Iron in PDB 6lvb: Structure of Dimethylformamidase, Tetramer

All present enzymatic activity of Structure of Dimethylformamidase, Tetramer:
3.5.1.56;

The binding sites of Iron atom in the Structure of Dimethylformamidase, Tetramer (pdb code 6lvb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Dimethylformamidase, Tetramer, PDB code: 6lvb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Dimethylformamidase, Tetramer


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Dimethylformamidase, Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:42.8 occ:1.00 OH A:TYR440 1.9 31.7 1.0 OH A:TYR399 1.9 31.9 1.0 OE1 A:GLU521 2.0 29.4 1.0 OE2 A:GLU521 2.0 29.4 1.0 O A:HOH901 2.1 35.7 1.0 CD A:GLU521 2.3 29.4 1.0 CZ A:TYR440 3.2 31.7 1.0 CZ A:TYR399 3.2 31.9 1.0 NE2 A:HIS519 3.4 33.5 1.0 ND2 A:ASN547 3.7 31.0 1.0 CG A:GLU521 3.8 29.4 1.0 CE2 A:TYR399 3.9 31.9 1.0 CE2 A:TYR440 4.0 31.7 1.0 CE1 A:HIS519 4.0 33.5 1.0 CE1 A:TYR440 4.2 31.7 1.0 CE1 A:TYR399 4.2 31.9 1.0 CB A:GLU521 4.5 29.4 1.0 CD2 A:HIS519 4.6 33.5 1.0 CE1 A:TYR522 4.7 26.5 1.0 CG A:ASN547 4.9 31.0 1.0 CZ2 A:TRP473 5.0 41.2 1.0

Iron binding site 2 out of 4 in the Structure of Dimethylformamidase, Tetramer


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Dimethylformamidase, Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe801 b:44.4 occ:1.00 OH C:TYR440 1.9 31.9 1.0 OH C:TYR399 1.9 32.1 1.0 OE1 C:GLU521 2.0 30.4 1.0 OE2 C:GLU521 2.0 30.4 1.0 O C:HOH901 2.1 34.5 1.0 CD C:GLU521 2.3 30.4 1.0 CZ C:TYR399 3.2 32.1 1.0 CZ C:TYR440 3.3 31.9 1.0 NE2 C:HIS519 3.3 33.9 1.0 ND2 C:ASN547 3.7 32.2 1.0 CG C:GLU521 3.8 30.4 1.0 CE1 C:HIS519 3.9 33.9 1.0 CE2 C:TYR399 3.9 32.1 1.0 CE2 C:TYR440 4.0 31.9 1.0 CE1 C:TYR440 4.2 31.9 1.0 CE1 C:TYR399 4.2 32.1 1.0 CD2 C:HIS519 4.4 33.9 1.0 CB C:GLU521 4.5 30.4 1.0 CE1 C:TYR522 4.6 27.3 1.0 CG C:ASN547 4.8 32.2 1.0 CZ2 C:TRP473 4.9 40.0 1.0

Iron binding site 3 out of 4 in the Structure of Dimethylformamidase, Tetramer


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Dimethylformamidase, Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe801 b:44.2 occ:1.00 OH E:TYR440 1.9 31.7 1.0 OH E:TYR399 1.9 31.8 1.0 OE1 E:GLU521 2.0 30.4 1.0 OE2 E:GLU521 2.0 30.4 1.0 O E:HOH901 2.1 34.4 1.0 CD E:GLU521 2.3 30.4 1.0 CZ E:TYR399 3.2 31.8 1.0 NE2 E:HIS519 3.3 33.8 1.0 CZ E:TYR440 3.3 31.7 1.0 ND2 E:ASN547 3.7 32.0 1.0 CG E:GLU521 3.8 30.4 1.0 CE1 E:HIS519 3.9 33.8 1.0 CE2 E:TYR399 3.9 31.8 1.0 CE2 E:TYR440 4.0 31.7 1.0 CE1 E:TYR440 4.2 31.7 1.0 CE1 E:TYR399 4.2 31.8 1.0 CD2 E:HIS519 4.4 33.8 1.0 CB E:GLU521 4.5 30.4 1.0 CE1 E:TYR522 4.6 27.2 1.0 CG E:ASN547 4.8 32.0 1.0 CZ2 E:TRP473 4.9 40.1 1.0

Iron binding site 4 out of 4 in the Structure of Dimethylformamidase, Tetramer


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Dimethylformamidase, Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe801 b:42.7 occ:1.00 OH G:TYR440 1.9 31.7 1.0 OH G:TYR399 1.9 32.0 1.0 OE1 G:GLU521 2.0 29.4 1.0 OE2 G:GLU521 2.0 29.4 1.0 O G:HOH901 2.1 35.9 1.0 CD G:GLU521 2.3 29.4 1.0 CZ G:TYR440 3.2 31.7 1.0 CZ G:TYR399 3.2 32.0 1.0 NE2 G:HIS519 3.4 33.5 1.0 ND2 G:ASN547 3.7 30.9 1.0 CG G:GLU521 3.8 29.4 1.0 CE2 G:TYR399 3.9 32.0 1.0 CE2 G:TYR440 4.0 31.7 1.0 CE1 G:HIS519 4.0 33.5 1.0 CE1 G:TYR440 4.2 31.7 1.0 CE1 G:TYR399 4.2 32.0 1.0 CB G:GLU521 4.5 29.4 1.0 CD2 G:HIS519 4.6 33.5 1.0 CE1 G:TYR522 4.7 26.4 1.0 CG G:ASN547 4.9 30.9 1.0 CZ2 G:TRP473 4.9 41.4 1.0

C.K.Arya, S.Yadav, J.Fine, A.Casanal, G.Chopra, G.Ramanathan, K.R.Vinothkumar, R.Subramanian. A 2-Tyr-1-Carboxylate Mononuclear Iron Center Is the Active Site of Dimethylformamidase. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32452120
DOI: 10.1002/ANIE.202005332