Magnesium in PDB 2qx0: Crystal Structure of Yersinia Pestis Hppk (Ternary Complex)

All present enzymatic activity of Crystal Structure of Yersinia Pestis Hppk (Ternary Complex):
2.7.6.3;

The structure of Crystal Structure of Yersinia Pestis Hppk (Ternary Complex), PDB code: 2qx0 was solved by J.Blaszczyk, S.Cherry, J.E.Tropea, D.S.Waugh, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.90 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.400, 78.620, 52.600, 90.00, 100.72, 90.00
R / Rfree (%)	23 / 26.9

The binding sites of Magnesium atom in the Crystal Structure of Yersinia Pestis Hppk (Ternary Complex) (pdb code 2qx0). 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 Yersinia Pestis Hppk (Ternary Complex), PDB code: 2qx0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Yersinia Pestis Hppk (Ternary Complex)


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 Yersinia Pestis Hppk (Ternary Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg161 b:14.7 occ:1.00 OD1 A:ASP96 2.0 13.2 1.0 OD1 A:ASP98 2.1 13.8 1.0 O1A A:APC171 2.1 12.5 1.0 O1B A:APC171 2.2 11.4 1.0 O A:HOH182 2.2 8.4 1.0 O A:HOH184 2.3 10.5 1.0 CG A:ASP96 3.0 16.0 1.0 CG A:ASP98 3.3 13.1 1.0 PA A:APC171 3.3 11.8 1.0 OD2 A:ASP96 3.3 12.8 1.0 PB A:APC171 3.3 11.6 1.0 MG A:MG162 3.5 13.5 1.0 C3A A:APC171 3.6 12.6 1.0 OD2 A:ASP98 3.8 10.0 1.0 O5' A:APC171 3.8 9.2 1.0 O2B A:APC171 4.0 13.0 1.0 OE2 A:GLU78 4.0 13.1 1.0 NH2 A:ARG93 4.1 22.0 1.0 O A:LEU97 4.1 8.0 1.0 O A:HOH188 4.3 14.4 1.0 O A:HOH185 4.3 11.0 1.0 CB A:ASP96 4.3 13.9 1.0 C A:LEU97 4.4 8.4 1.0 N A:LEU97 4.4 11.1 1.0 O A:HOH186 4.4 13.0 1.0 CB A:ASP98 4.5 8.9 1.0 N3 A:APC171 4.6 9.7 1.0 CA A:ASP98 4.6 7.9 1.0 N A:ASP98 4.6 10.1 1.0 O2A A:APC171 4.6 10.2 1.0 C2 A:APC171 4.6 12.0 1.0 O3B A:APC171 4.6 11.2 1.0 CA A:ASP96 4.7 13.5 1.0 C A:ASP96 4.8 12.5 1.0 NH1 A:ARG93 4.8 21.1 1.0 O3G A:APC171 4.8 10.8 1.0 O4 A:PH2181 4.8 13.3 1.0 CZ A:ARG93 4.9 21.7 1.0 O1G A:APC171 5.0 12.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Yersinia Pestis Hppk (Ternary Complex)


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 Yersinia Pestis Hppk (Ternary Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg162 b:13.5 occ:1.00 OD2 A:ASP98 2.1 10.0 1.0 OD2 A:ASP96 2.2 12.8 1.0 O3G A:APC171 2.2 10.8 1.0 O4 A:PH2181 2.2 13.3 1.0 O A:HOH183 2.2 9.4 1.0 O1B A:APC171 2.2 11.4 1.0 CG A:ASP98 2.9 13.1 1.0 OD1 A:ASP98 3.1 13.8 1.0 CG A:ASP96 3.2 16.0 1.0 PB A:APC171 3.3 11.6 1.0 PG A:APC171 3.3 10.1 1.0 C11 A:PH2181 3.4 14.1 1.0 O3B A:APC171 3.5 11.2 1.0 MG A:MG161 3.5 14.7 1.0 OD1 A:ASP96 3.6 13.2 1.0 NH1 A:ARG122 4.0 11.8 1.0 O2B A:APC171 4.0 13.0 1.0 O1G A:APC171 4.1 12.4 1.0 N1 A:PH2181 4.1 12.7 1.0 C2 A:PH2181 4.2 13.6 1.0 O A:HOH189 4.2 15.0 1.0 CB A:ASP98 4.3 8.9 1.0 O A:HOH206 4.4 19.3 1.0 NE2 A:HIS116 4.4 13.6 1.0 O A:HOH222 4.4 23.3 1.0 O A:HOH211 4.4 20.2 1.0 CB A:ASP96 4.5 13.9 1.0 O2G A:APC171 4.5 11.9 1.0 C3A A:APC171 4.8 12.6 1.0 O A:HOH184 4.9 10.5 1.0 O1A A:APC171 4.9 12.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Yersinia Pestis Hppk (Ternary Complex)


