Iron in PDB 2ws3: Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant

All present enzymatic activity of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant:
1.3.5.1; 1.3.99.1;

The structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant, PDB code: 2ws3 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)	49.03 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	119.850, 184.710, 203.310, 90.00, 90.00, 90.00
R / Rfree (%)	21.87 / 25.271

The structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE 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) Sdhd TYR83PHE Mutant (pdb code 2ws3). 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) Sdhd TYR83PHE Mutant, PDB code: 2ws3:
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) Sdhd TYR83PHE 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) Sdhd TYR83PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:43.5 occ:1.00 FE1 B:FES302 0.0 43.5 1.0 S2 B:FES302 2.2 41.7 1.0 S1 B:FES302 2.2 38.3 1.0 SG B:CYS60 2.2 47.1 1.0 SG B:CYS55 2.3 49.8 1.0 FE2 B:FES302 3.0 45.0 1.0 N B:CYS55 3.3 51.9 1.0 CB B:CYS60 3.4 47.3 1.0 CB B:CYS55 3.4 51.3 1.0 N B:CYS60 3.6 47.6 1.0 N B:GLY61 3.6 46.8 1.0 CA B:CYS55 3.8 52.6 1.0 CA B:CYS60 3.8 46.6 1.0 N B:ARG56 3.8 54.1 1.0 N B:SER62 3.9 47.4 1.0 C B:CYS60 4.0 46.3 1.0 OD1 B:ASP63 4.2 50.8 1.0 C B:CYS55 4.3 54.2 1.0 N B:SER54 4.3 51.7 1.0 CB B:SER62 4.3 48.7 1.0 N B:VAL59 4.4 50.0 1.0 C B:SER54 4.4 52.6 1.0 OG B:SER62 4.4 48.4 1.0 N B:GLY58 4.5 53.1 1.0 SG B:CYS75 4.5 51.3 1.0 CA B:GLY61 4.6 46.4 1.0 CA B:SER54 4.7 52.0 1.0 C B:GLY61 4.7 46.9 1.0 CA B:SER62 4.7 47.8 1.0 C B:VAL59 4.7 47.7 1.0 CA B:ARG56 4.7 55.4 1.0 N B:GLU57 4.7 54.4 1.0 CA B:GLY58 4.8 52.1 1.0 CB B:SER54 4.9 50.9 1.0

Iron binding site 2 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE 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) Sdhd TYR83PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:45.0 occ:1.00 FE2 B:FES302 0.0 45.0 1.0 OD1 B:ASP63 1.8 50.8 1.0 S1 B:FES302 2.2 38.3 1.0 S2 B:FES302 2.2 41.7 1.0 SG B:CYS75 2.3 51.3 1.0 CG B:ASP63 2.7 51.6 1.0 CB B:CYS75 3.0 54.8 1.0 FE1 B:FES302 3.0 43.5 1.0 OD2 B:ASP63 3.0 52.8 1.0 CB B:ASP63 4.0 51.6 1.0 N B:CYS75 4.0 55.5 1.0 CA B:CYS75 4.1 56.1 1.0 N B:ASP63 4.1 49.3 1.0 CB B:LEU73 4.3 52.0 1.0 N B:GLY58 4.4 53.1 1.0 SG B:CYS55 4.4 49.8 1.0 CA B:GLY58 4.5 52.1 1.0 CA B:ASP63 4.6 50.4 1.0 N B:ARG56 4.6 54.1 1.0 CA B:ARG56 4.6 55.4 1.0 CD2 B:LEU73 4.7 49.8 1.0 N B:SER62 4.8 47.4 1.0 CG B:LEU73 4.9 50.4 1.0 CD1 B:LEU73 4.9 50.1 1.0 CD2 B:LEU36 4.9 56.5 1.0 N B:GLU57 4.9 54.4 1.0 O B:ASP63 5.0 52.1 1.0 C B:ARG56 5.0 55.6 1.0 N B:ALA74 5.0 54.7 1.0

