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Chlorine in PDB 2vpy: Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp)

Protein crystallography data

The structure of Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp), PDB code: 2vpy was solved by M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.58 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.124, 165.194, 243.153, 90.00, 90.00, 90.00
R / Rfree (%) 28.3 / 28.9

Other elements in 2vpy:

The structure of Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp) also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Iron (Fe) 40 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp) (pdb code 2vpy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp), PDB code: 2vpy:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 2vpy

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Chlorine binding site 1 out of 10 in the Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1252

b:35.8
occ:1.00
 CL1 C:PCI1252 0.0 35.8 1.0
C2 C:PCI1252 1.7 37.8 1.0
C1 C:PCI1252 2.7 38.7 1.0
C3 C:PCI1252 2.7 38.5 1.0
O1 C:PCI1252 2.9 41.2 1.0
OH C:TYR130 3.0 57.5 1.0
CL2 C:PCI1252 3.2 34.5 1.0
CD1 C:LEU64 3.4 75.5 1.0
CZ C:TYR130 3.6 55.0 1.0
C6 C:PCI1252 4.0 37.1 1.0
N C:ALA93 4.0 59.8 1.0
C4 C:PCI1252 4.1 38.3 1.0
CD1 C:LEU96 4.1 61.5 1.0
C C:GLY92 4.1 59.0 1.0
O C:ILE89 4.1 50.5 1.0
CE1 C:TYR130 4.1 55.1 1.0
CG2 C:ILE89 4.2 48.3 1.0
CD2 C:LEU64 4.2 75.7 1.0
CA C:ALA93 4.3 60.6 1.0
O C:GLY92 4.4 58.9 1.0
CE2 C:TYR130 4.4 55.5 1.0
CG C:LEU64 4.5 75.6 1.0
CE1 C:HIS21 4.5 59.5 1.0
C5 C:PCI1252 4.5 38.4 1.0
CA C:GLY92 4.5 58.4 1.0
CB C:ALA93 4.6 60.5 1.0
CD1 C:ILE89 4.9 51.9 1.0

Chlorine binding site 2 out of 10 in 2vpy

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Chlorine binding site 2 out of 10 in the Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1252

b:34.5
occ:1.00
 CL2 C:PCI1252 0.0 34.5 1.0
C3 C:PCI1252 1.7 38.5 1.0
C2 C:PCI1252 2.7 37.8 1.0
C4 C:PCI1252 2.7 38.3 1.0
CL3 C:PCI1252 3.2 35.8 1.0
CL1 C:PCI1252 3.2 35.8 1.0
CD2 C:LEU79 3.5 60.4 1.0
CD2 C:LEU64 4.0 75.7 1.0
C5 C:PCI1252 4.0 38.4 1.0
C1 C:PCI1252 4.0 38.7 1.0
CD1 C:LEU64 4.0 75.5 1.0
CG2 C:ILE89 4.2 48.3 1.0
CG C:LEU64 4.4 75.6 1.0
C6 C:PCI1252 4.5 37.1 1.0
CD1 B:ILE91 4.5 44.8 1.0
CB C:LEU64 4.6 75.9 1.0
CD2 C:HIS76 4.7 66.6 1.0
CG C:LEU79 4.7 61.1 1.0
CB C:ALA93 4.8 60.5 1.0

Chlorine binding site 3 out of 10 in 2vpy

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Chlorine binding site 3 out of 10 in the Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1252

b:35.8
occ:1.00
 CL3 C:PCI1252 0.0 35.8 1.0
C4 C:PCI1252 1.7 38.3 1.0
O B:HOH2078 2.6 64.8 1.0
C5 C:PCI1252 2.6 38.4 1.0
C3 C:PCI1252 2.8 38.5 1.0
CL4 C:PCI1252 3.1 37.1 1.0
CL2 C:PCI1252 3.2 34.5 1.0
CD1 B:ILE91 3.5 44.8 1.0
CB B:CYS93 3.7 44.5 1.0
CD2 C:LEU64 3.9 75.7 1.0
C6 C:PCI1252 4.0 37.1 1.0
C2 C:PCI1252 4.0 37.8 1.0
CG1 B:ILE91 4.3 46.0 1.0
CA B:CYS93 4.3 46.9 1.0
NE2 C:HIS76 4.4 66.8 1.0
O C:LEU64 4.5 78.2 1.0
C1 C:PCI1252 4.5 38.7 1.0
CD2 C:HIS76 4.7 66.6 1.0
CG2 C:ILE89 4.8 48.3 1.0

