Iron in PDB 2wdv: E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket

All present enzymatic activity of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket:
1.3.5.1; 1.3.99.1;

The structure of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket, PDB code: 2wdv 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)	51.85 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	120.340, 184.847, 204.720, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23.3

The structure of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket 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 E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket (pdb code 2wdv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 30 binding sites of Iron where determined in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket, PDB code: 2wdv:
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 E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:34.9 occ:1.00 FE1 B:FES302 0.0 34.9 1.0 S2 B:FES302 2.1 31.2 1.0 S1 B:FES302 2.1 30.8 1.0 SG B:CYS60 2.3 54.1 1.0 SG B:CYS55 2.3 52.6 1.0 FE2 B:FES302 2.9 35.4 1.0 N B:CYS55 3.3 54.5 1.0 CB B:CYS60 3.4 54.4 1.0 CB B:CYS55 3.4 54.5 1.0 N B:CYS60 3.6 54.3 1.0 N B:ARG56 3.8 54.8 1.0 CA B:CYS55 3.8 54.4 1.0 CA B:CYS60 3.8 54.2 1.0 N B:GLY61 3.9 54.4 1.0 C B:CYS55 4.2 54.6 1.0 OD1 B:ASP63 4.2 53.5 1.0 N B:SER62 4.2 54.3 1.0 C B:CYS60 4.2 54.4 1.0 CB B:SER62 4.3 54.5 1.0 N B:SER54 4.3 54.7 1.0 N B:VAL59 4.3 54.6 1.0 C B:SER54 4.3 54.6 1.0 SG B:CYS75 4.4 52.4 1.0 N B:GLY58 4.5 54.6 1.0 CA B:ARG56 4.6 54.5 1.0 CA B:SER54 4.7 54.7 1.0 N B:GLU57 4.7 54.3 1.0 C B:VAL59 4.8 54.3 1.0 CA B:GLY58 4.8 54.7 1.0 CB B:SER54 4.8 54.9 1.0 CA B:SER62 4.9 54.5 1.0 CA B:GLY61 4.9 54.4 1.0 OG B:SER62 4.9 55.6 1.0 C B:GLY58 5.0 54.5 1.0

Iron binding site 2 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:35.4 occ:1.00 FE2 B:FES302 0.0 35.4 1.0 OD1 B:ASP63 1.8 53.5 1.0 S1 B:FES302 2.2 30.8 1.0 S2 B:FES302 2.2 31.2 1.0 SG B:CYS75 2.3 52.4 1.0 CG B:ASP63 2.8 54.8 1.0 FE1 B:FES302 2.9 34.9 1.0 OD2 B:ASP63 3.1 55.2 1.0 CB B:CYS75 3.2 54.5 1.0 CB B:ASP63 4.1 54.8 1.0 N B:CYS75 4.1 54.6 1.0 N B:ASP63 4.2 54.8 1.0 CB B:LEU73 4.2 54.8 1.0 CA B:CYS75 4.3 54.3 1.0 N B:GLY58 4.5 54.6 1.0 SG B:CYS55 4.5 52.6 1.0 CA B:ASP63 4.6 55.0 1.0 CA B:GLY58 4.6 54.7 1.0 CD1 B:LEU73 4.6 54.5 1.0 N B:ARG56 4.7 54.8 1.0 CA B:ARG56 4.7 54.5 1.0 CD2 B:LEU73 4.8 54.4 1.0 CG B:LEU73 4.8 54.4 1.0 SG B:CYS60 4.8 54.1 1.0 N B:ALA74 4.8 55.0 1.0 N B:SER62 4.9 54.3 1.0 O B:ASP63 4.9 55.2 1.0

Iron binding site 3 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:28.4 occ:1.00 FE1 B:SF4303 0.0 28.4 1.0 S4 B:SF4303 2.3 30.1 1.0 S3 B:SF4303 2.3 29.0 1.0 S2 B:SF4303 2.3 28.4 1.0 SG B:CYS155 2.3 53.2 1.0 FE4 B:SF4303 2.6 33.5 1.0 FE2 B:SF4303 2.6 29.0 1.0 FE3 B:SF4303 2.7 28.8 1.0 CB B:CYS155 3.4 54.6 1.0 S1 B:SF4303 3.9 30.1 1.0 N B:CYS155 4.0 54.6 1.0 CA B:CYS155 4.3 54.5 1.0 CB B:ALA173 4.4 55.9 1.0 CA B:ALA173 4.5 55.7 1.0 SG B:CYS149 4.5 51.5 1.0 SG B:CYS216 4.7 51.1 1.0 SG B:CYS152 4.7 52.2 1.0 N B:ALA173 4.9 55.9 1.0

