Iron in PDB 6pfy: Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A

All present enzymatic activity of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A:
1.97.1.12;

The structure of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A, PDB code: 6pfy was solved by R.Fromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.87 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	278.496, 165.126, 283.427, 90.00, 119.42, 90.00
R / Rfree (%)	30.3 / 34.3

The structure of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A also contains other interesting chemical elements:

Magnesium	(Mg)	285 atoms
Calcium	(Ca)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Iron atom in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A (pdb code 6pfy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 36 binding sites of Iron where determined in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A, PDB code: 6pfy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 36 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe845 b:37.9 occ:1.00 FE1 A:SF4845 0.0 37.9 1.0 S4 A:SF4845 2.2 36.1 1.0 S3 A:SF4845 2.3 38.3 1.0 S2 A:SF4845 2.3 40.3 1.0 SG B:CYS574 2.4 30.6 1.0 FE2 A:SF4845 2.7 41.5 1.0 FE3 A:SF4845 2.7 43.6 1.0 FE4 A:SF4845 2.8 41.1 1.0 CB B:CYS574 3.5 32.1 1.0 S1 A:SF4845 3.9 36.5 1.0 CZ3 B:TRP673 3.9 29.7 1.0 CD1 A:ILE724 4.1 37.5 1.0 SG A:CYS587 4.2 26.7 1.0 CG2 A:ILE724 4.3 38.9 1.0 CA B:CYS574 4.3 35.0 1.0 N B:CYS574 4.5 34.9 1.0 CE3 B:TRP673 4.5 29.8 1.0 NH2 A:ARG728 4.7 31.6 1.0 SG A:CYS578 4.7 29.8 1.0 SG B:CYS565 4.9 30.3 1.0 CH2 B:TRP673 4.9 30.5 1.0 CG1 A:ILE724 4.9 38.5 1.0

Iron binding site 2 out of 36 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe845 b:41.5 occ:1.00 FE2 A:SF4845 0.0 41.5 1.0 SG A:CYS587 1.7 26.7 1.0 S3 A:SF4845 2.2 38.3 1.0 S1 A:SF4845 2.3 36.5 1.0 S4 A:SF4845 2.3 36.1 1.0 FE4 A:SF4845 2.7 41.1 1.0 FE1 A:SF4845 2.7 37.9 1.0 FE3 A:SF4845 2.8 43.6 1.0 CB A:CYS587 3.2 26.6 1.0 S2 A:SF4845 3.9 40.3 1.0 CD1 B:ILE708 3.9 24.9 1.0 CA A:CYS587 4.0 26.1 1.0 CE3 B:TRP673 4.3 29.8 1.0 N A:CYS587 4.4 24.2 1.0 CB A:CYS578 4.4 31.8 1.0 CG1 B:ILE708 4.4 24.8 1.0 CZ3 B:TRP673 4.6 29.7 1.0 SG B:CYS565 4.6 30.3 1.0 SG A:CYS578 4.8 29.8 1.0 SG B:CYS574 4.9 30.6 1.0

Iron binding site 3 out of 36 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe845 b:43.6 occ:1.00 FE3 A:SF4845 0.0 43.6 1.0 S2 A:SF4845 2.2 40.3 1.0 S1 A:SF4845 2.3 36.5 1.0 S4 A:SF4845 2.3 36.1 1.0 SG A:CYS578 2.3 29.8 1.0 FE1 A:SF4845 2.7 37.9 1.0 FE4 A:SF4845 2.7 41.1 1.0 FE2 A:SF4845 2.8 41.5 1.0 CB A:CYS578 2.9 31.8 1.0 S3 A:SF4845 3.9 38.3 1.0 SG A:CYS587 4.1 26.7 1.0 N A:GLY580 4.3 26.0 1.0 CA A:GLY580 4.3 26.6 1.0 CA A:CYS578 4.4 31.2 1.0 CD B:PRO568 4.4 27.6 1.0 N B:PRO568 4.5 27.4 1.0 CD1 A:ILE724 4.6 37.5 1.0 C B:GLY567 4.6 26.6 1.0 CA B:GLY567 4.7 27.0 1.0 SG B:CYS565 4.7 30.3 1.0 C A:GLY580 4.8 25.9 1.0 SG B:CYS574 4.9 30.6 1.0 N A:CYS578 4.9 31.9 1.0 CB A:CYS587 5.0 26.6 1.0 CB A:PRO577 5.0 32.7 1.0

