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Iron in PDB 4ac5: Lipidic Sponge Phase Crystal Structure of the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography

Protein crystallography data

The structure of Lipidic Sponge Phase Crystal Structure of the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography, PDB code: 4ac5 was solved by L.C.Johansson, D.Arnlund, T.A.White, G.Katona, D.P.Deponte, U.Weierstall, R.B.Doak, R.L.Shoeman, L.Lomb, E.Malmerberg, J.Davidsson, K.Nass, M.Liang, J.Andreasson, A.Aquila, S.Bajt, M.Barthelmess, A.Barty, M.J.Bogan, C.Bostedt, J.D.Bozek, C.Caleman, R.Coffee, N.Coppola, T.Ekeberg, S.W.Epp, B.Erk, H.Fleckenstein, L.Foucar, H.Graafsma, L.Gumprecht, J.Hajdu, C.Y.Hampton, R.Hartmann, A.Hartmann, G.Hauser, H.Hirsemann, P.Holl, M.S.Hunter, S.Kassemeyer, N.Kimmel, R.A.Kirian, F.R.N.C.Maia, S.Marchesini, A.V.Martin, C.Reich, D.Rolles, B.Rudek, A.Rudenko, I.Schlichting, J.Schulz, M.M.Seibert, R.Sierra, H.Soltau, D.Starodub, F.Stellato, S.Stern, L.Struder, N.Timneanu, J.Ullrich, W.Y.Wahlgren, X.Wang, G.Weidenspointner, C.Wunderer, P.Fromme, H.N.Chapman, J.C.H.Spence, R.Neutze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.10 / 8.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.500, 84.600, 375.800, 90.00, 90.00, 90.00
R / Rfree (%) 35.1 / 38.4

Other elements in 4ac5:

The structure of Lipidic Sponge Phase Crystal Structure of the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Lipidic Sponge Phase Crystal Structure of the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography (pdb code 4ac5). 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 the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography, PDB code: 4ac5:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 4ac5

Go back to Iron Binding Sites List in 4ac5
Iron binding site 1 out of 5 in the Lipidic Sponge Phase Crystal Structure of the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography


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 the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1333

b:16.2
occ:1.00
FE C:HEM1333 0.0 16.2 1.0
NE2 C:HIS91 2.0 14.1 1.0
NC C:HEM1333 2.1 16.1 1.0
NA C:HEM1333 2.1 16.2 1.0
NB C:HEM1333 2.1 16.2 1.0
ND C:HEM1333 2.1 16.1 1.0
CE1 C:HIS91 3.0 14.1 1.0
CD2 C:HIS91 3.1 14.1 1.0
C4C C:HEM1333 3.1 16.1 1.0
C4A C:HEM1333 3.1 16.2 1.0
C1D C:HEM1333 3.1 16.1 1.0
C1B C:HEM1333 3.1 16.2 1.0
SD C:MET74 3.1 12.1 1.0
C1C C:HEM1333 3.1 16.1 1.0
C1A C:HEM1333 3.1 16.1 1.0
C4B C:HEM1333 3.1 16.2 1.0
C4D C:HEM1333 3.1 16.2 1.0
CHD C:HEM1333 3.4 16.1 1.0
CHB C:HEM1333 3.4 16.2 1.0
CHA C:HEM1333 3.5 16.1 1.0
CHC C:HEM1333 3.5 16.1 1.0
CG C:MET74 3.7 12.1 1.0
CE C:MET74 3.8 12.1 1.0
ND1 C:HIS91 4.1 14.1 1.0
CG C:HIS91 4.2 14.2 1.0
C2D C:HEM1333 4.3 16.2 1.0
C3A C:HEM1333 4.3 16.1 1.0
C3C C:HEM1333 4.3 16.0 1.0
C2B C:HEM1333 4.3 16.2 1.0
C2A C:HEM1333 4.3 16.1 1.0
C3D C:HEM1333 4.3 16.2 1.0
C2C C:HEM1333 4.3 16.0 1.0
C3B C:HEM1333 4.3 16.2 1.0
CB C:MET74 4.5 12.1 1.0
CE2 C:TYR104 5.0 13.4 1.0

Iron binding site 2 out of 5 in 4ac5

Go back to Iron Binding Sites List in 4ac5
Iron binding site 2 out of 5 in the Lipidic Sponge Phase Crystal Structure of the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography


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 the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1334

b:2.0
occ:1.00
FE C:HEM1334 0.0 2.0 1.0
NC C:HEM1334 2.1 2.0 1.0
NB C:HEM1334 2.1 2.0 1.0
NA C:HEM1334 2.1 2.0 1.0
ND C:HEM1334 2.1 2.0 1.0
NE2 C:HIS136 2.3 15.1 1.0
CE1 C:HIS136 3.0 15.2 1.0
C4C C:HEM1334 3.0 2.0 1.0
C1B C:HEM1334 3.1 2.0 1.0
C1C C:HEM1334 3.1 2.0 1.0
C4A C:HEM1334 3.1 2.0 1.0
C4B C:HEM1334 3.1 2.0 1.0
C1D C:HEM1334 3.1 2.0 1.0
C1A C:HEM1334 3.1 2.0 1.0
C4D C:HEM1334 3.1 2.0 1.0
SD C:MET110 3.1 13.3 1.0
CHD C:HEM1334 3.4 2.0 1.0
CHB C:HEM1334 3.4 2.0 1.0
CD2 C:HIS136 3.4 15.2 1.0
CHC C:HEM1334 3.4 2.0 1.0
CHA C:HEM1334 3.4 2.0 1.0
CG C:MET110 3.5 13.4 1.0
CE C:MET110 3.7 13.3 1.0
ND1 C:HIS136 4.2 15.2 1.0
C3C C:HEM1334 4.3 2.0 1.0
C2C C:HEM1334 4.3 2.0 1.0
C2B C:HEM1334 4.3 2.0 1.0
C3B C:HEM1334 4.3 2.0 1.0
C3A C:HEM1334 4.3 2.0 1.0
C2A C:HEM1334 4.3 2.0 1.0
CB C:MET110 4.3 13.5 1.0
C2D C:HEM1334 4.3 2.0 1.0
C3D C:HEM1334 4.3 2.0 1.0
CG C:HIS136 4.4 15.2 1.0

Iron binding site 3 out of 5 in 4ac5

Go back to Iron Binding Sites List in 4ac5
Iron binding site 3 out of 5 in the Lipidic Sponge Phase Crystal Structure of the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography


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 the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1335

b:4.4
occ:1.00
FE C:HEM1335 0.0 4.4 1.0
NC C:HEM1335 2.1 4.3 1.0
NB C:HEM1335 2.1 4.3 1.0
NA C:HEM1335 2.1 4.4 1.0
ND C:HEM1335 2.1 4.5 1.0
NE2 C:HIS248 2.2 14.4 1.0
SD C:MET233 2.8 14.0 1.0
CD2 C:HIS248 3.0 14.4 1.0
C1B C:HEM1335 3.0 4.3 1.0
C4B C:HEM1335 3.1 4.3 1.0
C4A C:HEM1335 3.1 4.4 1.0
C4C C:HEM1335 3.1 4.3 1.0
C1D C:HEM1335 3.1 4.5 1.0
CE1 C:HIS248 3.1 14.4 1.0
C1C C:HEM1335 3.1 4.3 1.0
C1A C:HEM1335 3.1 4.4 1.0
C4D C:HEM1335 3.1 4.6 1.0
CHB C:HEM1335 3.4 4.4 1.0
CHD C:HEM1335 3.4 4.4 1.0
CHC C:HEM1335 3.5 4.3 1.0
CHA C:HEM1335 3.5 4.5 1.0
CG C:MET233 3.7 13.9 1.0
CE C:MET233 3.8 14.0 1.0
CG C:HIS248 4.0 14.5 1.0
ND1 C:HIS248 4.0 14.4 1.0
C2B C:HEM1335 4.2 4.3 1.0
C3B C:HEM1335 4.3 4.3 1.0
C3A C:HEM1335 4.3 4.4 1.0
C3C C:HEM1335 4.3 4.3 1.0
C2C C:HEM1335 4.3 4.3 1.0
C2A C:HEM1335 4.3 4.4 1.0
C2D C:HEM1335 4.3 4.6 1.0
C3D C:HEM1335 4.3 4.6 1.0
CB C:MET233 4.5 13.9 1.0

Iron binding site 4 out of 5 in 4ac5

Go back to Iron Binding Sites List in 4ac5
Iron binding site 4 out of 5 in the Lipidic Sponge Phase Crystal Structure of the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography


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 the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1336

