Magnesium in PDB 6ojr: Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda

All present enzymatic activity of Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda:
1.13.11.43;

The structure of Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda, PDB code: 6ojr was solved by E.Kuatsjah, M.M.Verstraete, M.J.Kobylarz, A.K.N.Liu, M.E.P.Murphy, L.D.Eltis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.27 / 2.30
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	181.364, 181.364, 94.983, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 20.5

The binding sites of Magnesium atom in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda (pdb code 6ojr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda, PDB code: 6ojr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda


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 Sphingomonas Paucimobilis TMY1009 Apo-Lsda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:43.6 occ:1.00 OD2 A:ASP372 2.3 44.4 1.0 OG1 A:THR390 2.7 30.7 1.0 HE3 A:LYS375 2.8 53.7 1.0 HH22 A:ARG347 2.8 53.4 1.0 HB2 A:TRP405 2.9 35.8 1.0 HB2 A:ASP372 3.0 54.0 1.0 HB3 A:ASP372 3.1 54.0 1.0 CG A:ASP372 3.1 49.0 1.0 HG21 A:THR390 3.2 39.5 1.0 CB A:ASP372 3.3 45.0 1.0 HG1 A:THR390 3.3 36.8 1.0 HG3 A:LYS375 3.3 57.6 1.0 HE2 A:LYS375 3.4 53.7 1.0 NH2 A:ARG347 3.5 44.5 1.0 CE A:LYS375 3.5 44.7 1.0 HH21 A:ARG347 3.5 53.4 1.0 HG23 A:THR390 3.6 39.5 1.0 CG2 A:THR390 3.7 32.9 1.0 CB A:THR390 3.8 33.6 1.0 CB A:TRP405 3.8 29.9 1.0 HG2 A:LYS375 3.8 57.6 1.0 HD1 A:TRP405 3.9 41.4 1.0 CG A:LYS375 3.9 48.0 1.0 HA A:TRP405 4.1 38.3 1.0 CG A:TRP405 4.2 35.3 1.0 CD1 A:TRP405 4.2 34.5 1.0 HB A:THR390 4.2 40.3 1.0 CD A:LYS375 4.3 42.9 1.0 OD1 A:ASP372 4.3 49.4 1.0 HG A:SER403 4.4 39.9 1.0 CA A:TRP405 4.5 31.9 1.0 HB3 A:TRP405 4.5 35.8 1.0 HZ1 A:LYS375 4.5 74.5 1.0 HG22 A:THR390 4.6 39.5 1.0 NZ A:LYS375 4.6 62.1 1.0 HH12 A:ARG347 4.7 50.1 1.0 CZ A:ARG347 4.7 43.9 1.0 HD2 A:LYS375 4.7 51.5 1.0 OD1 A:ASN389 4.7 31.8 1.0 CA A:ASP372 4.8 45.4 1.0 N A:TRP405 4.8 31.2 1.0 HA A:THR390 4.9 39.4 1.0 OG A:SER403 4.9 33.2 1.0 CA A:THR390 5.0 32.8 1.0 HZ2 A:LYS375 5.0 74.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda


