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Iron in PDB 2wdr: E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound

Enzymatic activity of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound

All present enzymatic activity of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound:
1.3.5.1; 1.3.99.1;

Protein crystallography data

The structure of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound, PDB code: 2wdr 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) 46.52 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 119.955, 186.128, 204.034, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.8

Other elements in 2wdr:

The structure of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound also contains other interesting chemical elements:

Chlorine (Cl) 15 atoms
Sodium (Na) 3 atoms

Iron Binding Sites:

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 Pentachlorophenol Bound (pdb code 2wdr). 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 Pentachlorophenol Bound, PDB code: 2wdr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 30 in 2wdr

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Iron binding site 1 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound


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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:36.8
occ:1.00
 FE1 B:FES302 0.0 36.8 1.0
S1 B:FES302 2.2 31.3 1.0
S2 B:FES302 2.2 32.5 1.0
SG B:CYS60 2.3 47.0 1.0
SG B:CYS55 2.3 48.3 1.0
FE2 B:FES302 2.9 33.0 1.0
N B:CYS55 3.4 48.0 1.0
CB B:CYS60 3.4 48.0 1.0
CB B:CYS55 3.5 48.3 1.0
N B:ARG56 3.5 48.1 1.0
N B:CYS60 3.7 47.8 1.0
CA B:CYS55 3.8 48.2 1.0
N B:GLY61 3.8 48.0 1.0
CA B:CYS60 4.0 47.7 1.0
C B:CYS55 4.0 48.4 1.0
OD1 B:ASP63 4.2 49.3 1.0
N B:VAL59 4.2 47.9 1.0
N B:SER62 4.3 47.8 1.0
N B:GLY58 4.3 48.0 1.0
C B:CYS60 4.3 48.0 1.0
N B:SER54 4.4 47.6 1.0
C B:SER54 4.4 47.8 1.0
CA B:ARG56 4.4 47.8 1.0
N B:GLU57 4.4 47.6 1.0
SG B:CYS75 4.5 47.0 1.0
CB B:SER62 4.6 47.8 1.0
CA B:GLY58 4.7 48.1 1.0
CA B:SER54 4.8 47.6 1.0
C B:VAL59 4.8 48.0 1.0
CA B:GLY61 4.9 47.9 1.0
CB B:SER54 4.9 47.5 1.0
C B:ARG56 4.9 47.7 1.0

Iron binding site 2 out of 30 in 2wdr

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Iron binding site 2 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound


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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:33.0
occ:1.00
 FE2 B:FES302 0.0 33.0 1.0
OD1 B:ASP63 1.9 49.3 1.0
S2 B:FES302 2.2 32.5 1.0
S1 B:FES302 2.2 31.3 1.0
SG B:CYS75 2.3 47.0 1.0
CG B:ASP63 2.7 48.4 1.0
FE1 B:FES302 2.9 36.8 1.0
OD2 B:ASP63 3.0 48.4 1.0
CB B:CYS75 3.0 47.6 1.0
N B:CYS75 4.1 47.8 1.0
CB B:ASP63 4.1 47.9 1.0
CA B:CYS75 4.2 47.5 1.0
N B:ASP63 4.2 48.0 1.0
CB B:LEU73 4.2 48.0 1.0
N B:GLY58 4.3 48.0 1.0
CA B:GLY58 4.5 48.1 1.0
N B:ARG56 4.5 48.1 1.0
CA B:ARG56 4.6 47.8 1.0
SG B:CYS55 4.6 48.3 1.0
CA B:ASP63 4.7 47.8 1.0
SG B:CYS60 4.8 47.0 1.0
CD1 B:LEU73 4.8 48.2 1.0
CG B:LEU73 4.9 47.8 1.0
CD2 B:LEU73 4.9 47.4 1.0
N B:GLU57 4.9 47.6 1.0
CD2 B:LEU36 4.9 47.4 1.0
N B:ALA74 4.9 47.9 1.0
C B:ARG56 4.9 47.7 1.0
O B:ASP63 5.0 48.0 1.0
N B:SER62 5.0 47.8 1.0

