Magnesium in PDB 3dg7: Crystal Structure of Muconate Lactonizing Enzyme From Mucobacterium Smegmatis Complexed with Muconolactone

The structure of Crystal Structure of Muconate Lactonizing Enzyme From Mucobacterium Smegmatis Complexed with Muconolactone, PDB code: 3dg7 was solved by A.A.Fedorov, E.V.Fedorov, A.Sakai, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.42 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.047, 124.265, 117.485, 90.00, 133.39, 90.00
R / Rfree (%)	18.8 / 20.3

The binding sites of Magnesium atom in the Crystal Structure of Muconate Lactonizing Enzyme From Mucobacterium Smegmatis Complexed with Muconolactone (pdb code 3dg7). 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 Muconate Lactonizing Enzyme From Mucobacterium Smegmatis Complexed with Muconolactone, PDB code: 3dg7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Muconate Lactonizing Enzyme From Mucobacterium Smegmatis Complexed with Muconolactone


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 Muconate Lactonizing Enzyme From Mucobacterium Smegmatis Complexed with Muconolactone within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:20.6 occ:1.00 OE2 A:GLU217 2.0 17.4 1.0 O A:HOH2003 2.0 13.9 1.0 OD2 A:ASP191 2.1 16.6 1.0 O1 A:MUC1001 2.1 26.8 1.0 OD2 A:ASP242 2.2 16.2 1.0 O2 A:MUC1001 2.3 21.8 1.0 C1 A:MUC1001 2.5 27.1 1.0 CD A:GLU217 3.0 17.3 1.0 CG A:ASP191 3.1 16.6 1.0 CG A:ASP242 3.3 13.7 1.0 NZ A:LYS160 3.5 26.1 1.0 OD1 A:ASP191 3.5 16.0 1.0 CB A:ASP242 3.6 12.7 1.0 CG A:GLU217 3.7 15.6 1.0 O A:HOH2072 3.7 17.6 1.0 OE1 A:GLU217 4.0 16.5 1.0 C2 A:MUC1001 4.0 27.9 1.0 NZ A:LYS266 4.0 13.9 1.0 OE2 A:GLU243 4.1 20.7 1.0 O A:HOH2176 4.2 31.6 1.0 ND2 A:ASN193 4.2 20.7 1.0 OD1 A:ASP242 4.4 15.6 1.0 CB A:ASP191 4.4 15.9 1.0 NZ A:LYS162 4.6 35.0 1.0 CE A:LYS160 4.6 25.8 1.0 CE A:LYS266 4.6 11.3 1.0 CB A:GLU217 4.9 16.3 1.0 O A:HOH2030 5.0 14.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Muconate Lactonizing Enzyme From Mucobacterium Smegmatis Complexed with Muconolactone


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 Muconate Lactonizing Enzyme From Mucobacterium Smegmatis Complexed with Muconolactone within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:20.4 occ:1.00 OE2 B:GLU217 2.0 18.1 1.0 OD2 B:ASP191 2.1 14.9 1.0 O1 B:MUC1002 2.1 24.2 1.0 O B:HOH2085 2.1 16.4 1.0 OD2 B:ASP242 2.2 15.6 1.0 O2 B:MUC1002 2.4 19.6 1.0 C1 B:MUC1002 2.5 24.2 1.0 CD B:GLU217 3.0 17.7 1.0 CG B:ASP191 3.1 16.0 1.0 CG B:ASP242 3.3 13.8 1.0 OD1 B:ASP191 3.5 15.1 1.0 NZ B:LYS160 3.5 26.3 1.0 CB B:ASP242 3.6 13.0 1.0 O B:HOH2074 3.7 16.9 1.0 CG B:GLU217 3.7 16.8 1.0 OE1 B:GLU217 4.0 16.8 1.0 NZ B:LYS266 4.0 14.9 1.0 C2 B:MUC1002 4.0 25.6 1.0 OE2 B:GLU243 4.1 20.9 1.0 ND2 B:ASN193 4.2 21.7 1.0 O B:HOH2191 4.2 28.9 1.0 OD1 B:ASP242 4.4 15.4 1.0 CB B:ASP191 4.4 14.7 1.0 NZ B:LYS162 4.5 34.2 1.0 CE B:LYS160 4.6 25.7 1.0 CE B:LYS266 4.6 12.1 1.0 CB B:GLU217 4.9 16.0 1.0 O B:HOH2023 5.0 17.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Muconate Lactonizing Enzyme From Mucobacterium Smegmatis Complexed with Muconolactone


