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

The structure of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase, PDB code: 1ycg 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)	49.71 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	159.680, 159.680, 278.136, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 24.5

The structure of X-Ray 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)

14 atoms

The binding sites of Iron atom in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase (pdb code 1ycg). 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 Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase, PDB code: 1ycg:
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 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 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:52.4 occ:1.00 FE1 A:FEO501 0.0 52.4 1.0 NE2 A:HIS228 1.9 49.6 1.0 NE2 A:HIS86 2.0 59.1 1.0 OD1 A:ASP167 2.1 55.4 1.0 OD2 A:ASP85 2.2 50.8 1.0 O A:FEO501 2.5 56.3 1.0 CD2 A:HIS228 2.9 47.5 1.0 CE1 A:HIS228 2.9 48.5 1.0 C2 A:EDO602 2.9 58.5 1.0 CD2 A:HIS86 2.9 57.2 1.0 CG A:ASP167 3.0 56.2 1.0 CE1 A:HIS86 3.0 57.9 1.0 OD2 A:ASP167 3.1 57.2 1.0 C1 A:EDO602 3.3 56.1 1.0 CG A:ASP85 3.3 53.8 1.0 FE2 A:FEO501 3.8 56.7 1.0 OD1 A:ASP85 3.8 53.3 1.0 OG A:SER227 3.9 47.3 1.0 ND1 A:HIS228 4.0 46.7 1.0 CG A:HIS228 4.0 46.7 1.0 ND1 A:HIS86 4.0 57.4 1.0 CG A:HIS86 4.0 57.3 1.0 O2 A:EDO602 4.1 63.9 1.0 CB A:ASP167 4.4 56.0 1.0 O1 A:EDO602 4.5 52.0 1.0 CB A:ASP85 4.6 53.7 1.0 CD2 A:HIS81 4.6 58.4 1.0 OE2 A:GLU83 4.6 65.2 1.0 CE1 A:PHE24 4.7 72.8 1.0 CZ A:PHE24 4.7 73.1 1.0 OH A:TYR195 4.8 67.8 1.0 ND2 A:ASN166 4.9 67.1 1.0 CB A:SER227 4.9 46.0 1.0 CA A:ASP167 5.0 56.7 1.0 CD A:GLU83 5.0 65.5 1.0

Iron binding site 2 out of 8 in the X-Ray 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 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:56.7 occ:1.00 FE2 A:FEO501 0.0 56.7 1.0 NE2 A:HIS148 1.9 60.6 1.0 CD2 A:HIS148 2.0 59.6 1.0 OD2 A:ASP167 2.0 57.2 1.0 OE2 A:GLU83 2.2 65.2 1.0 NE2 A:HIS81 2.2 59.4 1.0 O A:FEO501 2.5 56.3 1.0 CD2 A:HIS81 2.9 58.4 1.0 O2 A:EDO602 3.1 63.9 1.0 CG A:ASP167 3.2 56.2 1.0 CE1 A:HIS148 3.3 58.5 1.0 CE1 A:HIS81 3.3 58.7 1.0 CG A:HIS148 3.3 58.4 1.0 C2 A:EDO602 3.4 58.5 1.0 CD A:GLU83 3.4 65.5 1.0 FE1 A:FEO501 3.8 52.4 1.0 OD1 A:ASP167 3.8 55.4 1.0 ND1 A:HIS148 3.9 57.4 1.0 C1 A:EDO602 4.0 56.1 1.0 CB A:GLU83 4.0 60.3 1.0 O1 A:EDO602 4.1 52.0 1.0 CG A:HIS81 4.1 57.6 1.0 OE1 A:GLU83 4.1 67.6 1.0 CB A:ASP167 4.2 56.0 1.0 ND1 A:HIS81 4.2 58.7 1.0 CG A:GLU83 4.3 62.8 1.0 CB A:HIS148 4.5 59.8 1.0 ND2 A:ASN166 4.7 67.1 1.0 CD2 A:HIS86 4.7 57.2 1.0 NE2 A:HIS86 4.8 59.1 1.0 OD1 A:ASP85 4.9 53.3 1.0

Iron binding site 3 out of 8 in the X-Ray 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 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:54.1 occ:1.00 FE1 B:FEO511 0.0 54.1 1.0 OE2 B:GLU83 2.0 69.9 1.0 NE2 B:HIS148 2.1 56.6 1.0 NE2 B:HIS81 2.1 62.2 1.0 CD2 B:HIS148 2.1 55.8 1.0 OD2 B:ASP167 2.2 65.3 1.0 O B:FEO511 2.4 56.3 1.0 CD2 B:HIS81 2.8 59.7 1.0 O2 B:EDO612 2.8 65.8 1.0 CD B:GLU83 3.2 70.4 1.0 CE1 B:HIS81 3.2 60.3 1.0 CG B:ASP167 3.3 62.6 1.0 C2 B:EDO612 3.4 64.0 1.0 CE1 B:HIS148 3.4 55.3 1.0 CG B:HIS148 3.5 55.8 1.0 CB B:GLU83 3.7 66.4 1.0 FE2 B:FEO511 3.8 55.1 1.0 OD1 B:ASP167 3.8 64.6 1.0 CG B:HIS81 4.0 59.1 1.0 CG B:GLU83 4.0 68.2 1.0 ND1 B:HIS148 4.0 54.6 1.0 O1 B:EDO612 4.0 57.3 1.0 C1 B:EDO612 4.1 62.5 1.0 OE1 B:GLU83 4.1 71.8 1.0 ND1 B:HIS81 4.2 61.3 1.0 CB B:ASP167 4.5 59.5 1.0 CD2 B:HIS86 4.5 58.5 1.0 OD1 B:ASP85 4.5 59.6 1.0 NE2 B:HIS86 4.5 57.1 1.0 CB B:HIS148 4.7 57.6 1.0 OD2 B:ASP85 4.8 56.6 1.0 ND2 B:ASN166 4.9 61.5 1.0

