Iron in PDB 3pcq: Femtosecond X-Ray Protein Nanocrystallography

The structure of Femtosecond X-Ray Protein Nanocrystallography, PDB code: 3pcq was solved by H.N.Chapman, P.Fromme, A.Barty, T.A.White, R.A.Kirian, A.Aquila, M.S.Hunter, J.Schulz, D.P.Deponte, U.Weierstall, R.B.Doak, F.R.N.C.Maia, A.V.Martin, I.Schlichting, L.Lomb, N.Coppola, R.L.Shoeman, S.W.Epp, R.Hartmann, D.Rolles, A.Rudenko, L.Foucar, N.Kimmel, G.Weidenspointner, P.Holl, M.Liang, M.Barthelmess, C.Caleman, S.Boutet, M.J.Bogan, J.Krzywinski, C.Bostedt, S.Bajt, L.Gumprecht, B.Rudek, B.Erk, C.Schmidt, A.Homke, C.Reich, D.Pietschner, L.Struder, G.Hauser, H.Gorke, J.Ullrich, S.Herrmann, G.Schaller, F.Schopper, H.Soltau, K.-U.Kuhnel, M.Messerschmidt, J.D.Bozek, S.P.Hau-Riege, M.Frank, C.Y.Hampton, R.Sierra, D.Starodub, G.J.Williams, J.Hajdu, N.Timneanu, M.M.Seibert, J.Andreasson, A.Rocker, O.Jonsson, M.Svenda, S.Stern, K.Nass, R.Andritschke, C.-D.Schroter, F.Krasniqi, M.Bott, K.E.Schmidt, X.Wang, I.Grotjohann, J.M.Holton, T.R.M.Barends, R.Neutze, S.Marchesini, R.Fromme, S.Schorb, D.Rupp, M.Adolph, T.Gorkhover, I.Andersson, H.Hirsemann, G.Potdevin, H.Graafsma, B.Nilsson, J.C.H.Spence, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.12 / 8.98
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	281.000, 281.000, 165.200, 90.00, 90.00, 120.00
R / Rfree (%)	25.2 / 23.2

The structure of Femtosecond X-Ray Protein Nanocrystallography also contains other interesting chemical elements:

Magnesium	(Mg)	96 atoms
Calcium	(Ca)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Femtosecond X-Ray Protein Nanocrystallography (pdb code 3pcq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Femtosecond X-Ray Protein Nanocrystallography, PDB code: 3pcq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe848 b:26.9 occ:1.00 FE1 A:SF4848 0.0 26.9 1.0 S4 A:SF4848 2.3 25.9 1.0 S2 A:SF4848 2.3 25.9 1.0 S3 A:SF4848 2.3 25.8 1.0 SG B:CYS574 2.4 30.4 1.0 FE2 A:SF4848 2.7 27.5 1.0 FE4 A:SF4848 2.7 26.5 1.0 FE3 A:SF4848 2.7 27.0 1.0 CB B:CYS574 3.3 28.4 1.0 S1 A:SF4848 3.9 27.4 1.0 CA B:CYS574 3.9 29.7 1.0 CD1 A:ILE724 4.1 27.6 1.0 N B:CYS574 4.1 29.5 1.0 CZ3 B:TRP673 4.1 29.1 1.0 SG B:CYS565 4.6 27.2 1.0 CG2 A:ILE724 4.6 29.2 1.0 CE3 B:TRP673 4.7 29.2 1.0 SG A:CYS578 4.7 23.4 1.0 CB B:CYS565 4.8 29.6 1.0 CG1 A:ILE724 4.9 30.1 1.0 SG A:CYS587 5.0 27.4 1.0

Iron binding site 2 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe848 b:27.5 occ:1.00 FE2 A:SF4848 0.0 27.5 1.0 S1 A:SF4848 2.3 27.4 1.0 S3 A:SF4848 2.3 25.8 1.0 S4 A:SF4848 2.3 25.9 1.0 SG A:CYS587 2.4 27.4 1.0 FE1 A:SF4848 2.7 26.9 1.0 FE4 A:SF4848 2.7 26.5 1.0 FE3 A:SF4848 2.7 27.0 1.0 CB A:CYS587 3.3 21.9 1.0 S2 A:SF4848 3.9 25.9 1.0 CA A:CYS587 3.9 24.0 1.0 CD1 B:ILE708 3.9 23.3 1.0 CE3 B:TRP673 4.2 29.2 1.0 N A:CYS587 4.2 23.7 1.0 CZ3 B:TRP673 4.5 29.1 1.0 SG A:CYS578 4.5 23.4 1.0 CB A:CYS578 4.5 28.9 1.0 SG B:CYS565 4.7 27.2 1.0 CG1 B:ILE708 4.8 25.5 1.0 SG B:CYS574 4.9 30.4 1.0

