Iron in PDB 6tsi: CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1

All present enzymatic activity of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1:
1.7.2.1; 1.7.99.1;

The structure of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1, PDB code: 6tsi was solved by T.Kluenemann, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.61 / 2.38
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	163.762, 91.093, 112.706, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 28

The structure of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Iron atom in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 (pdb code 6tsi). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1, PDB code: 6tsi:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:28.4 occ:1.00 FE A:HEC601 0.0 28.4 1.0 ND A:HEC601 2.1 17.1 1.0 NC A:HEC601 2.1 19.9 1.0 NE2 A:HIS51 2.1 15.1 1.0 NA A:HEC601 2.1 14.8 1.0 NB A:HEC601 2.1 17.1 1.0 SD A:MET88 2.5 18.6 1.0 CE1 A:HIS51 3.0 15.3 1.0 C1D A:HEC601 3.1 15.1 1.0 C4C A:HEC601 3.1 16.5 1.0 C4D A:HEC601 3.1 12.8 1.0 C1C A:HEC601 3.1 16.7 1.0 C1A A:HEC601 3.1 15.0 1.0 CD2 A:HIS51 3.1 13.6 1.0 C4A A:HEC601 3.1 13.8 1.0 C4B A:HEC601 3.1 11.6 1.0 C1B A:HEC601 3.1 14.8 1.0 HE1 A:HIS51 3.2 18.6 1.0 HD2 A:HIS51 3.3 16.5 1.0 CHD A:HEC601 3.4 14.1 1.0 HE2 A:MET88 3.5 18.0 1.0 CHA A:HEC601 3.5 14.7 1.0 CE A:MET88 3.5 14.8 1.0 CHC A:HEC601 3.5 13.5 1.0 CHB A:HEC601 3.5 14.8 1.0 HE1 A:MET88 3.6 18.0 1.0 CG A:MET88 3.9 19.0 1.0 HG2 A:MET88 3.9 23.0 1.0 HB2 A:MET88 4.0 26.0 1.0 HA A:MET88 4.0 21.1 1.0 HD11 A:LEU63 4.1 17.2 1.0 ND1 A:HIS51 4.2 11.2 1.0 HD2 A:PRO89 4.2 25.2 1.0 CG A:HIS51 4.2 12.5 1.0 CB A:MET88 4.3 21.5 1.0 HE3 A:MET88 4.4 18.0 1.0 C3C A:HEC601 4.4 14.7 1.0 C3D A:HEC601 4.4 18.1 1.0 C2D A:HEC601 4.4 13.9 1.0 C2C A:HEC601 4.4 16.7 1.0 C2A A:HEC601 4.4 16.9 1.0 C3B A:HEC601 4.4 14.3 1.0 C3A A:HEC601 4.4 14.8 1.0 C2B A:HEC601 4.5 17.9 1.0 HHD A:HEC601 4.5 17.2 1.0 HHA A:HEC601 4.5 17.9 1.0 HHC A:HEC601 4.6 16.4 1.0 HHB A:HEC601 4.6 18.0 1.0 HD21 A:LEU63 4.6 20.6 1.0 HG3 A:MET88 4.6 23.0 1.0 CA A:MET88 4.7 17.4 1.0 HE1 A:TRP91 4.8 20.7 1.0 HD1 A:HIS51 4.9 13.7 1.0