Iron binding site 3 out of 30 in 2wdr

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Iron binding site 3 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound


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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:30.0
occ:1.00
 FE1 B:SF4303 0.0 30.0 1.0
S4 B:SF4303 2.3 31.6 1.0
S2 B:SF4303 2.3 29.6 1.0
S3 B:SF4303 2.3 29.3 1.0
SG B:CYS155 2.3 44.7 1.0
FE2 B:SF4303 2.6 27.9 1.0
FE4 B:SF4303 2.6 31.5 1.0
FE3 B:SF4303 2.7 28.0 1.0
CB B:CYS155 3.4 47.6 1.0
S1 B:SF4303 3.9 31.7 1.0
N B:CYS155 4.0 48.0 1.0
CB B:ALA173 4.2 48.8 1.0
CA B:CYS155 4.3 47.5 1.0
CA B:ALA173 4.4 48.4 1.0
SG B:CYS149 4.5 44.3 1.0
SG B:CYS152 4.6 46.6 1.0
N B:ALA173 4.7 48.5 1.0
SG B:CYS216 4.8 45.6 1.0
N B:CYS154 4.9 48.0 1.0

Iron binding site 4 out of 30 in 2wdr

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Iron binding site 4 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound


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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:27.9
occ:1.00
 FE2 B:SF4303 0.0 27.9 1.0
S3 B:SF4303 2.3 29.3 1.0
S4 B:SF4303 2.3 31.6 1.0
SG B:CYS216 2.3 45.6 1.0
S1 B:SF4303 2.3 31.7 1.0
FE1 B:SF4303 2.6 30.0 1.0
FE3 B:SF4303 2.7 28.0 1.0
FE4 B:SF4303 2.7 31.5 1.0
CB B:CYS216 3.2 47.6 1.0
CA B:CYS216 3.7 47.5 1.0
S2 B:SF4303 3.9 29.6 1.0
CD B:PRO217 4.2 48.0 1.0
C B:CYS216 4.5 47.8 1.0
N B:PRO217 4.6 47.9 1.0
CD1 B:LEU220 4.6 47.3 1.0
SG B:CYS155 4.6 44.7 1.0
CB B:LEU220 4.7 47.7 1.0
CG B:LEU220 4.7 47.4 1.0
SG B:CYS152 4.8 46.6 1.0
SG B:CYS149 4.8 44.3 1.0
N B:LYS218 4.8 47.8 1.0
N B:CYS216 4.9 47.7 1.0

Iron binding site 5 out of 30 in 2wdr

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Iron binding site 5 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound


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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:28.0
occ:1.00
 FE3 B:SF4303 0.0 28.0 1.0
S4 B:SF4303 2.3 31.6 1.0
S2 B:SF4303 2.3 29.6 1.0
S1 B:SF4303 2.3 31.7 1.0
SG B:CYS149 2.3 44.3 1.0
FE4 B:SF4303 2.6 31.5 1.0
FE2 B:SF4303 2.7 27.9 1.0
FE1 B:SF4303 2.7 30.0 1.0
CB B:CYS149 3.3 47.1 1.0
CA B:CYS149 3.6 47.3 1.0
N B:ILE150 3.7 47.8 1.0
S3 B:SF4303 3.9 29.3 1.0
N B:LEU151 4.0 47.9 1.0
C B:CYS149 4.0 47.6 1.0
CA B:LEU151 4.6 47.8 1.0
N B:CYS152 4.6 48.0 1.0
SG B:CYS216 4.7 45.6 1.0
SG B:CYS152 4.7 46.6 1.0
CA B:ILE150 4.7 47.9 1.0
C B:ILE150 4.8 48.1 1.0
CD1 B:LEU220 4.8 47.3 1.0
SG B:CYS155 4.9 44.7 1.0
CG1 B:ILE150 4.9 47.1 1.0
N B:CYS149 5.0 47.6 1.0