Chlorine binding site 4 out of 10 in 2vpy

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Chlorine binding site 4 out of 10 in the Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1252

b:37.1
occ:1.00
 CL4 C:PCI1252 0.0 37.1 1.0
C5 C:PCI1252 1.7 38.4 1.0
C4 C:PCI1252 2.7 38.3 1.0
C6 C:PCI1252 2.7 37.1 1.0
CL5 C:PCI1252 3.0 37.3 1.0
CL3 C:PCI1252 3.1 35.8 1.0
O B:CYS93 3.6 47.9 1.0
CB B:CYS93 3.7 44.5 1.0
CA B:CYS93 3.8 46.9 1.0
CD2 C:LEU64 4.0 75.7 1.0
C1 C:PCI1252 4.0 38.7 1.0
C3 C:PCI1252 4.0 38.5 1.0
O B:HOH2079 4.0 86.3 1.0
ND2 C:ASN18 4.1 63.1 1.0
C B:CYS93 4.2 47.4 1.0
OE2 C:GLU67 4.3 80.0 1.0
O B:HOH2078 4.5 64.8 1.0
CD1 C:ILE89 4.5 51.9 1.0
C2 C:PCI1252 4.5 37.8 1.0
NE1 C:TRP14 4.7 44.2 1.0
OD1 C:ASN18 4.8 62.2 1.0
CG C:ASN18 4.8 62.2 1.0

Chlorine binding site 5 out of 10 in 2vpy

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Chlorine binding site 5 out of 10 in the Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1252

b:37.3
occ:1.00
 CL5 C:PCI1252 0.0 37.3 1.0
C6 C:PCI1252 1.7 37.1 1.0
C5 C:PCI1252 2.7 38.4 1.0
C1 C:PCI1252 2.7 38.7 1.0
O1 C:PCI1252 2.9 41.2 1.0
CL4 C:PCI1252 3.0 37.1 1.0
CD1 C:ILE89 3.2 51.9 1.0
NE2 C:HIS21 3.8 60.2 1.0
ND2 C:ASN18 3.9 63.1 1.0
C4 C:PCI1252 3.9 38.3 1.0
C2 C:PCI1252 4.0 37.8 1.0
CD2 C:LEU64 4.2 75.7 1.0
CD2 C:HIS21 4.2 59.9 1.0
CE1 C:HIS21 4.2 59.5 1.0
CE1 C:PHE22 4.3 52.9 1.0
C3 C:PCI1252 4.5 38.5 1.0
OH C:TYR130 4.6 57.5 1.0
CG1 C:ILE89 4.7 50.8 1.0
ND1 C:HIS21 4.8 59.1 1.0
CG C:HIS21 4.8 58.6 1.0
CZ C:PHE22 4.9 53.1 1.0
CE1 C:TYR130 5.0 55.1 1.0

Chlorine binding site 6 out of 10 in 2vpy

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Chlorine binding site 6 out of 10 in the Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1251

b:48.5
occ:1.00
 CL1 G:PCI1251 0.0 48.5 1.0
C2 G:PCI1251 1.7 49.5 1.0
C1 G:PCI1251 2.7 49.9 1.0
C3 G:PCI1251 2.8 50.9 1.0
O1 G:PCI1251 2.9 49.0 1.0
CL2 G:PCI1251 3.2 49.4 1.0
ND2 G:ASN17 3.3 74.5 1.0
NE2 G:HIS20 3.3 71.6 1.0
CD2 G:HIS20 3.4 71.6 1.0
CD1 G:ILE88 3.8 65.4 1.0
C6 G:PCI1251 4.0 49.5 1.0
C4 G:PCI1251 4.1 50.4 1.0
CD2 G:LEU63 4.2 87.2 1.0
CE1 G:PHE21 4.4 72.3 1.0
CG G:ASN17 4.5 73.5 1.0
CE1 G:HIS20 4.5 71.6 1.0
C5 G:PCI1251 4.5 50.3 1.0
CG G:HIS20 4.6 70.3 1.0
OH G:TYR129 4.8 68.2 1.0

