Magnesium in PDB 1p43: 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: 1p43 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 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.300, 115.100, 72.400, 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 1p43). 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: 1p43:
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:13.1 occ:1.00 OE2 A:GLU295 2.0 9.7 1.0 O A:HOH1002 2.1 10.9 1.0 OD2 A:ASP320 2.1 10.5 1.0 O1 A:2PG441 2.3 16.5 1.0 OD2 A:ASP246 2.4 14.3 1.0 O2 A:2PG441 2.5 18.9 1.0 C1 A:2PG441 2.7 16.9 1.0 CG A:ASP320 3.1 11.0 1.0 CG A:ASP246 3.2 13.7 1.0 CD A:GLU295 3.2 8.4 1.0 OD1 A:ASP246 3.3 13.6 1.0 CB A:ASP320 3.6 10.3 1.0 NZ A:LYS396 3.8 12.9 1.0 O A:HOH1001 3.8 6.5 1.0 OE1 A:GLU295 3.9 8.9 1.0 OD2 A:ASP296 4.1 14.2 1.0 CD2 A:LEU343 4.1 8.3 1.0 CG A:GLU295 4.1 9.6 1.0 NZ A:LYS345 4.2 11.6 1.0 OD1 A:ASP320 4.2 12.1 1.0 C2 A:2PG441 4.3 17.2 1.0 CB A:ASP246 4.6 11.3 1.0 CG A:ASP296 4.9 12.8 1.0 O1P A:2PG441 4.9 15.2 1.0 O A:HOH1004 4.9 32.9 1.0 CE A:LYS345 5.0 12.6 1.0 OE1 A:GLN168 5.0 17.9 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:28.0 occ:1.00 O A:HOH1867 2.2 33.1 1.0 O A:SER39 2.4 26.9 1.0 O A:HOH1001 2.5 6.5 1.0 O3P A:2PG441 2.6 12.1 1.0 O A:HOH1003 3.1 26.7 1.0 O A:HOH1004 3.3 32.9 1.0 C A:SER39 3.4 26.0 1.0 OD1 A:ASP321 3.5 17.6 1.0 P A:2PG441 3.8 10.4 1.0 O4P A:2PG441 3.9 13.4 1.0 O1 A:2PG441 3.9 16.5 1.0 OD2 A:ASP321 3.9 18.6 1.0 NZ A:LYS345 4.1 11.6 1.0 CG A:ASP321 4.1 16.2 1.0 N A:THR40 4.2 24.4 1.0 CA A:SER39 4.2 25.9 1.0 CB A:SER39 4.3 27.2 1.0 CA A:THR40 4.3 24.1 1.0 N A:SER39 4.4 24.4 1.0 O1P A:2PG441 4.4 15.2 1.0 OD2 A:ASP320 4.4 10.5 1.0 NH2 A:ARG374 4.5 12.0 1.0 C1 A:2PG441 4.7 16.9 1.0 OG A:SER39 4.7 30.2 1.0 N A:GLY41 4.8 23.2 1.0 C A:THR40 4.8 23.6 1.0 OE2 A:GLU44 4.8 19.0 1.0 O A:HOH1002 5.0 10.9 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:7.5 occ:1.00 OE2 B:GLU795 2.0 9.0 1.0 OD2 B:ASP820 2.1 8.7 1.0 O B:HOH1007 2.2 8.8 1.0 OD2 B:ASP746 2.2 9.9 1.0 O1 B:2PG941 2.3 14.0 1.0 O2 B:2PG941 2.3 17.6 1.0 C1 B:2PG941 2.6 12.8 1.0 CG B:ASP746 3.0 11.1 1.0 CD B:GLU795 3.1 7.9 1.0 CG B:ASP820 3.2 8.4 1.0 OD1 B:ASP746 3.3 9.9 1.0 CB B:ASP820 3.7 7.8 1.0 O B:HOH1005 3.7 1.0 1.0 OE1 B:GLU795 3.9 8.6 1.0 NZ B:LYS896 3.9 8.5 1.0 OD2 B:ASP796 4.0 9.8 1.0 CD2 B:LEU843 4.1 8.3 1.0 NZ B:LYS845 4.1 9.5 1.0 CG B:GLU795 4.1 7.2 1.0 C2 B:2PG941 4.2 15.3 1.0 OD1 B:ASP820 4.3 8.7 1.0 CB B:ASP746 4.4 10.1 1.0 CG B:ASP796 4.8 6.8 1.0 O1P B:2PG941 4.9 12.6 1.0 O3 B:2PG941 5.0 25.1 1.0 O B:HOH1516 5.0 35.5 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:27.1 occ:1.00 O B:HOH1006 2.3 32.1 1.0 O B:HOH1005 2.4 1.0 1.0 O B:SER539 2.5 23.4 1.0 O3P B:2PG941 2.6 9.9 1.0 O B:HOH1516 3.1 35.5 1.0 O B:HOH1515 3.2 27.2 1.0 C B:SER539 3.3 21.4 1.0 P B:2PG941 3.7 8.5 1.0 OD1 B:ASP821 3.7 13.5 1.0 O1 B:2PG941 3.8 14.0 1.0 O4P B:2PG941 3.8 8.8 1.0 N B:THR540 4.0 18.7 1.0 CA B:THR540 4.1 15.8 1.0 OD2 B:ASP821 4.2 14.2 1.0 CA B:SER539 4.2 22.1 1.0 N B:SER539 4.3 21.4 1.0 O1P B:2PG941 4.3 12.6 1.0 CB B:SER539 4.3 23.1 1.0 O B:HOH1782 4.3 34.1 1.0 NH2 B:ARG874 4.3 9.4 1.0 CG B:ASP821 4.4 13.5 1.0 NZ B:LYS845 4.4 9.5 1.0 C B:THR540 4.6 16.1 1.0 C1 B:2PG941 4.6 12.8 1.0 N B:GLY541 4.6 14.9 1.0 OD2 B:ASP820 4.7 8.7 1.0 O B:HOH1797 4.7 44.9 1.0 OE2 B:GLU544 4.9 9.8 1.0 C2 B:2PG941 4.9 15.3 1.0 OG B:SER539 5.0 26.0 1.0 O2P B:2PG941 5.0 7.1 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