Iron binding site 6 out of 30 in 2wdr

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Iron binding site 6 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound


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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:31.5
occ:1.00
 FE4 B:SF4303 0.0 31.5 1.0
S2 B:SF4303 2.3 29.6 1.0
S1 B:SF4303 2.3 31.7 1.0
S3 B:SF4303 2.3 29.3 1.0
SG B:CYS152 2.3 46.6 1.0
FE3 B:SF4303 2.6 28.0 1.0
FE1 B:SF4303 2.6 30.0 1.0
FE2 B:SF4303 2.7 27.9 1.0
CB B:CYS152 3.6 47.7 1.0
N B:CYS152 3.7 48.0 1.0
S4 B:SF4303 3.8 31.6 1.0
CD B:PRO217 4.1 48.0 1.0
N B:ALA153 4.1 48.1 1.0
CA B:CYS152 4.1 47.8 1.0
N B:CYS154 4.3 48.0 1.0
CG1 B:ILE150 4.4 47.1 1.0
CG B:PRO217 4.5 47.9 1.0
CB B:CYS154 4.5 48.4 1.0
C B:CYS152 4.5 48.0 1.0
SG B:CYS155 4.7 44.7 1.0
SG B:CYS216 4.7 45.6 1.0
SG B:CYS149 4.7 44.3 1.0
C B:LEU151 4.8 48.0 1.0
N B:LEU151 4.8 47.9 1.0
N B:CYS155 4.8 48.0 1.0
N B:ILE150 4.9 47.8 1.0
CA B:CYS154 4.9 48.4 1.0

Iron binding site 7 out of 30 in 2wdr

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Iron binding site 7 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound


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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:39.7
occ:1.00
 FE1 B:F3S304 0.0 39.7 1.0
S3 B:F3S304 2.2 39.6 1.0
S2 B:F3S304 2.2 39.1 1.0
S1 B:F3S304 2.2 40.4 1.0
FE4 B:F3S304 2.3 40.5 1.0
SG B:CYS159 2.3 47.1 1.0
FE3 B:F3S304 2.8 41.6 1.0
CB B:CYS159 3.2 47.5 1.0
CA B:CYS159 4.0 47.6 1.0
S4 B:F3S304 4.1 41.8 1.0
SG B:CYS212 4.2 43.0 1.0
CG B:PRO172 4.6 47.6 1.0
CB B:ILE209 4.6 47.9 1.0
CD1 B:ILE209 4.7 47.1 1.0
C B:CYS159 4.8 47.7 1.0
CE2 B:PHE169 4.9 47.5 1.0
SG B:CYS206 4.9 47.3 1.0
CD B:PRO160 4.9 47.6 1.0
CG1 B:ILE209 5.0 47.4 1.0
CB B:CYS212 5.0 47.1 1.0
CD B:PRO172 5.0 47.5 1.0

Iron binding site 8 out of 30 in 2wdr

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Iron binding site 8 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound


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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:41.6
occ:1.00
 FE3 B:F3S304 0.0 41.6 1.0
S1 B:F3S304 2.2 40.4 1.0
S3 B:F3S304 2.2 39.6 1.0
S4 B:F3S304 2.3 41.8 1.0
FE4 B:F3S304 2.3 40.5 1.0
SG B:CYS206 2.3 47.3 1.0
FE1 B:F3S304 2.8 39.7 1.0
CB B:CYS206 3.4 47.8 1.0
CA B:CYS206 3.9 48.0 1.0
S2 B:F3S304 4.0 39.1 1.0
N B:SER208 4.0 48.7 1.0
SG B:CYS212 4.2 43.0 1.0
N B:HIS207 4.2 48.6 1.0
C B:CYS206 4.3 48.4 1.0
CD1 B:ILE226 4.4 47.9 1.0
N B:ILE209 4.5 48.2 1.0
CA B:SER208 4.5 48.6 1.0
SG B:CYS159 4.7 47.1 1.0
CZ B:PHE169 4.9 48.0 1.0
C B:SER208 5.0 48.5 1.0

