Iron in PDB 6zid: Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure

The structure of Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure, PDB code: 6zid was solved by P.Baath, R.Dods, G.Braenden, R.Neutze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.31 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	226.500, 226.500, 113.900, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.3

The structure of Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Iron atom in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure (pdb code 6zid). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure, PDB code: 6zid:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:96.1 occ:1.00 FE C:HEC401 0.0 96.1 1.0 NB C:HEC401 2.0 95.8 1.0 NE2 C:HIS91 2.0 96.3 1.0 NA C:HEC401 2.1 97.4 1.0 NC C:HEC401 2.1 93.3 1.0 ND C:HEC401 2.1 98.0 1.0 SD C:MET74 2.4 92.3 1.0 CD2 C:HIS91 3.0 97.1 1.0 C4B C:HEC401 3.0 94.2 1.0 C1C C:HEC401 3.0 91.0 1.0 C4A C:HEC401 3.1 0.5 1.0 CE1 C:HIS91 3.1 96.0 1.0 C1B C:HEC401 3.1 98.1 1.0 C1A C:HEC401 3.1 0.1 1.0 C1D C:HEC401 3.1 0.9 1.0 C4D C:HEC401 3.1 97.6 1.0 C4C C:HEC401 3.1 92.2 1.0 CHC C:HEC401 3.4 93.9 1.0 CHB C:HEC401 3.4 0.7 1.0 CHA C:HEC401 3.4 0.0 1.0 CHD C:HEC401 3.5 95.1 1.0 CE C:MET74 3.5 92.8 1.0 CG C:MET74 3.6 91.6 1.0 CG C:HIS91 4.2 96.3 1.0 ND1 C:HIS91 4.2 95.8 1.0 C3B C:HEC401 4.3 96.7 1.0 C3A C:HEC401 4.3 0.2 1.0 C2B C:HEC401 4.3 97.9 1.0 C2C C:HEC401 4.3 86.4 1.0 C2A C:HEC401 4.3 0.9 1.0 C3D C:HEC401 4.3 95.9 1.0 C2D C:HEC401 4.3 0.2 1.0 CB C:MET74 4.3 94.5 1.0 C3C C:HEC401 4.3 91.9 1.0

Iron binding site 2 out of 6 in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:87.5 occ:1.00 FE C:HEC402 0.0 87.5 1.0 NE2 C:HIS136 2.0 84.2 1.0 NB C:HEC402 2.0 89.9 1.0 NC C:HEC402 2.1 91.0 1.0 NA C:HEC402 2.1 90.2 1.0 ND C:HEC402 2.1 92.6 1.0 SD C:MET110 2.3 89.2 1.0 CE1 C:HIS136 2.8 85.4 1.0 C4B C:HEC402 3.0 89.0 1.0 C1C C:HEC402 3.1 89.0 1.0 C4A C:HEC402 3.1 86.4 1.0 C1B C:HEC402 3.1 87.3 1.0 C1A C:HEC402 3.1 91.2 1.0 C1D C:HEC402 3.1 93.3 1.0 CD2 C:HIS136 3.1 84.2 1.0 C4C C:HEC402 3.1 86.1 1.0 C4D C:HEC402 3.1 97.2 1.0 CG C:MET110 3.4 90.2 1.0 CHC C:HEC402 3.4 91.1 1.0 CE C:MET110 3.4 85.6 1.0 CHB C:HEC402 3.4 86.7 1.0 CHD C:HEC402 3.4 90.2 1.0 CHA C:HEC402 3.4 94.2 1.0 ND1 C:HIS136 4.0 81.9 1.0 CB C:MET110 4.1 87.8 1.0 CG C:HIS136 4.1 84.7 1.0 C3B C:HEC402 4.3 87.5 1.0 C2B C:HEC402 4.3 89.4 1.0 C3A C:HEC402 4.3 89.8 1.0 C2A C:HEC402 4.3 91.2 1.0 C2C C:HEC402 4.3 84.8 1.0 C2D C:HEC402 4.3 92.6 1.0 C3C C:HEC402 4.3 86.7 1.0 C3D C:HEC402 4.3 94.3 1.0

