Iron in PDB 6de6: 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9

The structure of 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9, PDB code: 6de6 was solved by P.Goyal, S.Lovell, M.Richter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.43 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.223, 105.314, 140.038, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.2

The binding sites of Iron atom in the 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9 (pdb code 6de6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9, PDB code: 6de6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:26.6 occ:1.00 FE1 A:SF4703 0.0 26.6 1.0 S3 A:SF4703 2.3 28.9 1.0 S2 A:SF4703 2.3 27.3 1.0 S4 A:SF4703 2.3 27.6 1.0 SG A:CYS362 2.3 27.2 1.0 FE4 A:SF4703 2.7 28.1 1.0 FE2 A:SF4703 2.7 27.8 1.0 FE3 A:SF4703 2.8 26.7 1.0 CB A:CYS362 3.4 23.9 1.0 CA A:CYS362 3.7 24.0 1.0 N A:THR363 3.7 29.1 1.0 S1 A:SF4703 3.9 28.0 1.0 C A:CYS362 4.1 26.9 1.0 N A:GLN364 4.3 27.0 1.0 CB A:ALA325 4.4 26.5 1.0 CG2 A:ILE324 4.5 29.1 1.0 CA A:ALA325 4.6 31.6 1.0 N A:ALA325 4.7 26.5 1.0 SG A:CYS347 4.8 25.3 1.0 SG A:CYS350 4.8 29.0 1.0 CA A:THR363 4.8 36.5 1.0 CB A:GLN364 4.8 26.8 1.0 CB A:THR363 4.9 25.4 1.0 SG A:CYS344 4.9 28.2 1.0 CB A:CYS350 5.0 32.4 1.0

Iron binding site 2 out of 8 in the 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:27.8 occ:1.00 FE2 A:SF4703 0.0 27.8 1.0 S3 A:SF4703 2.3 28.9 1.0 S4 A:SF4703 2.3 27.6 1.0 S1 A:SF4703 2.3 28.0 1.0 SG A:CYS350 2.3 29.0 1.0 FE1 A:SF4703 2.7 26.6 1.0 FE4 A:SF4703 2.8 28.1 1.0 FE3 A:SF4703 2.8 26.7 1.0 CB A:CYS350 3.3 32.4 1.0 N A:CYS350 3.8 26.4 1.0 S2 A:SF4703 3.9 27.3 1.0 CG A:ARG321 4.0 30.2 1.0 CA A:CYS350 4.2 28.6 1.0 CD A:ARG321 4.3 30.9 1.0 CB A:ARG321 4.4 29.8 1.0 N A:ASN348 4.4 28.9 1.0 CA A:ASN348 4.4 26.6 1.0 N A:ILE349 4.4 27.7 1.0 SG A:CYS347 4.6 25.3 1.0 C A:ASN348 4.7 27.8 1.0 SG A:CYS344 4.7 28.2 1.0 SG A:CYS362 4.8 27.2 1.0 C A:ILE349 5.0 27.8 1.0

Iron binding site 3 out of 8 in the 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:26.7 occ:1.00 FE3 A:SF4703 0.0 26.7 1.0 S1 A:SF4703 2.3 28.0 1.0 SG A:CYS347 2.3 25.3 1.0 S4 A:SF4703 2.3 27.6 1.0 S2 A:SF4703 2.3 27.3 1.0 FE4 A:SF4703 2.7 28.1 1.0 FE2 A:SF4703 2.8 27.8 1.0 FE1 A:SF4703 2.8 26.6 1.0 N A:CYS347 3.6 26.6 1.0 CB A:CYS347 3.8 28.0 1.0 N A:ASN348 3.8 28.9 1.0 S3 A:SF4703 3.9 28.9 1.0 CG1 A:ILE345 4.0 26.9 1.0 CA A:CYS347 4.1 26.7 1.0 N A:ILE349 4.2 27.7 1.0 OG1 A:THR363 4.2 28.8 1.0 N A:GLY346 4.3 22.2 1.0 C A:CYS347 4.3 26.1 1.0 CB A:THR363 4.4 25.4 1.0 N A:THR363 4.5 29.1 1.0 C A:GLY346 4.6 26.9 1.0 CA A:ASN348 4.6 26.6 1.0 SG A:CYS344 4.6 28.2 1.0 CD1 A:ILE345 4.7 27.8 1.0 N A:ILE345 4.7 28.7 1.0 CA A:GLY346 4.8 28.6 1.0 SG A:CYS350 4.8 29.0 1.0 CB A:ILE349 4.9 27.4 1.0 C A:ASN348 4.9 27.8 1.0 SG A:CYS362 4.9 27.2 1.0 C A:ILE345 5.0 31.3 1.0 N A:CYS350 5.0 26.4 1.0

