Iron in PDB 3t6d: Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08

The structure of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08, PDB code: 3t6d was solved by A.W.Roszak, A.T.Gardiner, N.W.Isaacs, R.J.Cogdell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.34 / 1.95
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	220.440, 220.440, 113.100, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.6

The structure of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Iron atom in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 (pdb code 3t6d). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08, PDB code: 3t6d:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:47.4 occ:1.00 FE C:HEC401 0.0 47.4 1.0 NC C:HEC401 2.0 41.6 1.0 NA C:HEC401 2.0 44.9 1.0 ND C:HEC401 2.0 46.8 1.0 NB C:HEC401 2.1 45.6 1.0 NE2 C:HIS91 2.1 48.9 1.0 SD C:MET74 2.3 48.6 1.0 C1C C:HEC401 3.0 44.7 1.0 C4A C:HEC401 3.0 47.4 1.0 CE1 C:HIS91 3.0 52.8 1.0 C1D C:HEC401 3.0 45.6 1.0 C4C C:HEC401 3.0 46.0 1.0 C1A C:HEC401 3.0 48.1 1.0 CD2 C:HIS91 3.0 50.2 1.0 C1B C:HEC401 3.1 45.8 1.0 C4D C:HEC401 3.1 46.9 1.0 C4B C:HEC401 3.1 44.2 1.0 CHD C:HEC401 3.3 46.1 1.0 CHB C:HEC401 3.4 46.5 1.0 CHC C:HEC401 3.4 43.4 1.0 CG C:MET74 3.4 46.0 1.0 CHA C:HEC401 3.4 45.9 1.0 CE C:MET74 3.4 48.6 1.0 ND1 C:HIS91 4.1 51.0 1.0 CG C:HIS91 4.2 52.5 1.0 C2C C:HEC401 4.2 44.5 1.0 C2A C:HEC401 4.2 50.2 1.0 C3A C:HEC401 4.2 49.7 1.0 C2D C:HEC401 4.2 47.2 1.0 C3C C:HEC401 4.3 43.2 1.0 C3D C:HEC401 4.3 48.9 1.0 C2B C:HEC401 4.3 47.3 1.0 C3B C:HEC401 4.3 46.1 1.0 CB C:MET74 4.3 46.9 1.0

Iron binding site 2 out of 5 in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:45.2 occ:1.00 FE C:HEC402 0.0 45.2 1.0 NA C:HEC402 2.0 47.0 1.0 NC C:HEC402 2.0 42.1 1.0 ND C:HEC402 2.0 48.4 1.0 NB C:HEC402 2.0 45.1 1.0 NE2 C:HIS136 2.0 40.4 1.0 SD C:MET110 2.3 46.6 1.0 CE1 C:HIS136 3.0 41.1 1.0 C4A C:HEC402 3.0 45.8 1.0 C4D C:HEC402 3.0 45.5 1.0 C1A C:HEC402 3.0 46.2 1.0 C1D C:HEC402 3.0 41.9 1.0 C1C C:HEC402 3.0 40.2 1.0 C1B C:HEC402 3.1 43.4 1.0 C4C C:HEC402 3.1 44.1 1.0 CD2 C:HIS136 3.1 37.2 1.0 C4B C:HEC402 3.1 41.8 1.0 CE C:MET110 3.3 39.2 1.0 CHA C:HEC402 3.3 42.3 1.0 CHD C:HEC402 3.4 43.4 1.0 CHB C:HEC402 3.4 43.2 1.0 CHC C:HEC402 3.4 40.9 1.0 CG C:MET110 3.4 44.8 1.0 ND1 C:HIS136 4.1 42.4 1.0 CB C:MET110 4.2 44.2 1.0 CG C:HIS136 4.2 40.7 1.0 C3A C:HEC402 4.2 44.7 1.0 C3D C:HEC402 4.2 45.3 1.0 C2D C:HEC402 4.2 44.8 1.0 C2B C:HEC402 4.2 41.6 1.0 C2A C:HEC402 4.3 45.3 1.0 C2C C:HEC402 4.3 39.7 1.0 C3C C:HEC402 4.3 39.3 1.0 C3B C:HEC402 4.3 44.5 1.0

Iron binding site 3 out of 5 in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe403 b:37.8 occ:1.00 FE C:HEC403 0.0 37.8 1.0 NB C:HEC403 2.0 39.2 1.0 NC C:HEC403 2.0 39.2 1.0 NA C:HEC403 2.0 36.5 1.0 ND C:HEC403 2.0 36.7 1.0 NE2 C:HIS248 2.0 37.5 1.0 SD C:MET233 2.3 37.6 1.0 CE1 C:HIS248 3.0 36.5 1.0 C1B C:HEC403 3.0 37.7 1.0 C4B C:HEC403 3.0 34.8 1.0 CD2 C:HIS248 3.1 34.5 1.0 C4C C:HEC403 3.1 42.1 1.0 C1D C:HEC403 3.1 34.0 1.0 C1A C:HEC403 3.1 34.8 1.0 C4A C:HEC403 3.1 38.1 1.0 C1C C:HEC403 3.1 39.2 1.0 C4D C:HEC403 3.1 36.3 1.0 CG C:MET233 3.3 36.4 1.0 CHD C:HEC403 3.3 38.7 1.0 CHB C:HEC403 3.4 35.9 1.0 CHC C:HEC403 3.4 34.1 1.0 CHA C:HEC403 3.4 34.3 1.0 CE C:MET233 3.4 36.4 1.0 ND1 C:HIS248 4.1 35.4 1.0 CG C:HIS248 4.2 32.1 1.0 CB C:MET233 4.2 37.3 1.0 C3B C:HEC403 4.2 37.5 1.0 C2B C:HEC403 4.2 37.4 1.0 C2A C:HEC403 4.3 34.9 1.0 C2D C:HEC403 4.3 34.7 1.0 C3A C:HEC403 4.3 34.0 1.0 C3C C:HEC403 4.3 37.3 1.0 C2C C:HEC403 4.3 41.3 1.0 C3D C:HEC403 4.3 37.7 1.0

