Iron in PDB 4dik: Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima

The structure of Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima, PDB code: 4dik was solved by H.Fang, J.D.Caranto, A.B.Taylor, P.J.Hart, D.M.Kurtz Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.13 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.219, 96.007, 90.331, 90.00, 95.81, 90.00
R / Rfree (%)	19.1 / 21.5

The structure of Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Iron atom in the Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima (pdb code 4dik). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima, PDB code: 4dik:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:25.9 occ:0.77 FE1 A:FEO402 0.0 25.9 0.8 O A:FEO402 1.8 20.8 0.8 OD2 A:ASP168 2.1 28.8 1.0 OE1 A:GLU87 2.2 28.0 1.0 NE2 A:HIS151 2.3 35.0 1.0 NE2 A:HIS85 2.4 26.6 1.0 O A:HOH704 2.6 39.2 1.0 CD2 A:HIS85 3.1 27.1 1.0 CD2 A:HIS151 3.1 27.2 1.0 CD A:GLU87 3.1 31.1 1.0 CG A:ASP168 3.2 31.5 1.0 O A:HOH691 3.3 31.4 1.0 FE2 A:FEO402 3.3 23.7 0.8 CE1 A:HIS151 3.5 30.9 1.0 CE1 A:HIS85 3.6 33.2 1.0 OD1 A:ASP168 3.6 26.2 1.0 CB A:GLU87 3.8 27.5 1.0 OE2 A:GLU87 3.9 32.5 1.0 CG A:GLU87 4.0 25.8 1.0 OD1 A:ASP89 4.2 29.6 1.0 O A:HOH508 4.2 30.4 1.0 CG A:HIS85 4.4 28.1 1.0 CG A:HIS151 4.4 28.0 1.0 ND1 A:HIS151 4.5 30.4 1.0 CB A:ASP168 4.5 25.1 1.0 ND1 A:HIS85 4.5 26.4 1.0 OD2 A:ASP89 4.6 28.4 1.0 CG1 A:VAL201 4.8 24.2 1.0 CG A:ASP89 4.8 30.5 1.0 O A:HOH504 4.9 23.1 1.0 OH A:TYR197 4.9 27.8 1.0

Iron binding site 2 out of 4 in the Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:23.7 occ:0.75 FE2 A:FEO402 0.0 23.7 0.8 O A:FEO402 1.8 20.8 0.8 OD1 A:ASP168 2.2 26.2 1.0 OD2 A:ASP89 2.2 28.4 1.0 O A:HOH691 2.3 31.4 1.0 O A:HOH504 2.3 23.1 1.0 NE2 A:HIS228 2.4 22.9 1.0 CG A:ASP168 3.1 31.5 1.0 CG A:ASP89 3.2 30.5 1.0 CE1 A:HIS228 3.3 24.6 1.0 OD2 A:ASP168 3.3 28.8 1.0 FE1 A:FEO402 3.3 25.9 0.8 CD2 A:HIS228 3.4 22.6 1.0 OD1 A:ASP89 3.4 29.6 1.0 O A:HOH704 3.8 39.2 1.0 OH A:TYR197 3.9 27.8 1.0 O A:HOH535 4.3 29.0 1.0 ND1 A:HIS228 4.4 21.0 1.0 CZ A:PHE28 4.5 26.1 1.0 CG A:HIS228 4.5 21.9 1.0 CB A:ASP168 4.5 25.1 1.0 CD2 A:HIS85 4.5 27.1 1.0 CB A:ASP89 4.5 25.3 1.0 OE1 A:GLU87 4.7 28.0 1.0 NE2 A:HIS85 4.8 26.6 1.0 CA A:ASP168 4.9 27.2 1.0 CD A:GLU87 5.0 31.1 1.0

Iron binding site 3 out of 4 in the Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:27.5 occ:0.77 FE1 B:FEO402 0.0 27.5 0.8 O B:FEO402 1.8 21.8 0.8 OE1 B:GLU87 2.1 32.6 1.0 OD2 B:ASP168 2.2 31.4 1.0 NE2 B:HIS151 2.3 35.0 1.0 NE2 B:HIS85 2.4 29.5 1.0 O B:HOH710 2.6 37.0 1.0 CD2 B:HIS85 3.1 33.0 1.0 CD B:GLU87 3.1 33.6 1.0 CD2 B:HIS151 3.1 36.1 1.0 O B:HOH693 3.2 32.9 1.0 CG B:ASP168 3.2 32.4 1.0 FE2 B:FEO402 3.3 26.2 0.8 CE1 B:HIS151 3.4 34.5 1.0 OD1 B:ASP168 3.6 27.4 1.0 CE1 B:HIS85 3.6 32.5 1.0 CB B:GLU87 3.7 26.0 1.0 OE2 B:GLU87 3.7 34.5 1.0 CG B:GLU87 4.0 28.3 1.0 OD1 B:ASP89 4.2 28.2 1.0 O B:HOH657 4.3 39.5 1.0 CG B:HIS85 4.3 28.4 1.0 CG B:HIS151 4.4 31.1 1.0 ND1 B:HIS151 4.5 35.6 1.0 CB B:ASP168 4.5 31.9 1.0 ND1 B:HIS85 4.5 30.1 1.0 OD2 B:ASP89 4.6 25.9 1.0 OH B:TYR197 4.7 27.8 1.0 CG1 B:VAL201 4.8 29.1 1.0 CG B:ASP89 4.8 29.1 1.0 O B:HOH508 4.9 25.0 1.0

Iron binding site 4 out of 4 in the Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Flavo Di-Iron Protein H90A Mutant From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:26.2 occ:0.75 FE2 B:FEO402 0.0 26.2 0.8 O B:FEO402 1.8 21.8 0.8 OD2 B:ASP89 2.2 25.9 1.0 OD1 B:ASP168 2.2 27.4 1.0 O B:HOH693 2.3 32.9 1.0 NE2 B:HIS228 2.4 22.0 1.0 O B:HOH508 2.4 25.0 1.0 CG B:ASP89 3.1 29.1 1.0 CG B:ASP168 3.2 32.4 1.0 CE1 B:HIS228 3.3 24.5 1.0 FE1 B:FEO402 3.3 27.5 0.8 OD1 B:ASP89 3.4 28.2 1.0 OD2 B:ASP168 3.4 31.4 1.0 CD2 B:HIS228 3.4 26.5 1.0 OH B:TYR197 3.8 27.8 1.0 O B:HOH710 3.8 37.0 1.0 O B:HOH522 4.3 27.3 1.0 ND1 B:HIS228 4.4 20.4 1.0 CZ B:PHE28 4.5 25.5 1.0 CG B:HIS228 4.5 21.2 1.0 CD2 B:HIS85 4.5 33.0 1.0 CB B:ASP89 4.5 24.9 1.0 CB B:ASP168 4.5 31.9 1.0 OE1 B:GLU87 4.6 32.6 1.0 NE2 B:HIS85 4.8 29.5 1.0 CD B:GLU87 4.9 33.6 1.0 CA B:ASP168 4.9 32.5 1.0 CZ B:TYR197 5.0 30.0 1.0

H.Fang, J.D.Caranto, R.Mendoza, A.B.Taylor, P.J.Hart, D.M.Kurtz. Histidine Ligand Variants of A Flavo-Diiron Protein: Effects on Structure and Activities. J.Biol.Inorg.Chem. V. 17 1231 2012.
ISSN: ISSN 0949-8257
PubMed: 22990880
DOI: 10.1007/S00775-012-0938-4