Magnesium in PDB 3c9s: Aathil Complexed with Amppcp

All present enzymatic activity of Aathil Complexed with Amppcp:
2.7.4.16;

The structure of Aathil Complexed with Amppcp, PDB code: 3c9s was solved by K.M.Mcculloch, C.Kinsland, T.P.Begley, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.72 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.204, 67.137, 203.472, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.6

The binding sites of Magnesium atom in the Aathil Complexed with Amppcp (pdb code 3c9s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Aathil Complexed with Amppcp, PDB code: 3c9s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Aathil Complexed with Amppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aathil Complexed with Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:22.3 occ:1.00 O B:HOH972 2.4 25.9 1.0 OD1 A:ASP43 2.4 36.8 1.0 O1A B:ACP900 2.4 40.4 1.0 ND2 B:ASN119 2.4 34.3 1.0 O2B B:ACP900 2.5 38.7 1.0 O A:THR42 2.5 32.0 1.0 O B:HOH974 2.5 39.3 1.0 CG A:ASP43 3.6 36.7 1.0 C A:THR42 3.7 33.5 1.0 PA B:ACP900 3.7 38.8 1.0 PB B:ACP900 3.7 40.2 1.0 CG B:ASN119 3.7 34.7 1.0 O3A B:ACP900 3.8 45.6 1.0 MG A:MG903 3.9 23.7 1.0 CA A:ASP43 4.0 32.7 1.0 O2G B:ACP900 4.0 45.3 1.0 O5' B:ACP900 4.1 39.8 1.0 O B:HOH915 4.2 28.3 1.0 N A:ASP43 4.3 30.9 1.0 CB B:ASN119 4.3 30.6 1.0 O B:GLY118 4.4 33.1 1.0 CB A:ASP43 4.4 36.0 1.0 O A:HOH921 4.5 33.2 1.0 OD2 A:ASP43 4.5 38.9 1.0 O B:HOH905 4.6 27.6 1.0 OD2 A:ASP71 4.6 33.9 1.0 OD1 B:ASN119 4.7 36.2 1.0 O1B B:ACP900 4.7 47.0 1.0 C3B B:ACP900 4.8 46.8 1.0 N A:THR42 4.9 30.7 1.0 CA A:THR42 4.9 31.7 1.0 O2A B:ACP900 4.9 46.7 1.0 CA B:ASN119 4.9 32.0 1.0 OG1 A:THR41 5.0 35.0 1.0

Magnesium binding site 2 out of 6 in the Aathil Complexed with Amppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aathil Complexed with Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:23.1 occ:1.00 OD1 A:ASP71 2.3 31.0 1.0 OD1 A:ASP207 2.3 35.8 1.0 O A:HOH982 2.4 40.8 1.0 OD1 A:ASP27 2.4 34.2 1.0 C3B B:ACP900 2.6 46.8 1.0 O3G B:ACP900 2.9 44.7 1.0 O1B B:ACP900 3.1 47.0 1.0 CG A:ASP207 3.3 37.7 1.0 PB B:ACP900 3.4 40.2 1.0 CG A:ASP27 3.4 35.9 1.0 CG A:ASP71 3.5 33.9 1.0 PG B:ACP900 3.6 42.1 1.0 MG A:MG903 3.6 23.7 1.0 OD2 A:ASP207 3.6 35.8 1.0 CB A:ASP27 3.7 34.6 1.0 NH2 A:ARG142 3.7 48.4 1.0 O2B B:ACP900 4.0 38.7 1.0 O A:HOH980 4.0 36.0 1.0 O A:ASP207 4.3 40.8 1.0 OD2 A:ASP71 4.3 33.9 1.0 CA A:ASP27 4.4 37.0 1.0 CB A:ASP71 4.5 30.4 1.0 N A:ASP207 4.5 38.8 1.0 OD2 A:ASP27 4.5 39.1 1.0 O1G B:ACP900 4.6 41.7 1.0 CB A:ASP207 4.6 36.4 1.0 CA A:ASP71 4.7 32.2 1.0 O2G B:ACP900 4.7 45.3 1.0 O3A B:ACP900 4.9 45.6 1.0 CA A:ASP207 4.9 39.3 1.0 C A:ASP207 4.9 39.4 1.0 CZ A:ARG142 5.0 47.4 1.0 CB A:SER209 5.0 47.7 1.0

Magnesium binding site 3 out of 6 in the Aathil Complexed with Amppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Aathil Complexed with Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:23.7 occ:1.00 OD2 A:ASP71 2.3 33.9 1.0 OD2 A:ASP43 2.5 38.9 1.0 O A:HOH980 2.5 36.0 1.0 O3G B:ACP900 2.6 44.7 1.0 OD1 A:ASP43 2.7 36.8 1.0 O2G B:ACP900 2.7 45.3 1.0 O2B B:ACP900 2.7 38.7 1.0 OD1 A:ASP71 2.7 31.0 1.0 CG A:ASP71 2.8 33.9 1.0 CG A:ASP43 2.9 36.7 1.0 PG B:ACP900 3.0 42.1 1.0 C3B B:ACP900 3.3 46.8 1.0 PB B:ACP900 3.4 40.2 1.0 MG A:MG902 3.6 23.1 1.0 O B:HOH972 3.9 25.9 1.0 MG A:MG901 3.9 22.3 1.0 O A:VAL67 4.2 38.1 1.0 CB A:ASP71 4.3 30.4 1.0 O1B B:ACP900 4.4 47.0 1.0 O A:HOH947 4.4 48.2 1.0 CB A:ASP43 4.4 36.0 1.0 O1G B:ACP900 4.5 41.7 1.0 OD2 A:ASP207 4.7 35.8 1.0 O B:HOH974 4.7 39.3 1.0 O3A B:ACP900 4.9 45.6 1.0 OD1 A:ASN68 4.9 53.0 1.0

