Iron in PDB 3lm4: Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1)

All present enzymatic activity of Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1):
1.13.11.2;

The structure of Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1), PDB code: 3lm4 was solved by B.Syed Ibrahim, D.Kumaran, S.K.Burley, S.Swaminathan, New Yorksgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.67 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.923, 76.189, 251.373, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21

The binding sites of Iron atom in the Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1) (pdb code 3lm4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1), PDB code: 3lm4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:13.9 occ:1.00 OE1 A:GLU268 2.2 8.4 1.0 NE2 A:HIS217 2.3 5.8 1.0 NE2 A:HIS155 2.3 9.6 1.0 O A:HOH504 2.4 21.2 1.0 O1 A:PEO401 2.5 20.4 1.0 O A:HOH505 2.5 10.0 1.0 O2 A:PEO401 2.8 19.8 1.0 CE1 A:HIS217 3.0 3.5 1.0 CE1 A:HIS155 3.2 7.8 1.0 CD A:GLU268 3.2 9.2 1.0 CD2 A:HIS155 3.3 6.7 1.0 CD2 A:HIS217 3.4 4.9 1.0 OE2 A:GLU268 3.6 11.1 1.0 OH A:TYR258 3.9 10.0 1.0 ND1 A:HIS217 4.2 5.7 1.0 NE2 A:HIS200 4.3 16.0 1.0 ND1 A:HIS155 4.4 7.8 1.0 CE1 A:TYR258 4.4 7.5 1.0 CG A:HIS217 4.4 4.4 1.0 CG A:HIS155 4.4 7.6 1.0 CG A:GLU268 4.5 7.1 1.0 CZ A:TYR258 4.6 8.8 1.0 ND2 A:ASN157 4.7 13.8 1.0 CB A:ALA219 4.8 4.9 1.0 CB A:GLU268 4.8 4.9 1.0 OA1 A:HPX406 4.8 30.9 1.0 CB A:ASN157 4.9 9.6 1.0 OA2 A:HPX406 5.0 35.0 1.0 CE1 A:HIS200 5.0 16.9 1.0

Iron binding site 2 out of 4 in the Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:14.6 occ:1.00 OE1 B:GLU268 2.1 6.5 1.0 NE2 B:HIS155 2.2 7.8 1.0 O B:HOH500 2.3 16.7 1.0 NE2 B:HIS217 2.3 4.9 1.0 O B:HOH501 2.5 10.7 1.0 O1 B:PEO401 2.5 31.6 1.0 O2 B:PEO401 2.6 18.8 1.0 CE1 B:HIS155 3.1 7.5 1.0 CD B:GLU268 3.2 9.2 1.0 CE1 B:HIS217 3.2 6.0 1.0 CD2 B:HIS155 3.3 6.9 1.0 CD2 B:HIS217 3.4 5.0 1.0 OE2 B:GLU268 3.5 10.8 1.0 OH B:TYR258 3.7 7.5 1.0 ND1 B:HIS155 4.3 6.5 1.0 CG B:HIS155 4.4 6.7 1.0 ND1 B:HIS217 4.4 4.2 1.0 CE1 B:TYR258 4.4 6.9 1.0 NE2 B:HIS200 4.4 14.8 1.0 CG B:HIS217 4.5 5.9 1.0 CG B:GLU268 4.5 7.2 1.0 CZ B:TYR258 4.5 8.2 1.0 ND2 B:ASN157 4.6 9.0 1.0 OA1 B:HPX406 4.7 30.5 1.0 CB B:ALA219 4.7 2.9 1.0 OA2 B:HPX406 4.7 34.3 1.0 CB B:GLU268 4.7 6.5 1.0 CB B:ASN157 4.8 7.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe400 b:14.8 occ:1.00 OE1 C:GLU268 2.2 8.1 1.0 NE2 C:HIS155 2.2 10.1 1.0 O C:HOH502 2.3 16.2 1.0 O C:HOH503 2.3 18.1 1.0 O2 C:PEO401 2.3 20.8 1.0 NE2 C:HIS217 2.4 6.2 1.0 O1 C:PEO401 2.8 22.9 1.0 CE1 C:HIS217 3.1 7.1 1.0 CE1 C:HIS155 3.2 10.9 1.0 CD C:GLU268 3.2 10.3 1.0 CD2 C:HIS155 3.2 8.7 1.0 CD2 C:HIS217 3.5 7.9 1.0 OE2 C:GLU268 3.5 11.8 1.0 OH C:TYR258 3.8 10.7 1.0 NE2 C:HIS200 4.2 16.4 1.0 ND1 C:HIS155 4.3 8.9 1.0 ND1 C:HIS217 4.3 6.7 1.0 CG C:HIS155 4.3 8.9 1.0 CE1 C:TYR258 4.5 7.0 1.0 OA1 C:HPX406 4.6 27.3 1.0 CG C:GLU268 4.6 6.9 1.0 CG C:HIS217 4.6 7.6 1.0 CZ C:TYR258 4.6 8.9 1.0 ND2 C:ASN157 4.7 10.5 1.0 CB C:ALA219 4.8 4.4 1.0 CB C:GLU268 4.8 5.9 1.0 CE1 C:HIS200 4.9 17.0 1.0 CB C:ASN157 4.9 9.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe400 b:15.8 occ:1.00 OE1 D:GLU268 2.2 9.0 1.0 NE2 D:HIS155 2.2 7.7 1.0 O D:HOH506 2.3 23.6 1.0 NE2 D:HIS217 2.4 9.0 1.0 O D:HOH507 2.4 14.0 1.0 O1 D:PEO401 2.5 18.6 1.0 O2 D:PEO401 2.6 21.4 1.0 CE1 D:HIS155 3.1 7.5 1.0 CE1 D:HIS217 3.2 8.0 1.0 CD D:GLU268 3.2 10.9 1.0 CD2 D:HIS155 3.3 7.6 1.0 CD2 D:HIS217 3.5 8.4 1.0 OE2 D:GLU268 3.6 10.5 1.0 OH D:TYR258 3.8 10.7 1.0 ND1 D:HIS155 4.3 6.9 1.0 NE2 D:HIS200 4.3 15.3 1.0 ND1 D:HIS217 4.3 7.5 1.0 CG D:HIS155 4.4 7.8 1.0 CE1 D:TYR258 4.4 7.3 1.0 CG D:HIS217 4.5 7.6 1.0 CG D:GLU268 4.5 6.9 1.0 CZ D:TYR258 4.6 9.3 1.0 CB D:ALA219 4.7 3.1 1.0 OA1 D:HPX406 4.8 35.0 1.0 ND2 D:ASN157 4.8 9.2 1.0 CB D:GLU268 4.8 5.3 1.0 CB D:ASN157 4.9 9.8 1.0

B.Syed Ibrahim, D.Kumaran, S.K.Burley, S.Swaminathan. Crystal Structure of 2,3-Dihydroxy Biphenyl Dioxygenase From Rhodococcus Sp. (Strain RHA1) To Be Published.