Manganese in PDB 3b59: Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans

The structure of Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans, PDB code: 3b59 was solved by M.Madegowda, S.Eswaramoorthy, S.K.Burley, S.Swaminathan, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.57 / 2.53
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	144.997, 168.348, 202.790, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25.7

The binding sites of Manganese atom in the Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans (pdb code 3b59). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans, PDB code: 3b59:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:27.4 occ:1.00 OE1 A:GLU249 2.0 19.3 1.0 O A:HOH659 2.0 15.3 1.0 O A:HOH658 2.2 22.5 1.0 NE2 A:HIS198 2.2 17.2 1.0 NE2 A:HIS144 2.3 13.6 1.0 OH A:TYR239 2.8 12.3 1.0 CE1 A:HIS198 3.0 16.2 1.0 CD A:GLU249 3.0 19.4 1.0 CE1 A:HIS144 3.2 13.9 1.0 CD2 A:HIS198 3.3 13.4 1.0 CD2 A:HIS144 3.3 15.0 1.0 OE2 A:GLU249 3.5 20.4 1.0 CE2 A:TYR239 3.5 14.2 1.0 CZ A:TYR239 3.6 14.0 1.0 ND1 A:HIS198 4.1 18.6 1.0 CB A:ALA200 4.2 18.4 1.0 CG A:HIS198 4.3 17.2 1.0 CG2 A:VAL146 4.3 14.2 1.0 CG A:GLU249 4.3 17.7 1.0 ND1 A:HIS144 4.4 14.3 1.0 CG A:HIS144 4.4 15.9 1.0 CB A:GLU249 4.7 17.1 1.0 CD2 A:TYR239 4.8 14.6 1.0 CE1 A:TYR239 4.8 16.1 1.0 NE2 A:HIS230 4.9 17.5 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:21.3 occ:1.00 NE2 B:HIS198 2.0 24.6 1.0 O B:HOH643 2.1 26.4 1.0 OE1 B:GLU249 2.2 29.2 1.0 NE2 B:HIS144 2.3 22.4 1.0 O B:HOH644 2.5 28.0 1.0 OH B:TYR239 2.7 20.3 1.0 CE1 B:HIS198 2.9 22.3 1.0 CD2 B:HIS198 3.1 21.5 1.0 CD2 B:HIS144 3.2 20.2 1.0 CD B:GLU249 3.2 26.5 1.0 CE1 B:HIS144 3.4 20.2 1.0 OE2 B:GLU249 3.6 26.6 1.0 CZ B:TYR239 3.6 17.1 1.0 CE2 B:TYR239 3.8 16.1 1.0 ND1 B:HIS198 4.0 20.9 1.0 CG B:HIS198 4.1 21.7 1.0 CB B:ALA200 4.2 19.0 1.0 CG B:HIS144 4.4 22.1 1.0 CG2 B:VAL146 4.4 21.6 1.0 ND1 B:HIS144 4.4 21.5 1.0 CG B:GLU249 4.5 23.8 1.0 NE2 B:HIS230 4.7 21.7 1.0 CE1 B:TYR239 4.8 18.8 1.0 CB B:GLU249 4.8 20.4 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn603 b:25.3 occ:1.00 OE1 C:GLU249 1.9 21.0 1.0 O C:HOH641 2.0 17.0 1.0 O C:HOH642 2.0 32.3 1.0 NE2 C:HIS144 2.2 15.9 1.0 NE2 C:HIS198 2.4 21.6 1.0 OH C:TYR239 2.6 16.0 1.0 CD C:GLU249 2.9 20.3 1.0 OE2 C:GLU249 3.1 18.7 1.0 CD2 C:HIS144 3.2 17.4 1.0 CE1 C:HIS144 3.2 16.3 1.0 CD2 C:HIS198 3.3 20.4 1.0 CE1 C:HIS198 3.3 20.4 1.0 CZ C:TYR239 3.5 18.0 1.0 CE2 C:TYR239 3.7 17.5 1.0 CB C:ALA200 4.2 15.5 1.0 CG C:GLU249 4.3 20.1 1.0 ND1 C:HIS144 4.3 16.0 1.0 CG C:HIS144 