Magnesium in PDB 2pmq: Crystal Structure of A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601

The structure of Crystal Structure of A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601, PDB code: 2pmq was solved by J.B.Bonanno, M.Rutter, K.T.Bain, C.Lau, V.Sridhar, D.Smith, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.72
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	136.381, 136.381, 80.925, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.1

The binding sites of Magnesium atom in the Crystal Structure of A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601 (pdb code 2pmq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601, PDB code: 2pmq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601


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 A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:31.9 occ:1.00 O A:HOH1056 2.1 27.1 1.0 O A:HOH1250 2.2 38.8 1.0 O A:HOH1258 2.2 42.7 1.0 OE2 A:GLU79 4.2 33.2 1.0 OE1 A:GLU79 4.6 28.4 1.0 CD A:GLU79 4.7 27.0 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601


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 A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:18.1 occ:1.00 O A:HOH913 2.0 15.6 1.0 OE2 A:GLU218 2.0 20.3 1.0 OD1 A:ASP241 2.1 17.2 1.0 O A:HOH1239 2.1 35.5 1.0 OD2 A:ASP193 2.1 17.4 1.0 O A:HOH965 2.1 20.1 1.0 CD A:GLU218 3.1 21.0 1.0 CG A:ASP193 3.1 15.9 1.0 CG A:ASP241 3.2 16.6 1.0 OD1 A:ASP193 3.5 16.2 1.0 CB A:ASP241 3.6 14.4 1.0 ND2 A:ASN195 3.7 23.6 1.0 NE2 A:GLN161 3.7 23.2 1.0 CG A:GLU218 3.8 18.7 1.0 OH A:TYR56 3.9 17.3 0.5 O A:HOH1080 3.9 28.3 1.0 OE1 A:GLU218 3.9 25.2 1.0 NZ A:LYS163 4.0 27.2 1.0 OE1 A:GLU242 4.1 18.4 1.0 OD2 A:ASP241 4.2 17.3 1.0 O A:HOH997 4.4 25.1 1.0 CB A:ASP193 4.4 15.6 1.0 NZ A:LYS265 4.4 22.5 1.0 OH A:TYR56 4.4 20.6 0.5 CG A:ASN195 4.6 21.4 1.0 O A:HOH1024 4.6 24.3 1.0 OE2 A:GLU242 4.6 20.5 1.0 CD A:GLU242 4.7 19.3 1.0 CD A:GLN161 4.7 22.0 1.0 OD1 A:ASN195 4.8 24.7 1.0 CB A:GLU218 4.9 17.1 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601


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 A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:12.0 occ:0.25 O A:HOH1118 2.1 16.6 0.2 O A:HOH945 2.1 18.1 0.2 NE2 A:HIS235 2.3 18.1 1.0 CE1 A:HIS235 3.2 17.6 1.0 CD2 A:HIS235 3.3 18.5 1.0 ND1 A:HIS235 4.3 17.1 1.0 O A:HOH1112 4.4 36.4 1.0 CG A:HIS235 4.4 16.4 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601


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 A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg904 b:19.9 occ:1.00 OE2 B:GLU218 2.0 19.3 1.0 O B:HOH921 2.0 19.7 1.0 O B:HOH933 2.0 19.6 1.0 O B:HOH1005 2.1 35.4 1.0 OD2 B:ASP241 2.1 20.8 1.0 OD2 B:ASP193 2.1 20.4 1.0 CD B:GLU218 3.0 21.9 1.0 CG B:ASP193 3.1 18.4 1.0 CG B:ASP241 3.2 18.4 1.0 OD1 B:ASP193 3.4 18.0 1.0 CB B:ASP241 3.7 16.5 1.0 NE2 B:GLN161 3.8 21.8 1.0 CG B:GLU218 3.8 18.5 1.0 OE1 B:GLU218 3.9 25.5 1.0 O B:HOH1053 4.0 29.4 1.0 O B:HOH1065 4.0 38.3 1.0 OE1 B:GLU242 4.1 20.6 1.0 OD1 B:ASP241 4.2 18.1 1.0 OE2 B:GLU242 4.4 26.0 1.0 CB B:ASP193 4.4 18.6 1.0 OH B:TYR56 4.5 32.9 1.0 CD B:GLU242 4.6 20.5 1.0 O B:HOH994 4.6 27.1 1.0 CD B:GLN161 4.6 22.1 1.0 NZ B:LYS265 4.7 25.4 1.0 ND2 B:ASN195 4.8 26.9 1.0 OE1 B:GLN161 4.9 27.1 1.0 CB B:GLU218 4.9 16.3 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Mandelate Racemase/Muconate Lactonizing Enzyme From Roseovarius Sp. HTCC2601 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg905 b:14.7 occ:0.25 O B:HOH1134 2.2 20.8 0.2 O B:HOH963 2.2 16.5 0.2 NE2 B:HIS235 2.3 18.4 1.0 CE1 B:HIS235 3.2 18.7 1.0 CD2 B:HIS235 3.3 18.9 1.0 ND1 B:HIS235 4.4 17.4 1.0 O B:HOH1133 4.4 31.2 1.0 CG B:HIS235 4.5 17.5 1.0

S.Zhao, R.Kumar, A.Sakai, M.W.Vetting, B.M.Wood, S.Brown, J.B.Bonanno, B.S.Hillerich, R.D.Seidel, P.C.Babbitt, S.C.Almo, J.V.Sweedler, J.A.Gerlt, J.E.Cronan, M.P.Jacobson. Discovery of New Enzymes and Metabolic Pathways By Using Structure and Genome Context. Nature V. 502 698 2013.
ISSN: ISSN 0028-0836
PubMed: 24056934
DOI: 10.1038/NATURE12576