Magnesium in PDB 1p48: Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase

All present enzymatic activity of Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase:
4.2.1.11;

The structure of Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase, PDB code: 1p48 was solved by P.A.Sims, T.M.Larsen, R.R.Poyner, W.W.Cleland, G.H.Reed, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.800, 114.500, 73.100, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.3

The binding sites of Magnesium atom in the Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase (pdb code 1p48). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase, PDB code: 1p48:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg438 b:11.4 occ:1.00 OE2 A:GLU295 2.0 8.4 1.0 OD2 A:ASP320 2.0 8.4 1.0 O A:HOH1003 2.1 1.9 1.0 O1 A:PEP440 2.2 6.8 1.0 OD2 A:ASP246 2.5 11.5 1.0 O2' A:PEP440 2.6 8.6 1.0 C1 A:PEP440 2.7 8.5 1.0 CG A:ASP320 3.0 10.3 1.0 CD A:GLU295 3.2 7.2 1.0 CG A:ASP246 3.3 10.8 1.0 OD1 A:ASP246 3.3 10.6 1.0 CB A:ASP320 3.4 8.4 1.0 O A:HOH1001 3.7 2.1 1.0 OD2 A:ASP296 3.9 8.8 1.0 CD2 A:LEU343 3.9 3.4 1.0 OE1 A:GLU295 3.9 7.0 1.0 O A:HOH1002 3.9 16.1 1.0 NZ A:LYS396 4.0 7.0 1.0 NZ A:LYS345 4.0 3.8 1.0 CG A:GLU295 4.1 7.4 1.0 OD1 A:ASP320 4.1 11.8 1.0 C2 A:PEP440 4.2 8.1 1.0 MG A:MG439 4.3 17.9 1.0 CB A:ASP246 4.7 7.9 1.0 NE2 A:GLN167 4.7 10.2 1.0 CG A:ASP296 4.8 10.1 1.0 CE A:LYS345 4.9 8.2 1.0 CA A:ASP320 5.0 9.3 1.0

Magnesium binding site 2 out of 4 in the Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg439 b:17.9 occ:1.00 O A:SER39 2.1 20.5 1.0 O A:HOH1001 2.1 2.1 1.0 OG A:SER39 2.2 24.0 1.0 O1P A:PEP440 2.3 7.8 1.0 O A:HOH1002 2.3 16.1 1.0 O2' A:PEP440 2.6 8.6 1.0 C A:SER39 2.9 19.7 1.0 CB A:SER39 2.9 21.2 1.0 P A:PEP440 3.4 8.4 1.0 CA A:SER39 3.4 19.9 1.0 C1 A:PEP440 3.5 8.5 1.0 O2 A:PEP440 3.6 8.2 1.0 O2P A:PEP440 3.8 7.2 1.0 N A:SER39 3.9 19.0 1.0 N A:THR40 4.0 17.8 1.0 OD1 A:ASP321 4.0 8.9 1.0 C2 A:PEP440 4.1 8.1 1.0 NZ A:LYS345 4.1 3.8 1.0 OD2 A:ASP320 4.1 8.4 1.0 OD2 A:ASP321 4.1 10.1 1.0 MG A:MG438 4.3 11.4 1.0 NH2 A:ARG374 4.4 3.8 1.0 O A:HOH1003 4.5 1.9 1.0 O1 A:PEP440 4.5 6.8 1.0 CG A:ASP321 4.5 9.3 1.0 CA A:THR40 4.5 16.0 1.0 NE2 A:GLN167 4.6 10.2 1.0 O3P A:PEP440 4.6 6.7 1.0 OE1 A:GLN167 4.7 8.6 1.0 O A:HOH1547 5.0 23.3 1.0

Magnesium binding site 3 out of 4 in the Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg938 b:7.6 occ:1.00 OE2 B:GLU795 2.1 10.6 1.0 OD2 B:ASP820 2.1 5.1 1.0 O B:HOH1006 2.2 9.3 1.0 O1 B:PEP940 2.2 7.1 1.0 OD2 B:ASP746 2.2 8.6 1.0 O2' B:PEP940 2.4 10.6 1.0 C1 B:PEP940 2.6 8.0 1.0 CG B:ASP746 3.0 11.6 1.0 CG B:ASP820 3.2 7.6 1.0 OD1 B:ASP746 3.2 10.1 1.0 CD B:GLU795 3.2 9.9 1.0 CB B:ASP820 3.6 5.9 1.0 O B:HOH1004 3.7 2.8 1.0 NZ B:LYS896 3.8 6.8 1.0 OE1 B:GLU795 4.0 7.8 1.0 O B:HOH1005 4.0 12.8 1.0 OD2 B:ASP796 4.1 10.8 1.0 CD2 B:LEU843 4.1 6.5 1.0 C2 B:PEP940 4.1 7.9 1.0 NZ B:LYS845 4.1 6.0 1.0 MG B:MG939 4.2 21.1 1.0 CG B:GLU795 4.2 7.2 1.0 OD1 B:ASP820 4.2 6.8 1.0 CB B:ASP746 4.4 6.7 1.0 NE2 B:GLN667 4.7 8.5 1.0 CG B:ASP796 4.9 9.7 1.0 OE2 B:GLU668 4.9 6.8 1.0 O2 B:PEP940 5.0 8.4 1.0 CE B:LYS896 5.0 6.0 1.0 C3 B:PEP940 5.0 8.4 1.0

Magnesium binding site 4 out of 4 in the Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg939 b:21.1 occ:1.00 O B:HOH1004 2.1 2.8 1.0 O B:SER539 2.1 14.8 1.0 OG B:SER539 2.2 12.3 1.0 O B:HOH1005 2.2 12.8 1.0 O1P B:PEP940 2.3 8.7 1.0 O2' B:PEP940 2.3 10.6 1.0 CB B:SER539 3.0 13.9 1.0 C B:SER539 3.0 13.3 1.0 C1 B:PEP940 3.3 8.0 1.0 P B:PEP940 3.4 9.0 1.0 CA B:SER539 3.5 13.5 1.0 O2 B:PEP940 3.5 8.4 1.0 O2P B:PEP940 3.9 11.7 1.0 C2 B:PEP940 4.0 7.9 1.0 N B:SER539 4.0 13.2 1.0 OD2 B:ASP820 4.0 5.1 1.0 N B:THR540 4.1 13.1 1.0 OD2 B:ASP821 4.1 10.8 1.0 OD1 B:ASP821 4.2 8.8 1.0 NZ B:LYS845 4.2 6.0 1.0 MG B:MG938 4.2 7.6 1.0 O B:HOH1006 4.3 9.3 1.0 O1 B:PEP940 4.4 7.1 1.0 OE1 B:GLN667 4.4 10.0 1.0 NE2 B:GLN667 4.5 8.5 1.0 NH2 B:ARG874 4.5 6.8 1.0 CG B:ASP821 4.6 10.0 1.0 O3P B:PEP940 4.7 6.9 1.0 CA B:THR540 4.7 12.4 1.0 CD B:GLN667 4.9 9.2 1.0

P.A.Sims, T.M.Larsen, R.R.Poyner, W.W.Cleland, G.H.Reed. Reverse Protonation Is the Key to General Acid-Base Catalysis in Enolase Biochemistry V. 42 8298 2003.
ISSN: ISSN 0006-2960
PubMed: 12846578
DOI: 10.1021/BI0346345