Iron in PDB 2wp9: Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant

All present enzymatic activity of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant:
1.3.5.1; 1.3.99.1;

The structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant, PDB code: 2wp9 was solved by J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, G.Cecchini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.85 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	119.853, 183.803, 202.777, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.2

The structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant (pdb code 2wp9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 30 binding sites of Iron where determined in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant, PDB code: 2wp9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:43.1 occ:1.00 FE1 B:FES302 0.0 43.1 1.0 S1 B:FES302 2.2 47.2 1.0 S2 B:FES302 2.2 37.8 1.0 SG B:CYS60 2.2 37.0 1.0 SG B:CYS55 2.2 37.8 1.0 FE2 B:FES302 3.0 46.0 1.0 CB B:CYS60 3.3 37.6 1.0 N B:CYS55 3.4 38.4 1.0 CB B:CYS55 3.4 38.1 1.0 N B:CYS60 3.5 38.6 1.0 N B:ARG56 3.7 39.8 1.0 CA B:CYS55 3.8 38.6 1.0 CA B:CYS60 3.8 37.5 1.0 N B:GLY61 3.8 37.6 1.0 OD1 B:ASP63 4.1 37.8 1.0 C B:CYS55 4.1 39.6 1.0 C B:CYS60 4.1 37.3 1.0 N B:SER62 4.1 37.5 1.0 N B:VAL59 4.3 41.0 1.0 N B:GLY58 4.3 41.8 1.0 C B:SER54 4.4 39.4 1.0 N B:GLU57 4.5 41.2 1.0 N B:SER54 4.5 38.8 1.0 SG B:CYS75 4.5 39.5 1.0 CB B:SER62 4.5 37.5 1.0 CA B:ARG56 4.6 41.0 1.0 C B:VAL59 4.7 39.4 1.0 CA B:GLY61 4.8 37.2 1.0 CA B:GLY58 4.8 41.4 1.0 CA B:SER54 4.8 39.0 1.0 CA B:SER62 4.9 37.4 1.0 C B:GLY61 5.0 38.1 1.0 CB B:SER54 5.0 38.0 1.0 OG B:SER62 5.0 39.2 1.0 C B:GLY58 5.0 41.3 1.0

Iron binding site 2 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:46.0 occ:1.00 FE2 B:FES302 0.0 46.0 1.0 OD1 B:ASP63 1.8 37.8 1.0 S1 B:FES302 2.2 47.2 1.0 S2 B:FES302 2.2 37.8 1.0 SG B:CYS75 2.2 39.5 1.0 CG B:ASP63 2.7 40.1 1.0 OD2 B:ASP63 3.0 40.5 1.0 CB B:CYS75 3.0 41.5 1.0 FE1 B:FES302 3.0 43.1 1.0 CB B:ASP63 4.1 39.0 1.0 N B:CYS75 4.1 43.1 1.0 CB B:LEU73 4.1 41.9 1.0 N B:GLY58 4.2 41.8 1.0 N B:ASP63 4.2 38.2 1.0 CA B:CYS75 4.2 42.6 1.0 CA B:GLY58 4.4 41.4 1.0 CD2 B:LEU73 4.4 39.0 1.0 SG B:CYS55 4.5 37.8 1.0 CA B:ASP63 4.6 38.5 1.0 CD1 B:LEU73 4.6 39.0 1.0 CG B:LEU73 4.7 40.3 1.0 CA B:ARG56 4.7 41.0 1.0 N B:ARG56 4.7 39.8 1.0 N B:GLU57 4.8 41.2 1.0 N B:SER62 4.9 37.5 1.0 SG B:CYS60 4.9 37.0 1.0

