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Iron in PDB 6zi6: Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 20 Ps Structure

Protein crystallography data

The structure of Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 20 Ps Structure, PDB code: 6zi6 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 (%) 16.8 / 19.2

Other elements in 6zi6:

The structure of Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 20 Ps Structure also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 20 Ps Structure (pdb code 6zi6). 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 - 20 Ps Structure, PDB code: 6zi6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 6zi6

Go back to Iron Binding Sites List in 6zi6
Iron binding site 1 out of 6 in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 20 Ps 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 - 20 Ps Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:85.0
occ:1.00
FE C:HEC401 0.0 85.0 1.0
NB C:HEC401 2.0 84.7 1.0
NE2 C:HIS91 2.0 85.5 1.0
NA C:HEC401 2.1 86.3 1.0
NC C:HEC401 2.1 82.2 1.0
ND C:HEC401 2.1 86.9 1.0
SD C:MET74 2.4 82.2 1.0
CD2 C:HIS91 3.0 86.3 1.0
C4B C:HEC401 3.0 83.0 1.0
C1C C:HEC401 3.0 79.9 1.0
C4A C:HEC401 3.1 90.4 1.0
CE1 C:HIS91 3.1 85.2 1.0
C1B C:HEC401 3.1 87.0 1.0
C1A C:HEC401 3.1 89.0 1.0
C1D C:HEC401 3.1 89.8 1.0
C4D C:HEC401 3.1 86.5 1.0
C4C C:HEC401 3.1 81.1 1.0
CHC C:HEC401 3.4 82.8 1.0
CHB C:HEC401 3.4 89.6 1.0
CHA C:HEC401 3.4 92.9 1.0
CHD C:HEC401 3.5 84.0 1.0
CE C:MET74 3.5 82.7 1.0
CG C:MET74 3.6 81.5 1.0
CG C:HIS91 4.1 85.6 1.0
ND1 C:HIS91 4.1 85.1 1.0
C3B C:HEC401 4.3 85.6 1.0
C3A C:HEC401 4.3 93.1 1.0
C2B C:HEC401 4.3 86.8 1.0
C2C C:HEC401 4.3 75.3 1.0
C2A C:HEC401 4.3 90.8 1.0
C3D C:HEC401 4.3 84.8 1.0
C2D C:HEC401 4.3 90.1 1.0
CB C:MET74 4.3 84.4 1.0
C3C C:HEC401 4.3 80.8 1.0

Iron binding site 2 out of 6 in 6zi6

Go back to Iron Binding Sites List in 6zi6
Iron binding site 2 out of 6 in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 20 Ps 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 - 20 Ps Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:76.0
occ:1.00
FE C:HEC402 0.0 76.0 1.0
NE2 C:HIS136 2.0 73.3 1.0
NB C:HEC402 2.0 78.3 1.0
NC C:HEC402 2.1 79.4 1.0
NA C:HEC402 2.1 78.7 1.0
ND C:HEC402 2.1 81.0 1.0
SD C:MET110 2.3 78.3 1.0
CE1 C:HIS136 2.8 74.5 1.0
C4B C:HEC402 3.0 77.4 1.0
C1C C:HEC402 3.1 77.5 1.0
C4A C:HEC402 3.1 74.8 1.0
C1B C:HEC402 3.1 75.8 1.0
CD2 C:HIS136 3.1 73.3 1.0
C1A C:HEC402 3.1 79.7 1.0
C1D C:HEC402 3.1 81.7 1.0
C4C C:HEC402 3.1 74.5 1.0
C4D C:HEC402 3.1 85.7 1.0
CG C:MET110 3.4 79.2 1.0
CHC C:HEC402 3.4 79.6 1.0
CE C:MET110 3.4 74.7 1.0
CHB C:HEC402 3.4 75.2 1.0
CHD C:HEC402 3.4 78.7 1.0
CHA C:HEC402 3.4 82.7 1.0
ND1 C:HIS136 4.0 71.0 1.0
CB C:MET110 4.1 76.8 1.0
CG C:HIS136 4.1 73.8 1.0
C3B C:HEC402 4.3 76.0 1.0
C2B C:HEC402 4.3 77.9 1.0
C3A C:HEC402 4.3 78.2 1.0
C2A C:HEC402 4.3 79.7 1.0
C2C C:HEC402 4.3 73.2 1.0
C2D C:HEC402 4.3 81.1 1.0
C3C C:HEC402 4.3 75.2 1.0
C3D C:HEC402 4.3 82.8 1.0

