Magnesium in PDB 7ed9: Crystal Structure of Selenomethionine-Labeled Thermus Thermophilus Faka Atp-Binding Domain

The structure of Crystal Structure of Selenomethionine-Labeled Thermus Thermophilus Faka Atp-Binding Domain, PDB code: 7ed9 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)	47.84 / 2.02
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.74, 90.74, 112.6, 90, 90, 90
R / Rfree (%)	22.7 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Selenomethionine-Labeled Thermus Thermophilus Faka Atp-Binding Domain (pdb code 7ed9). 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 Selenomethionine-Labeled Thermus Thermophilus Faka Atp-Binding Domain, PDB code: 7ed9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Selenomethionine-Labeled 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 Selenomethionine-Labeled Thermus Thermophilus Faka Atp-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:16.1 occ:1.00 OD1 A:ASP40 2.0 29.9 1.0 O2A A:ADP201 2.0 28.3 1.0 O2B A:ADP201 2.1 29.2 1.0 O A:HOH313 2.2 25.1 1.0 OD1 A:ASP38 2.2 34.6 1.0 OD1 A:ASN32 2.2 28.1 1.0 CG A:ASP38 3.1 34.8 1.0 CG A:ASP40 3.1 30.5 1.0 PB A:ADP201 3.2 29.0 1.0 CG A:ASN32 3.2 27.9 1.0 PA A:ADP201 3.3 28.2 1.0 OD2 A:ASP38 3.3 34.7 1.0 OD2 A:ASP40 3.6 30.5 1.0 MG A:MG203 3.6 33.4 1.0 O3A A:ADP201 3.6 28.6 1.0 O3B A:ADP201 3.6 29.3 1.0 ND2 A:ASN32 3.7 27.6 1.0 O A:VAL36 4.0 32.5 1.0 OG1 A:THR41 4.1 25.6 1.0 O1A A:ADP201 4.1 28.1 1.0 N A:ASP40 4.2 30.5 1.0 N A:THR41 4.4 27.8 1.0 CB A:ASP40 4.4 31.0 1.0 O5' A:ADP201 4.5 27.9 1.0 CB A:ASP38 4.5 35.8 1.0 CB A:ASN32 4.5 28.5 1.0 O1B A:ADP201 4.5 28.6 1.0 C A:ASP40 4.6 28.6 1.0 ND2 A:ASN44 4.6 30.1 1.0 CA A:ASP40 4.6 30.1 1.0 N A:ASP38 4.6 34.2 1.0 N A:GLY39 4.7 32.4 1.0 C A:ASP38 4.7 33.7 1.0 C5' A:ADP201 4.8 27.6 1.0 CG2 A:VAL36 4.8 36.0 1.0 CA A:ASP38 4.8 35.1 1.0 CA A:THR41 4.9 27.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Selenomethionine-Labeled 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 Selenomethionine-Labeled Thermus Thermophilus Faka Atp-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:33.4 occ:1.00 OD2 A:ASP38 2.2 34.7 1.0 OD2 A:ASP40 2.4 30.5 1.0 O A:HOH360 2.5 33.4 1.0 O A:HOH349 2.5 36.2 1.0 O2B A:ADP201 2.5 29.2 1.0 O A:HOH359 2.8 48.0 1.0 CG A:ASP38 3.3 34.8 1.0 CG A:ASP40 3.3 30.5 1.0 PB A:ADP201 3.5 29.0 1.0 OD1 A:ASP40 3.6 29.9 1.0 MG A:MG202 3.6 16.1 1.0 O1B A:ADP201 3.7 28.6 1.0 OD1 A:ASP38 3.8 34.6 1.0 O A:HOH309 4.0 41.8 1.0 O A:HOH350 4.2 38.4 1.0 O3B A:ADP201 4.3 29.3 1.0 ND2 A:ASN44 4.4 30.1 1.0 CB A:ASP38 4.5 35.8 1.0 CB A:ASP40 4.7 31.0 1.0 O A:HOH313 4.7 25.1 1.0 O3A A:ADP201 4.8 28.6 1.0 O A:HOH305 4.9 32.4 1.0 O A:HOH322 4.9 41.8 1.0 O2A A:ADP201 4.9 28.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Selenomethionine-Labeled 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 Selenomethionine-Labeled Thermus Thermophilus Faka Atp-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:20.3 occ:1.00 OD1 B:ASP40 2.0 36.2 1.0 O1B B:ADP201 2.0 32.7 1.0 O1A B:ADP201 2.1 31.9 1.0 OD1 B:ASP38 2.2 39.9 1.0 O B:HOH309 2.2 28.1 1.0 OD1 B:ASN32 2.2 36.0 1.0 CG B:ASP38 3.1 41.4 1.0 CG B:ASP40 3.1 37.2 1.0 CG B:ASN32 3.2 35.7 1.0 PB B:ADP201 3.2 32.7 1.0 OD2 B:ASP38 3.3 41.6 1.0 PA B:ADP201 3.3 32.3 1.0 MG B:MG203 3.4 40.6 1.0 OD2 B:ASP40 3.6 37.2 1.0 O3A B:ADP201 3.6 32.6 1.0 ND2 B:ASN32 3.6 36.1 1.0 O3B B:ADP201 3.7 32.3 1.0 O B:VAL36 4.1 42.1 1.0 N B:ASP40 4.1 37.3 1.0 O2A B:ADP201 4.2 32.3 1.0 OG1 B:THR41 4.2 29.3 1.0 CB B:ASP40 4.4 38.7 1.0 N B:THR41 4.4 32.6 1.0 CB B:ASP38 4.4 42.8 1.0 O2B B:ADP201 4.5 32.6 1.0 O5' B:ADP201 4.5 32.0 1.0 CB B:ASN32 4.6 35.5 1.0 CA B:ASP40 4.6 37.5 1.0 N B:GLY39 4.6 38.8 1.0 N B:ASP38 4.6 40.6 1.0 C B:ASP40 4.6 34.9 1.0 C B:ASP38 4.7 40.7 1.0 ND2 B:ASN44 4.7 34.1 1.0 CG2 B:VAL36 4.7 45.4 1.0 CA B:ASP38 4.8 41.8 1.0 C5' B:ADP201 4.8 31.9 1.0 O B:HOH326 4.9 52.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Selenomethionine-Labeled 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 Selenomethionine-Labeled Thermus Thermophilus Faka Atp-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:40.6 occ:1.00 OD2 B:ASP38 2.1 41.6 1.0 O B:HOH326 2.3 52.0 1.0 OD2 B:ASP40 2.3 37.2 1.0 O1B B:ADP201 2.5 32.7 1.0 O B:HOH336 2.5 51.2 1.0 O B:HOH335 3.0 57.5 1.0 CG B:ASP40 3.1 37.2 1.0 CG B:ASP38 3.2 41.4 1.0 OD1 B:ASP40 3.3 36.2 1.0 MG B:MG202 3.4 20.3 1.0 PB B:ADP201 3.6 32.7 1.0 OD1 B:ASP38 3.6 39.9 1.0 O2B B:ADP201 3.8 32.6 1.0 O B:HOH316 3.9 55.0 1.0 ND2 B:ASN44 4.3 34.1 1.0 O3B B:ADP201 4.3 32.3 1.0 CB B:ASP38 4.4 42.8 1.0 CB B:ASP40 4.5 38.7 1.0 O B:HOH309 4.7 28.1 1.0 O1A B:ADP201 4.8 31.9 1.0 O3A B:ADP201 4.8 32.6 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.