Magnesium in PDB 1rdf: G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate

The structure of G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate, PDB code: 1rdf was solved by S.D.Lahiri, G.Zhang, D.Dunaway-Mariano, K.N.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.09 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	181.714, 147.348, 131.308, 90.00, 125.21, 90.00
R / Rfree (%)	23 / 26

The binding sites of Magnesium atom in the G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate (pdb code 1rdf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate, PDB code: 1rdf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:4.5 occ:1.00 O A:ALA14 2.1 37.4 1.0 O2 A:ESA500 2.5 33.6 1.0 O A:HOH541 2.6 22.8 1.0 OD1 A:ASP186 2.7 30.4 1.0 OD2 A:ASP12 2.7 40.3 1.0 O1 A:ESA500 2.9 30.3 1.0 C A:ALA14 3.0 37.5 1.0 S A:ESA500 3.2 34.9 1.0 OD2 A:ASP186 3.2 32.9 1.0 CG A:ASP186 3.3 30.6 1.0 CG A:ASP12 3.7 39.4 1.0 N A:GLY15 3.9 36.4 1.0 N A:ALA14 3.9 39.5 1.0 CA A:ALA14 3.9 38.7 1.0 CA A:GLY15 4.0 35.9 1.0 OD1 A:ASP12 4.2 40.2 1.0 C2 A:ESA500 4.2 33.3 1.0 O3 A:ESA500 4.4 32.9 1.0 SG A:CYS22 4.4 39.6 1.0 C A:TRP13 4.4 38.6 1.0 OG1 A:THR16 4.4 33.8 1.0 CB A:ALA14 4.4 39.0 1.0 N A:THR16 4.6 36.5 1.0 C A:GLY15 4.6 36.1 1.0 CB A:ASP186 4.7 30.3 1.0 N A:TRP13 4.8 38.6 1.0 CB A:ASP12 4.8 38.3 1.0 OD1 A:ASP190 4.8 32.5 1.0 O A:TRP13 4.8 39.2 1.0 CG2 A:THR187 5.0 27.1 1.0

Magnesium binding site 2 out of 6 in the G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:8.9 occ:1.00 O B:ALA14 2.3 19.8 1.0 O B:HOH547 2.4 32.0 1.0 OD1 B:ASP186 2.5 15.8 1.0 O2 B:ESA500 2.6 33.3 1.0 OD1 B:ASP12 3.0 16.2 1.0 OD2 B:ASP186 3.1 16.1 1.0 CG B:ASP186 3.2 17.9 1.0 C B:ALA14 3.3 18.4 1.0 C2 B:ESA500 3.3 35.6 1.0 S B:ESA500 3.5 36.0 1.0 CB B:ALA14 4.0 18.5 1.0 CA B:ALA14 4.1 18.8 1.0 CG B:ASP12 4.2 21.4 1.0 CG2 B:THR187 4.2 19.3 1.0 O1 B:ESA500 4.3 35.9 1.0 N B:GLY15 4.3 18.3 1.0 N B:ALA14 4.4 18.2 1.0 SG B:CYS22 4.4 34.5 1.0 OD2 B:ASP190 4.4 23.3 1.0 CA B:GLY15 4.5 20.7 1.0 C1 B:ESA500 4.5 36.1 1.0 O3 B:ESA500 4.7 35.0 1.0 OD2 B:ASP12 4.7 21.1 1.0 CB B:ASP186 4.7 19.1 1.0 C B:TRP13 4.9 18.3 1.0 OG1 B:THR16 4.9 31.4 1.0 N B:ASP186 4.9 18.6 1.0

Magnesium binding site 3 out of 6 in the G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:2.0 occ:1.00 O C:ALA14 2.3 32.5 1.0 O2 C:ESA500 2.6 41.7 1.0 OD1 C:ASP186 2.7 36.2 1.0 O C:HOH539 2.7 31.9 1.0 OD2 C:ASP12 2.8 36.1 1.0 O1 C:ESA500 2.9 39.7 1.0 OD2 C:ASP186 3.0 35.2 1.0 S C:ESA500 3.1 44.2 1.0 OD1 C:ASP12 3.2 36.7 1.0 C C:ALA14 3.2 34.0 1.0 CG C:ASP186 3.2 34.7 1.0 CG C:ASP12 3.3 37.8 1.0 C2 C:ESA500 3.6 43.7 1.0 OD2 C:ASP190 3.9 34.8 1.0 CA C:ALA14 4.0 36.1 1.0 N C:GLY15 4.0 33.4 1.0 N C:ALA14 4.0 39.3 1.0 CA C:GLY15 4.2 32.2 1.0 CB C:ALA14 4.3 36.1 1.0 CG2 C:THR187 4.3 24.2 1.0 O3 C:ESA500 4.5 44.2 1.0 NH1 C:ARG160 4.5 33.4 1.0 C1 C:ESA500 4.6 43.2 1.0 O C:HOH521 4.6 43.9 1.0 CB C:ASP186 4.7 32.9 1.0 CB C:ASP12 4.8 40.1 1.0 CG C:ASP190 4.9 34.5 1.0 SG C:CYS22 5.0 37.0 1.0