Iron binding site 3 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe848 b:27.0 occ:1.00 FE3 A:SF4848 0.0 27.0 1.0 SG A:CYS578 2.2 23.4 1.0 S2 A:SF4848 2.2 25.9 1.0 S1 A:SF4848 2.3 27.4 1.0 S4 A:SF4848 2.3 25.9 1.0 FE4 A:SF4848 2.7 26.5 1.0 FE1 A:SF4848 2.7 26.9 1.0 FE2 A:SF4848 2.7 27.5 1.0 CB A:CYS578 3.3 28.9 1.0 S3 A:SF4848 3.9 25.8 1.0 CD B:PRO568 4.3 25.0 1.0 N A:GLY580 4.4 25.7 1.0 CA A:GLY580 4.5 23.5 1.0 N B:PRO568 4.5 26.5 1.0 CD1 A:ILE724 4.6 27.6 1.0 CA A:CYS578 4.7 29.7 1.0 C B:GLY567 4.7 27.1 1.0 O A:PRO577 4.7 32.6 1.0 CB B:PRO568 4.8 27.2 1.0 C A:GLY580 4.8 24.6 1.0 SG B:CYS565 4.8 27.2 1.0 SG A:CYS587 4.8 27.4 1.0 CA B:GLY567 4.9 27.2 1.0 SG B:CYS574 4.9 30.4 1.0 CA B:PRO568 5.0 28.3 1.0 C A:PRO577 5.0 31.9 1.0 CG B:PRO568 5.0 25.4 1.0 CA A:CYS587 5.0 24.0 1.0

Iron binding site 4 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe848 b:26.5 occ:1.00 FE4 A:SF4848 0.0 26.5 1.0 SG B:CYS565 2.3 27.2 1.0 S1 A:SF4848 2.3 27.4 1.0 S2 A:SF4848 2.3 25.9 1.0 S3 A:SF4848 2.3 25.8 1.0 FE3 A:SF4848 2.7 27.0 1.0 FE2 A:SF4848 2.7 27.5 1.0 FE1 A:SF4848 2.7 26.9 1.0 CB B:CYS565 3.3 29.6 1.0 S4 A:SF4848 3.9 25.9 1.0 N B:GLY567 4.3 30.2 1.0 CA B:GLY567 4.4 27.2 1.0 CD1 B:ILE708 4.4 23.3 1.0 CD A:PRO581 4.4 22.5 1.0 N A:PRO581 4.5 23.8 1.0 CA B:CYS565 4.7 31.7 1.0 CB A:PRO581 4.8 23.1 1.0 SG A:CYS578 4.8 23.4 1.0 C B:GLY567 4.8 27.1 1.0 SG B:CYS574 4.8 30.4 1.0 C A:GLY580 4.9 24.6 1.0 CA A:PRO581 4.9 23.9 1.0 O B:PRO564 4.9 32.9 1.0 SG A:CYS587 4.9 27.4 1.0 CA B:CYS574 5.0 29.7 1.0

Iron binding site 5 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:25.8 occ:1.00 FE1 C:SF4101 0.0 25.8 1.0 S2 C:SF4101 2.2 26.4 1.0 S3 C:SF4101 2.3 25.6 1.0 S4 C:SF4101 2.3 25.3 1.0 SG C:CYS50 2.4 28.6 1.0 FE4 C:SF4101 2.7 26.0 1.0 FE3 C:SF4101 2.7 26.1 1.0 FE2 C:SF4101 2.8 26.8 1.0 N C:CYS50 3.4 24.2 1.0 N C:LYS51 3.5 29.3 1.0 CB C:CYS50 3.7 26.1 1.0 S1 C:SF4101 3.9 24.6 1.0 CA C:CYS50 3.9 25.3 1.0 CD C:PRO21 4.1 34.5 1.0 N C:GLY49 4.1 25.9 1.0 C C:CYS50 4.2 28.3 1.0 C C:GLY49 4.2 25.1 1.0 N C:ARG52 4.2 29.3 1.0 CA C:LYS51 4.4 29.0 1.0 CA C:GLY49 4.4 23.3 1.0 CG2 C:VAL48 4.5 26.7 1.0 CG C:PRO21 4.7 34.2 1.0 SG C:CYS47 4.7 23.4 1.0 SG C:CYS53 4.7 33.7 1.0 C C:LYS51 4.8 29.1 1.0 SG C:CYS20 4.8 36.2 1.0 N C:VAL48 4.9 25.6 1.0 N C:CYS53 4.9 30.6 1.0