Iron binding site 3 out of 6 in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe403 b:77.5 occ:1.00 FE C:HEC403 0.0 77.5 1.0 NE2 C:HIS248 1.9 79.5 1.0 NB C:HEC403 2.0 73.8 1.0 NA C:HEC403 2.1 77.3 1.0 NC C:HEC403 2.1 75.5 1.0 ND C:HEC403 2.1 75.5 1.0 SD C:MET233 2.3 81.3 1.0 CD2 C:HIS248 2.9 77.5 1.0 CE1 C:HIS248 2.9 79.0 1.0 C4B C:HEC403 3.0 75.8 1.0 C4A C:HEC403 3.0 76.9 1.0 C1B C:HEC403 3.0 76.7 1.0 C1D C:HEC403 3.1 78.2 1.0 C1C C:HEC403 3.1 74.6 1.0 C1A C:HEC403 3.1 77.7 1.0 C4C C:HEC403 3.1 77.7 1.0 C4D C:HEC403 3.1 76.7 1.0 CHB C:HEC403 3.4 77.3 1.0 CHC C:HEC403 3.4 74.6 1.0 CHD C:HEC403 3.4 80.1 1.0 CG C:MET233 3.4 82.5 1.0 CHA C:HEC403 3.5 77.5 1.0 CE C:MET233 3.5 85.2 1.0 ND1 C:HIS248 4.0 77.3 1.0 CG C:HIS248 4.1 76.6 1.0 CB C:MET233 4.2 83.6 1.0 C3B C:HEC403 4.3 74.3 1.0 C2B C:HEC403 4.3 75.4 1.0 C3A C:HEC403 4.3 77.3 1.0 C2D C:HEC403 4.3 78.6 1.0 C2C C:HEC403 4.3 77.8 1.0 C2A C:HEC403 4.3 77.8 1.0 C3D C:HEC403 4.3 77.8 1.0 C3C C:HEC403 4.3 77.5 1.0

Iron binding site 4 out of 6 in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe404 b:81.8 occ:1.00 FE C:HEC404 0.0 81.8 1.0 NE2 C:HIS309 2.0 77.0 1.0 NB C:HEC404 2.0 83.1 1.0 NE2 C:HIS124 2.1 83.3 1.0 NC C:HEC404 2.1 83.7 1.0 NA C:HEC404 2.1 85.3 1.0 ND C:HEC404 2.1 85.5 1.0 CE1 C:HIS124 2.8 83.6 1.0 CE1 C:HIS309 2.9 78.3 1.0 C4B C:HEC404 3.0 81.4 1.0 C1C C:HEC404 3.1 83.2 1.0 CD2 C:HIS309 3.1 78.2 1.0 C1B C:HEC404 3.1 81.3 1.0 C1D C:HEC404 3.1 86.3 1.0 C4A C:HEC404 3.1 81.3 1.0 C1A C:HEC404 3.1 83.8 1.0 C4C C:HEC404 3.1 80.7 1.0 C4D C:HEC404 3.1 87.3 1.0 CD2 C:HIS124 3.2 84.7 1.0 CHC C:HEC404 3.4 84.4 1.0 CHD C:HEC404 3.4 83.9 1.0 CHB C:HEC404 3.4 83.0 1.0 CHA C:HEC404 3.5 82.6 1.0 ND1 C:HIS124 4.0 83.0 1.0 ND1 C:HIS309 4.0 78.0 1.0 CG C:HIS309 4.2 78.7 1.0 CG C:HIS124 4.2 82.2 1.0 C3B C:HEC404 4.3 80.0 1.0 C2B C:HEC404 4.3 81.8 1.0 C2C C:HEC404 4.3 79.6 1.0 C2A C:HEC404 4.3 80.6 1.0 C3A C:HEC404 4.3 81.3 1.0 C2D C:HEC404 4.3 88.3 1.0 C3D C:HEC404 4.3 88.7 1.0 C3C C:HEC404 4.3 81.4 1.0 CG C:PRO315 4.9 80.6 1.0

