Iron in PDB 1ych: X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase

The structure of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase, PDB code: 1ych was solved by R.Silaghi-Dumitrescu, D.M.Kurtz, W.N.Lanzilotta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.91 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	160.327, 160.327, 279.144, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 24.5

The structure of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Iron atom in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase (pdb code 1ych). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase, PDB code: 1ych:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:59.8 occ:1.00 FE1 A:FEO501 0.0 59.8 1.0 O A:FEO501 2.0 63.7 1.0 NE2 A:HIS86 2.1 63.1 1.0 NE2 A:HIS228 2.2 59.4 1.0 OD2 A:ASP85 2.3 59.0 1.0 OD1 A:ASP167 2.3 61.9 1.0 OD2 A:ASP167 2.9 61.6 1.0 CG A:ASP167 2.9 62.6 1.0 CD2 A:HIS228 3.1 57.8 1.0 CD2 A:HIS86 3.1 63.3 1.0 CE1 A:HIS86 3.1 64.2 1.0 O A:HOH705 3.2 52.9 1.0 FE2 A:FEO501 3.2 61.2 1.0 CE1 A:HIS228 3.3 58.7 1.0 CG A:ASP85 3.4 60.3 1.0 OD1 A:ASP85 3.8 59.8 1.0 OG A:SER227 4.1 58.0 1.0 ND1 A:HIS86 4.2 63.8 1.0 CG A:HIS86 4.2 63.8 1.0 CG A:HIS228 4.3 56.8 1.0 CB A:ASP167 4.3 62.2 1.0 ND1 A:HIS228 4.3 57.0 1.0 OH A:TYR195 4.5 76.6 1.0 CE1 A:PHE24 4.5 79.7 1.0 CZ A:PHE24 4.6 78.7 1.0 CD2 A:HIS81 4.6 67.5 1.0 CB A:ASP85 4.7 59.5 1.0 OE2 A:GLU83 4.7 73.5 1.0 NE2 A:HIS81 5.0 68.4 1.0

Iron binding site 2 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:61.2 occ:1.00 FE2 A:FEO501 0.0 61.2 1.0 O A:FEO501 2.0 63.7 1.0 OD2 A:ASP167 2.2 61.6 1.0 OE2 A:GLU83 2.3 73.5 1.0 NE2 A:HIS81 2.4 68.4 1.0 NE2 A:HIS148 2.4 62.3 1.0 CD2 A:HIS148 2.5 61.9 1.0 CD2 A:HIS81 2.9 67.5 1.0 FE1 A:FEO501 3.2 59.8 1.0 CG A:ASP167 3.3 62.6 1.0 CD A:GLU83 3.4 72.6 1.0 CE1 A:HIS81 3.5 68.2 1.0 O A:HOH705 3.5 52.9 1.0 CE1 A:HIS148 3.7 62.8 1.0 CB A:GLU83 3.8 66.9 1.0 CG A:HIS148 3.9 63.7 1.0 OD1 A:ASP167 4.0 61.9 1.0 CG A:HIS81 4.2 66.3 1.0 CG A:GLU83 4.2 70.3 1.0 CD2 A:HIS86 4.3 63.3 1.0 OE1 A:GLU83 4.3 72.6 1.0 NE2 A:HIS86 4.4 63.1 1.0 ND1 A:HIS148 4.4 62.3 1.0 ND1 A:HIS81 4.4 68.0 1.0 OD1 A:ASP85 4.4 59.8 1.0 CB A:ASP167 4.5 62.2 1.0 OD2 A:ASP85 4.5 59.0 1.0 ND2 A:ASN166 4.7 71.2 1.0 O A:HOH721 4.8 65.6 1.0 CG A:ASP85 4.9 60.3 1.0 NE2 A:HIS25 5.0 85.2 1.0

Iron binding site 3 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe511 b:62.9 occ:1.00 FE1 B:FEO511 0.0 62.9 1.0 O B:FEO511 2.0 65.9 1.0 OE2 B:GLU83 2.2 73.2 1.0 OD2 B:ASP167 2.3 71.0 1.0 NE2 B:HIS81 2.3 70.6 1.0 NE2 B:HIS148 2.4 64.7 1.0 CD2 B:HIS148 2.5 63.8 1.0 CD2 B:HIS81 3.0 68.7 1.0 CD B:GLU83 3.2 72.4 1.0 FE2 B:FEO511 3.3 59.6 1.0 CG B:ASP167 3.4 69.9 1.0 O B:HOH714 3.4 57.2 1.0 CE1 B:HIS81 3.5 69.2 1.0 CB B:GLU83 3.7 67.8 1.0 CE1 B:HIS148 3.7 65.9 1.0 OD1 B:ASP167 3.8 70.5 1.0 CG B:HIS148 3.9 65.8 1.0 CG B:GLU83 4.0 68.6 1.0 OE1 B:GLU83 4.1 74.8 1.0 OD1 B:ASP85 4.2 67.3 1.0 CG B:HIS81 4.2 67.9 1.0 ND1 B:HIS148 4.4 64.6 1.0 OD2 B:ASP85 4.4 65.9 1.0 NE2 B:HIS86 4.4 62.4 1.0 CD2 B:HIS86 4.4 64.7 1.0 ND1 B:HIS81 4.5 69.6 1.0 CB B:ASP167 4.6 67.5 1.0 CG B:ASP85 4.7 67.1 1.0 NE2 B:HIS25 4.9 85.0 1.0 ND2 B:ASN166 5.0 68.7 1.0