Magnesium binding site 4 out of 6 in the Aathil Complexed with Amppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Aathil Complexed with Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:25.3 occ:1.00 OD1 B:ASP71 2.3 31.5 1.0 OD1 B:ASP207 2.3 39.5 1.0 OD2 B:ASP27 2.4 38.3 1.0 C3B A:ACP900 2.5 46.8 1.0 O B:HOH971 2.5 39.1 1.0 O3G A:ACP900 2.9 46.7 1.0 O1B A:ACP900 3.1 47.9 1.0 CG B:ASP207 3.3 38.7 1.0 PB A:ACP900 3.4 39.9 1.0 CG B:ASP27 3.4 39.7 1.0 CG B:ASP71 3.5 35.3 1.0 PG A:ACP900 3.6 39.1 1.0 OD2 B:ASP207 3.6 39.2 1.0 MG B:MG903 3.7 22.4 1.0 CB B:ASP27 3.7 38.8 1.0 O B:HOH973 3.9 31.1 1.0 NH2 B:ARG142 3.9 45.3 1.0 O2B A:ACP900 4.0 40.1 1.0 O B:ASP207 4.3 33.0 1.0 OD2 B:ASP71 4.3 33.9 1.0 N B:ASP207 4.5 38.2 1.0 CA B:ASP27 4.5 39.5 1.0 CB B:ASP71 4.5 32.3 1.0 O1G A:ACP900 4.5 40.7 1.0 OD1 B:ASP27 4.6 39.9 1.0 O B:HOH919 4.6 37.0 1.0 CB B:ASP207 4.6 37.8 1.0 CA B:ASP71 4.6 34.5 1.0 O2G A:ACP900 4.7 43.5 1.0 O3A A:ACP900 4.9 45.8 1.0 CA B:ASP207 4.9 37.6 1.0 C B:ASP207 4.9 38.1 1.0

Magnesium binding site 5 out of 6 in the Aathil Complexed with Amppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Aathil Complexed with Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:23.8 occ:1.00 O A:HOH981 2.4 28.9 1.0 OD1 B:ASP43 2.4 30.7 1.0 O B:THR42 2.4 32.9 1.0 O A:HOH984 2.5 36.3 1.0 O2B A:ACP900 2.5 40.1 1.0 OD1 A:ASN119 2.5 35.4 1.0 O1A A:ACP900 2.6 41.9 1.0 O B:HOH970 3.3 51.2 1.0 C B:THR42 3.5 33.4 1.0 CG B:ASP43 3.6 35.2 1.0 CG A:ASN119 3.7 35.1 1.0 PB A:ACP900 3.8 39.9 1.0 PA A:ACP900 3.8 39.3 1.0 CA B:ASP43 3.9 35.0 1.0 MG B:MG903 3.9 22.4 1.0 O3A A:ACP900 4.0 45.8 1.0 O2G A:ACP900 4.1 43.5 1.0 N B:ASP43 4.1 32.0 1.0 O5' A:ACP900 4.2 42.6 1.0 O A:HOH923 4.2 31.5 1.0 O B:HOH917 4.3 38.9 1.0 CB B:ASP43 4.3 33.7 1.0 O A:HOH909 4.4 29.0 1.0 CB A:ASN119 4.4 29.6 1.0 OD2 B:ASP43 4.5 34.3 1.0 O A:GLY118 4.5 32.2 1.0 OD2 B:ASP71 4.6 33.9 1.0 ND2 A:ASN119 4.7 29.7 1.0 CA B:THR42 4.7 31.5 1.0 N B:THR42 4.8 31.8 1.0 O1B A:ACP900 4.8 47.9 1.0 OG1 B:THR41 4.9 34.5 1.0 C3B A:ACP900 4.9 46.8 1.0

Magnesium binding site 6 out of 6 in the Aathil Complexed with Amppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Aathil Complexed with Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:22.4 occ:1.00 OD2 B:ASP71 2.3 33.9 1.0 O B:HOH973 2.5 31.1 1.0 OD2 B:ASP43 2.5 34.3 1.0 O3G A:ACP900 2.5 46.7 1.0 OD1 B:ASP43 2.6 30.7 1.0 O2G A:ACP900 2.7 43.5 1.0 O2B A:ACP900 2.7 40.1 1.0 OD1 B:ASP71 2.8 31.5 1.0 CG B:ASP71 2.9 35.3 1.0 CG B:ASP43 2.9 35.2 1.0 PG A:ACP900 3.0 39.1 1.0 C3B A:ACP900 3.2 46.8 1.0 PB A:ACP900 3.4 39.9 1.0 MG B:MG901 3.7 25.3 1.0 O B:HOH970 3.7 51.2 1.0 O A:HOH981 3.9 28.9 1.0 MG B:MG902 3.9 23.8 1.0 O B:VAL67 4.1 37.5 1.0 O1B A:ACP900 4.3 47.9 1.0 CB B:ASP71 4.4 32.3 1.0 O1G A:ACP900 4.4 40.7 1.0 CB B:ASP43 4.4 33.7 1.0 OD2 B:ASP207 4.6 39.2 1.0 O A:HOH984 4.7 36.3 1.0 O3A A:ACP900 4.8 45.8 1.0 C B:VAL67 5.0 36.3 1.0

K.M.Mcculloch, C.Kinsland, T.P.Begley, S.E.Ealick. Structural Studies of Thiamin Monophosphate Kinase in Complex with Substrates and Products. Biochemistry V. 47 3810 2008.
ISSN: ISSN 0006-2960
PubMed: 18311927
DOI: 10.1021/BI800041H