Iron binding site 6 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:26.8 occ:1.00 FE2 C:SF4101 0.0 26.8 1.0 S1 C:SF4101 2.2 24.6 1.0 S4 C:SF4101 2.3 25.3 1.0 S3 C:SF4101 2.3 25.6 1.0 SG C:CYS20 2.4 36.2 1.0 FE3 C:SF4101 2.7 26.1 1.0 FE4 C:SF4101 2.7 26.0 1.0 FE1 C:SF4101 2.8 25.8 1.0 CB C:CYS20 3.2 33.1 1.0 CA C:CYS20 3.8 35.3 1.0 S2 C:SF4101 3.9 26.4 1.0 CD C:PRO21 4.0 34.5 1.0 CG2 C:VAL24 4.1 30.8 1.0 CB C:VAL24 4.1 29.9 1.0 OG1 C:THR22 4.3 30.4 1.0 C C:CYS20 4.6 36.3 1.0 N C:PRO21 4.6 36.0 1.0 SG C:CYS50 4.7 28.6 1.0 CD1 C:LEU25 4.8 30.6 1.0 SG C:CYS47 4.9 23.4 1.0 CB C:CYS53 4.9 28.2 1.0 SG C:CYS53 4.9 33.7 1.0 CG C:LEU25 4.9 30.3 1.0 N C:CYS20 4.9 34.9 1.0 CG1 C:VAL24 4.9 27.2 1.0 N C:VAL24 5.0 32.6 1.0

Iron binding site 7 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:26.1 occ:1.00 FE3 C:SF4101 0.0 26.1 1.0 S4 C:SF4101 2.2 25.3 1.0 S1 C:SF4101 2.3 24.6 1.0 S2 C:SF4101 2.4 26.4 1.0 SG C:CYS53 2.4 33.7 1.0 FE2 C:SF4101 2.7 26.8 1.0 FE1 C:SF4101 2.7 25.8 1.0 FE4 C:SF4101 2.8 26.0 1.0 CB C:CYS53 3.1 28.2 1.0 S3 C:SF4101 3.9 25.6 1.0 N C:CYS53 4.0 30.6 1.0 CA C:CYS53 4.2 31.5 1.0 CG2 C:VAL66 4.2 31.0 1.0 N C:LYS51 4.5 29.3 1.0 CA C:LYS51 4.6 29.0 1.0 SG C:CYS50 4.7 28.6 1.0 N C:ARG52 4.7 29.3 1.0 CD1 C:LEU25 4.7 30.6 1.0 SG C:CYS47 4.8 23.4 1.0 C C:LYS51 4.9 29.1 1.0 SG C:CYS20 4.9 36.2 1.0

Iron binding site 8 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:26.0 occ:1.00 FE4 C:SF4101 0.0 26.0 1.0 S3 C:SF4101 2.2 25.6 1.0 S2 C:SF4101 2.3 26.4 1.0 SG C:CYS47 2.3 23.4 1.0 S1 C:SF4101 2.3 24.6 1.0 FE1 C:SF4101 2.7 25.8 1.0 FE2 C:SF4101 2.7 26.8 1.0 FE3 C:SF4101 2.8 26.1 1.0 CB C:CYS47 3.5 25.7 1.0 N C:GLY49 3.8 25.9 1.0 CA C:CYS47 3.8 25.7 1.0 S4 C:SF4101 3.9 25.3 1.0 N C:VAL48 4.0 25.6 1.0 C C:CYS47 4.2 25.9 1.0 CG2 C:VAL24 4.3 30.8 1.0 CA C:GLY49 4.3 23.3 1.0 CG2 C:VAL4 4.6 29.3 1.0 CB C:VAL24 4.7 29.9 1.0 N C:CYS50 4.8 24.2 1.0 SG C:CYS20 4.8 36.2 1.0 C C:VAL48 4.9 28.1 1.0 CG1 C:VAL24 4.9 27.2 1.0 C C:GLY49 5.0 25.1 1.0 SG C:CYS53 5.0 33.7 1.0