Iron binding site 3 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:39.2 occ:1.00 FE1 B:SF4303 0.0 39.2 1.0 S4 B:SF4303 2.3 40.3 1.0 S3 B:SF4303 2.3 41.9 1.0 SG B:CYS149 2.3 35.7 1.0 S2 B:SF4303 2.3 41.8 1.0 FE2 B:SF4303 2.6 38.6 1.0 FE4 B:SF4303 2.7 39.9 1.0 FE3 B:SF4303 2.7 40.1 1.0 CB B:CYS149 3.4 38.4 1.0 CA B:CYS149 3.7 38.6 1.0 N B:ILE150 3.8 38.1 1.0 S1 B:SF4303 3.9 39.1 1.0 N B:LEU151 4.1 36.4 1.0 C B:CYS149 4.1 38.6 1.0 CD1 B:LEU220 4.5 37.8 1.0 CA B:LEU151 4.6 36.5 1.0 N B:CYS152 4.7 37.0 1.0 SG B:CYS216 4.8 42.3 1.0 SG B:CYS155 4.8 38.5 1.0 SG B:CYS152 4.8 37.7 1.0 CB B:ALA173 4.9 37.8 1.0 CA B:ILE150 4.9 36.7 1.0 C B:ILE150 4.9 36.6 1.0 CD2 B:LEU176 4.9 40.0 1.0

Iron binding site 4 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:38.6 occ:1.00 FE2 B:SF4303 0.0 38.6 1.0 S3 B:SF4303 2.2 41.9 1.0 S4 B:SF4303 2.3 40.3 1.0 SG B:CYS152 2.3 37.7 1.0 S1 B:SF4303 2.4 39.1 1.0 FE1 B:SF4303 2.6 39.2 1.0 FE4 B:SF4303 2.8 39.9 1.0 FE3 B:SF4303 2.8 40.1 1.0 CB B:CYS152 3.6 37.5 1.0 N B:CYS152 3.6 37.0 1.0 S2 B:SF4303 3.9 41.8 1.0 N B:ALA153 3.9 38.8 1.0 CA B:CYS152 4.0 37.3 1.0 CD B:PRO217 4.2 43.0 1.0 N B:CYS154 4.2 40.3 1.0 C B:CYS152 4.3 38.9 1.0 CG1 B:ILE150 4.3 36.9 1.0 CG B:PRO217 4.5 41.6 1.0 N B:LEU151 4.6 36.4 1.0 SG B:CYS149 4.6 35.7 1.0 C B:LEU151 4.6 37.1 1.0 CB B:CYS154 4.7 41.9 1.0 SG B:CYS155 4.7 38.5 1.0 SG B:CYS216 4.8 42.3 1.0 CA B:ALA153 4.8 38.8 1.0 N B:ILE150 4.8 38.1 1.0 N B:CYS155 4.9 41.2 1.0 CA B:LEU151 4.9 36.5 1.0 C B:ALA153 4.9 39.9 1.0 CD1 B:ILE150 5.0 37.6 1.0 CA B:CYS154 5.0 41.6 1.0

Iron binding site 5 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:40.1 occ:1.00 FE3 B:SF4303 0.0 40.1 1.0 S2 B:SF4303 2.2 41.8 1.0 S1 B:SF4303 2.3 39.1 1.0 SG B:CYS155 2.3 38.5 1.0 S4 B:SF4303 2.3 40.3 1.0 FE4 B:SF4303 2.6 39.9 1.0 FE1 B:SF4303 2.7 39.2 1.0 FE2 B:SF4303 2.8 38.6 1.0 CB B:CYS155 3.3 40.5 1.0 S3 B:SF4303 3.9 41.9 1.0 N B:CYS155 3.9 41.2 1.0 CB B:ALA173 4.1 37.8 1.0 CA B:CYS155 4.2 41.0 1.0 CA B:ALA173 4.5 38.4 1.0 SG B:CYS149 4.6 35.7 1.0 SG B:CYS152 4.7 37.7 1.0 SG B:CYS216 4.7 42.3 1.0 N B:ALA173 4.8 39.4 1.0 N B:CYS154 4.9 40.3 1.0 N B:ALA153 5.0 38.8 1.0 CB B:CYS216 5.0 43.7 1.0