Iron binding site 4 out of 36 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe845 b:41.1 occ:1.00 FE4 A:SF4845 0.0 41.1 1.0 S1 A:SF4845 2.2 36.5 1.0 SG B:CYS565 2.2 30.3 1.0 S3 A:SF4845 2.3 38.3 1.0 S2 A:SF4845 2.3 40.3 1.0 FE2 A:SF4845 2.7 41.5 1.0 FE3 A:SF4845 2.7 43.6 1.0 FE1 A:SF4845 2.8 37.9 1.0 CB B:CYS565 3.1 28.9 1.0 S4 A:SF4845 3.9 36.1 1.0 SG A:CYS587 4.3 26.7 1.0 SG B:CYS574 4.4 30.6 1.0 CA B:GLY567 4.5 27.0 1.0 CA B:CYS565 4.5 27.9 1.0 N B:GLY567 4.5 28.8 1.0 CD A:PRO581 4.5 24.0 1.0 OG1 B:THR573 4.6 33.7 1.0 CD1 B:ILE708 4.6 24.9 1.0 CA B:CYS574 4.8 35.0 1.0 CB B:CYS574 4.8 32.1 1.0 C B:GLY567 4.9 26.6 1.0 N A:PRO581 4.9 25.2 1.0 SG A:CYS578 4.9 29.8 1.0 N B:CYS574 5.0 34.9 1.0

Iron binding site 5 out of 36 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:33.1 occ:1.00 FE1 C:SF4101 0.0 33.1 1.0 S2 C:SF4101 2.2 33.5 1.0 S3 C:SF4101 2.3 34.9 1.0 S4 C:SF4101 2.3 33.9 1.0 SG C:CYS50 2.7 29.2 1.0 FE4 C:SF4101 2.7 36.9 1.0 FE3 C:SF4101 2.7 31.8 1.0 FE2 C:SF4101 2.8 34.4 1.0 N C:CYS50 3.6 29.1 1.0 S1 C:SF4101 3.9 34.3 1.0 N C:LYS51 4.0 30.0 1.0 CB C:CYS50 4.0 28.9 1.0 N C:GLY49 4.1 36.2 1.0 CD C:PRO21 4.2 31.6 1.0 N C:ARG52 4.3 27.1 1.0 CA C:CYS50 4.3 29.4 1.0 C C:GLY49 4.4 30.2 1.0 CA C:GLY49 4.5 34.1 1.0 C C:CYS50 4.6 28.9 1.0 SG C:CYS20 4.6 52.8 1.0 CB C:ARG52 4.7 25.5 1.0 SG C:CYS47 4.8 26.3 1.0 N C:VAL48 4.9 35.2 1.0 CA C:LYS51 4.9 28.8 1.0 CG C:PRO21 4.9 30.7 1.0 N C:CYS53 5.0 32.9 1.0