4.4 18.1 1.0 CG C:HIS198 4.4 21.5 1.0 ND1 C:HIS198 4.4 22.4 1.0 NE2 C:HIS230 4.5 23.1 1.0 CG2 C:VAL146 4.6 12.9 1.0 CB C:GLU249 4.7 20.3 1.0 CE1 C:TYR239 4.7 17.9 1.0 CD2 C:HIS230 4.8 22.6 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn604 b:21.6 occ:1.00 OE1 D:GLU249 1.9 27.6 1.0 NE2 D:HIS144 2.2 17.8 1.0 O D:HOH645 2.3 31.3 1.0 NE2 D:HIS198 2.4 24.9 1.0 O D:HOH644 2.4 20.0 1.0 OH D:TYR239 2.7 18.6 1.0 CD D:GLU249 2.8 25.2 1.0 OE2 D:GLU249 3.1 26.3 1.0 CD2 D:HIS144 3.2 17.2 1.0 CE1 D:HIS144 3.2 17.5 1.0 CE1 D:HIS198 3.3 23.8 1.0 CD2 D:HIS198 3.3 24.4 1.0 CZ D:TYR239 3.6 14.9 1.0 CE2 D:TYR239 3.9 14.7 1.0 CB D:ALA200 4.2 16.6 1.0 CG D:GLU249 4.2 25.2 1.0 ND1 D:HIS144 4.3 18.6 1.0 CG D:HIS144 4.3 18.4 1.0 ND1 D:HIS198 4.4 25.3 1.0 CG D:HIS198 4.5 25.1 1.0 NE2 D:HIS230 4.5 23.4 1.0 CB D:GLU249 4.5 23.1 1.0 CG2 D:VAL146 4.6 26.3 1.0 CE1 D:TYR239 4.7 14.9 1.0 ND2 D:ASN235 4.9 25.4 1.0 CD2 D:HIS230 4.9 21.9 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn606 b:30.6 occ:1.00 O E:HOH623 2.1 26.7 1.0 OE1 E:GLU249 2.1 27.5 1.0 O E:HOH622 2.3 28.2 1.0 NE2 E:HIS198 2.3 19.4 1.0 NE2 E:HIS144 2.4 30.6 1.0 OH E:TYR239 2.8 36.1 1.0 CD E:GLU249 3.0 26.6 1.0 CE1 E:HIS198 3.1 19.9 1.0 OE2 E:GLU249 3.3 27.8 1.0 CD2 E:HIS144 3.3 30.6 1.0 CD2 E:HIS198 3.4 20.8 1.0 CE1 E:HIS144 3.5 31.3 1.0 CZ E:TYR239 3.6 33.4 1.0 CE2 E:TYR239 3.8 32.2 1.0 ND1 E:HIS198 4.3 21.5 1.0 NE2 E:HIS230 4.3 23.5 1.0 CB E:ALA200 4.3 29.6 1.0 CG E:HIS198 4.5 22.0 1.0 CG E:GLU249 4.5 26.2 1.0 CG2 E:VAL146 4.5 27.5 1.0 CG E:HIS144 4.5 30.5 1.0 ND1 E:HIS144 4.5 30.1 1.0 CE1 E:TYR239 4.7 33.0 1.0 CD2 E:HIS230 4.7 24.0 1.0 CB E:GLU249 4.8 26.6 1.0 ND2 E:ASN235 5.0 29.8 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn605 b:31.6 occ:1.00 NE2 F:HIS144 2.1 27.8 1.0 O F:HOH639 2.1 20.7 1.0 OE1 F:GLU249 2.1 30.2 1.0 O F:HOH640 2.3 33.1 1.0 NE2 F:HIS198 2.4 24.0 1.0 OH F:TYR239 2.9 25.7 1.0 CD F:GLU249 3.0 26.8 1.0 CE1 F:HIS144 3.0 27.7 1.0 CD2 F:HIS144 3.1 27.8 1.0 OE2 F:GLU249 3.3 27.3 1.0 CD2 F:HIS198 3.3 24.1 1.0 CE1 F:HIS198 3.3 24.1 1.0 CZ F:TYR239 3.7 23.2 1.0 CE2 F:TYR239 3.9 21.3 1.0 CB F:ALA200 4.0 22.7 1.0 ND1 F:HIS144 4.2 28.0 1.0 CG F:HIS144 4.2 27.0 1.0 CG F:GLU249 4.3 25.8 1.0 CG2 F:VAL146 4.4 27.9 1.0 ND1 F:HIS198 4.4 25.8 1.0 CG F:HIS198 4.5 24.6 1.0 NE2 F:HIS230 4.7 29.1 1.0 CE1 F:TYR239 4.8 23.9 1.0 CB F:GLU249 4.9 25.2 1.0 ND2 F:ASN235 4.9 33.1 1.0 CD2 F:HIS230 5.0 29.4 1.0

M.Madegowda, S.Eswaramoorthy, S.K.Burley, S.Swaminathan. Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans. To Be Published.