Iron in PDB 3wr9: Crystal Structure of the Anaerobic Desb-Gallate Complex

All present enzymatic activity of Crystal Structure of the Anaerobic Desb-Gallate Complex:
1.13.11.58;

The structure of Crystal Structure of the Anaerobic Desb-Gallate Complex, PDB code: 3wr9 was solved by K.Sugimoto, M.Senda, D.Kasai, M.Fukuda, E.Masai, T.Senda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.17 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	123.523, 159.182, 104.498, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.9

The binding sites of Iron atom in the Crystal Structure of the Anaerobic Desb-Gallate Complex (pdb code 3wr9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of the Anaerobic Desb-Gallate Complex, PDB code: 3wr9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of the Anaerobic Desb-Gallate Complex


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 the Anaerobic Desb-Gallate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:14.4 occ:0.50 FE A:FE2501 0.0 14.4 0.5 OAE A:GDE503 2.0 21.9 1.0 FE A:FE2501 2.0 17.9 0.5 NE2 A:HIS59 2.3 19.3 1.0 OAC A:GDE503 2.5 22.2 1.0 NE2 A:HIS12 2.5 21.5 1.0 CAL A:GDE503 2.9 22.7 1.0 O A:HOH691 3.0 30.2 1.0 CD2 A:HIS59 3.1 20.6 1.0 CD2 A:HIS12 3.1 22.3 1.0 CAI A:GDE503 3.1 21.5 1.0 OE1 A:GLU239 3.3 32.8 1.0 CE1 A:HIS59 3.3 18.5 1.0 OE2 A:GLU239 3.3 31.4 1.0 CD A:GLU239 3.7 30.1 1.0 CE1 A:HIS12 3.8 22.6 1.0 CAJ A:GDE503 4.2 21.0 1.0 CG A:HIS59 4.2 19.9 1.0 NE2 A:HIS124 4.2 16.9 1.0 NE2 A:HIS192 4.2 22.3 1.0 ND1 A:HIS59 4.3 18.3 1.0 OD1 A:ASN57 4.3 26.1 1.0 CG A:HIS12 4.4 23.0 1.0 CAF A:GDE503 4.5 22.4 1.0 O A:HOH610 4.7 16.0 1.0 ND1 A:HIS12 4.7 25.1 1.0 OAD A:GDE503 4.7 21.5 1.0 CE1 A:HIS192 4.9 21.7 1.0 CE1 B:PHE374 4.9 16.6 1.0 ND2 A:ASN57 4.9 25.2 1.0 CD2 A:HIS124 4.9 19.3 1.0

Iron binding site 2 out of 6 in the Crystal Structure of the Anaerobic Desb-Gallate Complex


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 the Anaerobic Desb-Gallate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:17.9 occ:0.50 FE A:FE2501 0.0 17.9 0.5 NE2 A:HIS59 1.9 19.3 1.0 FE A:FE2501 2.0 14.4 0.5 NE2 A:HIS12 2.1 21.5 1.0 O A:HOH691 2.1 30.2 1.0 OE1 A:GLU239 2.1 32.8 1.0 OD1 A:ASN57 2.3 26.1 1.0 CE1 A:HIS59 2.7 18.5 1.0 CE1 A:HIS12 2.7 22.6 1.0 CD2 A:HIS59 3.1 20.6 1.0 CD A:GLU239 3.1 30.1 1.0 CG A:ASN57 3.1 22.8 1.0 ND2 A:ASN57 3.2 25.2 1.0 OE2 A:GLU239 3.3 31.4 1.0 CD2 A:HIS12 3.4 22.3 1.0 OAE A:GDE503 3.7 21.9 1.0 ND1 A:HIS59 3.8 18.3 1.0 ND1 A:HIS12 4.0 25.1 1.0 CG A:HIS59 4.0 19.9 1.0 CG A:HIS12 4.3 23.0 1.0 OAC A:GDE503 4.3 22.2 1.0 CG A:GLU239 4.4 25.4 1.0 O A:ASN57 4.5 18.7 1.0 CB A:ASN57 4.6 20.9 1.0 CB A:GLU239 4.8 24.4 1.0 CAL A:GDE503 4.8 22.7 1.0 CA A:GLY188 4.9 23.5 1.0

Iron binding site 3 out of 6 in the Crystal Structure of the Anaerobic Desb-Gallate Complex


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 the Anaerobic Desb-Gallate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:21.9 occ:1.00 NE2 A:HIS20 2.0 27.5 1.0 NE2 A:HIS136 2.0 19.7 1.0 CE1 A:HIS136 2.8 20.1 1.0 CE1 A:HIS20 2.9 27.7 1.0 CD2 A:HIS20 3.1 27.2 1.0 CD2 A:HIS136 3.2 21.1 1.0 ND1 A:HIS136 4.0 18.8 1.0 ND1 A:HIS20 4.1 26.4 1.0 CG A:HIS20 4.2 27.9 1.0 CG A:HIS136 4.2 23.0 1.0 CD2 A:LEU90 4.6 21.3 1.0 O A:SER131 4.9 23.3 1.0