Iron binding site 4 out of 8 in the X-Ray 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 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:55.1 occ:1.00 FE2 B:FEO511 0.0 55.1 1.0 NE2 B:HIS228 1.8 52.8 1.0 OD1 B:ASP167 2.0 64.6 1.0 NE2 B:HIS86 2.0 57.1 1.0 OD2 B:ASP85 2.3 56.6 1.0 O B:FEO511 2.4 56.3 1.0 C2 B:EDO612 2.7 64.0 1.0 CD2 B:HIS228 2.7 48.9 1.0 CE1 B:HIS228 2.8 50.5 1.0 CE1 B:HIS86 2.9 56.3 1.0 CG B:ASP167 3.0 62.6 1.0 C1 B:EDO612 3.1 62.5 1.0 CD2 B:HIS86 3.1 58.5 1.0 OD2 B:ASP167 3.3 65.3 1.0 CG B:ASP85 3.4 60.3 1.0 FE1 B:FEO511 3.8 54.1 1.0 OG B:SER227 3.8 47.6 1.0 O2 B:EDO612 3.8 65.8 1.0 CG B:HIS228 3.9 48.7 1.0 ND1 B:HIS228 3.9 49.2 1.0 OD1 B:ASP85 3.9 59.6 1.0 ND1 B:HIS86 4.0 57.4 1.0 CG B:HIS86 4.2 58.6 1.0 O1 B:EDO612 4.3 57.3 1.0 CB B:ASP167 4.3 59.5 1.0 OH B:TYR195 4.5 63.4 1.0 CB B:ASP85 4.7 59.5 1.0 CD2 B:HIS81 4.7 59.7 1.0 CE1 B:PHE24 4.7 74.6 1.0 OE2 B:GLU83 4.8 69.9 1.0 CA B:ASP167 4.8 58.2 1.0 CB B:SER227 4.9 46.2 1.0 ND2 B:ASN166 4.9 61.5 1.0 CZ B:PHE24 4.9 74.6 1.0

Iron binding site 5 out of 8 in the X-Ray 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 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:46.8 occ:1.00 FE1 C:FEO521 0.0 46.8 1.0 OE2 C:GLU83 2.0 51.1 1.0 NE2 C:HIS81 2.0 51.4 1.0 NE2 C:HIS148 2.1 57.2 1.0 OD2 C:ASP167 2.2 45.9 1.0 CD2 C:HIS148 2.2 55.8 1.0 O C:FEO521 2.4 45.0 1.0 CD2 C:HIS81 2.8 50.3 1.0 CE1 C:HIS81 3.1 50.8 1.0 CD C:GLU83 3.2 52.1 1.0 CG C:ASP167 3.3 48.1 1.0 CE1 C:HIS148 3.4 55.2 1.0 O1 C:EDO622 3.5 40.2 1.0 CG C:HIS148 3.5 53.4 1.0 C1 C:EDO622 3.5 45.6 1.0 O2 C:EDO622 3.6 59.3 1.0 C2 C:EDO622 3.6 48.6 1.0 FE2 C:FEO521 3.7 43.5 1.0 OD1 C:ASP167 3.8 50.6 1.0 CB C:GLU83 3.8 50.1 1.0 OE1 C:GLU83 4.0 56.1 1.0 ND1 C:HIS148 4.0 53.0 1.0 CG C:HIS81 4.0 51.1 1.0 CG C:GLU83 4.1 51.4 1.0 ND1 C:HIS81 4.2 52.5 1.0 CB C:ASP167 4.4 47.2 1.0 OD1 C:ASP85 4.5 47.1 1.0 CB C:HIS148 4.7 53.2 1.0 CD2 C:HIS86 4.8 47.2 1.0 OD2 C:ASP85 4.8 41.7 1.0 ND2 C:ASN166 4.8 52.5 1.0 NE2 C:HIS86 4.9 47.6 1.0

