Iron in PDB 4d8g: Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn)

All present enzymatic activity of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn):
1.17.4.1;

The structure of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn), PDB code: 4d8g 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)	29.74 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.387, 98.264, 100.390, 90.00, 97.67, 90.00
R / Rfree (%)	19.4 / 22.1

The structure of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low 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 2 - Low Mn) (pdb code 4d8g). 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 2 - Low Mn), PDB code: 4d8g:
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 2 - Low 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 2 - Low Mn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:17.1 occ:0.50 OE2 A:GLU193 1.8 27.4 1.0 OE1 A:GLU227 2.1 28.5 1.0 ND1 A:HIS230 2.2 16.7 1.0 OE2 A:GLU227 2.2 26.4 1.0 OE2 A:GLU120 2.3 26.5 1.0 O A:HOH619 2.3 23.2 0.5 CD A:GLU227 2.5 29.7 1.0 CD A:GLU193 2.9 27.0 1.0 CE1 A:HIS230 3.0 18.2 1.0 CD A:GLU120 3.2 22.9 1.0 CG A:HIS230 3.3 15.2 1.0 MN A:MN401 3.3 14.8 0.5 OE1 A:GLU120 3.4 29.4 1.0 CG A:GLU193 3.5 23.2 1.0 CB A:HIS230 3.8 14.5 1.0 OE1 A:GLU193 4.0 29.5 1.0 CG A:GLU227 4.0 23.5 1.0 OE1 A:GLN116 4.1 20.3 1.0 NE2 A:HIS230 4.2 17.1 1.0 CD2 A:HIS230 4.3 14.9 1.0 CG1 A:VAL92 4.3 16.1 1.0 CB A:GLU193 4.5 19.7 1.0 O A:HOH618 4.5 18.2 0.5 CE2 A:PHE197 4.6 25.2 1.0 CG A:GLU120 4.6 17.7 1.0 CA A:GLU227 4.7 17.3 1.0 CB A:GLU227 4.8 18.4 1.0 CD2 A:PHE197 4.8 25.2 1.0 CE1 A:HIS123 4.9 16.3 1.0 CD A:GLN116 4.9 14.4 1.0 CG A:GLN116 4.9 13.8 1.0 ND1 A:HIS123 4.9 15.9 1.0

Iron binding site 2 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low 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 2 - Low Mn) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:24.2 occ:0.50 OE2 B:GLU193 1.8 28.5 1.0 ND1 B:HIS230 2.0 19.7 1.0 OE2 B:GLU227 2.2 27.8 1.0 OE2 B:GLU120 2.2 29.3 1.0 OE1 B:GLU227 2.3 27.7 1.0 O B:HOH578 2.4 23.6 0.5 CD B:GLU227 2.6 28.1 1.0 CE1 B:HIS230 2.8 17.5 1.0 CD B:GLU193 3.0 27.7 1.0 CD B:GLU120 3.1 27.3 1.0 CG B:HIS230 3.2 14.8 1.0 OE1 B:GLU120 3.3 30.1 1.0 MN B:MN401 3.3 24.9 0.5 CG B:GLU193 3.7 22.7 1.0 CB B:HIS230 3.7 15.6 1.0 OE1 B:GLU193 4.0 30.6 1.0 NE2 B:HIS230 4.0 15.6 1.0 CG B:GLU227 4.1 21.5 1.0 OE1 B:GLN116 4.1 21.7 1.0 CG1 B:VAL92 4.2 19.1 1.0 CD2 B:HIS230 4.2 17.8 1.0 CB B:GLU193 4.5 19.8 1.0 O B:HOH590 4.5 26.9 0.5 CG B:GLU120 4.5 19.3 1.0 CE2 B:PHE197 4.6 25.1 1.0 CA B:GLU227 4.6 18.9 1.0 CE1 B:HIS123 4.8 16.3 1.0 CB B:GLU227 4.8 19.9 1.0 CG B:GLN116 4.8 14.6 1.0 CD B:GLN116 4.9 16.0 1.0 ND1 B:HIS123 4.9 16.5 1.0 OE1 B:GLU89 5.0 35.4 1.0