Iron binding site 4 out of 8 in the 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:28.1 occ:1.00 FE4 A:SF4703 0.0 28.1 1.0 S3 A:SF4703 2.3 28.9 1.0 S1 A:SF4703 2.3 28.0 1.0 SG A:CYS344 2.3 28.2 1.0 S2 A:SF4703 2.3 27.3 1.0 FE3 A:SF4703 2.7 26.7 1.0 FE1 A:SF4703 2.7 26.6 1.0 FE2 A:SF4703 2.8 27.8 1.0 CB A:CYS344 3.4 29.2 1.0 CA A:CYS344 3.8 33.0 1.0 S4 A:SF4703 3.9 27.6 1.0 N A:ILE345 3.9 28.7 1.0 N A:GLY346 3.9 22.2 1.0 CB A:ARG321 4.1 29.8 1.0 C A:CYS344 4.2 36.2 1.0 O A:ARG321 4.3 29.3 1.0 CB A:ALA325 4.4 26.5 1.0 CG A:ARG321 4.6 30.2 1.0 CA A:GLY346 4.6 28.6 1.0 C A:ARG321 4.7 25.3 1.0 SG A:CYS362 4.7 27.2 1.0 CD A:ARG321 4.8 30.9 1.0 CA A:ARG321 4.8 27.5 1.0 N A:CYS347 4.9 26.6 1.0 C A:ILE345 4.9 31.3 1.0 SG A:CYS347 4.9 25.3 1.0 SG A:CYS350 4.9 29.0 1.0 CA A:ILE345 4.9 27.8 1.0

Iron binding site 5 out of 8 in the 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe703 b:42.4 occ:1.00 FE1 B:SF4703 0.0 42.4 1.0 S3 B:SF4703 2.3 50.5 1.0 S2 B:SF4703 2.3 44.9 1.0 SG B:CYS362 2.3 33.7 1.0 S4 B:SF4703 2.4 53.8 1.0 FE4 B:SF4703 2.7 73.3 1.0 FE3 B:SF4703 2.8 66.4 1.0 FE2 B:SF4703 2.8 58.4 1.0 CB B:CYS362 3.3 33.7 1.0 CA B:CYS362 3.6 36.7 1.0 N B:THR363 3.7 33.0 1.0 S1 B:SF4703 4.0 56.7 1.0 C B:CYS362 4.0 39.8 1.0 N B:GLN364 4.3 34.7 1.0 CB B:ALA325 4.5 33.6 1.0 CG2 B:ILE324 4.5 33.7 1.0 CA B:ALA325 4.6 35.9 1.0 N B:ALA325 4.7 32.9 1.0 CA B:THR363 4.8 34.0 1.0 SG B:CYS347 4.8 54.1 1.0 SG B:CYS350 4.9 52.8 1.0 CB B:GLN364 4.9 38.0 1.0 N B:CYS362 4.9 35.5 1.0 CB B:THR363 5.0 40.5 1.0