Iron binding site 6 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:39.9 occ:1.00 FE4 B:SF4303 0.0 39.9 1.0 S2 B:SF4303 2.2 41.8 1.0 S1 B:SF4303 2.2 39.1 1.0 SG B:CYS216 2.3 42.3 1.0 S3 B:SF4303 2.3 41.9 1.0 FE3 B:SF4303 2.6 40.1 1.0 FE1 B:SF4303 2.7 39.2 1.0 FE2 B:SF4303 2.8 38.6 1.0 CB B:CYS216 3.2 43.7 1.0 CA B:CYS216 3.8 44.2 1.0 S4 B:SF4303 3.9 40.3 1.0 CD B:PRO217 4.0 43.0 1.0 CD1 B:LEU220 4.5 37.8 1.0 C B:CYS216 4.5 44.2 1.0 N B:PRO217 4.6 43.2 1.0 CB B:LEU220 4.6 40.6 1.0 CG B:LEU220 4.7 39.4 1.0 SG B:CYS152 4.7 37.7 1.0 SG B:CYS155 4.7 38.5 1.0 N B:LYS218 4.8 42.2 1.0 CG B:PRO217 4.9 41.6 1.0 SG B:CYS149 4.9 35.7 1.0 CB B:LYS218 4.9 41.1 1.0

Iron binding site 7 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe304 b:44.1 occ:1.00 FE1 B:F3S304 0.0 44.1 1.0 S3 B:F3S304 2.2 43.6 1.0 S1 B:F3S304 2.2 41.1 1.0 S2 B:F3S304 2.2 41.5 1.0 FE4 B:F3S304 2.3 46.4 1.0 SG B:CYS159 2.3 41.9 1.0 FE3 B:F3S304 2.9 47.8 1.0 CB B:CYS159 3.1 42.9 1.0 CA B:CYS159 4.0 44.1 1.0 S4 B:F3S304 4.1 49.4 1.0 SG B:CYS212 4.2 43.2 1.0 CB B:ILE209 4.5 50.8 1.0 CE2 B:PHE169 4.7 39.3 1.0 C B:CYS159 4.7 44.7 1.0 CG B:PRO172 4.8 42.0 1.0 CD B:PRO172 4.8 41.1 1.0 CD1 B:ILE209 4.9 48.0 1.0 CD B:PRO160 4.9 47.4 1.0 CB B:SER161 4.9 47.1 1.0 N B:PRO160 5.0 46.3 1.0 CZ B:PHE169 5.0 40.3 1.0

Iron binding site 8 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe304 b:47.8 occ:1.00 FE3 B:F3S304 0.0 47.8 1.0 S1 B:F3S304 2.2 41.1 1.0 SG B:CYS206 2.3 43.1 1.0 S4 B:F3S304 2.3 49.4 1.0 S3 B:F3S304 2.3 43.6 1.0 FE4 B:F3S304 2.4 46.4 1.0 FE1 B:F3S304 2.9 44.1 1.0 CB B:CYS206 3.2 46.1 1.0 CA B:CYS206 3.6 47.3 1.0 N B:SER208 3.9 51.2 1.0 N B:THR207 3.9 50.4 1.0 C B:CYS206 4.0 49.5 1.0 S2 B:F3S304 4.1 41.5 1.0 CA B:SER208 4.3 51.8 1.0 SG B:CYS212 4.3 43.2 1.0 CD1 B:ILE226 4.4 43.8 1.0 N B:ILE209 4.4 51.8 1.0 N B:MET210 4.8 52.5 1.0 C B:SER208 4.8 52.5 1.0 SG B:CYS159 4.8 41.9 1.0 C B:THR207 4.8 52.9 1.0 O B:CYS206 4.9 49.8 1.0 CZ B:PHE169 4.9 40.3 1.0 CA B:THR207 5.0 52.5 1.0 N B:CYS206 5.0 48.1 1.0