Iron binding site 2 out of 4 in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:30.4 occ:1.00 FE A:DHE602 0.0 30.4 1.0 NE2 A:HIS182 2.0 24.1 1.0 NA A:DHE602 2.0 19.1 1.0 NC A:DHE602 2.1 19.3 1.0 ND A:DHE602 2.1 16.4 1.0 O A:HOH742 2.1 18.3 1.0 NB A:DHE602 2.1 18.8 1.0 CE1 A:HIS182 2.7 18.1 1.0 HE1 A:HIS182 2.8 21.9 1.0 C1A A:DHE602 3.1 19.7 1.0 C1C A:DHE602 3.1 18.0 1.0 C4C A:DHE602 3.1 17.4 1.0 C1D A:DHE602 3.1 16.1 1.0 C4A A:DHE602 3.1 15.1 1.0 C4D A:DHE602 3.1 14.2 1.0 CD2 A:HIS182 3.1 21.2 1.0 C1B A:DHE602 3.2 18.6 1.0 C4B A:DHE602 3.2 15.9 1.0 HH B:TYR10 3.4 19.2 1.0 HD2 A:HIS182 3.4 25.7 1.0 CHD A:DHE602 3.5 14.6 1.0 CHA A:DHE602 3.5 16.1 1.0 CHC A:DHE602 3.5 16.8 1.0 CHB A:DHE602 3.5 18.9 1.0 ND1 A:HIS182 3.9 15.4 1.0 CG A:HIS182 4.1 13.4 1.0 OH B:TYR10 4.2 15.8 1.0 HE1 B:TYR10 4.3 20.3 1.0 C2C A:DHE602 4.3 11.7 1.0 HD2 A:ARG225 4.3 17.4 1.0 C3A A:DHE602 4.4 17.3 1.0 C2A A:DHE602 4.4 17.5 1.0 HE2 A:HIS327 4.4 15.8 1.0 C2B A:DHE602 4.4 16.2 1.0 C2D A:DHE602 4.4 16.7 1.0 C3D A:DHE602 4.4 15.2 1.0 C3C A:DHE602 4.5 14.4 1.0 O A:HOH739 4.5 15.2 1.0 HHD A:DHE602 4.5 17.7 1.0 HHA A:DHE602 4.5 19.5 1.0 C3B A:DHE602 4.5 15.2 1.0 HHC A:DHE602 4.6 20.4 1.0 HHB A:DHE602 4.6 22.9 1.0 HD1 A:HIS182 4.6 18.8 1.0 O2B A:DHE602 4.7 18.9 1.0 HZ A:PHE425 4.8 26.2 1.0 HE A:ARG225 4.9 17.7 1.0 CE1 B:TYR10 4.9 16.7 1.0 CZ B:TYR10 5.0 15.3 1.0

Iron binding site 3 out of 4 in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:35.2 occ:1.00 FE B:HEC601 0.0 35.2 1.0 NE2 B:HIS51 2.0 19.9 1.0 ND B:HEC601 2.1 21.4 1.0 NC B:HEC601 2.1 21.5 1.0 NA B:HEC601 2.1 15.5 1.0 NB B:HEC601 2.1 19.2 1.0 SD B:MET88 2.4 23.6 1.0 CE1 B:HIS51 2.7 17.1 1.0 HE1 B:HIS51 2.8 20.8 1.0 C1D B:HEC601 3.1 17.2 1.0 C1A B:HEC601 3.1 15.1 1.0 C4C B:HEC601 3.1 16.4 1.0 C4D B:HEC601 3.1 17.0 1.0 C4A B:HEC601 3.1 16.1 1.0 C4B B:HEC601 3.1 14.4 1.0 C1C B:HEC601 3.1 17.3 1.0 C1B B:HEC601 3.1 19.0 1.0 CD2 B:HIS51 3.2 17.6 1.0 CE B:MET88 3.4 21.5 1.0 HE2 B:MET88 3.4 26.0 1.0 CHD B:HEC601 3.5 16.5 1.0 CHA B:HEC601 3.5 15.7 1.0 CHB B:HEC601 3.5 16.9 1.0 CHC B:HEC601 3.5 14.4 1.0 HD2 B:HIS51 3.5 21.4 1.0 HE1 B:MET88 3.5 26.0 1.0 CG B:MET88 3.7 20.8 1.0 HB2 B:MET88 3.8 25.1 1.0 HG2 B:MET88 3.8 25.2 1.0 ND1 B:HIS51 4.0 14.6 1.0 CG B:HIS51 4.2 15.1 1.0 HA B:MET88 4.2 26.4 1.0 CB B:MET88 4.2 20.8 1.0 HE3 B:MET88 4.3 26.0 1.0 HD11 B:LEU63 4.3 19.3 1.0 C3C B:HEC601 4.4 15.3 1.0 C2D B:HEC601 4.4 13.8 1.0 C3D B:HEC601 4.4 17.7 1.0 C3B B:HEC601 4.4 15.4 1.0 C2A B:HEC601 4.4 18.9 1.0 C3A B:HEC601 4.4 17.1 1.0 C2C B:HEC601 4.5 18.7 1.0 HD2 B:PRO89 4.5 27.7 1.0 HG3 B:MET88 4.5 25.2 1.0 C2B B:HEC601 4.5 19.8 1.0 HHD B:HEC601 4.5 20.0 1.0 HD21 B:LEU63 4.5 17.8 1.0 HHA B:HEC601 4.5 19.0 1.0 HHB B:HEC601 4.6 20.5 1.0 HHC B:HEC601 4.6 17.5 1.0 HD1 B:HIS51 4.7 17.8 1.0 CA B:MET88 4.8 21.8 1.0 HE1 B:TRP91 4.9 21.0 1.0