Iron binding site 3 out of 6 in 6zi6

Go back to Iron Binding Sites List in 6zi6
Iron binding site 3 out of 6 in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 20 Ps 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 - 20 Ps Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe403

b:66.0
occ:1.00
FE C:HEC403 0.0 66.0 1.0
NE2 C:HIS248 1.9 67.1 1.0
NB C:HEC403 2.0 62.4 1.0
NA C:HEC403 2.1 65.8 1.0
NC C:HEC403 2.1 64.1 1.0
ND C:HEC403 2.1 64.1 1.0
SD C:MET233 2.3 69.7 1.0
CD2 C:HIS248 2.9 65.1 1.0
CE1 C:HIS248 2.9 66.5 1.0
C4B C:HEC403 3.0 64.4 1.0
C4A C:HEC403 3.0 65.5 1.0
C1B C:HEC403 3.0 65.3 1.0
C1D C:HEC403 3.1 66.8 1.0
C1C C:HEC403 3.1 63.2 1.0
C1A C:HEC403 3.1 66.2 1.0
C4C C:HEC403 3.1 66.3 1.0
C4D C:HEC403 3.1 65.2 1.0
CHB C:HEC403 3.4 65.9 1.0
CHC C:HEC403 3.4 63.2 1.0
CHD C:HEC403 3.4 68.7 1.0
CG C:MET233 3.4 70.9 1.0
CHA C:HEC403 3.5 66.1 1.0
CE C:MET233 3.5 73.7 1.0
ND1 C:HIS248 4.0 64.9 1.0
CG C:HIS248 4.1 64.1 1.0
CB C:MET233 4.2 72.1 1.0
C3B C:HEC403 4.3 62.9 1.0
C2B C:HEC403 4.3 64.0 1.0
C3A C:HEC403 4.3 65.9 1.0
C2D C:HEC403 4.3 67.2 1.0
C2C C:HEC403 4.3 66.4 1.0
C2A C:HEC403 4.3 66.4 1.0
C3D C:HEC403 4.3 66.4 1.0
C3C C:HEC403 4.3 66.1 1.0

Iron binding site 4 out of 6 in 6zi6

Go back to Iron Binding Sites List in 6zi6
Iron binding site 4 out of 6 in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 20 Ps 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 - 20 Ps Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe404

b:68.8
occ:1.00
FE C:HEC404 0.0 68.8 1.0
NE2 C:HIS309 2.0 65.5 1.0
NB C:HEC404 2.0 70.0 1.0
NC C:HEC404 2.1 70.6 1.0
NE2 C:HIS124 2.1 71.7 1.0
NA C:HEC404 2.1 72.2 1.0
ND C:HEC404 2.1 72.5 1.0
CE1 C:HIS124 2.8 72.0 1.0
CE1 C:HIS309 2.9 66.9 1.0
C4B C:HEC404 3.0 68.3 1.0
C1C C:HEC404 3.1 70.1 1.0
CD2 C:HIS309 3.1 66.8 1.0
C1B C:HEC404 3.1 68.2 1.0
C1D C:HEC404 3.1 73.2 1.0
C4A C:HEC404 3.1 68.3 1.0
C1A C:HEC404 3.1 70.7 1.0
C4C C:HEC404 3.1 67.7 1.0
C4D C:HEC404 3.1 74.3 1.0
CD2 C:HIS124 3.2 73.1 1.0
CHC C:HEC404 3.4 71.3 1.0
CHD C:HEC404 3.4 70.8 1.0
CHB C:HEC404 3.4 69.9 1.0
CHA C:HEC404 3.5 69.5 1.0
ND1 C:HIS309 4.0 66.6 1.0
ND1 C:HIS124 4.0 71.4 1.0
CG C:HIS309 4.1 67.3 1.0
CG C:HIS124 4.2 70.6 1.0
C3B C:HEC404 4.3 67.0 1.0
C2B C:HEC404 4.3 68.7 1.0
C2C C:HEC404 4.3 66.5 1.0
C2A C:HEC404 4.3 67.5 1.0
C3A C:HEC404 4.3 68.2 1.0
C2D C:HEC404 4.3 75.2 1.0
C3D C:HEC404 4.3 75.6 1.0
C3C C:HEC404 4.3 68.3 1.0
CG C:PRO315 4.9 70.7 1.0