Iron binding site 6 out of 36 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:34.4 occ:1.00 FE2 C:SF4101 0.0 34.4 1.0 S1 C:SF4101 2.3 34.3 1.0 S4 C:SF4101 2.3 33.9 1.0 SG C:CYS20 2.3 52.8 1.0 S3 C:SF4101 2.3 34.9 1.0 FE3 C:SF4101 2.7 31.8 1.0 FE4 C:SF4101 2.7 36.9 1.0 FE1 C:SF4101 2.8 33.1 1.0 CB C:CYS20 3.6 41.5 1.0 S2 C:SF4101 3.9 33.5 1.0 CB C:VAL24 4.0 32.2 1.0 CA C:CYS20 4.2 39.0 1.0 CG2 C:VAL24 4.3 30.8 1.0 CD1 C:LEU25 4.4 32.3 1.0 CD C:PRO21 4.4 31.6 1.0 OG1 C:THR22 4.4 31.3 1.0 SG C:CYS47 4.5 26.3 1.0 CG1 C:VAL24 4.7 31.4 1.0 N C:VAL24 4.8 33.4 1.0 C C:CYS20 4.9 35.9 1.0 N C:PRO21 5.0 32.3 1.0

Iron binding site 7 out of 36 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:31.8 occ:1.00 FE3 C:SF4101 0.0 31.8 1.0 S4 C:SF4101 2.3 33.9 1.0 S1 C:SF4101 2.3 34.3 1.0 S2 C:SF4101 2.3 33.5 1.0 SG C:CYS53 2.7 31.2 1.0 FE2 C:SF4101 2.7 34.4 1.0 FE1 C:SF4101 2.7 33.1 1.0 FE4 C:SF4101 2.8 36.9 1.0 CB C:CYS53 3.5 32.7 1.0 S3 C:SF4101 3.9 34.9 1.0 N C:CYS53 3.9 32.9 1.0 CG1 C:VAL66 4.1 30.3 1.0 CA C:CYS53 4.3 34.2 1.0 CD1 C:LEU25 4.5 32.3 1.0 N C:ARG52 4.6 27.1 1.0 SG C:CYS47 4.7 26.3 1.0 N C:LYS51 4.7 30.0 1.0 SG C:CYS20 4.7 52.8 1.0 CA C:LYS51 4.8 28.8 1.0 C C:LYS51 4.9 28.8 1.0 SG C:CYS50 4.9 29.2 1.0

Iron binding site 8 out of 36 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:36.9 occ:1.00 FE4 C:SF4101 0.0 36.9 1.0 SG C:CYS47 2.2 26.3 1.0 S3 C:SF4101 2.2 34.9 1.0 S2 C:SF4101 2.3 33.5 1.0 S1 C:SF4101 2.4 34.3 1.0 FE1 C:SF4101 2.7 33.1 1.0 FE2 C:SF4101 2.7 34.4 1.0 FE3 C:SF4101 2.8 31.8 1.0 N C:GLY49 3.6 36.2 1.0 CB C:CYS47 3.7 30.9 1.0 N C:VAL48 3.8 35.2 1.0 S4 C:SF4101 3.9 33.9 1.0 CA C:CYS47 3.9 31.9 1.0 CA C:GLY49 4.1 34.1 1.0 C C:CYS47 4.4 32.5 1.0 C C:VAL48 4.6 36.9 1.0 CG2 C:VAL4 4.7 28.0 1.0 N C:CYS50 4.7 29.1 1.0 CG2 C:VAL24 4.7 30.8 1.0 CA C:VAL48 4.7 36.8 1.0 C C:GLY49 4.8 30.2 1.0 CB C:VAL24 4.9 32.2 1.0 CG1 C:VAL24 4.9 31.4 1.0 SG C:CYS20 5.0 52.8 1.0