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 Sphingomonas Paucimobilis TMY1009 Apo-Lsda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:36.6 occ:1.00 H A:ILE354 2.3 30.2 1.0 OE2 A:GLU356 2.4 45.4 1.0 HD2 A:ARG353 2.5 31.8 1.0 O A:HOH750 2.6 34.0 1.0 HA A:ARG353 2.7 30.2 1.0 HH11 A:ARG353 2.7 39.3 1.0 HG12 A:ILE354 2.8 36.1 1.0 N A:ILE354 3.1 25.2 1.0 CD A:ARG353 3.4 26.5 1.0 HB3 A:ARG353 3.4 29.7 1.0 CD A:GLU356 3.4 46.3 1.0 CA A:ARG353 3.4 25.1 1.0 HG13 A:ILE354 3.5 36.1 1.0 HD3 A:ARG353 3.5 31.8 1.0 NH1 A:ARG353 3.5 32.8 1.0 O A:HOH870 3.6 38.2 1.0 CG1 A:ILE354 3.6 30.1 1.0 HG3 A:GLU356 3.6 52.7 1.0 C A:ARG353 3.7 28.9 1.0 O A:HOH741 3.7 29.7 1.0 O A:ILE354 3.8 29.7 1.0 CB A:ARG353 3.8 24.8 1.0 HH12 A:ARG353 4.0 39.3 1.0 CA A:ILE354 4.1 31.4 1.0 CG A:GLU356 4.1 43.9 1.0 O A:HOH858 4.2 38.6 1.0 CG A:ARG353 4.2 27.0 1.0 HG23 A:ILE354 4.3 34.6 1.0 C A:ILE354 4.3 30.9 1.0 NE A:ARG353 4.3 39.6 1.0 OE1 A:GLU356 4.3 61.6 1.0 CB A:ILE354 4.4 30.2 1.0 CZ A:ARG353 4.4 30.6 1.0 O A:PRO352 4.5 30.9 1.0 HD11 A:ILE354 4.6 38.6 1.0 N A:ARG353 4.6 27.4 1.0 HG2 A:GLU356 4.7 52.7 1.0 CD1 A:ILE354 4.7 32.2 1.0 O A:HOH846 4.7 44.0 1.0 HB2 A:ARG353 4.7 29.7 1.0 HG2 A:ARG353 4.8 32.4 1.0 O A:MET284 4.8 25.4 1.0 CG2 A:ILE354 4.9 28.8 1.0 HA A:ILE354 4.9 37.7 1.0 HG3 A:ARG353 4.9 32.4 1.0 O A:ARG353 4.9 24.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda


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 Sphingomonas Paucimobilis TMY1009 Apo-Lsda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:46.0 occ:1.00 HE22 A:GLN469 1.6 44.9 1.0 NE2 A:GLN469 2.4 37.5 1.0 HE21 A:GLN469 2.7 44.9 1.0 O A:ILE412 2.8 27.1 1.0 HG1 A:THR388 2.9 46.9 1.0 HB1 A:ALA411 3.0 41.0 1.0 OG1 A:THR388 3.1 39.1 1.0 O A:HOH735 3.2 45.0 1.0 HG2 A:GLN413 3.3 36.6 1.0 CD A:GLN469 3.5 37.7 1.0 C A:ILE412 3.5 27.9 1.0 HB3 A:ALA411 3.5 41.0 1.0 H A:ILE412 3.5 34.4 1.0 HA A:GLN413 3.6 35.8 1.0 CB A:ALA411 3.7 34.1 1.0 O A:HOH616 3.7 33.9 1.0 OE1 A:GLN469 3.8 40.2 1.0 N A:ILE412 3.8 28.7 1.0 CG A:GLN413 4.1 30.5 1.0 N A:GLN413 4.1 25.1 1.0 HG3 A:GLN413 4.1 36.6 1.0 H A:THR388 4.2 42.2 1.0 CA A:GLN413 4.3 29.8 1.0 CA A:ILE412 4.3 29.2 1.0 HB2 A:ALA411 4.3 41.0 1.0 C A:ALA411 4.4 28.4 1.0 O A:THR388 4.4 35.1 1.0 CB A:THR388 4.5 35.7 1.0 CA A:ALA411 4.7 31.9 1.0 HA A:ILE412 4.8 35.0 1.0 H A:GLN413 4.8 30.1 1.0 HD13 A:LEU369 4.8 31.2 1.0 CG A:GLN469 4.8 39.2 1.0 HB2 A:GLN469 4.8 35.1 1.0 CB A:GLN413 4.8 27.9 1.0 OD2 A:ASP436 4.9 27.7 1.0 HG2 A:GLN469 4.9 47.0 1.0 HB A:THR388 5.0 42.8 1.0 N A:THR388 5.0 35.1 1.0 HE1 A:HIS438 5.0 56.4 1.0 HA A:GLN469 5.0 33.1 1.0

E.Kuatsjah, M.M.Verstraete, M.J.Kobylarz, A.K.N.Liu, M.E.P.Murphy, L.D.Eltis. Identification of Functionally Important Residues and Structural Features in A Bacterial Lignostilbene Dioxygenase. J.Biol.Chem. V. 294 12911 2019.
ISSN: ESSN 1083-351X
PubMed: 31292192
DOI: 10.1074/JBC.RA119.009428