Magnesium binding site 4 out of 6 in the G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:12.0 occ:1.00 O D:HOH522 2.2 2.0 1.0 O D:ALA14 2.4 15.2 1.0 OD1 D:ASP186 2.4 17.2 1.0 O2 D:ESA500 2.5 29.1 1.0 OD1 D:ASP12 2.9 4.6 1.0 CG D:ASP186 3.1 17.1 1.0 OD2 D:ASP186 3.2 16.4 1.0 C D:ALA14 3.3 15.6 1.0 S D:ESA500 3.7 29.5 1.0 OG D:SER209 3.9 35.5 1.0 CG D:ASP12 4.0 8.3 1.0 CB D:ALA14 4.0 14.9 1.0 OD2 D:ASP190 4.0 2.0 1.0 CG2 D:THR187 4.1 2.0 1.0 CA D:ALA14 4.2 14.1 1.0 O1 D:ESA500 4.2 27.8 1.0 N D:GLY15 4.2 17.5 1.0 SG D:CYS22 4.3 33.1 1.0 O3 D:ESA500 4.3 29.5 1.0 CA D:GLY15 4.3 19.2 1.0 OD2 D:ASP12 4.3 4.5 1.0 O D:HOH505 4.5 31.7 1.0 OG1 D:THR16 4.6 33.0 1.0 CB D:ASP186 4.6 15.7 1.0 N D:ALA14 4.6 12.7 1.0 N D:ASP186 4.7 13.1 1.0 C D:GLY15 4.8 20.4 1.0 N D:THR16 4.8 22.2 1.0 O D:TRP13 4.9 14.0 1.0 C2 D:ESA500 4.9 29.4 1.0 CB D:CYS22 5.0 34.1 1.0 C D:TRP13 5.0 13.1 1.0

Magnesium binding site 5 out of 6 in the G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg501 b:3.8 occ:1.00 OD1 E:ASP186 2.5 14.0 1.0 OD1 E:ASP12 2.5 20.2 1.0 O3 E:ESA500 2.6 25.7 1.0 O E:ALA14 2.8 9.7 1.0 OD2 E:ASP12 2.9 19.5 1.0 CG E:ASP12 3.0 19.4 1.0 CG E:ASP186 3.3 15.1 1.0 OD2 E:ASP190 3.3 24.5 1.0 OD2 E:ASP186 3.4 15.0 1.0 S E:ESA500 3.5 24.9 1.0 O1 E:ESA500 3.6 25.4 1.0 C E:ALA14 3.9 11.4 1.0 O E:HOH550 3.9 35.4 1.0 NH1 E:ARG160 4.0 42.1 1.0 CG2 E:THR187 4.1 17.3 1.0 O2 E:ESA500 4.3 27.1 1.0 OG1 E:THR187 4.3 16.8 1.0 CB E:ASP12 4.4 17.3 1.0 CG E:ASP190 4.5 24.4 1.0 N E:ALA14 4.5 12.7 1.0 CA E:ALA14 4.5 11.3 1.0 OG1 E:THR16 4.6 27.3 1.0 CB E:ALA14 4.6 11.6 1.0 CB E:ASP186 4.7 15.5 1.0 N E:ASP186 4.7 13.7 1.0 N E:GLY15 4.9 12.0 1.0 CB E:THR187 4.9 19.3 1.0 C2 E:ESA500 4.9 26.1 1.0 N E:TRP13 4.9 17.6 1.0 C E:TRP13 5.0 15.1 1.0 SG E:CYS22 5.0 27.2 1.0 OD1 E:ASP190 5.0 25.1 1.0

Magnesium binding site 6 out of 6 in the G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of G50P Mutant of Phosphonoacetaldehyde Hydrolase in Complex with Substrate Analogue Vinyl Sulfonate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg501 b:18.2 occ:1.00 O F:ALA14 2.3 28.4 1.0 O F:HOH502 2.5 12.7 1.0 OD1 F:ASP186 2.7 24.8 1.0 O2 F:ESA500 2.8 36.0 1.0 OD2 F:ASP12 2.9 26.9 1.0 OD2 F:ASP186 2.9 26.7 1.0 C F:ALA14 3.2 29.1 1.0 CG F:ASP186 3.2 25.6 1.0 C1 F:ESA500 3.6 39.0 1.0 O3 F:ESA500 3.6 36.2 1.0 S F:ESA500 3.7 38.7 1.0 CB F:ALA14 3.8 30.6 1.0 CA F:ALA14 3.9 29.6 1.0 CG F:ASP12 4.0 27.5 1.0 C2 F:ESA500 4.0 38.5 1.0 N F:GLY15 4.1 28.5 1.0 O F:HOH504 4.2 21.3 1.0 N F:ALA14 4.2 29.2 1.0 CG2 F:THR187 4.2 23.1 1.0 SG F:CYS22 4.2 22.1 1.0 OD1 F:ASP12 4.3 24.4 1.0 CA F:GLY15 4.3 28.5 1.0 OD1 F:ASP190 4.5 27.1 1.0 CB F:ASP186 4.7 25.3 1.0 OG1 F:THR16 4.8 16.3 1.0 CB F:CYS22 4.9 22.6 1.0 C F:GLY15 5.0 28.6 1.0

S.D.Lahiri, G.Zhang, J.Dai, D.Dunaway-Mariano, K.N.Allen. Analysis of the Substrate Specificity Loop of the Had Superfamily Cap Domain Biochemistry V. 43 2812 2004.
ISSN: ISSN 0006-2960
PubMed: 15005616
DOI: 10.1021/BI0356810