Iron in PDB 2wjn: Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose)

The structure of Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose), PDB code: 2wjn was solved by A.B.Wohri, W.Y.Wahlgren, E.Malmerberg, L.C.Johansson, R.Neutze, G.Katona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.97 / 1.86
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.760, 139.430, 178.240, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.3

The structure of Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose) also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Iron atom in the Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose) (pdb code 2wjn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose), PDB code: 2wjn:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:31.9 occ:1.00 FE C:HEC401 0.0 31.9 1.0 NE2 C:HIS91 1.9 27.6 1.0 ND C:HEC401 2.1 32.9 1.0 NB C:HEC401 2.1 32.5 1.0 NC C:HEC401 2.1 28.9 1.0 NA C:HEC401 2.1 31.5 1.0 SD C:MET74 2.3 33.3 1.0 CD2 C:HIS91 2.9 31.8 1.0 CE1 C:HIS91 2.9 32.4 1.0 C4C C:HEC401 3.0 32.6 1.0 C1D C:HEC401 3.0 35.0 1.0 C1B C:HEC401 3.1 35.7 1.0 C4A C:HEC401 3.1 35.8 1.0 C4D C:HEC401 3.1 35.3 1.0 C1A C:HEC401 3.1 33.6 1.0 C4B C:HEC401 3.1 35.9 1.0 C1C C:HEC401 3.1 31.5 1.0 CHD C:HEC401 3.3 31.4 1.0 CHB C:HEC401 3.4 32.6 1.0 CHA C:HEC401 3.5 33.9 1.0 CE C:MET74 3.5 33.9 1.0 CG C:MET74 3.5 33.8 1.0 CHC C:HEC401 3.5 33.4 1.0 ND1 C:HIS91 4.0 29.9 1.0 CG C:HIS91 4.1 28.1 1.0 CB C:MET74 4.3 33.0 1.0 C2D C:HEC401 4.3 33.9 1.0 C2B C:HEC401 4.3 36.5 1.0 C3C C:HEC401 4.3 30.3 1.0 C3B C:HEC401 4.3 33.1 1.0 C3A C:HEC401 4.3 35.5 1.0 C3D C:HEC401 4.3 33.5 1.0 C2A C:HEC401 4.3 34.0 1.0 C2C C:HEC401 4.3 29.5 1.0

Iron binding site 2 out of 5 in the Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:30.2 occ:1.00 FE C:HEC402 0.0 30.2 1.0 NE2 C:HIS136 2.0 32.8 1.0 NA C:HEC402 2.0 30.7 1.0 NC C:HEC402 2.1 29.4 1.0 ND C:HEC402 2.1 28.9 1.0 NB C:HEC402 2.1 29.3 1.0 SD C:MET110 2.4 33.9 1.0 CE1 C:HIS136 2.9 31.1 1.0 C4A C:HEC402 3.0 32.9 1.0 C1D C:HEC402 3.0 31.4 1.0 CD2 C:HIS136 3.0 33.1 1.0 C1B C:HEC402 3.0 32.4 1.0 C4C C:HEC402 3.1 29.9 1.0 C1A C:HEC402 3.1 34.0 1.0 C4B C:HEC402 3.2 30.0 1.0 C4D C:HEC402 3.2 32.0 1.0 C1C C:HEC402 3.2 30.2 1.0 CHB C:HEC402 3.3 31.6 1.0 CHD C:HEC402 3.3 31.0 1.0 CG C:MET110 3.4 32.2 1.0 CE C:MET110 3.5 34.0 1.0 CHC C:HEC402 3.5 30.4 1.0 CHA C:HEC402 3.6 31.7 1.0 ND1 C:HIS136 4.1 32.9 1.0 CG C:HIS136 4.2 30.9 1.0 CB C:MET110 4.2 32.9 1.0 C3A C:HEC402 4.2 32.1 1.0 C3C C:HEC402 4.3 28.7 1.0 C2A C:HEC402 4.3 32.9 1.0 C2D C:HEC402 4.3 31.0 1.0 C2B C:HEC402 4.3 30.0 1.0 C2C C:HEC402 4.4 28.2 1.0 C3D C:HEC402 4.4 29.9 1.0 C3B C:HEC402 4.4 29.1 1.0 CG C:PRO142 5.0 32.5 1.0

Iron binding site 3 out of 5 in the Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe403 b:25.8 occ:1.00 FE C:HEC403 0.0 25.8 1.0 NE2 C:HIS248 2.0 33.7 1.0 NC C:HEC403 2.0 27.6 1.0 NA C:HEC403 2.1 26.3 1.0 NB C:HEC403 2.1 25.2 1.0 ND C:HEC403 2.1 23.9 1.0 SD C:MET233 2.3 35.7 1.0 CE1 C:HIS248 2.9 35.3 1.0 C4C C:HEC403 3.0 25.5 1.0 C1D C:HEC403 3.0 25.7 1.0 C4B C:HEC403 3.1 23.9 1.0 C4A C:HEC403 3.1 23.6 1.0 C1A C:HEC403 3.1 25.6 1.0 C1B C:HEC403 3.1 25.2 1.0 C4D C:HEC403 3.1 24.7 1.0 C1C C:HEC403 3.1 23.9 1.0 CD2 C:HIS248 3.1 36.0 1.0 CHD C:HEC403 3.3 24.3 1.0 CG C:MET233 3.4 34.6 1.0 CHB C:HEC403 3.4 26.6 1.0 CE C:MET233 3.5 35.1 1.0 CHA C:HEC403 3.5 25.7 1.0 CHC C:HEC403 3.5 22.3 1.0 ND1 C:HIS248 4.1 32.9 1.0 CG C:HIS248 4.2 34.6 1.0 C3C C:HEC403 4.2 25.1 1.0 C3B C:HEC403 4.3 22.4 1.0 C2A C:HEC403 4.3 26.6 1.0 C2C C:HEC403 4.3 23.4 1.0 C3A C:HEC403 4.3 24.2 1.0 C2D C:HEC403 4.3 26.1 1.0 C2B C:HEC403 4.3 24.6 1.0 CB C:MET233 4.3 33.1 1.0 C3D C:HEC403 4.4 23.2 1.0