Iron binding site 3 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE 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) Sdhd TYR83PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:41.6 occ:1.00 FE1 B:SF4303 0.0 41.6 1.0 S3 B:SF4303 2.3 40.9 1.0 S4 B:SF4303 2.3 40.8 1.0 S2 B:SF4303 2.3 40.2 1.0 SG B:CYS155 2.3 48.8 1.0 FE4 B:SF4303 2.6 40.9 1.0 FE2 B:SF4303 2.7 40.4 1.0 FE3 B:SF4303 2.8 38.7 1.0 CB B:CYS155 3.2 50.4 1.0 S1 B:SF4303 3.8 39.7 1.0 N B:CYS155 4.0 50.0 1.0 CB B:ALA173 4.0 47.5 1.0 CA B:CYS155 4.2 50.6 1.0 CA B:ALA173 4.4 47.7 1.0 SG B:CYS149 4.5 43.1 1.0 SG B:CYS216 4.7 48.5 1.0 SG B:CYS152 4.7 47.6 1.0 N B:ALA173 4.8 49.0 1.0 N B:SER156 5.0 49.8 1.0

Iron binding site 4 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE 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) Sdhd TYR83PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:40.4 occ:1.00 FE2 B:SF4303 0.0 40.4 1.0 S4 B:SF4303 2.2 40.8 1.0 SG B:CYS216 2.3 48.5 1.0 S3 B:SF4303 2.3 40.9 1.0 S1 B:SF4303 2.3 39.7 1.0 FE1 B:SF4303 2.7 41.6 1.0 FE4 B:SF4303 2.7 40.9 1.0 FE3 B:SF4303 2.7 38.7 1.0 CB B:CYS216 3.5 51.5 1.0 S2 B:SF4303 3.9 40.2 1.0 CA B:CYS216 3.9 51.7 1.0 CD1 B:LEU220 4.0 48.6 1.0 CD B:PRO217 4.2 50.4 1.0 CG B:LEU220 4.6 49.6 1.0 C B:CYS216 4.6 52.4 1.0 CB B:LEU220 4.6 50.6 1.0 N B:PRO217 4.7 51.8 1.0 SG B:CYS152 4.7 47.6 1.0 N B:LYS218 4.8 51.0 1.0 SG B:CYS155 4.8 48.8 1.0 SG B:CYS149 4.9 43.1 1.0 CG B:PRO217 4.9 49.5 1.0 CB B:CYS155 5.0 50.4 1.0

Iron binding site 5 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE 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) Sdhd TYR83PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:38.7 occ:1.00 FE3 B:SF4303 0.0 38.7 1.0 S1 B:SF4303 2.3 39.7 1.0 S4 B:SF4303 2.3 40.8 1.0 SG B:CYS149 2.3 43.1 1.0 S2 B:SF4303 2.3 40.2 1.0 FE4 B:SF4303 2.7 40.9 1.0 FE2 B:SF4303 2.7 40.4 1.0 FE1 B:SF4303 2.8 41.6 1.0 CB B:CYS149 3.2 45.6 1.0 CA B:CYS149 3.6 45.8 1.0 N B:ILE150 3.7 45.5 1.0 S3 B:SF4303 3.9 40.9 1.0 C B:CYS149 4.0 45.3 1.0 N B:LEU151 4.1 44.7 1.0 CD1 B:LEU220 4.3 48.6 1.0 CA B:LEU151 4.7 44.5 1.0 CA B:ILE150 4.8 45.2 1.0 SG B:CYS152 4.8 47.6 1.0 N B:CYS152 4.8 45.5 1.0 SG B:CYS216 4.9 48.5 1.0 C B:ILE150 4.9 45.0 1.0 CB B:ALA173 4.9 47.5 1.0 SG B:CYS155 4.9 48.8 1.0 CD2 B:LEU176 4.9 47.9 1.0 N B:CYS149 4.9 46.5 1.0