Iron binding site 4 out of 6 in the Crystal Structure of the Anaerobic Desb-Gallate Complex


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 the Anaerobic Desb-Gallate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:27.8 occ:0.50 FE B:FE2501 0.0 27.8 0.5 OE1 B:GLU239 2.1 35.5 1.0 FE B:FE2501 2.1 18.5 0.5 NE2 B:HIS59 2.2 23.9 1.0 NE2 B:HIS12 2.2 30.9 1.0 CE1 B:HIS12 2.4 31.2 1.0 OD1 B:ASN57 2.5 26.8 1.0 CE1 B:HIS59 2.9 22.1 1.0 O B:HOH616 3.0 32.2 1.0 ND2 B:ASN57 3.0 29.3 1.0 CD B:GLU239 3.1 31.9 1.0 CG B:ASN57 3.1 25.7 1.0 CD2 B:HIS59 3.2 24.1 1.0 OE2 B:GLU239 3.4 32.3 1.0 CD2 B:HIS12 3.6 29.0 1.0 ND1 B:HIS12 3.7 31.6 1.0 OAE B:GDE503 3.8 27.5 1.0 ND1 B:HIS59 4.0 21.8 1.0 CG B:HIS59 4.2 23.8 1.0 CG B:HIS12 4.3 29.3 1.0 CG B:GLU239 4.4 28.4 1.0 O B:ASN57 4.5 24.5 1.0 CB B:ASN57 4.6 24.5 1.0 CB B:GLU239 4.7 27.2 1.0 OAD B:GDE503 4.7 30.4 1.0

Iron binding site 5 out of 6 in the Crystal Structure of the Anaerobic Desb-Gallate Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Anaerobic Desb-Gallate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:18.5 occ:0.50 FE B:FE2501 0.0 18.5 0.5 O B:HOH616 1.9 32.2 1.0 OAE B:GDE503 1.9 27.5 1.0 NE2 B:HIS12 2.0 30.9 1.0 FE B:FE2501 2.1 27.8 0.5 NE2 B:HIS59 2.4 23.9 1.0 OAD B:GDE503 2.7 30.4 1.0 CD2 B:HIS12 2.8 29.0 1.0 CAL B:GDE503 3.0 28.6 1.0 CE1 B:HIS12 3.1 31.2 1.0 OE1 B:GLU239 3.2 35.5 1.0 OE2 B:GLU239 3.3 32.3 1.0 CAJ B:GDE503 3.3 30.4 1.0 CD2 B:HIS59 3.3 24.1 1.0 CE1 B:HIS59 3.4 22.1 1.0 CD B:GLU239 3.6 31.9 1.0 CG B:HIS12 4.0 29.3 1.0 NE2 B:HIS124 4.1 26.0 1.0 ND1 B:HIS12 4.1 31.6 1.0 CAI B:GDE503 4.3 28.8 1.0 NE2 B:HIS192 4.4 31.0 1.0 ND1 B:HIS59 4.4 21.8 1.0 CG B:HIS59 4.5 23.8 1.0 OD1 B:ASN57 4.5 26.8 1.0 O B:HOH612 4.6 15.5 1.0 CAG B:GDE503 4.7 29.3 1.0 OAC B:GDE503 4.7 28.8 1.0 CD2 B:HIS124 4.8 25.5 1.0 ND2 B:ASN57 5.0 29.3 1.0 CE1 B:HIS192 5.0 29.5 1.0

Iron binding site 6 out of 6 in the Crystal Structure of the Anaerobic Desb-Gallate Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Anaerobic Desb-Gallate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:32.6 occ:1.00 NE2 B:HIS136 1.9 40.4 1.0 NE2 B:HIS20 1.9 38.0 1.0 O B:HOH608 2.3 32.6 1.0 CE1 B:HIS136 2.8 39.8 1.0 CE1 B:HIS20 2.9 38.5 1.0 CD2 B:HIS20 2.9 38.3 1.0 CD2 B:HIS136 3.0 38.9 1.0 CD2 B:LEU90 3.9 36.3 1.0 ND1 B:HIS136 3.9 39.1 1.0 ND1 B:HIS20 4.0 38.7 1.0 CG B:HIS136 4.0 38.4 1.0 CG B:HIS20 4.1 37.4 1.0 O B:ASP89 4.7 37.3 1.0 O B:SER131 4.9 34.9 1.0 OD1 B:ASP21 5.0 41.2 1.0

K.Sugimoto, M.Senda, D.Kasai, M.Fukuda, E.Masai, T.Senda. Molecular Mechanism of Strict Substrate Specificity of An Extradiol Dioxygenase, Desb, Derived From Sphingobium Sp. Syk-6 Plos One V. 9 92249 2014.
ISSN: ESSN 1932-6203
PubMed: 24657997
DOI: 10.1371/JOURNAL.PONE.0092249