Iron in PDB 3hx9: Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site

The structure of Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site, PDB code: 3hx9 was solved by N.Chim, T.Q.Nguyen, A.Iniguez, C.W.Goulding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.35 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	43.971, 64.622, 71.082, 90.00, 90.01, 90.00
R / Rfree (%)	18.6 / 23.1

The structure of Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site (pdb code 3hx9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site, PDB code: 3hx9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:21.7 occ:1.00 FE A:HEM300 0.0 21.7 1.0 NC A:HEM300 2.0 19.7 1.0 NA A:HEM300 2.0 21.9 1.0 NB A:HEM300 2.0 19.9 1.0 ND A:HEM300 2.1 20.7 1.0 NE2 A:HIS75 2.2 20.4 1.0 CE1 A:HIS75 3.0 20.1 1.0 C4B A:HEM300 3.0 20.2 1.0 C1A A:HEM300 3.0 23.4 1.0 C4D A:HEM300 3.0 20.8 1.0 C4C A:HEM300 3.1 18.2 1.0 C1C A:HEM300 3.1 20.4 1.0 C4A A:HEM300 3.1 23.0 1.0 C1B A:HEM300 3.1 18.6 1.0 C1D A:HEM300 3.1 19.4 1.0 CD2 A:HIS75 3.3 21.9 1.0 CHA A:HEM300 3.4 21.8 1.0 CHC A:HEM300 3.4 21.9 1.0 CHD A:HEM300 3.4 19.3 1.0 CHB A:HEM300 3.5 20.6 1.0 CHA A:HEM200 3.8 18.4 1.0 C1A A:HEM200 3.8 19.8 1.0 C4D A:HEM200 3.8 19.9 1.0 NA A:HEM200 4.0 20.1 1.0 ND A:HEM200 4.0 17.8 1.0 ND1 A:HIS75 4.2 22.3 1.0 C2A A:HEM300 4.2 26.1 1.0 C3B A:HEM300 4.2 21.9 1.0 C3A A:HEM300 4.3 27.6 1.0 C3D A:HEM300 4.3 18.7 1.0 C2B A:HEM300 4.3 19.9 1.0 C2C A:HEM300 4.3 20.4 1.0 C3C A:HEM300 4.3 18.0 1.0 C2D A:HEM300 4.3 18.9 1.0 CG A:HIS75 4.4 21.2 1.0 C3D A:HEM200 4.4 19.8 1.0 C2A A:HEM200 4.5 21.8 1.0 FE A:HEM200 4.6 18.2 1.0 C1D A:HEM200 4.7 19.0 1.0 C4A A:HEM200 4.7 18.8 1.0 C3A A:HEM200 4.9 22.4 1.0 C2D A:HEM200 5.0 17.5 1.0

Iron binding site 2 out of 4 in the Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:18.2 occ:1.00 FE A:HEM200 0.0 18.2 1.0 NA A:HEM200 2.0 20.1 1.0 NC A:HEM200 2.0 19.3 1.0 ND A:HEM200 2.1 17.8 1.0 NB A:HEM200 2.1 19.2 1.0 CL A:CL301 2.4 18.2 1.0 C1A A:HEM200 3.0 19.8 1.0 C4C A:HEM200 3.0 17.6 1.0 C4D A:HEM200 3.0 19.9 1.0 C4A A:HEM200 3.1 18.8 1.0 C1D A:HEM200 3.1 19.0 1.0 C1B A:HEM200 3.1 16.7 1.0 C4B A:HEM200 3.1 19.5 1.0 C1C A:HEM200 3.1 18.7 1.0 CHA A:HEM200 3.4 18.4 1.0 CHD A:HEM200 3.4 21.8 1.0 CHB A:HEM200 3.5 20.6 1.0 CHC A:HEM200 3.5 16.9 1.0 CHD A:HEM300 3.7 19.3 1.0 C1D A:HEM300 3.9 19.4 1.0 C4C A:HEM300 3.9 18.2 1.0 ND A:HEM300 4.1 20.7 1.0 NC A:HEM300 4.1 19.7 1.0 OD1 A:ASN7 4.2 22.5 1.0 C3C A:HEM200 4.2 20.8 1.0 C2A A:HEM200 4.2 21.8 1.0 C3A A:HEM200 4.2 22.4 1.0 C3D A:HEM200 4.3 19.8 1.0 C2C A:HEM200 4.3 16.3 1.0 C2D A:HEM200 4.3 17.5 1.0 C2B A:HEM200 4.3 17.4 1.0 C3B A:HEM200 4.3 19.6 1.0 CZ A:PHE23 4.6 16.5 1.0 C3C A:HEM300 4.6 18.0 1.0 FE A:HEM300 4.6 21.7 1.0 C2D A:HEM300 4.7 18.9 1.0 C4D A:HEM300 4.9 20.8 1.0 C1C A:HEM300 4.9 20.4 1.0 CE1 A:PHE23 4.9 19.7 1.0 CG A:ASN7 5.0 15.7 1.0