Iron binding site 3 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low 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 2 - Low Mn) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:23.5 occ:0.50 OE2 C:GLU193 1.7 31.4 1.0 O C:HOH574 2.0 34.0 0.5 ND1 C:HIS230 2.1 22.6 1.0 OE1 C:GLU227 2.2 33.6 1.0 OE2 C:GLU227 2.2 32.6 1.0 OE2 C:GLU120 2.2 30.4 1.0 CD C:GLU227 2.5 33.0 1.0 CD C:GLU193 2.9 31.0 1.0 CE1 C:HIS230 2.9 22.1 1.0 CD C:GLU120 3.1 30.5 1.0 CG C:HIS230 3.2 19.4 1.0 MN C:MN401 3.3 23.0 0.5 OE1 C:GLU120 3.3 31.9 1.0 CG C:GLU193 3.6 27.8 1.0 CB C:HIS230 3.7 18.3 1.0 OE1 C:GLU193 3.9 32.4 1.0 CG C:GLU227 4.0 26.5 1.0 OE1 C:GLN116 4.1 23.1 1.0 NE2 C:HIS230 4.1 19.0 1.0 CD2 C:HIS230 4.3 20.3 1.0 CG1 C:VAL92 4.4 20.3 1.0 CB C:GLU193 4.4 24.3 1.0 O C:HOH575 4.5 26.6 0.5 CG C:GLU120 4.6 23.1 1.0 CA C:GLU227 4.7 21.8 1.0 CE2 C:PHE197 4.7 29.6 1.0 CE1 C:HIS123 4.7 22.2 1.0 CB C:GLU227 4.7 22.4 1.0 ND1 C:HIS123 4.8 18.4 1.0 OE1 C:GLU89 4.8 32.1 1.0 CD2 C:PHE197 4.9 27.6 1.0 CD C:GLN116 4.9 19.8 1.0 CG C:GLN116 4.9 17.8 1.0

Iron binding site 4 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low 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 2 - Low Mn) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe402 b:26.8 occ:0.50 OE2 D:GLU193 1.8 31.6 1.0 ND1 D:HIS230 2.1 20.8 1.0 OE1 D:GLU227 2.2 30.2 1.0 OE2 D:GLU227 2.2 28.4 1.0 OE2 D:GLU120 2.3 30.9 1.0 CD D:GLU227 2.5 29.3 1.0 O D:HOH568 2.6 20.2 0.5 CE1 D:HIS230 2.9 22.2 1.0 CD D:GLU193 2.9 30.9 1.0 CG D:HIS230 3.2 17.8 1.0 CD D:GLU120 3.3 28.7 1.0 MN D:MN401 3.3 24.8 0.5 OE1 D:GLU120 3.5 34.3 1.0 CG D:GLU193 3.6 27.1 1.0 CB D:HIS230 3.7 18.6 1.0 OE1 D:GLU193 3.9 31.6 1.0 CG D:GLU227 4.0 24.2 1.0 OE1 D:GLN116 4.0 23.5 1.0 NE2 D:HIS230 4.1 17.6 1.0 CD2 D:HIS230 4.3 19.7 1.0 CG1 D:VAL92 4.3 20.8 1.0 CB D:GLU193 4.4 25.2 1.0 CE2 D:PHE197 4.5 27.0 1.0 CG D:GLU120 4.6 23.4 1.0 CA D:GLU227 4.7 20.3 1.0 O D:HOH501 4.8 35.0 0.5 CB D:GLU227 4.8 21.3 1.0 CE1 D:HIS123 4.8 16.3 1.0 CG D:GLN116 4.9 16.3 1.0 CD D:GLN116 4.9 19.7 1.0 OE1 D:GLU89 4.9 35.1 1.0 ND1 D:HIS123 4.9 16.9 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