Iron binding site 4 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:29.0 occ:1.00 FE2 B:SF4303 0.0 29.0 1.0 S4 B:SF4303 2.2 30.1 1.0 S3 B:SF4303 2.3 29.0 1.0 SG B:CYS216 2.3 51.1 1.0 S1 B:SF4303 2.3 30.1 1.0 FE3 B:SF4303 2.6 28.8 1.0 FE1 B:SF4303 2.6 28.4 1.0 FE4 B:SF4303 2.7 33.5 1.0 CB B:CYS216 3.5 53.9 1.0 S2 B:SF4303 3.9 28.4 1.0 CA B:CYS216 4.0 53.7 1.0 CD1 B:LEU220 4.3 54.8 1.0 CD B:PRO217 4.4 54.0 1.0 CG B:LEU220 4.5 54.1 1.0 CB B:LEU220 4.6 54.4 1.0 C B:CYS216 4.6 53.9 1.0 SG B:CYS155 4.7 53.2 1.0 N B:LYS218 4.7 54.3 1.0 SG B:CYS152 4.7 52.2 1.0 SG B:CYS149 4.7 51.5 1.0 N B:PRO217 4.7 53.9 1.0 CB B:LYS218 4.9 54.5 1.0

Iron binding site 5 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:28.8 occ:1.00 FE3 B:SF4303 0.0 28.8 1.0 S4 B:SF4303 2.3 30.1 1.0 S1 B:SF4303 2.3 30.1 1.0 S2 B:SF4303 2.3 28.4 1.0 SG B:CYS149 2.3 51.5 1.0 FE2 B:SF4303 2.6 29.0 1.0 FE4 B:SF4303 2.6 33.5 1.0 FE1 B:SF4303 2.7 28.4 1.0 CB B:CYS149 3.3 53.8 1.0 CA B:CYS149 3.7 53.8 1.0 N B:ILE150 3.7 54.2 1.0 S3 B:SF4303 3.8 29.0 1.0 N B:LEU151 4.0 54.4 1.0 C B:CYS149 4.1 54.1 1.0 CD1 B:LEU220 4.5 54.8 1.0 CA B:LEU151 4.6 54.5 1.0 SG B:CYS152 4.7 52.2 1.0 SG B:CYS216 4.7 51.1 1.0 N B:CYS152 4.7 54.8 1.0 CA B:ILE150 4.8 54.3 1.0 C B:ILE150 4.8 54.5 1.0 SG B:CYS155 4.9 53.2 1.0

Iron binding site 6 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:33.5 occ:1.00 FE4 B:SF4303 0.0 33.5 1.0 S2 B:SF4303 2.3 28.4 1.0 S1 B:SF4303 2.3 30.1 1.0 S3 B:SF4303 2.3 29.0 1.0 SG B:CYS152 2.3 52.2 1.0 FE3 B:SF4303 2.6 28.8 1.0 FE1 B:SF4303 2.6 28.4 1.0 FE2 B:SF4303 2.7 29.0 1.0 N B:CYS152 3.7 54.8 1.0 CB B:CYS152 3.8 54.5 1.0 S4 B:SF4303 3.8 30.1 1.0 N B:ALA153 3.9 54.4 1.0 CA B:CYS152 4.2 54.6 1.0 N B:CYS154 4.2 54.4 1.0 CD B:PRO217 4.4 54.0 1.0 C B:CYS152 4.4 54.8 1.0 SG B:CYS155 4.5 53.2 1.0 SG B:CYS149 4.6 51.5 1.0 CG1 B:ILE150 4.6 53.9 1.0 N B:LEU151 4.6 54.4 1.0 CB B:CYS154 4.6 55.0 1.0 CG B:PRO217 4.7 53.9 1.0 SG B:CYS216 4.7 51.1 1.0 N B:CYS155 4.7 54.6 1.0 CA B:ALA153 4.7 54.4 1.0 C B:LEU151 4.8 54.8 1.0 CA B:LEU151 4.9 54.5 1.0 C B:ALA153 4.9 54.5 1.0 CA B:CYS154 4.9 54.9 1.0 N B:ILE150 5.0 54.2 1.0

Iron binding site 7 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe304 b:43.9 occ:1.00 FE1 B:F3S304 0.0 43.9 1.0 S3 B:F3S304 2.2 45.3 1.0 S1 B:F3S304 2.2 45.6 1.0 S2 B:F3S304 2.2 49.4 1.0 FE4 B:F3S304 2.3 49.6 1.0 SG B:CYS159 2.3 53.3 1.0 FE3 B:F3S304 2.8 49.8 1.0 CB B:CYS159 3.1 54.1 1.0 CA B:CYS159 3.9 54.2 1.0 S4 B:F3S304 4.0 46.1 1.0 SG B:CYS212 4.1 52.2 1.0 CD B:PRO172 4.7 54.4 1.0 C B:CYS159 4.7 54.5 1.0 CD B:PRO160 4.7 54.7 1.0 CB B:ILE209 4.7 55.2 1.0 CG B:PRO172 4.8 54.5 1.0 CE2 B:PHE169 4.9 54.2 1.0 CD1 B:ILE209 4.9 54.9 1.0 N B:PRO160 4.9 54.6 1.0

