Atomistry » Manganese » PDB 3auz-3c5m » 3b59
Atomistry »
  Manganese »
    PDB 3auz-3c5m »
      3b59 »

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

Protein crystallography data

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

Manganese Binding Sites:

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 3b59

Go back to Manganese Binding Sites List in 3b59
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 3b59

Go back to Manganese Binding Sites List in 3b59
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 3b59

Go back to Manganese Binding Sites List in 3b59
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 3b59

Go back to Manganese Binding Sites List in 3b59
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 3b59

Go back to Manganese Binding Sites List in 3b59
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 3b59

Go back to Manganese Binding Sites List in 3b59
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

Reference:

M.Madegowda, S.Eswaramoorthy, S.K.Burley, S.Swaminathan. Crystal Structure of the Mn(II)-Bound Glyoxalase From Novosphingobium Aromaticivorans. To Be Published.
Page generated: Sat Oct 5 15:55:14 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy