Iron in PDB 2gyq: Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.

The structure of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris., PDB code: 2gyq was solved by J.Osipiuk, E.Evdokimova, M.Kudritska, A.Savchenko, A.Edwards, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.70 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	33.451, 101.125, 103.802, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 17.6

The structure of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. also contains other interesting chemical elements:

Zinc	(Zn)	6 atoms
Sodium	(Na)	1 atom

The binding sites of Iron atom in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. (pdb code 2gyq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris., PDB code: 2gyq:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:17.1 occ:1.00 OE1 A:GLU114 2.0 9.5 0.5 OE1 A:GLU117 2.1 16.1 1.0 OE1 A:GLU147 2.1 22.1 1.0 NE2 A:HIS52 2.2 10.1 0.7 O A:HOH585 2.3 25.0 1.0 OE2 A:GLU114 2.3 17.1 0.5 O A:HOH534 2.3 18.1 1.0 OE1 A:GLU114 2.4 15.6 0.5 CD A:GLU114 2.7 14.2 0.5 CD A:GLU147 3.1 14.6 1.0 CD A:GLU114 3.1 8.3 0.5 CD A:GLU117 3.1 12.5 1.0 CD2 A:HIS52 3.2 15.5 0.7 CE1 A:HIS52 3.2 11.5 0.7 ZN A:ZN409 3.3 13.5 0.6 O A:HOH591 3.3 18.3 0.3 ZN A:ZN407 3.4 17.6 1.0 OE2 A:GLU147 3.4 13.8 1.0 OE2 A:GLU114 3.5 11.6 0.5 OE2 A:GLU117 3.5 16.1 1.0 O A:HOH459 3.8 25.6 1.0 CG A:GLU114 4.2 12.5 0.5 CG A:GLU147 4.3 13.8 1.0 ND1 A:HIS52 4.3 10.7 0.7 CG A:HIS52 4.3 16.5 0.7 CG A:GLU117 4.4 11.5 1.0 O A:HOH577 4.4 28.1 1.0 CG A:GLU114 4.5 9.7 0.5 CA A:GLU114 4.6 9.1 0.5 CB A:GLU147 4.6 12.5 1.0 CA A:GLU114 4.6 9.5 0.5 CA A:GLU147 4.7 13.5 1.0 OG1 A:THR56 4.8 15.3 1.0 O A:HOH572 4.8 27.9 1.0 CB A:GLU114 4.8 9.8 0.5 CB A:GLU117 4.8 8.9 1.0 CD1 A:ILE29 4.8 11.5 1.0 CB A:GLU114 4.8 10.3 0.5 OE1 A:GLN59 4.9 10.0 0.6 CG1 A:VAL113 4.9 11.1 1.0

Iron binding site 2 out of 5 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:10.3 occ:1.00 OH A:TYR116 1.9 11.5 1.0 OD2 A:ASP21 2.1 10.6 1.0 OE2 B:GLU88 2.1 14.7 1.0 SG A:CYS79 2.3 11.7 1.0 OE1 B:GLU88 2.5 17.0 1.0 OD1 A:ASP21 2.6 12.2 1.0 CG A:ASP21 2.7 10.4 1.0 CD B:GLU88 2.7 14.3 1.0 CZ A:TYR116 3.1 10.3 1.0 CB A:CYS79 3.3 9.7 1.0 CE2 A:TYR116 3.6 11.4 1.0 CA A:CYS79 3.8 9.1 1.0 NE A:ARG120 4.1 12.4 1.0 CB A:ALA81 4.1 8.7 1.0 CB A:ASP21 4.2 9.3 1.0 NH2 A:ARG120 4.2 13.6 1.0 CG B:GLU88 4.2 11.8 1.0 CE1 A:TYR116 4.2 10.6 1.0 O B:HOH460 4.4 21.1 1.0 C A:CYS79 4.5 9.2 1.0 O A:HOH424 4.5 12.5 1.0 O A:HOH422 4.6 13.7 1.0 N A:ALA81 4.6 8.6 1.0 CZ A:ARG120 4.6 11.6 1.0 O A:ASP21 4.8 8.6 1.0 N A:PRO80 4.9 9.0 1.0 C A:ASP21 4.9 7.9 1.0 CA A:ALA81 4.9 8.3 1.0 N A:ILE82 4.9 7.5 1.0 CA A:ASP21 5.0 8.7 1.0

Iron binding site 3 out of 5 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:14.4 occ:1.00 OE2 A:GLU88 1.5 6.6 0.6 OH B:TYR116 2.0 12.1 0.7 OD2 B:ASP21 2.1 12.8 1.0 SG B:CYS79 2.2 16.1 1.0 CD A:GLU88 2.4 10.6 0.6 OD1 B:ASP21 2.5 13.9 1.0 OE1 A:GLU88 2.6 14.4 0.6 CG B:ASP21 2.7 9.9 1.0 OE2 A:GLU88 3.1 13.6 0.4 OH B:TYR116 3.1 10.8 0.3 CZ B:TYR116 3.2 10.1 0.7 CB B:CYS79 3.2 10.6 1.0 CE2 B:TYR116 3.8 10.0 0.7 CA B:CYS79 3.8 10.0 1.0 CE1 B:TYR116 3.8 10.8 0.3 CZ B:TYR116 3.9 11.5 0.3 CG A:GLU88 4.0 10.8 0.6 NH2 B:ARG120 4.1 18.0 1.0 O B:HOH516 4.1 30.6 1.0 CD A:GLU88 4.1 11.9 0.4 NE B:ARG120 4.1 15.3 1.0 CB B:ASP21 4.2 10.1 1.0 CE1 B:TYR116 4.3 10.3 0.7 CB B:ALA81 4.3 11.6 1.0 CG A:GLU88 4.5 12.3 0.4 C B:CYS79 4.5 9.4 1.0 O A:HOH590 4.6 18.4 1.0 O B:HOH418 4.6 14.1 1.0 N B:ALA81 4.6 9.4 1.0 CZ B:ARG120 4.7 16.6 1.0 O B:ASP21 4.8 8.9 1.0 N B:PRO80 4.9 9.2 1.0 C B:ASP21 4.9 8.4 1.0 O1 B:EDO413 4.9 27.9 1.0 CA B:ASP21 5.0 8.0 1.0

Iron binding site 4 out of 5 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe404 b:11.2 occ:1.00 OE2 B:GLU117 2.0 17.2 1.0 OE1 B:GLU147 2.0 12.2 1.0 OE1 B:GLN59 2.0 9.8 1.0 O B:HOH428 2.1 16.3 1.0 OE1 B:GLU26 2.1 9.3 1.0 OE2 B:GLU26 2.3 10.7 1.0 CD B:GLU26 2.5 11.8 1.0 CD B:GLU117 3.0 11.0 1.0 CD B:GLU147 3.0 9.1 1.0 CD B:GLN59 3.1 9.9 1.0 OE2 B:GLU147 3.2 10.8 1.0 OE1 B:GLU117 3.4 14.1 1.0 FE B:FE405 3.6 13.3 1.0 NE2 B:GLN59 3.6 11.2 1.0 O B:HOH567 3.6 25.9 1.0 CG B:GLU26 4.1 10.6 1.0 CG B:GLU117 4.2 9.2 1.0 OG1 B:THR56 4.3 13.6 1.0 CG B:GLU147 4.3 10.4 1.0 CG2 B:THR56 4.4 13.3 1.0 CG B:GLN59 4.4 10.2 1.0 CE2 B:TYR121 4.5 9.2 1.0 CB B:GLN59 4.6 9.0 1.0 OH B:TYR121 4.6 9.4 1.0 CD1 B:ILE29 4.6 14.3 1.0 CB B:GLU117 4.7 8.3 1.0 NE2 B:HIS52 4.7 10.9 1.0 CB B:THR56 4.8 11.6 1.0 CB B:GLU26 4.9 9.1 1.0 CA B:THR56 5.0 12.0 1.0

Iron binding site 5 out of 5 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe405 b:13.3 occ:1.00 O B:HOH567 1.5 25.9 1.0 OE2 B:GLU147 2.0 10.8 1.0 OE1 B:GLU117 2.1 14.1 1.0 OE1 B:GLU114 2.1 15.2 1.0 NE2 B:HIS52 2.1 10.9 1.0 OE2 B:GLU114 2.4 19.1 1.0 O B:HOH428 2.5 16.3 1.0 CD B:GLU114 2.6 13.9 1.0 CD B:GLU147 2.9 9.1 1.0 CE1 B:HIS52 3.1 11.0 1.0 CD B:GLU117 3.1 11.0 1.0 CD2 B:HIS52 3.2 12.3 1.0 OE1 B:GLU147 3.4 12.2 1.0 OE2 B:GLU117 3.5 17.2 1.0 FE B:FE404 3.6 11.2 1.0 CG B:GLU147 4.0 10.4 1.0 CB B:GLU147 4.1 7.8 1.0 CG B:GLU114 4.1 12.2 1.0 CH3 B:ACT415 4.2 26.6 1.0 CA B:GLU147 4.2 7.8 1.0 ND1 B:HIS52 4.2 12.1 1.0 CG B:HIS52 4.3 11.0 1.0 CG B:GLU117 4.4 9.2 1.0 NE2 B:GLN59 4.6 11.2 1.0 OE1 B:GLN59 4.7 9.8 1.0 CA B:GLU114 4.7 10.0 1.0 OG1 B:THR56 4.7 13.6 1.0 CB B:GLU117 4.8 8.3 1.0 CB B:GLU114 4.8 10.5 1.0 O B:ACT415 4.9 24.0 1.0 CB B:ALA150 4.9 10.9 1.0 N B:GLU147 4.9 7.5 1.0 C B:ACT415 5.0 27.9 1.0

J.Osipiuk, E.Evdokimova, M.Kudritska, A.Savchenko, A.Edwards, A.Joachimiak. X-Ray Crystal Structure of Ycfi Protein, A Putative Structural Protein From Rhodopseudomonas Palustris. To Be Published.