Iron binding site 6 out of 8 in the 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe703 b:58.4 occ:1.00 FE2 B:SF4703 0.0 58.4 1.0 S1 B:SF4703 2.3 56.7 1.0 S4 B:SF4703 2.3 53.8 1.0 SG B:CYS350 2.3 52.8 1.0 S3 B:SF4703 2.4 50.5 1.0 FE4 B:SF4703 2.8 73.3 1.0 FE3 B:SF4703 2.8 66.4 1.0 FE1 B:SF4703 2.8 42.4 1.0 CB B:CYS350 3.4 48.8 1.0 N B:CYS350 3.9 50.8 1.0 S2 B:SF4703 4.0 44.9 1.0 CG B:ARG321 4.0 44.8 1.0 CD B:ARG321 4.3 43.3 1.0 N B:ASN348 4.3 52.6 1.0 CA B:CYS350 4.3 46.1 1.0 CA B:ASN348 4.3 54.3 1.0 CB B:ARG321 4.5 41.1 1.0 N B:ILE349 4.5 53.7 1.0 SG B:CYS344 4.6 65.7 1.0 SG B:CYS347 4.7 54.1 1.0 C B:ASN348 4.7 48.4 1.0 SG B:CYS362 4.9 33.7 1.0 OD1 B:ASN348 4.9 53.1 1.0

Iron binding site 7 out of 8 in the 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe703 b:66.4 occ:1.00 FE3 B:SF4703 0.0 66.4 1.0 S4 B:SF4703 2.3 53.8 1.0 S2 B:SF4703 2.3 44.9 1.0 SG B:CYS347 2.3 54.1 1.0 S1 B:SF4703 2.3 56.7 1.0 FE4 B:SF4703 2.8 73.3 1.0 FE2 B:SF4703 2.8 58.4 1.0 FE1 B:SF4703 2.8 42.4 1.0 N B:CYS347 3.6 54.7 1.0 N B:ASN348 3.7 52.6 1.0 CB B:CYS347 3.8 50.2 1.0 S3 B:SF4703 3.9 50.5 1.0 CA B:CYS347 4.1 50.0 1.0 CG1 B:ILE345 4.1 50.6 1.0 OG1 B:THR363 4.2 37.7 1.0 N B:ILE349 4.3 53.7 1.0 C B:CYS347 4.3 57.1 1.0 N B:GLY346 4.3 47.0 1.0 N B:THR363 4.4 33.0 1.0 CB B:THR363 4.5 40.5 1.0 C B:GLY346 4.6 60.0 1.0 CA B:ASN348 4.6 54.3 1.0 SG B:CYS344 4.7 65.7 1.0 N B:ILE345 4.7 42.5 1.0 CA B:GLY346 4.8 54.0 1.0 SG B:CYS350 4.8 52.8 1.0 CD1 B:ILE345 4.8 47.8 1.0 CB B:ILE349 4.9 49.1 1.0 SG B:CYS362 4.9 33.7 1.0 C B:ASN348 4.9 48.4 1.0

Iron binding site 8 out of 8 in the 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 2.1 A Resolution Structure of Histamine Dehydrogenase From Rhizobium Sp. 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe703 b:73.3 occ:1.00 FE4 B:SF4703 0.0 73.3 1.0 S3 B:SF4703 2.3 50.5 1.0 S1 B:SF4703 2.3 56.7 1.0 SG B:CYS344 2.3 65.7 1.0 S2 B:SF4703 2.3 44.9 1.0 FE1 B:SF4703 2.7 42.4 1.0 FE2 B:SF4703 2.8 58.4 1.0 FE3 B:SF4703 2.8 66.4 1.0 CB B:CYS344 3.3 41.5 1.0 CA B:CYS344 3.7 39.6 1.0 N B:ILE345 3.8 42.5 1.0 S4 B:SF4703 3.9 53.8 1.0 N B:GLY346 4.0 47.0 1.0 CB B:ARG321 4.2 41.1 1.0 C B:CYS344 4.2 38.9 1.0 O B:ARG321 4.5 29.2 1.0 CB B:ALA325 4.5 33.6 1.0 CG B:ARG321 4.6 44.8 1.0 CA B:GLY346 4.7 54.0 1.0 SG B:CYS362 4.7 33.7 1.0 CD B:ARG321 4.8 43.3 1.0 C B:ARG321 4.9 31.2 1.0 CA B:ILE345 4.9 44.6 1.0 CA B:ARG321 5.0 35.8 1.0 C B:ILE345 5.0 46.1 1.0 N B:CYS347 5.0 54.7 1.0 N B:CYS344 5.0 35.8 1.0 SG B:CYS350 5.0 52.8 1.0

P.Goyal, S.Lovell, M.Richter. Structure of Histamine Dehydrogenase To Be Published.