Iron in PDB 4d8f: Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)

All present enzymatic activity of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn):
1.17.4.1;

The structure of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn), PDB code: 4d8f was solved by L.M.K.Dassama, A.K.Boal, C.Krebs, A.C.Rosenzweig, J.M.Bollinger Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.66 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.221, 97.998, 100.291, 90.00, 97.79, 90.00
R / Rfree (%)	18.6 / 23.5

The structure of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn) also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Iron atom in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn) (pdb code 4d8f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn), PDB code: 4d8f:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:38.4 occ:1.00 OE2 A:GLU193 1.8 22.1 1.0 OE2 A:GLU227 2.0 26.6 1.0 OE2 A:GLU120 2.3 20.4 1.0 ND1 A:HIS230 2.3 13.9 1.0 CD A:GLU227 2.7 25.8 1.0 OE1 A:GLU227 2.7 28.8 1.0 CD A:GLU193 3.0 21.5 1.0 CE1 A:HIS230 3.0 15.4 1.0 MN A:MN402 3.1 36.8 1.0 CD A:GLU120 3.2 18.5 1.0 OE1 A:GLU120 3.4 19.3 1.0 CG A:HIS230 3.4 14.8 1.0 CG A:GLU193 3.6 20.1 1.0 CB A:HIS230 3.9 14.7 1.0 OE1 A:GLU193 4.0 22.8 1.0 NE2 A:GLN116 4.1 15.7 1.0 CG A:GLU227 4.2 21.7 1.0 NE2 A:HIS230 4.3 15.4 1.0 CG1 A:VAL92 4.4 14.2 1.0 CB A:GLU193 4.5 19.2 1.0 CD2 A:HIS230 4.5 15.7 1.0 O A:HOH642 4.5 20.1 1.0 CG A:GLU120 4.6 16.2 1.0 CE2 A:PHE197 4.6 21.1 1.0 CE1 A:HIS123 4.7 15.4 1.0 ND1 A:HIS123 4.7 16.0 1.0 CA A:GLU227 4.8 18.0 1.0 OE1 A:GLU89 4.8 23.4 1.0 CD2 A:PHE197 4.8 20.6 1.0 CB A:GLU227 5.0 18.7 1.0 CG A:GLN116 5.0 14.2 1.0

Iron binding site 2 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:45.5 occ:1.00 OE2 B:GLU193 1.9 24.8 1.0 ND1 B:HIS230 2.1 15.2 1.0 OE2 B:GLU120 2.2 22.9 1.0 OE1 B:GLU227 2.3 27.5 1.0 OE2 B:GLU227 2.5 28.8 1.0 CD B:GLU227 2.7 27.3 1.0 CE1 B:HIS230 2.9 15.2 1.0 CD B:GLU193 3.1 23.8 1.0 MN B:MN401 3.1 43.1 1.0 CD B:GLU120 3.2 21.5 1.0 CG B:HIS230 3.2 15.8 1.0 OE1 B:GLU120 3.4 23.6 1.0 CB B:HIS230 3.7 16.6 1.0 CG B:GLU193 3.7 22.7 1.0 OE1 B:GLU193 4.1 25.9 1.0 NE2 B:HIS230 4.1 15.6 1.0 CG B:GLU227 4.1 22.8 1.0 CD2 B:HIS230 4.3 15.1 1.0 CG1 B:VAL92 4.4 16.4 1.0 OE1 B:GLN116 4.4 17.4 1.0 O B:HOH573 4.6 39.9 1.0 CG B:GLU120 4.6 18.1 1.0 CA B:GLU227 4.6 19.8 1.0 CB B:GLU193 4.6 22.2 1.0 CE2 B:PHE197 4.6 28.0 1.0 OE1 B:GLU89 4.8 27.8 1.0 CB B:GLU227 4.8 20.2 1.0 CE1 B:HIS123 4.8 15.4 1.0 ND1 B:HIS123 4.8 14.7 1.0 CG B:GLN116 5.0 14.4 1.0