Iron binding site 4 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe511 b:59.6 occ:1.00 FE2 B:FEO511 0.0 59.6 1.0 O B:FEO511 2.0 65.9 1.0 OD2 B:ASP85 2.0 65.9 1.0 NE2 B:HIS86 2.2 62.4 1.0 NE2 B:HIS228 2.2 62.3 1.0 OD1 B:ASP167 2.3 70.5 1.0 CE1 B:HIS86 3.0 62.2 1.0 O B:HOH714 3.1 57.2 1.0 CD2 B:HIS228 3.1 60.6 1.0 CG B:ASP167 3.1 69.9 1.0 CG B:ASP85 3.1 67.1 1.0 CE1 B:HIS228 3.1 62.9 1.0 CD2 B:HIS86 3.2 64.7 1.0 OD2 B:ASP167 3.2 71.0 1.0 FE1 B:FEO511 3.3 62.9 1.0 OD1 B:ASP85 3.6 67.3 1.0 OG B:SER227 4.1 57.1 1.0 ND1 B:HIS86 4.1 63.7 1.0 ND1 B:HIS228 4.2 61.1 1.0 CG B:HIS228 4.2 60.1 1.0 CG B:HIS86 4.2 65.2 1.0 CB B:ASP85 4.5 65.6 1.0 CB B:ASP167 4.5 67.5 1.0 CZ B:PHE24 4.7 77.3 1.0 CD2 B:HIS81 4.7 68.7 1.0 OH B:TYR195 4.7 77.3 1.0 CE1 B:PHE24 4.7 77.4 1.0 OE2 B:GLU83 4.8 73.2 1.0 NE2 B:HIS81 5.0 70.6 1.0

Iron binding site 5 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe521 b:46.9 occ:1.00 FE1 C:FEO521 0.0 46.9 1.0 O C:FEO521 2.0 49.0 1.0 OE2 C:GLU83 2.1 56.1 1.0 OD2 C:ASP167 2.1 49.2 1.0 NE2 C:HIS81 2.2 56.9 1.0 NE2 C:HIS148 2.5 56.0 1.0 CD2 C:HIS148 2.6 54.4 1.0 CD2 C:HIS81 2.9 56.4 1.0 O C:HOH724 3.2 51.7 1.0 CG C:ASP167 3.2 52.3 1.0 CD C:GLU83 3.3 59.5 1.0 FE2 C:FEO521 3.3 45.3 1.0 CE1 C:HIS81 3.3 57.7 1.0 OD1 C:ASP167 3.7 53.2 1.0 CE1 C:HIS148 3.8 55.5 1.0 CB C:GLU83 3.8 56.9 1.0 CG C:HIS148 3.9 54.5 1.0 OE1 C:GLU83 4.1 62.7 1.0 CG C:HIS81 4.1 57.5 1.0 CG C:GLU83 4.1 58.6 1.0 OD1 C:ASP85 4.3 52.7 1.0 ND1 C:HIS81 4.3 58.3 1.0 OD2 C:ASP85 4.3 47.6 1.0 ND1 C:HIS148 4.5 53.8 1.0 CB C:ASP167 4.5 51.0 1.0 CD2 C:HIS86 4.5 53.5 1.0 NE2 C:HIS86 4.6 54.0 1.0 CG C:ASP85 4.8 50.3 1.0 ND2 C:ASN166 4.8 53.4 1.0 NE2 C:HIS25 5.0 81.6 1.0 CB C:HIS148 5.0 55.9 1.0