Iron binding site 6 out of 8 in the X-Ray 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 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:43.5 occ:1.00 FE2 C:FEO521 0.0 43.5 1.0 NE2 C:HIS228 1.8 36.4 1.0 OD1 C:ASP167 2.1 50.6 1.0 OD2 C:ASP85 2.3 41.7 1.0 O C:FEO521 2.3 45.0 1.0 NE2 C:HIS86 2.4 47.6 1.0 CD2 C:HIS228 2.7 32.8 1.0 CE1 C:HIS228 2.8 34.5 1.0 CG C:ASP167 3.1 48.1 1.0 C1 C:EDO622 3.1 45.6 1.0 CE1 C:HIS86 3.2 47.4 1.0 OD2 C:ASP167 3.3 45.9 1.0 CD2 C:HIS86 3.3 47.2 1.0 CG C:ASP85 3.4 45.8 1.0 C2 C:EDO622 3.6 48.6 1.0 FE1 C:FEO521 3.7 46.8 1.0 CG C:HIS228 3.9 32.4 1.0 ND1 C:HIS228 3.9 33.2 1.0 OD1 C:ASP85 3.9 47.1 1.0 OG C:SER227 3.9 42.5 1.0 O1 C:EDO622 4.2 40.2 1.0 ND1 C:HIS86 4.3 46.9 1.0 OH C:TYR195 4.4 62.0 1.0 CG C:HIS86 4.4 45.9 1.0 CB C:ASP167 4.4 47.2 1.0 OE2 C:GLU83 4.5 51.1 1.0 CE1 C:PHE24 4.6 72.5 1.0 CB C:ASP85 4.7 44.9 1.0 CD2 C:HIS81 4.7 50.3 1.0 O2 C:EDO622 4.8 59.3 1.0 CA C:ASP167 4.9 48.2 1.0 NE2 C:HIS81 5.0 51.4 1.0

Iron binding site 7 out of 8 in the X-Ray 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 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:46.1 occ:1.00 FE1 D:FEO531 0.0 46.1 1.0 OE2 D:GLU83 1.6 61.2 1.0 NE2 D:HIS148 2.0 54.8 1.0 NE2 D:HIS81 2.1 50.6 1.0 CD2 D:HIS148 2.2 52.5 1.0 OD2 D:ASP167 2.3 48.4 1.0 O D:FEO531 2.5 46.3 1.0 CD D:GLU83 2.7 57.5 1.0 CD2 D:HIS81 2.8 48.7 1.0 CE1 D:HIS148 3.2 52.0 1.0 CE1 D:HIS81 3.2 49.7 1.0 CG D:GLU83 3.3 56.2 1.0 O2 D:EDO632 3.4 58.2 1.0 CG D:ASP167 3.4 48.3 1.0 CG D:HIS148 3.5 52.0 1.0 OE1 D:GLU83 3.7 60.6 1.0 CB D:GLU83 3.8 53.6 1.0 ND1 D:HIS148 3.9 51.4 1.0 CG D:HIS81 4.0 49.5 1.0 FE2 D:FEO531 4.0 42.4 1.0 OD1 D:ASP167 4.1 48.7 1.0 C2 D:EDO632 4.1 63.1 1.0 ND1 D:HIS81 4.2 50.7 1.0 O1 D:EDO632 4.4 61.6 1.0 CB D:ASP167 4.5 44.3 1.0 OD1 D:ASP85 4.6 46.3 1.0 CD2 D:HIS86 4.6 50.5 1.0 C1 D:EDO632 4.6 61.5 1.0 CB D:HIS148 4.6 53.0 1.0 NE2 D:HIS86 4.7 52.1 1.0 OD2 D:ASP85 4.9 39.6 1.0 ND2 D:ASN166 4.9 53.2 1.0

Iron binding site 8 out of 8 in the X-Ray 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 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:42.4 occ:1.00 FE2 D:FEO531 0.0 42.4 1.0 NE2 D:HIS228 1.8 37.5 1.0 NE2 D:HIS86 2.0 52.1 1.0 OD2 D:ASP85 2.0 39.6 1.0 O D:FEO531 2.3 46.3 1.0 OD1 D:ASP167 2.4 48.7 1.0 C2 D:EDO632 2.8 63.1 1.0 CD2 D:HIS228 2.8 35.4 1.0 CE1 D:HIS228 2.8 36.4 1.0 CE1 D:HIS86 2.8 51.8 1.0 CD2 D:HIS86 3.0 50.5 1.0 CG D:ASP85 3.1 43.9 1.0 CG D:ASP167 3.2 48.3 1.0 OD2 D:ASP167 3.4 48.4 1.0 O2 D:EDO632 3.5 58.2 1.0 C1 D:EDO632 3.7 61.5 1.0 OD1 D:ASP85 3.7 46.3 1.0 ND1 D:HIS228 3.9 35.6 1.0 OG D:SER227 3.9 44.8 1.0 CG D:HIS228 3.9 35.5 1.0 ND1 D:HIS86 4.0 51.5 1.0 FE1 D:FEO531 4.0 46.1 1.0 CG D:HIS86 4.1 50.6 1.0 CB D:ASP85 4.3 45.6 1.0 OE2 D:GLU83 4.6 61.2 1.0 CE1 D:PHE24 4.6 69.8 1.0 CB D:ASP167 4.6 44.3 1.0 O1 D:EDO632 4.6 61.6 1.0 OH D:TYR195 4.7 58.1 1.0 CD2 D:HIS81 4.9 48.7 1.0 CB D:SER227 5.0 42.3 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