Iron in PDB 3wpm: Crystal Structure of the Anaerobic Desb-Gallate Complex By Co- Crystallization

The structure of Crystal Structure of the Anaerobic Desb-Gallate Complex By Co- Crystallization, PDB code: 3wpm 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)	43.89 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.105, 64.185, 117.896, 90.00, 97.19, 90.00
R / Rfree (%)	22.5 / 29.6

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

Iron binding site 1 out of 3 in the Crystal Structure of the Anaerobic Desb-Gallate Complex By Co- Crystallization


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 By Co- Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:55.3 occ:1.00 OE1 A:GLU239 2.1 45.5 1.0 NE2 A:HIS59 2.3 36.5 1.0 CD A:GLU239 2.7 42.4 1.0 OE2 A:GLU239 2.7 44.8 1.0 OD1 A:ASN57 2.7 48.1 1.0 NE2 A:HIS12 2.8 53.0 1.0 CE1 A:HIS59 3.1 44.9 1.0 CE1 A:HIS12 3.2 51.8 1.0 ND2 A:ASN57 3.4 37.2 1.0 CD2 A:HIS59 3.4 40.3 1.0 CG A:ASN57 3.4 43.4 1.0 CD2 A:HIS12 3.9 56.4 1.0 CG A:GLU239 4.2 36.8 1.0 ND1 A:HIS59 4.3 46.7 1.0 ND1 A:HIS12 4.4 59.8 1.0 CG A:HIS59 4.4 43.2 1.0 CB A:GLU239 4.7 36.5 1.0 CG A:HIS12 4.7 61.3 1.0 O A:ASN57 4.9 46.7 1.0 CB A:ASN57 4.9 41.0 1.0 CE A:MET242 5.0 42.4 1.0

Iron binding site 2 out of 3 in the Crystal Structure of the Anaerobic Desb-Gallate Complex By Co- Crystallization


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 By Co- Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:11.0 occ:0.50 FE B:FE501 0.0 11.0 0.5 OE1 B:GLU239 2.0 19.6 1.0 NE2 B:HIS59 2.1 22.5 1.0 OD1 B:ASN57 2.2 21.6 1.0 NE2 B:HIS12 2.3 28.1 1.0 FE B:FE501 2.3 29.7 0.5 CD B:GLU239 3.0 20.7 1.0 CE1 B:HIS59 3.0 23.3 1.0 CE1 B:HIS12 3.1 22.2 1.0 CG B:ASN57 3.1 21.2 1.0 CD2 B:HIS59 3.1 24.2 1.0 ND2 B:ASN57 3.2 18.2 1.0 OE2 B:GLU239 3.3 23.6 1.0 CD2 B:HIS12 3.4 24.4 1.0 O B:HOH601 3.8 14.1 1.0 OAE B:GDE502 4.0 21.7 1.0 ND1 B:HIS59 4.1 19.5 1.0 CG B:HIS59 4.2 21.2 1.0 ND1 B:HIS12 4.2 21.4 1.0 CG B:GLU239 4.4 17.4 1.0 CG B:HIS12 4.4 23.6 1.0 CB B:ASN57 4.5 21.6 1.0 O B:ASN57 4.7 22.0 1.0 CB B:GLU239 4.8 20.4 1.0 OAD B:GDE502 4.8 24.3 1.0

Iron binding site 3 out of 3 in the Crystal Structure of the Anaerobic Desb-Gallate Complex By Co- Crystallization


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 By Co- Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:29.7 occ:0.50 FE B:FE501 0.0 29.7 0.5 FE B:FE501 2.3 11.0 0.5 O B:HOH601 2.5 14.1 1.0 OAD B:GDE502 2.5 24.3 1.0 OE2 B:GLU239 2.6 23.6 1.0 OAE B:GDE502 2.7 21.7 1.0 NE2 B:HIS12 2.9 28.1 1.0 OE1 B:GLU239 2.9 19.6 1.0 CD2 B:HIS12 3.1 24.4 1.0 CD B:GLU239 3.1 20.7 1.0 NE2 B:HIS59 3.3 22.5 1.0 CAJ B:GDE502 3.4 23.9 1.0 CAL B:GDE502 3.5 25.8 1.0 NE2 B:HIS192 3.9 18.8 1.0 CD2 B:HIS59 4.1 24.2 1.0 CE1 B:HIS59 4.1 23.3 1.0 CE1 B:HIS12 4.1 22.2 1.0 CE1 B:HIS192 4.3 19.5 1.0 CG B:HIS12 4.4 23.6 1.0 OD1 B:ASN57 4.5 21.6 1.0 CG B:GLU239 4.6 17.4 1.0 CAG B:GDE502 4.8 22.0 1.0 CAI B:GDE502 4.8 23.1 1.0 ND1 B:HIS12 4.9 21.4 1.0 CD2 B:HIS192 5.0 18.6 1.0 CA B:GLY188 5.0 21.5 1.0 NE2 B:HIS124 5.0 24.8 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