Iron binding site 6 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe521 b:45.3 occ:1.00 FE2 C:FEO521 0.0 45.3 1.0 O C:FEO521 2.0 49.0 1.0 NE2 C:HIS228 2.0 42.8 1.0 OD2 C:ASP85 2.1 47.6 1.0 OD1 C:ASP167 2.2 53.2 1.0 NE2 C:HIS86 2.4 54.0 1.0 CD2 C:HIS228 3.0 41.5 1.0 CE1 C:HIS228 3.0 41.9 1.0 CG C:ASP167 3.1 52.3 1.0 OD2 C:ASP167 3.2 49.2 1.0 CG C:ASP85 3.2 50.3 1.0 CE1 C:HIS86 3.2 53.6 1.0 O C:HOH724 3.2 51.7 1.0 CD2 C:HIS86 3.3 53.5 1.0 FE1 C:FEO521 3.3 46.9 1.0 OD1 C:ASP85 3.7 52.7 1.0 ND1 C:HIS228 4.1 41.9 1.0 CG C:HIS228 4.1 41.6 1.0 OG C:SER227 4.1 46.9 1.0 ND1 C:HIS86 4.3 52.7 1.0 CG C:HIS86 4.3 52.5 1.0 CB C:ASP85 4.5 49.6 1.0 CE1 C:PHE24 4.5 77.6 1.0 OH C:TYR195 4.5 70.3 1.0 CB C:ASP167 4.5 51.0 1.0 OE2 C:GLU83 4.6 56.1 1.0 CD2 C:HIS81 4.6 56.4 1.0 CZ C:PHE24 4.8 79.2 1.0 NE2 C:HIS81 4.9 56.9 1.0

Iron binding site 7 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe531 b:48.6 occ:1.00 FE1 D:FEO531 0.0 48.6 1.0 OE2 D:GLU83 1.8 59.6 1.0 O D:FEO531 2.0 53.0 1.0 OD2 D:ASP167 2.2 55.8 1.0 NE2 D:HIS148 2.3 58.0 1.0 NE2 D:HIS81 2.4 54.0 1.0 CD2 D:HIS148 2.5 56.5 1.0 CD D:GLU83 2.9 59.5 1.0 CD2 D:HIS81 3.0 53.2 1.0 O D:HOH737 3.2 50.4 1.0 CG D:ASP167 3.3 56.2 1.0 CG D:GLU83 3.4 58.9 1.0 CE1 D:HIS81 3.5 55.2 1.0 CE1 D:HIS148 3.6 58.8 1.0 FE2 D:FEO531 3.6 49.0 1.0 CG D:HIS148 3.8 57.8 1.0 OD1 D:ASP167 3.9 58.4 1.0 CB D:GLU83 3.9 57.4 1.0 OE1 D:GLU83 3.9 62.0 1.0 CG D:HIS81 4.3 54.0 1.0 ND1 D:HIS148 4.3 57.6 1.0 NE2 D:HIS86 4.3 52.9 1.0 OD2 D:ASP85 4.4 47.9 1.0 OD1 D:ASP85 4.4 55.3 1.0 CD2 D:HIS86 4.4 53.8 1.0 ND1 D:HIS81 4.5 56.0 1.0 CB D:ASP167 4.5 52.8 1.0 NE2 D:HIS25 4.7 81.5 1.0 CG D:ASP85 4.8 52.6 1.0 ND2 D:ASN166 4.9 58.4 1.0 CB D:HIS148 5.0 58.0 1.0

Iron binding site 8 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe531 b:49.0 occ:1.00 FE2 D:FEO531 0.0 49.0 1.0 O D:FEO531 2.0 53.0 1.0 OD2 D:ASP85 2.1 47.9 1.0 NE2 D:HIS228 2.1 45.4 1.0 NE2 D:HIS86 2.2 52.9 1.0 OD1 D:ASP167 2.4 58.4 1.0 CD2 D:HIS228 2.8 43.1 1.0 CE1 D:HIS86 3.0 55.0 1.0 O D:HOH737 3.1 50.4 1.0 CG D:ASP167 3.2 56.2 1.0 CE1 D:HIS228 3.2 43.5 1.0 OD2 D:ASP167 3.2 55.8 1.0 CG D:ASP85 3.3 52.6 1.0 CD2 D:HIS86 3.3 53.8 1.0 FE1 D:FEO531 3.6 48.6 1.0 OD1 D:ASP85 3.9 55.3 1.0 OG D:SER227 4.0 50.2 1.0 CG D:HIS228 4.0 43.1 1.0 ND1 D:HIS86 4.2 54.8 1.0 ND1 D:HIS228 4.2 44.0 1.0 CG D:HIS86 4.4 53.9 1.0 CE1 D:PHE24 4.4 80.0 1.0 CB D:ASP85 4.4 52.5 1.0 OH D:TYR195 4.5 69.9 1.0 CB D:ASP167 4.6 52.8 1.0 OE2 D:GLU83 4.6 59.6 1.0 CD2 D:HIS81 4.9 53.2 1.0 CZ D:PHE24 4.9 81.2 1.0

R.Silaghi-Dumitrescu, D.M.Kurtz Jr, L.G.Ljungdahl, W.N.Lanzilotta. X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase. Biochemistry V. 44 6492 2005.
ISSN: ISSN 0006-2960
PubMed: 15850383
DOI: 10.1021/BI0473049