Iron binding site 6 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE 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) Sdhd TYR83PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:40.9 occ:1.00 FE4 B:SF4303 0.0 40.9 1.0 S2 B:SF4303 2.3 40.2 1.0 S1 B:SF4303 2.3 39.7 1.0 S3 B:SF4303 2.3 40.9 1.0 SG B:CYS152 2.3 47.6 1.0 FE1 B:SF4303 2.6 41.6 1.0 FE3 B:SF4303 2.7 38.7 1.0 FE2 B:SF4303 2.7 40.4 1.0 CB B:CYS152 3.7 46.5 1.0 N B:CYS152 3.7 45.5 1.0 S4 B:SF4303 3.8 40.8 1.0 N B:ALA153 4.0 46.3 1.0 CA B:CYS152 4.2 46.1 1.0 CD B:PRO217 4.3 50.4 1.0 N B:CYS154 4.3 48.4 1.0 C B:CYS152 4.4 46.6 1.0 CG1 B:ILE150 4.5 45.8 1.0 SG B:CYS155 4.5 48.8 1.0 CG B:PRO217 4.6 49.5 1.0 SG B:CYS216 4.6 48.5 1.0 SG B:CYS149 4.7 43.1 1.0 N B:CYS155 4.7 50.0 1.0 N B:LEU151 4.7 44.7 1.0 CB B:CYS154 4.7 50.2 1.0 C B:LEU151 4.8 45.1 1.0 CA B:ALA153 4.8 47.1 1.0 N B:ILE150 4.9 45.5 1.0 C B:ALA153 4.9 48.2 1.0 CA B:LEU151 5.0 44.5 1.0 CA B:CYS154 5.0 49.8 1.0

Iron binding site 7 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE 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) Sdhd TYR83PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe304 b:52.0 occ:1.00 FE1 B:F3S304 0.0 52.0 1.0 S3 B:F3S304 2.2 49.6 1.0 FE4 B:F3S304 2.2 58.0 1.0 S2 B:F3S304 2.2 55.8 1.0 S1 B:F3S304 2.2 54.8 1.0 SG B:CYS159 2.3 56.2 1.0 FE3 B:F3S304 2.8 56.7 1.0 CB B:CYS159 3.0 55.6 1.0 CA B:CYS159 3.9 56.8 1.0 S4 B:F3S304 4.0 59.3 1.0 SG B:CYS212 4.1 53.2 1.0 CD B:PRO172 4.6 51.6 1.0 C B:CYS159 4.7 58.4 1.0 CB B:ILE209 4.7 64.2 1.0 CE2 B:PHE169 4.7 56.5 1.0 CD B:PRO160 4.8 61.2 1.0 CZ B:PHE169 4.9 56.6 1.0 N B:PRO160 4.9 60.3 1.0 CB B:CYS212 5.0 53.4 1.0 CG B:PRO172 5.0 51.0 1.0

Iron binding site 8 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE 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) Sdhd TYR83PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe304 b:56.7 occ:1.00 FE3 B:F3S304 0.0 56.7 1.0 S1 B:F3S304 2.2 54.8 1.0 S3 B:F3S304 2.2 49.6 1.0 S4 B:F3S304 2.2 59.3 1.0 SG B:CYS206 2.3 60.1 1.0 FE4 B:F3S304 2.3 58.0 1.0 FE1 B:F3S304 2.8 52.0 1.0 CB B:CYS206 3.2 60.2 1.0 CA B:CYS206 3.6 61.9 1.0 N B:HIS207 3.7 64.4 1.0 N B:SER208 3.9 65.3 1.0 C B:CYS206 4.0 64.0 1.0 S2 B:F3S304 4.1 55.8 1.0 SG B:CYS212 4.3 53.2 1.0 CA B:SER208 4.4 65.5 1.0 N B:ILE209 4.4 65.0 1.0 CD1 B:ILE226 4.5 55.1 1.0 SG B:CYS159 4.7 56.2 1.0 CZ B:PHE169 4.8 56.6 1.0 C B:HIS207 4.8 67.2 1.0 CA B:HIS207 4.8 67.0 1.0 N B:CYS206 4.9 62.2 1.0 C B:SER208 4.9 66.2 1.0