Iron binding site 9 out of 36 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe102 b:37.7 occ:1.00 FE1 C:SF4102 0.0 37.7 1.0 O C:HOH205 2.0 46.7 1.0 S4 C:SF4102 2.3 38.9 1.0 S3 C:SF4102 2.3 42.6 1.0 S2 C:SF4102 2.3 42.9 1.0 FE2 C:SF4102 2.7 52.8 1.0 FE3 C:SF4102 2.7 41.3 1.0 FE4 C:SF4102 2.8 47.7 1.0 SG C:CYS57 2.8 46.1 1.0 CA C:CYS57 3.8 39.5 1.0 CB C:CYS57 3.8 40.9 1.0 S1 C:SF4102 3.9 44.1 1.0 CG2 C:ILE64 4.0 26.0 1.0 CD C:PRO58 4.1 42.0 1.0 CB C:SER63 4.4 39.9 1.0 N C:ILE64 4.6 34.7 1.0 CB C:ILE64 4.7 26.8 1.0 CB C:CYS16 4.7 47.6 1.0 N C:CYS57 4.7 38.7 1.0 N C:PRO58 4.7 43.1 1.0 C C:CYS57 4.7 42.2 1.0 SG C:CYS13 4.8 49.1 1.0 SG C:CYS10 4.9 46.3 1.0 OG C:SER63 4.9 43.7 1.0 OG1 C:THR59 5.0 39.0 1.0 N C:SER63 5.0 38.5 1.0 O C:ALA56 5.0 44.5 1.0

Iron binding site 10 out of 36 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe102 b:52.8 occ:1.00 FE2 C:SF4102 0.0 52.8 1.0 S3 C:SF4102 2.3 42.6 1.0 S1 C:SF4102 2.3 44.1 1.0 S4 C:SF4102 2.3 38.9 1.0 FE4 C:SF4102 2.7 47.7 1.0 FE1 C:SF4102 2.7 37.7 1.0 SG C:CYS16 2.7 53.2 1.0 FE3 C:SF4102 2.8 41.3 1.0 CB C:CYS16 3.0 47.6 1.0 O C:HOH205 3.4 46.7 1.0 N C:CYS16 3.8 43.7 1.0 S2 C:SF4102 3.9 42.9 1.0 CA C:CYS16 4.0 45.6 1.0 CB C:ALA39 4.3 32.3 1.0 SG C:CYS13 4.5 49.1 1.0 SG C:CYS10 4.7 46.3 1.0 N C:GLN15 4.7 46.9 1.0 CG2 C:ILE64 4.7 26.0 1.0 N C:THR14 4.8 45.1 1.0 C C:GLN15 5.0 44.7 1.0

C.Gisriel, J.Coe, R.Letrun, O.M.Yefanov, C.Luna-Chavez, N.E.Stander, S.Lisova, V.Mariani, M.Kuhn, S.Aplin, T.D.Grant, K.Dorner, T.Sato, A.Echelmeier, J.Cruz Villarreal, M.S.Hunter, M.O.Wiedorn, J.Knoska, V.Mazalova, S.Roy-Chowdhury, J.H.Yang, A.Jones, R.Bean, J.Bielecki, Y.Kim, G.Mills, B.Weinhausen, J.D.Meza, N.Al-Qudami, S.Bajt, G.Brehm, S.Botha, D.Boukhelef, S.Brockhauser, B.D.Bruce, M.A.Coleman, C.Danilevski, E.Discianno, Z.Dobson, H.Fangohr, J.M.Martin-Garcia, Y.Gevorkov, S.Hauf, A.Hosseinizadeh, F.Januschek, G.K.Ketawala, C.Kupitz, L.Maia, M.Manetti, M.Messerschmidt, T.Michelat, J.Mondal, A.Ourmazd, G.Previtali, I.Sarrou, S.Schon, P.Schwander, M.L.Shelby, A.Silenzi, J.Sztuk-Dambietz, J.Szuba, M.Turcato, T.A.White, K.Wrona, C.Xu, M.H.Abdellatif, J.D.Zook, J.C.H.Spence, H.N.Chapman, A.Barty, R.A.Kirian, M.Frank, A.Ros, M.Schmidt, R.Fromme, A.P.Mancuso, P.Fromme, N.A.Zatsepin. Membrane Protein Megahertz Crystallography at the European Xfel. Nat Commun V. 10 5021 2019.
ISSN: ESSN 2041-1723
PubMed: 31685819
DOI: 10.1038/S41467-019-12955-3