Iron binding site 9 out of 30 in 2wdr

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Iron binding site 9 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound


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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:40.5
occ:1.00
 FE4 B:F3S304 0.0 40.5 1.0
S2 B:F3S304 2.1 39.1 1.0
S3 B:F3S304 2.1 39.6 1.0
S4 B:F3S304 2.2 41.8 1.0
FE3 B:F3S304 2.3 41.6 1.0
FE1 B:F3S304 2.3 39.7 1.0
SG B:CYS212 2.3 43.0 1.0
S1 B:F3S304 3.3 40.4 1.0
CB B:CYS212 3.7 47.1 1.0
N B:MET210 3.7 48.3 1.0
N B:CYS212 4.1 48.0 1.0
CA B:MET210 4.2 48.7 1.0
OG1 B:THR223 4.4 47.9 1.0
SG B:CYS206 4.4 47.3 1.0
N B:ASN211 4.5 48.3 1.0
N B:ILE209 4.5 48.2 1.0
SG B:CYS159 4.5 47.1 1.0
CA B:CYS212 4.6 47.5 1.0
CB B:ILE209 4.7 47.9 1.0
C B:MET210 4.7 48.7 1.0
C B:ILE209 4.7 48.2 1.0
CG B:PRO172 4.8 47.6 1.0
CA B:ILE209 4.9 48.0 1.0

Iron binding site 10 out of 30 in 2wdr

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Iron binding site 10 out of 30 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound


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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1130

b:41.1
occ:1.00
 FE C:HEM1130 0.0 41.1 1.0
NE2 C:HIS84 1.9 46.9 1.0
NE2 D:HIS71 1.9 47.0 1.0
NC C:HEM1130 2.0 40.8 1.0
ND C:HEM1130 2.0 40.8 1.0
NB C:HEM1130 2.1 41.2 1.0
NA C:HEM1130 2.1 40.8 1.0
CE1 D:HIS71 2.7 47.8 1.0
CD2 C:HIS84 2.8 48.0 1.0
C4C C:HEM1130 2.9 39.6 1.0
C1D C:HEM1130 2.9 40.4 1.0
CE1 C:HIS84 3.0 47.8 1.0
C1C C:HEM1130 3.1 41.5 1.0
C4D C:HEM1130 3.1 40.7 1.0
CD2 D:HIS71 3.1 47.7 1.0
C1B C:HEM1130 3.1 41.5 1.0
C4B C:HEM1130 3.1 41.3 1.0
C4A C:HEM1130 3.2 40.9 1.0
C1A C:HEM1130 3.2 40.6 1.0
CHD C:HEM1130 3.2 40.2 1.0
CHB C:HEM1130 3.5 41.7 1.0
CHC C:HEM1130 3.5 41.1 1.0
CHA C:HEM1130 3.5 40.7 1.0
ND1 D:HIS71 3.9 47.8 1.0
CG C:HIS84 4.0 48.2 1.0
ND1 C:HIS84 4.1 47.9 1.0
CG D:HIS71 4.1 47.5 1.0
C2D C:HEM1130 4.1 40.8 1.0
C3C C:HEM1130 4.1 39.1 1.0
C3D C:HEM1130 4.2 40.8 1.0
C2C C:HEM1130 4.2 40.3 1.0
C2B C:HEM1130 4.4 41.6 1.0
C3B C:HEM1130 4.4 41.5 1.0
C3A C:HEM1130 4.4 40.2 1.0
C2A C:HEM1130 4.4 40.6 1.0
NE2 C:HIS30 4.9 48.2 1.0

Reference:

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
Page generated: Sun Aug 4 03:45:34 2024

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