Iron binding site 5 out of 6 in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure within 5.0Å range: probe atom residue distance (Å) B Occ M:Fe401 b:81.4 occ:0.70 FE M:FE401 0.0 81.4 0.7 FE M:FE401 0.2 81.4 0.3 NE2 L:HIS190 2.0 80.6 0.3 NE2 L:HIS190 2.0 80.6 0.7 OE2 M:GLU232 2.1 78.6 0.3 OE2 M:GLU232 2.2 78.6 0.7 NE2 M:HIS217 2.2 79.7 0.7 NE2 M:HIS264 2.2 79.2 0.7 OE1 M:GLU232 2.3 80.8 0.3 NE2 M:HIS217 2.3 79.7 0.3 NE2 L:HIS230 2.3 85.8 0.7 NE2 M:HIS264 2.3 79.2 0.3 OE1 M:GLU232 2.3 80.8 0.7 NE2 L:HIS230 2.4 85.8 0.3 CD M:GLU232 2.5 79.2 0.3 CD M:GLU232 2.6 79.2 0.7 CE1 L:HIS190 2.9 81.9 0.7 CE1 L:HIS190 2.9 81.9 0.3 CD2 L:HIS190 3.1 78.7 0.3 CE1 M:HIS217 3.1 80.4 0.7 CD2 L:HIS190 3.1 78.7 0.7 CE1 M:HIS217 3.2 80.4 0.3 CE1 M:HIS264 3.2 80.7 0.7 CE1 L:HIS230 3.2 84.3 0.7 CE1 M:HIS264 3.2 80.7 0.3 CD2 M:HIS264 3.2 78.0 0.7 CD2 M:HIS217 3.3 75.9 0.7 CE1 L:HIS230 3.3 84.3 0.3 CD2 M:HIS217 3.3 75.9 0.3 CD2 M:HIS264 3.3 78.0 0.3 CD2 L:HIS230 3.3 83.8 0.7 CD2 L:HIS230 3.3 83.8 0.3 ND1 L:HIS190 4.0 77.7 0.7 ND1 L:HIS190 4.0 77.7 0.3 CG M:GLU232 4.1 82.2 0.3 CG M:GLU232 4.1 82.2 0.7 CG L:HIS190 4.2 75.2 0.3 CG L:HIS190 4.2 75.2 0.7 ND1 M:HIS217 4.3 79.1 0.7 ND1 M:HIS217 4.3 79.1 0.3 ND1 M:HIS264 4.3 82.9 0.7 ND1 L:HIS230 4.4 85.9 0.7 ND1 M:HIS264 4.4 82.9 0.3 CG M:HIS264 4.4 79.2 0.7 CG M:HIS217 4.4 79.9 0.7 CG M:HIS217 4.4 79.9 0.3 ND1 L:HIS230 4.4 85.9 0.3 CG L:HIS230 4.4 83.7 0.7 CG M:HIS264 4.5 79.2 0.3 CG L:HIS230 4.5 83.7 0.3 CG1 M:ILE221 4.5 85.0 0.3 CG1 L:ILE194 4.5 86.4 1.0 CG1 M:ILE221 4.6 85.0 0.7 CD1 M:ILE221 4.8 82.4 0.3 CB M:GLU232 4.9 82.9 0.3 CD1 L:ILE194 5.0 87.0 1.0 CB M:GLU232 5.0 82.9 0.7