Iron binding site 5 out of 6 in 6zi6

Go back to Iron Binding Sites List in 6zi6
Iron binding site 5 out of 6 in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 20 Ps 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 - 20 Ps Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe401

b:70.5
occ:0.70
FE M:FE401 0.0 70.5 0.7
FE M:FE401 0.1 70.5 0.3
NE2 L:HIS190 2.0 69.5 0.3
NE2 L:HIS190 2.0 69.5 0.7
OE2 M:GLU232 2.1 67.7 0.3
OE2 M:GLU232 2.1 67.7 0.7
NE2 M:HIS217 2.2 68.7 0.7
NE2 M:HIS264 2.2 67.5 0.3
OE1 M:GLU232 2.3 69.9 0.3
NE2 L:HIS230 2.3 74.2 0.7
NE2 M:HIS264 2.3 67.5 0.7
NE2 M:HIS217 2.3 68.7 0.3
OE1 M:GLU232 2.4 69.9 0.7
NE2 L:HIS230 2.4 74.2 0.3
CD M:GLU232 2.5 68.3 0.3
CD M:GLU232 2.6 68.3 0.7
CE1 L:HIS190 2.9 70.8 0.3
CE1 L:HIS190 2.9 70.8 0.7
CE1 M:HIS217 3.1 69.3 0.7
CD2 L:HIS190 3.1 67.6 0.3
CE1 M:HIS264 3.1 69.1 0.3
CD2 L:HIS190 3.1 67.6 0.7
CE1 M:HIS217 3.2 69.3 0.3
CE1 L:HIS230 3.2 72.8 0.7
CE1 M:HIS264 3.2 69.1 0.7
CD2 M:HIS217 3.3 64.8 0.7
CD2 L:HIS230 3.3 72.3 0.7
CD2 M:HIS264 3.3 66.3 0.7
CD2 M:HIS264 3.3 66.3 0.3
CD2 M:HIS217 3.3 64.8 0.3
CE1 L:HIS230 3.3 72.8 0.3
CD2 L:HIS230 3.3 72.3 0.3
CG M:GLU232 4.0 71.3 0.3
ND1 L:HIS190 4.0 66.6 0.3
ND1 L:HIS190 4.1 66.6 0.7
CG M:GLU232 4.1 71.3 0.7
CG L:HIS190 4.2 64.1 0.3
CG L:HIS190 4.2 64.1 0.7
ND1 M:HIS217 4.2 68.0 0.7
ND1 M:HIS217 4.3 68.0 0.3
ND1 M:HIS264 4.3 71.2 0.3
ND1 L:HIS230 4.3 74.4 0.7
ND1 M:HIS264 4.3 71.2 0.7
CG M:HIS217 4.4 68.8 0.7
CG L:HIS230 4.4 72.1 0.7
CG M:HIS217 4.4 68.8 0.3
CG M:HIS264 4.4 67.5 0.3
CG M:HIS264 4.4 67.5 0.7
ND1 L:HIS230 4.4 74.4 0.3
CG L:HIS230 4.5 72.1 0.3
CG1 M:ILE221 4.5 73.5 0.3
CG1 M:ILE221 4.6 73.5 0.7
CG1 L:ILE194 4.6 72.4 1.0
CD1 M:ILE221 4.7 71.0 0.3
CB M:GLU232 4.9 72.0 0.3
CB M:GLU232 5.0 72.0 0.7