Iron binding site 8 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe304 b:49.8 occ:1.00 FE3 B:F3S304 0.0 49.8 1.0 S1 B:F3S304 2.2 45.6 1.0 S3 B:F3S304 2.2 45.3 1.0 S4 B:F3S304 2.3 46.1 1.0 FE4 B:F3S304 2.3 49.6 1.0 SG B:CYS206 2.3 54.9 1.0 FE1 B:F3S304 2.8 43.9 1.0 CB B:CYS206 3.3 54.7 1.0 CA B:CYS206 3.7 54.6 1.0 N B:HIS207 3.9 54.9 1.0 N B:SER208 4.0 55.2 1.0 S2 B:F3S304 4.1 49.4 1.0 C B:CYS206 4.1 54.8 1.0 CD1 B:ILE226 4.3 54.8 1.0 SG B:CYS212 4.3 52.2 1.0 SG B:CYS159 4.6 53.3 1.0 CA B:SER208 4.6 55.4 1.0 N B:ILE209 4.7 55.5 1.0 CZ B:PHE169 4.7 54.4 1.0 C B:HIS207 4.9 55.0 1.0 N B:CYS206 5.0 54.5 1.0

Iron binding site 9 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe304 b:49.6 occ:1.00 FE4 B:F3S304 0.0 49.6 1.0 S2 B:F3S304 2.1 49.4 1.0 S4 B:F3S304 2.1 46.1 1.0 S3 B:F3S304 2.2 45.3 1.0 FE1 B:F3S304 2.3 43.9 1.0 FE3 B:F3S304 2.3 49.8 1.0 SG B:CYS212 2.3 52.2 1.0 S1 B:F3S304 3.1 45.6 1.0 CB B:CYS212 3.9 54.8 1.0 N B:MET210 3.9 55.6 1.0 N B:CYS212 4.3 55.4 1.0 SG B:CYS206 4.3 54.9 1.0 CA B:MET210 4.4 55.8 1.0 OG1 B:THR223 4.5 55.1 1.0 SG B:CYS159 4.5 53.3 1.0 N B:ILE209 4.6 55.5 1.0 N B:ASN211 4.7 55.7 1.0 CA B:CYS212 4.8 55.0 1.0 CB B:ILE209 4.8 55.2 1.0 C B:MET210 4.8 56.0 1.0 C B:ILE209 4.9 55.4 1.0

Iron binding site 10 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1129 b:45.2 occ:1.00 FE C:HEM1129 0.0 45.2 1.0 NE2 D:HIS71 1.9 53.4 1.0 NE2 C:HIS84 1.9 54.2 1.0 NC C:HEM1129 1.9 45.9 1.0 ND C:HEM1129 2.0 45.6 1.0 NA C:HEM1129 2.1 47.0 1.0 NB C:HEM1129 2.1 45.8 1.0 CE1 D:HIS71 2.8 54.4 1.0 CE1 C:HIS84 2.9 54.9 1.0 C4C C:HEM1129 2.9 45.7 1.0 C1D C:HEM1129 2.9 46.0 1.0 CD2 C:HIS84 3.0 55.0 1.0 CD2 D:HIS71 3.0 54.6 1.0 C4D C:HEM1129 3.0 46.2 1.0 C1C C:HEM1129 3.0 46.4 1.0 C4B C:HEM1129 3.1 46.9 1.0 C1A C:HEM1129 3.1 47.1 1.0 C1B C:HEM1129 3.1 46.5 1.0 C4A C:HEM1129 3.1 47.9 1.0 CHD C:HEM1129 3.3 46.0 1.0 CHA C:HEM1129 3.4 46.4 1.0 CHC C:HEM1129 3.4 46.3 1.0 CHB C:HEM1129 3.5 47.1 1.0 ND1 D:HIS71 4.0 54.5 1.0 ND1 C:HIS84 4.0 54.5 1.0 CG D:HIS71 4.1 54.3 1.0 CG C:HIS84 4.1 54.8 1.0 C2D C:HEM1129 4.2 46.5 1.0 C3C C:HEM1129 4.2 45.5 1.0 C3D C:HEM1129 4.2 46.9 1.0 C2C C:HEM1129 4.2 46.2 1.0 C3B C:HEM1129 4.3 48.0 1.0 C2A C:HEM1129 4.3 47.8 1.0 C2B C:HEM1129 4.3 47.5 1.0 C3A C:HEM1129 4.3 48.0 1.0

J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, G.Cecchini. Structure of Escherichia Coli Succinate:Quinone Oxidoreductase with An Occupied and Empty Quinone- Binding Site. J.Biol.Chem. V. 284 29836 2009.
ISSN: ISSN 0021-9258
PubMed: 19710024
DOI: 10.1074/JBC.M109.010058