Iron binding site 9 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE 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) Sdhd TYR83PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe304 b:58.0 occ:1.00 FE4 B:F3S304 0.0 58.0 1.0 S2 B:F3S304 2.1 55.8 1.0 S3 B:F3S304 2.2 49.6 1.0 S4 B:F3S304 2.2 59.3 1.0 FE1 B:F3S304 2.2 52.0 1.0 FE3 B:F3S304 2.3 56.7 1.0 SG B:CYS212 2.3 53.2 1.0 S1 B:F3S304 3.0 54.8 1.0 N B:MET210 3.8 62.4 1.0 CB B:CYS212 3.8 53.4 1.0 CA B:MET210 4.3 61.8 1.0 N B:CYS212 4.3 56.4 1.0 SG B:CYS206 4.4 60.1 1.0 N B:ILE209 4.4 65.0 1.0 OG1 B:THR223 4.5 58.9 1.0 SG B:CYS159 4.5 56.2 1.0 N B:ASN211 4.6 60.5 1.0 CA B:CYS212 4.7 54.0 1.0 CB B:ILE209 4.8 64.2 1.0 C B:ILE209 4.8 64.2 1.0 CB B:CYS159 4.8 55.6 1.0 C B:MET210 4.8 61.1 1.0 CA B:ILE209 4.9 65.2 1.0

Iron binding site 10 out of 30 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE 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) Sdhd TYR83PHE Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1130 b:46.0 occ:1.00 FE C:HEM1130 0.0 46.0 1.0 NE2 C:HIS84 1.9 65.3 1.0 NE2 D:HIS71 1.9 58.0 1.0 ND C:HEM1130 2.0 47.4 1.0 NC C:HEM1130 2.0 45.0 1.0 NB C:HEM1130 2.1 47.8 1.0 NA C:HEM1130 2.1 47.9 1.0 CE1 C:HIS84 2.8 64.1 1.0 CE1 D:HIS71 2.9 56.4 1.0 CD2 D:HIS71 3.0 57.5 1.0 C4D C:HEM1130 3.0 48.3 1.0 C1D C:HEM1130 3.0 47.1 1.0 CD2 C:HIS84 3.0 65.1 1.0 C4C C:HEM1130 3.0 44.0 1.0 C1A C:HEM1130 3.0 48.2 1.0 C4B C:HEM1130 3.0 49.0 1.0 C1C C:HEM1130 3.1 44.6 1.0 C1B C:HEM1130 3.1 49.2 1.0 C4A C:HEM1130 3.1 49.0 1.0 CHD C:HEM1130 3.4 46.2 1.0 CHA C:HEM1130 3.4 48.1 1.0 CHC C:HEM1130 3.4 45.7 1.0 CHB C:HEM1130 3.5 48.8 1.0 ND1 D:HIS71 4.0 56.8 1.0 ND1 C:HIS84 4.0 64.2 1.0 CG D:HIS71 4.1 57.2 1.0 CG C:HIS84 4.1 65.3 1.0 C3D C:HEM1130 4.2 48.9 1.0 C2D C:HEM1130 4.2 47.4 1.0 C3B C:HEM1130 4.3 52.2 1.0 C3C C:HEM1130 4.3 42.8 1.0 C2A C:HEM1130 4.3 49.4 1.0 C2C C:HEM1130 4.3 43.4 1.0 C3A C:HEM1130 4.3 49.0 1.0 C2B C:HEM1130 4.3 51.6 1.0 NE2 C:HIS30 5.0 63.4 1.0

J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, G.Cecchini. Succinate Dehydrogenase Activity To Be Published.