Iron binding site 3 out of 4 in the Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe300 b:21.7 occ:1.00 FE B:HEM300 0.0 21.7 1.0 NC B:HEM300 2.0 20.4 1.0 NA B:HEM300 2.0 21.9 1.0 NB B:HEM300 2.0 20.3 1.0 ND B:HEM300 2.1 19.6 1.0 NE2 B:HIS75 2.2 18.2 1.0 CE1 B:HIS75 3.0 18.4 1.0 C4B B:HEM300 3.0 18.6 1.0 C4C B:HEM300 3.0 19.1 1.0 C1A B:HEM300 3.0 23.8 1.0 C4D B:HEM300 3.0 21.6 1.0 C1C B:HEM300 3.1 21.6 1.0 C1B B:HEM300 3.1 19.6 1.0 C4A B:HEM300 3.1 23.0 1.0 C1D B:HEM300 3.1 20.0 1.0 CD2 B:HIS75 3.3 21.9 1.0 CHA B:HEM300 3.4 21.4 1.0 CHC B:HEM300 3.4 22.5 1.0 CHD B:HEM300 3.5 19.5 1.0 CHB B:HEM300 3.5 20.4 1.0 CHA B:HEM200 3.8 18.4 1.0 C4D B:HEM200 3.8 18.4 1.0 C1A B:HEM200 3.8 20.8 1.0 ND B:HEM200 4.0 17.6 1.0 NA B:HEM200 4.0 21.8 1.0 ND1 B:HIS75 4.2 22.2 1.0 C3B B:HEM300 4.2 21.3 1.0 C2B B:HEM300 4.3 21.4 1.0 C2A B:HEM300 4.3 25.2 1.0 C2C B:HEM300 4.3 20.7 1.0 C3C B:HEM300 4.3 18.3 1.0 C3A B:HEM300 4.3 26.9 1.0 C3D B:HEM300 4.3 19.4 1.0 C2D B:HEM300 4.3 19.7 1.0 CG B:HIS75 4.4 21.5 1.0 C3D B:HEM200 4.5 18.2 1.0 C2A B:HEM200 4.5 23.4 1.0 C1D B:HEM200 4.6 19.3 1.0 FE B:HEM200 4.7 18.5 1.0 C4A B:HEM200 4.7 21.4 1.0 C3A B:HEM200 4.9 24.3 1.0 C2D B:HEM200 5.0 17.4 1.0

Iron binding site 4 out of 4 in the Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Heme-Degrader, Mhud (RV3592), From Mycobacterium Tuberculosis with Two Hemes Bound in Its Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:18.5 occ:1.00 FE B:HEM200 0.0 18.5 1.0 NC B:HEM200 2.0 19.6 1.0 NA B:HEM200 2.0 21.8 1.0 ND B:HEM200 2.1 17.6 1.0 NB B:HEM200 2.1 21.2 1.0 CL B:CL301 2.3 18.4 1.0 C4C B:HEM200 3.0 16.9 1.0 C1A B:HEM200 3.0 20.8 1.0 C1D B:HEM200 3.0 19.3 1.0 C1B B:HEM200 3.1 16.7 1.0 C4D B:HEM200 3.1 18.4 1.0 C1C B:HEM200 3.1 18.1 1.0 C4B B:HEM200 3.1 20.2 1.0 C4A B:HEM200 3.1 21.4 1.0 CHD B:HEM200 3.4 20.3 1.0 CHA B:HEM200 3.4 18.4 1.0 CHB B:HEM200 3.5 19.8 1.0 CHC B:HEM200 3.5 17.2 1.0 CHD B:HEM300 3.8 19.5 1.0 C1D B:HEM300 3.9 20.0 1.0 C4C B:HEM300 4.0 19.1 1.0 ND B:HEM300 4.1 19.6 1.0 C3C B:HEM200 4.2 21.1 1.0 NC B:HEM300 4.2 20.4 1.0 OD1 B:ASN7 4.2 21.7 1.0 C2A B:HEM200 4.2 23.4 1.0 C3A B:HEM200 4.3 24.3 1.0 C2C B:HEM200 4.3 15.8 1.0 C2D B:HEM200 4.3 17.4 1.0 C3D B:HEM200 4.3 18.2 1.0 C2B B:HEM200 4.3 19.6 1.0 C3B B:HEM200 4.3 19.0 1.0 CZ B:PHE23 4.6 14.7 1.0 C3C B:HEM300 4.6 18.3 1.0 FE B:HEM300 4.7 21.7 1.0 C2D B:HEM300 4.7 19.7 1.0 CE1 B:PHE23 4.9 17.7 1.0 C4D B:HEM300 4.9 21.6 1.0 C1C B:HEM300 4.9 21.6 1.0 CG B:ASN7 5.0 15.3 1.0

N.Chim, A.Iniguez, T.Q.Nguyen, C.W.Goulding. Unusual Diheme Conformation of the Heme-Degrading Protein From Mycobacterium Tuberculosis J.Mol.Biol. V. 395 595 2009.
ISSN: ISSN 0022-2836
PubMed: 19917297
DOI: 10.1016/J.JMB.2009.11.025