Iron binding site 9 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe304 b:46.4 occ:1.00 FE4 B:F3S304 0.0 46.4 1.0 S2 B:F3S304 2.1 41.5 1.0 S3 B:F3S304 2.1 43.6 1.0 S4 B:F3S304 2.2 49.4 1.0 SG B:CYS212 2.3 43.2 1.0 FE1 B:F3S304 2.3 44.1 1.0 FE3 B:F3S304 2.4 47.8 1.0 S1 B:F3S304 3.2 41.1 1.0 N B:MET210 3.8 52.5 1.0 CB B:CYS212 3.8 43.6 1.0 CA B:MET210 4.1 54.0 1.0 N B:CYS212 4.2 48.1 1.0 N B:ASN211 4.2 53.0 1.0 OG1 B:THR223 4.4 46.4 1.0 SG B:CYS206 4.5 43.1 1.0 SG B:CYS159 4.5 41.9 1.0 CA B:CYS212 4.6 45.0 1.0 C B:MET210 4.7 54.2 1.0 N B:ILE209 4.8 51.8 1.0 C B:ILE209 4.8 52.2 1.0 CB B:ILE209 4.9 50.8 1.0 CB B:PRO172 4.9 41.2 1.0 CB B:CYS159 4.9 42.9 1.0

Iron binding site 10 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1129 b:53.1 occ:1.00 FE C:HEM1129 0.0 53.1 1.0 NE2 C:HIS84 1.9 54.5 1.0 NC C:HEM1129 2.0 53.0 1.0 NE2 D:HIS71 2.0 47.6 1.0 NA C:HEM1129 2.1 55.0 1.0 ND C:HEM1129 2.1 56.2 1.0 NB C:HEM1129 2.2 56.8 1.0 CE1 D:HIS71 2.8 47.4 1.0 CD2 C:HIS84 2.9 58.2 1.0 C4C C:HEM1129 2.9 53.7 1.0 CE1 C:HIS84 2.9 55.4 1.0 C1D C:HEM1129 3.0 54.5 1.0 C1C C:HEM1129 3.1 53.6 1.0 C1A C:HEM1129 3.1 55.9 1.0 C4A C:HEM1129 3.1 55.3 1.0 C4D C:HEM1129 3.2 55.5 1.0 C1B C:HEM1129 3.2 57.0 1.0 C4B C:HEM1129 3.2 55.6 1.0 CD2 D:HIS71 3.2 47.6 1.0 CHD C:HEM1129 3.3 54.8 1.0 CHC C:HEM1129 3.5 54.0 1.0 CHB C:HEM1129 3.5 56.6 1.0 CHA C:HEM1129 3.5 55.4 1.0 ND1 D:HIS71 4.0 46.8 1.0 ND1 C:HIS84 4.0 56.4 1.0 CG C:HIS84 4.0 57.0 1.0 C3C C:HEM1129 4.2 54.7 1.0 CG D:HIS71 4.2 47.7 1.0 C2D C:HEM1129 4.2 53.6 1.0 C2C C:HEM1129 4.2 54.9 1.0 C3D C:HEM1129 4.3 55.8 1.0 C2A C:HEM1129 4.3 56.4 1.0 C3A C:HEM1129 4.3 55.8 1.0 C3B C:HEM1129 4.4 56.6 1.0 C2B C:HEM1129 4.4 56.4 1.0 NE2 C:HIS30 4.9 53.8 1.0

J.Ruprecht, S.Iwata, R.A.Rothery, J.H.Weiner, E.Maklashina, G.Cecchini. Perturbation of the Quinone-Binding Site of Complex II Alters the Electronic Properties of the Proximal [3FE-4S] Iron-Sulfur Cluster. J. Biol. Chem. V. 286 12756 2011.
ISSN: ESSN 1083-351X
PubMed: 21310949
DOI: 10.1074/JBC.M110.209874