Iron binding site 3 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:47.1 occ:1.00 OE2 C:GLU193 1.9 28.5 1.0 OE2 C:GLU227 2.2 31.5 1.0 ND1 C:HIS230 2.3 21.3 1.0 OE2 C:GLU120 2.4 25.4 1.0 CD C:GLU227 2.8 30.3 1.0 OE1 C:GLU227 2.9 31.9 1.0 CD C:GLU193 3.0 27.4 1.0 CE1 C:HIS230 3.0 21.6 1.0 MN C:MN402 3.1 42.9 1.0 CD C:GLU120 3.2 23.9 1.0 OE1 C:GLU120 3.3 26.2 1.0 CG C:HIS230 3.3 21.3 1.0 CG C:GLU193 3.5 26.0 1.0 CB C:HIS230 3.8 20.3 1.0 OE1 C:GLU193 4.1 29.9 1.0 NE2 C:HIS230 4.2 21.8 1.0 CG C:GLU227 4.2 26.5 1.0 CD2 C:HIS230 4.4 21.1 1.0 OE1 C:GLN116 4.4 20.0 1.0 CB C:GLU193 4.4 25.0 1.0 CG1 C:VAL92 4.5 18.7 1.0 CE2 C:PHE197 4.6 24.3 1.0 CA C:GLU227 4.6 23.4 1.0 CG C:GLU120 4.6 20.9 1.0 OE1 C:GLU89 4.8 30.5 1.0 CE1 C:HIS123 4.8 17.1 1.0 CD2 C:PHE197 4.8 25.2 1.0 ND1 C:HIS123 4.9 17.8 1.0 CB C:GLU227 4.9 24.1 1.0

Iron binding site 4 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:48.4 occ:1.00 OE2 D:GLU193 1.9 26.8 1.0 OE1 D:GLU227 2.2 27.5 1.0 ND1 D:HIS230 2.3 18.8 1.0 OE2 D:GLU120 2.4 24.2 1.0 OE2 D:GLU227 2.5 28.2 1.0 CD D:GLU227 2.7 26.7 1.0 CD D:GLU193 2.9 26.6 1.0 CE1 D:HIS230 3.1 18.9 1.0 MN D:MN402 3.2 43.9 1.0 CD D:GLU120 3.3 22.9 1.0 CG D:HIS230 3.4 18.6 1.0 CG D:GLU193 3.4 26.0 1.0 OE1 D:GLU120 3.4 24.1 1.0 CB D:HIS230 3.7 18.3 1.0 OE1 D:GLU193 4.0 27.9 1.0 CG D:GLU227 4.2 23.6 1.0 OE1 D:GLN116 4.2 20.9 1.0 NE2 D:HIS230 4.3 17.5 1.0 CG1 D:VAL92 4.3 18.9 1.0 CB D:GLU193 4.3 25.3 1.0 CD2 D:HIS230 4.4 18.1 1.0 CE2 D:PHE197 4.5 27.9 1.0 CG D:GLU120 4.7 20.4 1.0 CA D:GLU227 4.8 21.2 1.0 OE1 D:GLU89 4.9 30.4 1.0 CE1 D:HIS123 4.9 18.4 1.0 CD2 D:PHE197 4.9 28.4 1.0 CB D:GLU227 4.9 21.5 1.0 ND1 D:HIS123 4.9 18.4 1.0

L.M.Dassama, A.K.Boal, C.Krebs, A.C.Rosenzweig, J.M.Bollinger. Evidence That the Beta Subunit of Chlamydia Trachomatis Ribonucleotide Reductase Is Active with the Manganese Ion of Its Manganese(IV)/Iron(III) Cofactor in Site 1. J.Am.Chem.Soc. V. 134 2520 2012.
ISSN: ISSN 0002-7863
PubMed: 22242660
DOI: 10.1021/JA211314P