Magnesium in PDB 1sjc: X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine

The structure of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine, PDB code: 1sjc was solved by J.B.Thoden, E.A.Taylor-Ringia, J.B.Garrett, J.A.Gerlt, H.M.Holden, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	215.700, 215.700, 259.000, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine (pdb code 1sjc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine, PDB code: 1sjc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:47.8 occ:1.00 O12 A:SMG1000 2.1 70.1 1.0 OD2 A:ASP189 2.1 33.5 1.0 O A:HOH1186 2.3 39.8 1.0 OE2 A:GLU214 2.4 45.7 1.0 OD2 A:ASP239 2.4 39.1 1.0 C2 A:SMG1000 2.7 39.4 1.0 O11 A:SMG1000 2.7 73.8 1.0 CD A:GLU214 2.9 35.6 1.0 CG A:ASP189 3.0 40.0 1.0 OD1 A:ASP189 3.3 39.5 1.0 OE1 A:GLU214 3.4 77.7 1.0 NZ A:LYS161 3.5 33.9 1.0 CG A:ASP239 3.6 27.5 1.0 CG A:GLU214 3.7 40.5 1.0 ND2 A:ASN191 3.8 40.2 1.0 CB A:ASP239 3.9 33.5 1.0 NZ A:LYS163 4.0 47.2 1.0 C1 A:SMG1000 4.0 0.0 1.0 NZ A:LYS263 4.1 62.1 1.0 ND2 A:ASN261 4.2 35.5 1.0 CB A:ASP189 4.2 26.2 1.0 CG A:ASN191 4.4 51.1 1.0 OD1 A:ASN191 4.4 45.9 1.0 OE1 A:GLU240 4.4 44.0 1.0 CE A:LYS263 4.4 40.6 1.0 CE A:LYS161 4.5 28.5 1.0 O A:HOH1008 4.6 28.2 1.0 OD1 A:ASP239 4.6 41.2 1.0 CB A:GLU214 4.7 31.0 1.0 CB A:SMG1000 4.9 57.1 1.0 N1 A:SMG1000 4.9 57.4 1.0

Magnesium binding site 2 out of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1101 b:33.2 occ:1.00 OE2 B:GLU214 2.2 36.5 1.0 O12 B:SMG1100 2.2 50.9 1.0 O11 B:SMG1100 2.3 51.5 1.0 OD2 B:ASP239 2.4 30.1 1.0 O B:HOH1113 2.4 30.8 1.0 OD2 B:ASP189 2.6 36.7 1.0 C2 B:SMG1100 2.6 32.7 1.0 CD B:GLU214 3.0 30.9 1.0 CG B:ASP189 3.3 28.5 1.0 OD1 B:ASP189 3.4 42.2 1.0 CG B:ASP239 3.5 34.5 1.0 ND2 B:ASN191 3.6 46.5 1.0 CB B:ASP239 3.7 29.9 1.0 OE1 B:GLU214 3.7 33.5 1.0 CG B:GLU214 3.7 29.5 1.0 NZ B:LYS161 3.8 26.3 1.0 NZ B:LYS263 3.8 51.5 1.0 NZ B:LYS163 3.9 49.8 1.0 C1 B:SMG1100 4.1 31.2 1.0 OE1 B:GLU240 4.2 30.7 1.0 O B:HOH1176 4.3 49.6 1.0 ND2 B:ASN261 4.4 35.4 1.0 CG B:ASN191 4.4 33.0 1.0 OD1 B:ASP239 4.6 37.4 1.0 CB B:ASP189 4.6 29.8 1.0 OD1 B:ASN191 4.7 28.9 1.0 CE B:LYS263 4.8 28.0 1.0 CE2 B:TYR55 4.8 29.3 1.0 CB B:SMG1100 4.9 45.2 1.0 CE B:LYS161 4.9 28.6 1.0 N1 B:SMG1100 4.9 43.0 1.0 CB B:GLU214 4.9 28.7 1.0 CD B:GLU240 5.0 35.3 1.0