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 Muconate Lactonizing Enzyme From Mucobacterium Smegmatis Complexed with Muconolactone within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2003 b:20.3 occ:1.00 OE2 C:GLU217 2.0 18.0 1.0 O1 C:MUC1003 2.1 24.4 1.0 OD2 C:ASP191 2.1 16.0 1.0 O C:HOH2008 2.1 13.2 1.0 OD2 C:ASP242 2.2 16.4 1.0 O2 C:MUC1003 2.4 19.4 1.0 C1 C:MUC1003 2.5 24.2 1.0 CD C:GLU217 3.0 16.9 1.0 CG C:ASP191 3.1 15.6 1.0 CG C:ASP242 3.3 14.3 1.0 OD1 C:ASP191 3.5 15.6 1.0 NZ C:LYS160 3.5 26.8 1.0 O C:HOH2114 3.6 16.7 1.0 CB C:ASP242 3.6 13.5 1.0 CG C:GLU217 3.7 16.1 1.0 OE1 C:GLU217 4.0 17.5 1.0 NZ C:LYS266 4.0 15.9 1.0 C2 C:MUC1003 4.0 26.2 1.0 OE2 C:GLU243 4.1 20.6 1.0 O C:HOH2167 4.1 25.6 1.0 ND2 C:ASN193 4.2 22.5 1.0 OD1 C:ASP242 4.4 15.3 1.0 CB C:ASP191 4.4 14.9 1.0 NZ C:LYS162 4.5 35.1 1.0 CE C:LYS160 4.6 26.2 1.0 CE C:LYS266 4.6 13.3 1.0 CB C:GLU217 4.9 16.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Muconate Lactonizing Enzyme From Mucobacterium Smegmatis Complexed with Muconolactone


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 Muconate Lactonizing Enzyme From Mucobacterium Smegmatis Complexed with Muconolactone within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2004 b:19.6 occ:1.00 OE2 D:GLU217 2.0 16.4 1.0 O D:HOH2013 2.0 14.1 1.0 OD2 D:ASP191 2.1 15.8 1.0 O1 D:MUC1004 2.1 25.4 1.0 OD2 D:ASP242 2.2 16.5 1.0 O2 D:MUC1004 2.4 20.3 1.0 C1 D:MUC1004 2.5 25.7 1.0 CD D:GLU217 3.0 16.2 1.0 CG D:ASP191 3.1 16.4 1.0 CG D:ASP242 3.3 13.5 1.0 NZ D:LYS160 3.5 25.4 1.0 OD1 D:ASP191 3.5 15.6 1.0 CB D:ASP242 3.6 14.2 1.0 O D:HOH2073 3.7 17.2 1.0 CG D:GLU217 3.7 15.1 1.0 OE1 D:GLU217 4.0 16.8 1.0 NZ D:LYS266 4.0 16.5 1.0 OE2 D:GLU243 4.1 21.7 1.0 C2 D:MUC1004 4.1 26.8 1.0 ND2 D:ASN193 4.2 22.3 1.0 O D:HOH2162 4.3 28.2 1.0 OD1 D:ASP242 4.4 15.7 1.0 CB D:ASP191 4.4 15.7 1.0 NZ D:LYS162 4.6 34.4 1.0 CE D:LYS160 4.6 25.4 1.0 CE D:LYS266 4.6 14.4 1.0 CB D:GLU217 4.9 15.9 1.0

A.Sakai, A.A.Fedorov, E.V.Fedorov, A.M.Schnoes, M.E.Glasner, S.Brown, M.E.Rutter, K.Bain, S.Chang, T.Gheyi, J.M.Sauder, S.K.Burley, P.C.Babbitt, S.C.Almo, J.A.Gerlt. Evolution of Enzymatic Activities in the Enolase Superfamily: Stereochemically Distinct Mechanisms in Two Families of Cis,Cis-Muconate Lactonizing Enzymes Biochemistry V. 48 1445 2009.
ISSN: ISSN 0006-2960
PubMed: 19220063
DOI: 10.1021/BI802277H