Iron binding site 6 out of 6 in 6zi6

Go back to Iron Binding Sites List in 6zi6
Iron binding site 6 out of 6 in the Ultrafast Structural Response to Charge Redistribution Within A Photosynthetic Reaction Centre - 20 Ps 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 - 20 Ps Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe401

b:70.5
occ:0.30
FE M:FE401 0.0 70.5 0.3
FE M:FE401 0.1 70.5 0.7
NE2 L:HIS190 2.0 69.5 0.3
NE2 L:HIS190 2.0 69.5 0.7
OE2 M:GLU232 2.1 67.7 0.3
NE2 M:HIS217 2.1 68.7 0.7
OE2 M:GLU232 2.2 67.7 0.7
NE2 L:HIS230 2.2 74.2 0.7
NE2 M:HIS217 2.3 68.7 0.3
NE2 L:HIS230 2.3 74.2 0.3
NE2 M:HIS264 2.3 67.5 0.3
OE1 M:GLU232 2.3 69.9 0.3
NE2 M:HIS264 2.4 67.5 0.7
OE1 M:GLU232 2.4 69.9 0.7
CD M:GLU232 2.5 68.3 0.3
CD M:GLU232 2.6 68.3 0.7
CE1 L:HIS190 2.9 70.8 0.3
CE1 L:HIS190 2.9 70.8 0.7
CE1 M:HIS217 3.1 69.3 0.7
CD2 L:HIS190 3.1 67.6 0.3
CD2 L:HIS190 3.1 67.6 0.7
CE1 L:HIS230 3.1 72.8 0.7
CE1 M:HIS217 3.2 69.3 0.3
CD2 L:HIS230 3.2 72.3 0.7
CD2 M:HIS217 3.2 64.8 0.7
CE1 M:HIS264 3.2 69.1 0.3
CD2 L:HIS230 3.2 72.3 0.3
CD2 M:HIS217 3.2 64.8 0.3
CE1 L:HIS230 3.3 72.8 0.3
CE1 M:HIS264 3.3 69.1 0.7
CD2 M:HIS264 3.3 66.3 0.7
CD2 M:HIS264 3.3 66.3 0.3
ND1 L:HIS190 4.0 66.6 0.3
ND1 L:HIS190 4.1 66.6 0.7
CG M:GLU232 4.1 71.3 0.3
CG M:GLU232 4.2 71.3 0.7
CG L:HIS190 4.2 64.1 0.3
CG L:HIS190 4.2 64.1 0.7
ND1 M:HIS217 4.2 68.0 0.7
ND1 L:HIS230 4.3 74.4 0.7
ND1 M:HIS217 4.3 68.0 0.3
CG M:HIS217 4.3 68.8 0.7
CG L:HIS230 4.3 72.1 0.7
CG M:HIS217 4.3 68.8 0.3
ND1 L:HIS230 4.4 74.4 0.3
ND1 M:HIS264 4.4 71.2 0.3
CG L:HIS230 4.4 72.1 0.3
ND1 M:HIS264 4.4 71.2 0.7
CG M:HIS264 4.5 67.5 0.3
CG M:HIS264 4.5 67.5 0.7
CG1 M:ILE221 4.5 73.5 0.3
CG1 M:ILE221 4.5 73.5 0.7
CG1 L:ILE194 4.6 72.4 1.0
CD1 M:ILE221 4.7 71.0 0.3

Reference:

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
Page generated: Wed Aug 7 18:33:09 2024

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