Iron binding site 4 out of 5 in the Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe404 b:28.7 occ:1.00 FE C:HEC404 0.0 28.7 1.0 NC C:HEC404 1.9 24.2 1.0 NA C:HEC404 2.0 27.7 1.0 ND C:HEC404 2.1 28.2 1.0 NB C:HEC404 2.1 28.2 1.0 NE2 C:HIS309 2.1 33.0 1.0 NE2 C:HIS124 2.1 32.3 1.0 C4C C:HEC404 3.0 25.1 1.0 C1D C:HEC404 3.0 25.6 1.0 CE1 C:HIS124 3.0 34.3 1.0 C1C C:HEC404 3.0 24.4 1.0 C4A C:HEC404 3.1 25.0 1.0 C1B C:HEC404 3.1 23.9 1.0 CE1 C:HIS309 3.1 32.2 1.0 C4D C:HEC404 3.1 27.4 1.0 CD2 C:HIS309 3.1 32.6 1.0 C4B C:HEC404 3.1 26.0 1.0 C1A C:HEC404 3.1 28.3 1.0 CD2 C:HIS124 3.1 33.3 1.0 CHD C:HEC404 3.4 26.3 1.0 CHB C:HEC404 3.4 26.6 1.0 CHC C:HEC404 3.5 26.8 1.0 CHA C:HEC404 3.5 28.4 1.0 ND1 C:HIS124 4.2 31.1 1.0 ND1 C:HIS309 4.2 30.7 1.0 C3C C:HEC404 4.2 26.7 1.0 C2C C:HEC404 4.2 25.5 1.0 CG C:HIS309 4.2 32.8 1.0 CG C:HIS124 4.2 33.1 1.0 C3A C:HEC404 4.3 25.3 1.0 C2A C:HEC404 4.3 27.4 1.0 C2B C:HEC404 4.3 24.0 1.0 C2D C:HEC404 4.3 27.5 1.0 C3B C:HEC404 4.3 20.7 1.0 C3D C:HEC404 4.3 27.9 1.0 CD C:PRO315 4.8 36.2 1.0 CG C:PRO315 4.9 35.2 1.0

Iron binding site 5 out of 5 in the Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Lipidic Sponge Phase Crystal Structure of Photosynthetic Reaction Centre From Blastochloris Viridis (High Dose) within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe306 b:27.8 occ:1.00 NE2 M:HIS217 2.2 35.1 1.0 OE2 M:GLU232 2.2 32.5 1.0 NE2 L:HIS190 2.3 31.3 1.0 NE2 L:HIS230 2.3 32.0 1.0 NE2 M:HIS264 2.3 32.2 1.0 OE1 M:GLU232 2.4 33.9 1.0 CD M:GLU232 2.6 32.3 1.0 CE1 M:HIS217 3.1 36.0 1.0 CE1 M:HIS264 3.2 32.7 1.0 CE1 L:HIS230 3.2 33.8 1.0 CE1 L:HIS190 3.2 33.7 1.0 CD2 L:HIS190 3.2 31.9 1.0 CD2 M:HIS217 3.3 33.2 1.0 CD2 L:HIS230 3.3 36.8 1.0 CD2 M:HIS264 3.3 32.6 1.0 CG M:GLU232 4.1 31.2 1.0 ND1 M:HIS217 4.3 33.9 1.0 ND1 M:HIS264 4.3 34.0 1.0 ND1 L:HIS230 4.3 33.0 1.0 ND1 L:HIS190 4.3 30.9 1.0 CG M:HIS217 4.4 35.9 1.0 CG L:HIS190 4.4 33.8 1.0 CG L:HIS230 4.4 33.8 1.0 CG M:HIS264 4.4 33.7 1.0 CG1 M:ILE221 4.6 33.0 1.0 CG1 L:ILE194 4.6 34.7 1.0 O M:HOH517 4.8 29.7 1.0 CB M:GLU232 5.0 32.3 1.0

A.B.Wohri, W.Y.Wahlgren, E.Malmerberg, L.C.Johansson, R.Neutze, G.Katona. Lipidic Sponge Phase Crystal Structure of A Photosynthetic Reaction Center Reveals Lipids on the Protein Surface. Biochemistry V. 48 9831 2009.
ISSN: ISSN 1520-4995
PubMed: 19743880
DOI: 10.1021/BI900545E