Iron binding site 9 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe102 b:35.7 occ:1.00 FE1 C:SF4102 0.0 35.7 1.0 S4 C:SF4102 2.3 33.1 1.0 S2 C:SF4102 2.3 34.1 1.0 S3 C:SF4102 2.3 34.2 1.0 SG C:CYS57 2.4 39.7 1.0 FE2 C:SF4102 2.7 34.5 1.0 FE4 C:SF4102 2.7 35.0 1.0 FE3 C:SF4102 2.7 35.5 1.0 CB C:CYS57 3.3 36.6 1.0 CA C:CYS57 3.8 37.8 1.0 S1 C:SF4102 3.9 34.5 1.0 CD C:PRO58 3.9 41.6 1.0 CB C:SER63 4.0 35.7 1.0 CG2 C:ILE64 4.5 29.3 1.0 C C:CYS57 4.6 39.9 1.0 SG C:CYS13 4.6 35.8 1.0 N C:PRO58 4.6 41.2 1.0 N C:ILE64 4.7 34.1 1.0 OG C:SER63 4.7 32.9 1.0 CG2 C:THR59 4.7 39.8 1.0 N C:SER63 4.8 32.7 1.0 N C:CYS57 4.8 35.4 1.0 SG C:CYS16 4.9 40.9 1.0 CA C:SER63 4.9 35.1 1.0 CB C:ILE64 4.9 32.1 1.0 SG C:CYS10 4.9 35.5 1.0

Iron binding site 10 out of 12 in the Femtosecond X-Ray Protein Nanocrystallography


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Femtosecond X-Ray Protein Nanocrystallography within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe102 b:34.5 occ:1.00 FE2 C:SF4102 0.0 34.5 1.0 S3 C:SF4102 2.3 34.2 1.0 S1 C:SF4102 2.3 34.5 1.0 S4 C:SF4102 2.3 33.1 1.0 SG C:CYS16 2.4 40.9 1.0 FE4 C:SF4102 2.7 35.0 1.0 FE1 C:SF4102 2.7 35.7 1.0 FE3 C:SF4102 2.7 35.5 1.0 CB C:CYS16 3.3 36.6 1.0 CB C:ALA39 3.8 34.9 1.0 N C:CYS16 3.9 39.0 1.0 S2 C:SF4102 3.9 34.1 1.0 CA C:CYS16 4.2 38.5 1.0 SG C:CYS10 4.6 35.5 1.0 SG C:CYS13 4.6 35.8 1.0 CG2 C:ILE64 4.8 29.3 1.0 N C:GLN15 4.8 39.6 1.0 CB C:ILE64 4.9 32.1 1.0 N C:THR14 4.9 33.1 1.0 SG C:CYS57 4.9 39.7 1.0 N C:VAL17 5.0 37.1 1.0

H.N.Chapman, P.Fromme, A.Barty, T.A.White, R.A.Kirian, A.Aquila, M.S.Hunter, J.Schulz, D.P.Deponte, U.Weierstall, R.B.Doak, F.R.Maia, A.V.Martin, I.Schlichting, L.Lomb, N.Coppola, R.L.Shoeman, S.W.Epp, R.Hartmann, D.Rolles, A.Rudenko, L.Foucar, N.Kimmel, G.Weidenspointner, P.Holl, M.Liang, M.Barthelmess, C.Caleman, S.Boutet, M.J.Bogan, J.Krzywinski, C.Bostedt, S.Bajt, L.Gumprecht, B.Rudek, B.Erk, C.Schmidt, A.Homke, C.Reich, D.Pietschner, L.Struder, G.Hauser, H.Gorke, J.Ullrich, S.Herrmann, G.Schaller, F.Schopper, H.Soltau, K.U.Kuhnel, M.Messerschmidt, J.D.Bozek, S.P.Hau-Riege, M.Frank, C.Y.Hampton, R.G.Sierra, D.Starodub, G.J.Williams, J.Hajdu, N.Timneanu, M.M.Seibert, J.Andreasson, A.Rocker, O.Jonsson, M.Svenda, S.Stern, K.Nass, R.Andritschke, C.D.Schroter, F.Krasniqi, M.Bott, K.E.Schmidt, X.Wang, I.Grotjohann, J.M.Holton, T.R.Barends, R.Neutze, S.Marchesini, R.Fromme, S.Schorb, D.Rupp, M.Adolph, T.Gorkhover, I.Andersson, H.Hirsemann, G.Potdevin, H.Graafsma, B.Nilsson, J.C.Spence. Femtosecond X-Ray Protein Nanocrystallography. Nature V. 470 73 2011.
ISSN: ISSN 0028-0836
PubMed: 21293373
DOI: 10.1038/NATURE09750