Magnesium binding site 3 out of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1201 b:47.6 occ:1.00 OD2 C:ASP239 2.1 51.4 1.0 O C:HOH1386 2.1 36.0 1.0 OD2 C:ASP189 2.2 33.6 1.0 OE2 C:GLU214 2.4 41.7 1.0 O11 C:SMG1200 2.6 38.7 1.0 O12 C:SMG1200 2.7 34.8 1.0 CG C:ASP189 3.0 35.0 1.0 C2 C:SMG1200 3.0 0.0 1.0 OD1 C:ASP189 3.1 41.6 1.0 CD C:GLU214 3.2 21.3 1.0 CG C:ASP239 3.2 70.0 1.0 CB C:ASP239 3.7 36.0 1.0 NZ C:LYS161 3.8 39.1 1.0 OE1 C:GLU214 3.8 58.6 1.0 NZ C:LYS263 3.9 50.2 1.0 ND2 C:ASN191 3.9 43.7 1.0 CG C:GLU214 4.0 32.5 1.0 OE1 C:GLU240 4.1 38.9 1.0 OD1 C:ASP239 4.3 34.3 1.0 OD1 C:ASN191 4.3 34.6 1.0 CB C:ASP189 4.4 29.2 1.0 CG C:ASN191 4.4 40.2 1.0 NZ C:LYS163 4.5 51.8 1.0 C1 C:SMG1200 4.5 37.6 1.0 CE C:LYS263 4.6 40.0 1.0 ND2 C:ASN261 4.7 32.1 1.0 CB C:GLU214 4.7 46.9 1.0 O C:HOH1280 4.7 47.0 1.0 OE2 C:GLU240 4.8 37.6 1.0 CD C:GLU240 4.8 33.1 1.0 CE C:LYS161 4.8 22.2 1.0 CE1 C:TYR55 4.9 50.1 1.0

Magnesium binding site 4 out of 4 in the X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of O-Succinylbenzoate Synthase Complexed with N-Succinyl Methionine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1301 b:66.7 occ:1.00 O12 D:SMG1300 1.9 78.8 1.0 OE2 D:GLU214 2.1 43.3 1.0 OD2 D:ASP239 2.3 38.1 1.0 O D:HOH1437 2.4 47.6 1.0 OD2 D:ASP189 2.4 62.0 1.0 C2 D:SMG1300 2.7 59.0 1.0 O11 D:SMG1300 2.7 0.0 1.0 CD D:GLU214 2.8 67.2 1.0 CG D:ASP189 3.3 49.1 1.0 NZ D:LYS161 3.4 39.6 1.0 OE1 D:GLU214 3.5 35.5 1.0 OD1 D:ASP189 3.5 45.9 1.0 CG D:ASP239 3.5 62.2 1.0 CG D:GLU214 3.6 37.5 1.0 ND2 D:ASN191 3.7 42.0 1.0 NZ D:LYS263 3.7 42.6 1.0 CB D:ASP239 3.8 49.9 1.0 C1 D:SMG1300 4.1 90.5 1.0 O D:HOH1421 4.1 49.4 1.0 OE1 D:GLU240 4.2 55.4 1.0 CE D:LYS161 4.3 60.9 1.0 ND2 D:ASN261 4.3 27.1 1.0 CG D:ASN191 4.4 59.6 1.0 OD1 D:ASP239 4.5 37.6 1.0 OD1 D:ASN191 4.5 46.1 1.0 NZ D:LYS163 4.6 42.0 1.0 CB D:ASP189 4.6 33.0 1.0 CE D:LYS263 4.6 41.1 1.0 CB D:GLU214 4.7 29.8 1.0 CE2 D:TYR55 4.9 67.9 1.0 CB D:SMG1300 4.9 55.5 1.0 N1 D:SMG1300 4.9 51.5 1.0

J.B.Thoden, E.A.Taylor-Ringia, J.B.Garrett, J.A.Gerlt, H.M.Holden, I.Rayment. Evolution of Enzymatic Activity in the Enolase Superfamily: Structural Studies of the Promiscuous O-Succinylbenzoate Synthase From Amycolatopsis Biochemistry V. 43 5716 2004.
ISSN: ISSN 0006-2960
PubMed: 15134446
DOI: 10.1021/BI0497897