 O A:HOH328 2.0 33.0 1.0 O3B A:ADP203 2.1 24.6 1.0 OD2 A:ASP40 2.2 32.4 1.0 CG A:ASP38 3.1 34.3 1.0 CG A:ASP40 3.1 27.7 1.0 PB A:ADP203 3.2 30.7 1.0 OD1 A:ASP40 3.4 28.3 1.0 MG A:MG201 3.4 27.6 1.0 OD1 A:ASP38 3.4 30.5 1.0 O1B A:ADP203 3.5 29.7 1.0 O A:HOH338 4.0 40.5 1.0 O2B A:ADP203 4.0 26.7 1.0 ND2 A:ASN44 4.2 26.3 1.0 O A:HOH352 4.3 45.0 1.0 CB A:ASP38 4.4 34.9 1.0 O3A A:ADP203 4.5 29.5 1.0 CB A:ASP40 4.5 28.7 1.0 O A:HOH325 4.6 23.9 1.0 O2A A:ADP203 4.7 26.3 1.0 O A:HOH314 4.9 44.1 1.0 PA A:ADP203 4.9 26.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus Faka Atp-Binding Domain


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 Thermus Thermophilus Faka Atp-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:38.3 occ:1.00 O1B B:ADP203 2.0 40.8 1.0 O1A B:ADP203 2.1 36.5 1.0 OD1 B:ASP40 2.1 40.5 1.0 O B:HOH312 2.1 38.7 1.0 OD1 B:ASN32 2.2 34.1 1.0 OD1 B:ASP38 2.2 42.9 1.0 PB B:ADP203 3.1 39.8 1.0 CG B:ASP40 3.1 40.1 1.0 PA B:ADP203 3.1 35.1 1.0 CG B:ASN32 3.1 33.5 1.0 CG B:ASP38 3.2 40.6 1.0 O3A B:ADP203 3.4 38.3 1.0 MG B:MG202 3.4 42.1 1.0 OD2 B:ASP38 3.4 40.5 1.0 O3B B:ADP203 3.5 35.8 1.0 ND2 B:ASN32 3.5 32.7 1.0 OD2 B:ASP40 3.5 41.9 1.0 O B:VAL36 3.9 46.4 1.0 O2A B:ADP203 3.9 35.6 1.0 OG1 B:THR41 4.1 37.2 1.0 N B:ASP40 4.2 38.1 1.0 O5' B:ADP203 4.4 34.3 1.0 O2B B:ADP203 4.4 37.5 1.0 N B:THR41 4.4 33.9 1.0 CB B:ASP40 4.4 36.9 1.0 CB B:ASN32 4.5 31.4 1.0 CB B:ASP38 4.5 39.9 1.0 N B:ASP38 4.6 43.8 1.0 O B:HOH321 4.6 42.6 1.0 C5' B:ADP203 4.6 28.5 1.0 CG2 B:VAL36 4.6 42.4 1.0 CA B:ASP40 4.7 38.4 1.0 C B:ASP40 4.7 38.5 1.0 O B:HOH339 4.7 42.4 1.0 C B:ASP38 4.7 43.3 1.0 N B:GLY39 4.7 41.9 1.0 ND2 B:ASN44 4.7 36.8 1.0 CA B:ASP38 4.8 42.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus Faka Atp-Binding Domain


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 Thermus Thermophilus Faka Atp-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:42.1 occ:1.00 OD2 B:ASP40 2.0 41.9 1.0 O B:HOH321 2.0 42.6 1.0 OD2 B:ASP38 2.0 40.5 1.0 O B:HOH339 2.2 42.4 1.0 O1B B:ADP203 2.2 40.8 1.0 O B:HOH330 2.2 46.6 1.0 CG B:ASP40 3.0 40.1 1.0 CG B:ASP38 3.1 40.6 1.0 PB B:ADP203 3.3 39.8 1.0 OD1 B:ASP40 3.3 40.5 1.0 MG B:MG201 3.4 38.3 1.0 OD1 B:ASP38 3.5 42.9 1.0 O2B B:ADP203 3.6 37.5 1.0 O3B B:ADP203 4.0 35.8 1.0 ND2 B:ASN44 4.2 36.8 1.0 CB B:ASP40 4.3 36.9 1.0 CB B:ASP38 4.4 39.9 1.0 O3A B:ADP203 4.6 38.3 1.0 O B:HOH312 4.7 38.7 1.0 O1A B:ADP203 4.8 36.5 1.0 O B:HOH309 4.9 52.9 1.0 PA B:ADP203 5.0 35.1 1.0 CG2 B:VAL36 5.0 42.4 1.0

M.Nakatani, S.Nakahara, K.Fukui, T.Murakawa, S.Baba, T.Kumasaka, T.Yano, R.Masui. Crystal Structure of the Atp-Binding Domain of Fatty Acid Kinase Faka From Thermus Thermophilus To Be Published.