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 Yersinia Pestis Hppk (Ternary Complex) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg163 b:14.1 occ:1.00 OD1 B:ASP98 2.1 11.5 1.0 OD1 B:ASP96 2.1 11.8 1.0 O1A B:APC172 2.2 12.3 1.0 O1B B:APC172 2.2 11.0 1.0 O B:HOH186 2.2 7.8 1.0 O B:HOH185 2.2 7.7 1.0 CG B:ASP96 3.1 9.8 1.0 CG B:ASP98 3.2 13.4 1.0 PA B:APC172 3.3 11.1 1.0 PB B:APC172 3.3 11.2 1.0 OD2 B:ASP96 3.4 6.6 1.0 C3A B:APC172 3.6 11.7 1.0 MG B:MG164 3.6 9.4 1.0 OD2 B:ASP98 3.7 11.4 1.0 O5' B:APC172 3.8 9.7 1.0 OE2 B:GLU78 4.0 10.3 1.0 O B:LEU97 4.1 7.9 1.0 O2B B:APC172 4.1 10.9 1.0 NH2 B:ARG93 4.2 15.8 1.0 O B:HOH190 4.4 14.2 1.0 C B:LEU97 4.4 9.2 1.0 O B:HOH199 4.4 16.8 1.0 CB B:ASP98 4.4 9.6 1.0 CB B:ASP96 4.4 9.1 1.0 N B:LEU97 4.5 9.9 1.0 O B:HOH195 4.6 15.8 1.0 N3 B:APC172 4.6 8.5 1.0 CA B:ASP98 4.6 8.7 1.0 O3B B:APC172 4.6 9.4 1.0 O2A B:APC172 4.6 11.0 1.0 N B:ASP98 4.6 8.7 1.0 C2 B:APC172 4.6 10.1 1.0 NH1 B:ARG93 4.7 16.4 1.0 O3G B:APC172 4.8 12.1 1.0 CA B:ASP96 4.8 9.9 1.0 C B:ASP96 4.8 8.6 1.0 O1G B:APC172 4.9 12.9 1.0 O4 B:PH2182 4.9 11.1 1.0 CZ B:ARG93 4.9 16.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Yersinia Pestis Hppk (Ternary Complex)


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 Yersinia Pestis Hppk (Ternary Complex) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg164 b:9.4 occ:1.00 OD2 B:ASP98 2.1 11.4 1.0 O3G B:APC172 2.1 12.1 1.0 OD2 B:ASP96 2.2 6.6 1.0 O B:HOH187 2.2 9.5 1.0 O4 B:PH2182 2.2 11.1 1.0 O1B B:APC172 2.3 11.0 1.0 CG B:ASP98 3.0 13.4 1.0 CG B:ASP96 3.3 9.8 1.0 OD1 B:ASP98 3.3 11.5 1.0 PG B:APC172 3.3 11.8 1.0 PB B:APC172 3.3 11.2 1.0 C11 B:PH2182 3.4 13.2 1.0 O3B B:APC172 3.4 9.4 1.0 MG B:MG163 3.6 14.1 1.0 OD1 B:ASP96 3.7 11.8 1.0 NH1 B:ARG122 3.8 11.0 1.0 O2B B:APC172 4.1 10.9 1.0 N1 B:PH2182 4.1 12.6 1.0 O1G B:APC172 4.1 12.9 1.0 C2 B:PH2182 4.2 13.4 1.0 O B:HOH197 4.2 15.9 1.0 O B:HOH194 4.3 15.2 1.0 NE2 B:HIS116 4.3 15.5 1.0 CB B:ASP98 4.4 9.6 1.0 O B:HOH212 4.4 21.2 1.0 O2G B:APC172 4.4 12.1 1.0 O B:HOH200 4.5 17.8 1.0 CB B:ASP96 4.6 9.1 1.0 O B:HOH185 4.8 7.7 1.0 C3A B:APC172 4.8 11.7 1.0 CZ B:ARG122 5.0 9.4 1.0 O1A B:APC172 5.0 12.3 1.0 CE1 B:HIS116 5.0 16.2 1.0

J.Blaszczyk, Y.Li, S.Cherry, J.Alexandratos, Y.Wu, G.Shaw, J.E.Tropea, D.S.Waugh, H.Yan, X.Ji. Structure and Activity of Yersinia Pestis 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase As A Novel Target For the Development of Antiplague Therapeutics. Acta Crystallogr.,Sect.D V. 63 1169 2007.
ISSN: ISSN 0907-4449
PubMed: 18007032
DOI: 10.1107/S0907444907047452