b:2.0
occ:1.00
FE C:HEM1336 0.0 2.0 1.0
NA C:HEM1336 2.1 2.0 1.0
NB C:HEM1336 2.1 2.0 1.0
NC C:HEM1336 2.1 2.0 1.0
ND C:HEM1336 2.1 2.0 1.0
NE2 C:HIS309 2.2 14.4 1.0
NE2 C:HIS124 2.2 13.9 1.0
CE1 C:HIS309 3.0 14.4 1.0
CE1 C:HIS124 3.0 13.9 1.0
C1B C:HEM1336 3.1 2.0 1.0
C4B C:HEM1336 3.1 2.0 1.0
C4C C:HEM1336 3.1 2.0 1.0
C4A C:HEM1336 3.1 2.0 1.0
C1C C:HEM1336 3.1 2.0 1.0
C1A C:HEM1336 3.1 2.0 1.0
C1D C:HEM1336 3.1 2.0 1.0
C4D C:HEM1336 3.1 2.0 1.0
CD2 C:HIS124 3.3 13.9 1.0
CD2 C:HIS309 3.3 14.4 1.0
CHB C:HEM1336 3.4 2.0 1.0
CHC C:HEM1336 3.4 2.0 1.0
CHD C:HEM1336 3.4 2.0 1.0
CHA C:HEM1336 3.5 2.0 1.0
ND1 C:HIS309 4.1 14.4 1.0
ND1 C:HIS124 4.2 13.9 1.0
C2B C:HEM1336 4.3 2.0 1.0
C3B C:HEM1336 4.3 2.0 1.0
C3C C:HEM1336 4.3 2.0 1.0
C2C C:HEM1336 4.3 2.0 1.0
C3A C:HEM1336 4.3 2.0 1.0
C2A C:HEM1336 4.3 2.0 1.0
CG C:HIS124 4.3 13.9 1.0
CG C:HIS309 4.3 14.5 1.0
C2D C:HEM1336 4.4 2.0 1.0
C3D C:HEM1336 4.4 2.0 1.0
CG C:PRO315 5.0 14.9 1.0

Iron binding site 5 out of 5 in 4ac5

Go back to Iron Binding Sites List in 4ac5
Iron binding site 5 out of 5 in the Lipidic Sponge Phase Crystal Structure of the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography


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 the Bl. Viridis Reaction Centre Solved Using Serial Femtosecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Fe1327

b:2.0
occ:1.00
NE2 L:HIS190 2.0 11.8 1.0
NE2 M:HIS217 2.1 14.4 1.0
NE2 M:HIS264 2.2 14.9 1.0
OE2 M:GLU232 2.4 15.9 1.0
NE2 L:HIS230 2.6 14.5 1.0
CD2 L:HIS190 2.9 11.8 1.0
CE1 L:HIS190 3.0 11.8 1.0
CE1 M:HIS217 3.0 14.4 1.0
CE1 M:HIS264 3.1 15.0 1.0
OE1 M:GLU232 3.1 15.9 1.0
CD M:GLU232 3.1 15.9 1.0
CD2 M:HIS217 3.1 14.4 1.0
CD2 M:HIS264 3.1 14.9 1.0
CD2 L:HIS230 3.5 14.6 1.0
CE1 L:HIS230 3.5 14.6 1.0
ND1 L:HIS190 4.1 11.8 1.0
CG L:HIS190 4.1 11.9 1.0
ND1 M:HIS217 4.2 14.4 1.0
ND1 M:HIS264 4.2 15.0 1.0
CG M:HIS217 4.2 14.4 1.0
CG M:HIS264 4.2 15.0 1.0
CG1 L:ILE194 4.5 13.4 1.0
CG M:GLU232 4.6 16.0 1.0
ND1 L:HIS230 4.6 14.6 1.0
CG L:HIS230 4.7 14.5 1.0
CG1 M:ILE221 4.8 14.7 1.0

Reference:

L.C.Johansson, D.Arnlund, T.A.White, G.Katona, D.P.Deponte, U.Weierstall, R.B.Doak, R.L.Shoeman, L.Lomb, E.Malmerberg, J.Davidsson, K.Nass, M.Liang, J.Andreasson, A.Aquila, S.Bajt, M.Barthelmess, A.Barty, M.J.Bogan, C.Bostedt, J.D.Bozek, C.Caleman, R.Coffee, N.Coppola, T.Ekeberg, S.W.Epp, B.Erk, H.Fleckenstein, L.Foucar, H.Graafsma, L.Gumprecht, J.Hajdu, C.Y.Hampton, R.Hartmann, A.Hartmann, G.Hauser, H.Hirsemann, P.Holl, M.S.Hunter, S.Kassemeyer, N.Kimmel, R.A.Kirian, F.R.N.C.Maia, S.Marchesini, A.V.Martin, C.Reich, D.Rolles, B.Rudek, A.Rudenko, I.Schlichting, J.Schulz, M.M.Seibert, R.Sierra, H.Soltau, D.Starodub, F.Stellato, S.Stern, L.Struder, N.Timneanu, J.Ullrich, W.Y.Wahlgren, X.Wang, G.Weidenspointner, C.Wunderer, P.Fromme, H.N.Chapman, J.C.H.Spence, R.Neutze. Lipidic Phase Membrane Protein Serial Femtosecond Crystallography. Nat.Methods V. 9 263 2012.
ISSN: ISSN 1548-7091
PubMed: 22286383
DOI: 10.1038/NMETH.1867
Page generated: Sun Dec 13 15:27:55 2020

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