Iron binding site 6 out of 6 in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 5 Ps (B) Structure within 5.0Å range: probe atom residue distance (Å) B Occ M:Fe401 b:81.4 occ:0.30 FE M:FE401 0.0 81.4 0.3 FE M:FE401 0.2 81.4 0.7 OE2 M:GLU232 2.1 78.6 0.3 OE2 M:GLU232 2.1 78.6 0.7 NE2 L:HIS190 2.1 80.6 0.3 NE2 L:HIS190 2.1 80.6 0.7 NE2 M:HIS217 2.1 79.7 0.7 NE2 L:HIS230 2.2 85.8 0.7 NE2 M:HIS217 2.2 79.7 0.3 NE2 L:HIS230 2.2 85.8 0.3 OE1 M:GLU232 2.3 80.8 0.3 NE2 M:HIS264 2.4 79.2 0.7 OE1 M:GLU232 2.4 80.8 0.7 NE2 M:HIS264 2.4 79.2 0.3 CD M:GLU232 2.5 79.2 0.3 CD M:GLU232 2.6 79.2 0.7 CE1 L:HIS190 3.0 81.9 0.7 CE1 L:HIS190 3.0 81.9 0.3 CE1 M:HIS217 3.0 80.4 0.7 CE1 M:HIS217 3.1 80.4 0.3 CE1 L:HIS230 3.1 84.3 0.7 CD2 L:HIS190 3.2 78.7 0.3 CD2 L:HIS230 3.2 83.8 0.7 CD2 L:HIS190 3.2 78.7 0.7 CE1 L:HIS230 3.2 84.3 0.3 CD2 M:HIS217 3.2 75.9 0.7 CD2 L:HIS230 3.2 83.8 0.3 CD2 M:HIS217 3.2 75.9 0.3 CE1 M:HIS264 3.3 80.7 0.7 CE1 M:HIS264 3.3 80.7 0.3 CD2 M:HIS264 3.4 78.0 0.7 CD2 M:HIS264 3.5 78.0 0.3 CG M:GLU232 4.0 82.2 0.3 CG M:GLU232 4.1 82.2 0.7 ND1 L:HIS190 4.1 77.7 0.7 ND1 L:HIS190 4.1 77.7 0.3 ND1 M:HIS217 4.2 79.1 0.7 ND1 M:HIS217 4.2 79.1 0.3 ND1 L:HIS230 4.3 85.9 0.7 CG L:HIS190 4.3 75.2 0.3 CG L:HIS190 4.3 75.2 0.7 CG M:HIS217 4.3 79.9 0.7 CG L:HIS230 4.3 83.7 0.7 CG M:HIS217 4.3 79.9 0.3 ND1 L:HIS230 4.3 85.9 0.3 CG1 M:ILE221 4.3 85.0 0.3 CG L:HIS230 4.4 83.7 0.3 ND1 M:HIS264 4.4 82.9 0.7 CG1 M:ILE221 4.4 85.0 0.7 ND1 M:HIS264 4.5 82.9 0.3 CG M:HIS264 4.5 79.2 0.7 CG M:HIS264 4.6 79.2 0.3 CD1 M:ILE221 4.6 82.4 0.3 CG1 L:ILE194 4.7 86.4 1.0 CB M:GLU232 4.9 82.9 0.3

R.Dods, P.Baath, D.Morozov, V.A.Gagner, A.Arnlund, H.L.Luk, J.Kuebel, M.Maj, A.Vallejos, C.Wickstrand, R.Bosman, K.R.Beyerlein, G.Nelson, M.Liang, D.Milathianaki, J.Robinson, R.Harimoorthy, P.Berntsen, E.Malmerberg, L.Johansson, R.Andersson, S.Carbajo, E.Claesson, C.E.Conrad, P.Dahl, G.Hammarin, M.S.Hunter, C.Li, S.Lisova, A.Royant, C.Safari, A.Sharma, G.J.Williams, O.Yefanov, S.Westenhoff, J.Davidsson, D.P.Deponte, S.Boutet, A.Barty, G.Katona, G.Groenhof, G.Braenden, R.Neutze. Ultrafast Structural Changes Within A Photosynthetic Reaction Centre Nature 2020.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-020-3000-7