Iron binding site 4 out of 5 in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe404 b:39.3 occ:1.00 FE C:HEC404 0.0 39.3 1.0 ND C:HEC404 2.0 38.3 1.0 NB C:HEC404 2.0 38.4 1.0 NA C:HEC404 2.0 38.3 1.0 NC C:HEC404 2.0 40.8 1.0 NE2 C:HIS124 2.0 40.8 1.0 NE2 C:HIS309 2.0 41.8 1.0 CE1 C:HIS124 3.0 41.6 1.0 CE1 C:HIS309 3.0 37.3 1.0 C1D C:HEC404 3.0 40.4 1.0 C4A C:HEC404 3.0 36.0 1.0 C1B C:HEC404 3.0 34.6 1.0 C4D C:HEC404 3.0 39.4 1.0 C1A C:HEC404 3.0 36.8 1.0 C4B C:HEC404 3.0 38.0 1.0 C1C C:HEC404 3.1 37.1 1.0 C4C C:HEC404 3.1 38.1 1.0 CD2 C:HIS124 3.1 37.6 1.0 CD2 C:HIS309 3.1 36.1 1.0 CHB C:HEC404 3.3 36.9 1.0 CHD C:HEC404 3.3 40.5 1.0 CHA C:HEC404 3.4 41.2 1.0 CHC C:HEC404 3.4 38.7 1.0 ND1 C:HIS124 4.1 38.2 1.0 ND1 C:HIS309 4.1 38.7 1.0 CG C:HIS124 4.2 37.1 1.0 CG C:HIS309 4.2 36.1 1.0 C3A C:HEC404 4.2 33.9 1.0 C3D C:HEC404 4.2 40.1 1.0 C2D C:HEC404 4.2 39.4 1.0 C2B C:HEC404 4.3 33.7 1.0 C2A C:HEC404 4.3 35.8 1.0 C3B C:HEC404 4.3 34.2 1.0 C3C C:HEC404 4.3 36.8 1.0 C2C C:HEC404 4.3 37.4 1.0 CD C:PRO315 4.9 40.8 1.0 CG C:PRO315 5.0 41.9 1.0

Iron binding site 5 out of 5 in the Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Reaction Centre From Blastochloris Viridis Strain Dsm 133 (Atcc 19567) Substrain-08 within 5.0Å range: probe atom residue distance (Å) B Occ M:Fe500 b:37.3 occ:1.00 NE2 M:HIS217 2.1 32.7 1.0 NE2 L:HIS190 2.2 39.0 1.0 OE2 M:GLU232 2.2 39.2 1.0 NE2 M:HIS264 2.3 37.0 1.0 NE2 L:HIS230 2.3 41.6 1.0 OE1 M:GLU232 2.7 37.2 1.0 CD M:GLU232 2.7 36.7 1.0 CE1 L:HIS190 3.0 37.7 1.0 CE1 M:HIS217 3.1 34.2 1.0 CD2 M:HIS217 3.2 30.5 1.0 CD2 M:HIS264 3.2 34.7 1.0 CD2 L:HIS190 3.2 41.7 1.0 CE1 M:HIS264 3.2 38.0 1.0 CD2 L:HIS230 3.2 39.0 1.0 CE1 L:HIS230 3.3 41.3 1.0 ND1 M:HIS217 4.2 31.8 1.0 ND1 L:HIS190 4.2 37.9 1.0 CG M:GLU232 4.3 37.7 1.0 CG M:HIS217 4.3 31.8 1.0 CG L:HIS190 4.3 36.5 1.0 ND1 M:HIS264 4.4 34.5 1.0 CG M:HIS264 4.4 39.2 1.0 CG L:HIS230 4.4 38.7 1.0 ND1 L:HIS230 4.4 39.9 1.0 CG1 M:ILE221 4.6 36.7 1.0 CG1 L:ILE194 4.8 42.2 1.0

A.W.Roszak, V.Moulisova, A.D.Reksodipuro, A.T.Gardiner, R.Fujii, H.Hashimoto, N.W.Isaacs, R.J.Cogdell. New Insights Into the Structure of the Reaction Centre From Blastochloris Viridis: Evolution in the Laboratory. Biochem.J. V. 442 27 2012.
ISSN: ISSN 0264-6021
PubMed: 22054235
DOI: 10.1042/BJ20111540