Iron binding site 4 out of 4 in the CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of CD1 Nitrite Reductase Nirs with Bound Dihydro-Heme D1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:33.5 occ:1.00 FE B:DHE602 0.0 33.5 1.0 NE2 B:HIS182 2.0 21.2 1.0 NA B:DHE602 2.0 20.1 1.0 NC B:DHE602 2.1 18.1 1.0 ND B:DHE602 2.1 19.8 1.0 NB B:DHE602 2.1 16.1 1.0 O A:HOH725 2.2 16.9 1.0 CD2 B:HIS182 2.9 15.4 1.0 CE1 B:HIS182 3.0 16.8 1.0 C1A B:DHE602 3.1 18.1 1.0 C4A B:DHE602 3.1 14.1 1.0 HD2 B:HIS182 3.1 18.6 1.0 C4C B:DHE602 3.1 16.4 1.0 C1C B:DHE602 3.1 18.3 1.0 C4D B:DHE602 3.1 16.1 1.0 C1D B:DHE602 3.1 14.2 1.0 C1B B:DHE602 3.1 15.6 1.0 C4B B:DHE602 3.2 16.1 1.0 HE1 B:HIS182 3.2 20.4 1.0 CHA B:DHE602 3.5 19.2 1.0 CHD B:DHE602 3.5 14.8 1.0 CHB B:DHE602 3.5 19.9 1.0 CHC B:DHE602 3.5 16.8 1.0 HH A:TYR10 3.6 19.4 1.0 ND1 B:HIS182 4.1 14.4 1.0 CG B:HIS182 4.1 10.9 1.0 OH A:TYR10 4.2 15.9 1.0 C3A B:DHE602 4.3 15.0 1.0 C2A B:DHE602 4.3 16.6 1.0 HE1 A:TYR10 4.3 21.7 1.0 C2C B:DHE602 4.3 14.4 1.0 HD2 B:ARG225 4.3 16.4 1.0 C2B B:DHE602 4.4 18.9 1.0 HE2 B:HIS327 4.4 20.4 1.0 C2D B:DHE602 4.4 13.8 1.0 C3D B:DHE602 4.4 12.8 1.0 O B:HOH719 4.4 15.9 1.0 HHA B:DHE602 4.5 23.2 1.0 C3C B:DHE602 4.5 15.4 1.0 HHD B:DHE602 4.5 18.0 1.0 C3B B:DHE602 4.5 17.0 1.0 HHB B:DHE602 4.6 24.1 1.0 HHC B:DHE602 4.6 20.3 1.0 O2B B:DHE602 4.7 22.5 1.0 HD1 B:HIS182 4.8 17.5 1.0 CE1 A:TYR10 5.0 17.9 1.0 HZ B:PHE425 5.0 22.2 1.0 O2C B:DHE602 5.0 13.7 1.0

T.Klunemann, W.Blankenfeldt. Structure of Heme D 1 -Free Cd 1 Nitrite Reductase Nirs. Acta Crystallogr.,Sect.F V. 76 250 2020.
ISSN: ESSN 2053-230X
PubMed: 32510465
DOI: 10.1107/S2053230X20006676