Chlorine binding site 7 out of 10 in 2vpy

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Chlorine binding site 7 out of 10 in the Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1251

b:49.4
occ:1.00
 CL2 G:PCI1251 0.0 49.4 1.0
C3 G:PCI1251 1.7 50.9 1.0
C2 G:PCI1251 2.7 49.5 1.0
C4 G:PCI1251 2.7 50.4 1.0
CL1 G:PCI1251 3.2 48.5 1.0
CL3 G:PCI1251 3.2 49.3 1.0
OE2 G:GLU66 3.6 87.8 1.0
ND2 G:ASN17 3.6 74.5 1.0
O F:CYS93 3.7 54.3 1.0
CA F:CYS93 3.8 55.7 1.0
OD1 G:ASN17 3.8 74.4 1.0
CB F:CYS93 3.9 54.4 1.0
C5 G:PCI1251 4.0 50.3 1.0
C1 G:PCI1251 4.0 49.9 1.0
CG G:ASN17 4.1 73.5 1.0
C F:CYS93 4.3 55.4 1.0
CD G:GLU66 4.4 87.6 1.0
C6 G:PCI1251 4.5 49.5 1.0
CD2 G:LEU63 4.6 87.2 1.0
NE1 G:TRP13 4.7 54.1 1.0
OE1 G:GLU66 4.7 87.6 1.0
CD1 G:ILE88 4.9 65.4 1.0

Chlorine binding site 8 out of 10 in 2vpy

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Chlorine binding site 8 out of 10 in the Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1251

b:49.3
occ:1.00
 CL3 G:PCI1251 0.0 49.3 1.0
C4 G:PCI1251 1.7 50.4 1.0
C5 G:PCI1251 2.7 50.3 1.0
C3 G:PCI1251 2.8 50.9 1.0
CL4 G:PCI1251 3.1 50.8 1.0
CL2 G:PCI1251 3.2 49.4 1.0
CD1 F:ILE91 3.6 61.7 1.0
O G:LEU63 3.7 86.9 1.0
NE2 G:HIS75 4.0 77.3 1.0
C6 G:PCI1251 4.0 49.5 1.0
CB F:CYS93 4.0 54.4 1.0
C2 G:PCI1251 4.1 49.5 1.0
O F:ILE91 4.3 60.3 1.0
CB G:SER67 4.3 85.8 1.0
OE2 G:GLU66 4.3 87.8 1.0
CA F:CYS93 4.3 55.7 1.0
CG1 F:ILE91 4.5 61.9 1.0
CD2 G:HIS75 4.5 77.4 1.0
C1 G:PCI1251 4.5 49.9 1.0
OG G:SER67 4.6 87.2 1.0
C G:LEU63 4.7 86.2 1.0
CD2 G:LEU63 4.7 87.2 1.0
N F:CYS93 4.9 57.8 1.0
CB F:ILE91 5.0 61.2 1.0
CB G:LEU63 5.0 86.4 1.0

Chlorine binding site 9 out of 10 in 2vpy

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Chlorine binding site 9 out of 10 in the Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1251

b:50.8
occ:1.00
 CL4 G:PCI1251 0.0 50.8 1.0
C5 G:PCI1251 1.7 50.3 1.0
C6 G:PCI1251 2.7 49.5 1.0
C4 G:PCI1251 2.7 50.4 1.0
CL5 G:PCI1251 3.0 50.3 1.0
CL3 G:PCI1251 3.1 49.3 1.0
CD2 G:LEU78 3.6 70.7 1.0
CD1 F:ILE91 3.8 61.7 1.0
CD1 G:LEU63 3.8 87.2 1.0
CD2 G:HIS75 3.9 77.4 1.0
C1 G:PCI1251 4.0 49.9 1.0
C3 G:PCI1251 4.0 50.9 1.0
CB G:LEU63 4.2 86.4 1.0
CD2 G:LEU63 4.2 87.2 1.0
CG G:LEU63 4.3 86.8 1.0
NE2 G:HIS75 4.3 77.3 1.0
C2 G:PCI1251 4.5 49.5 1.0
O G:LEU63 4.7 86.9 1.0
CG G:LEU78 4.9 71.6 1.0

Chlorine binding site 10 out of 10 in 2vpy

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Chlorine binding site 10 out of 10 in the Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Polysulfide Reductase with Bound Quinone Inhibitor, Pentachlorophenol (Pcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1251

b:50.3
occ:1.00
 CL5 G:PCI1251 0.0 50.3 1.0
C6 G:PCI1251 1.7 49.5 1.0
C5 G:PCI1251 2.7 50.3 1.0
C1 G:PCI1251 2.7 49.9 1.0
CD1 G:LEU63 2.8 87.2 1.0
O1 G:PCI1251 2.9 49.0 1.0
CL4 G:PCI1251 3.0 50.8 1.0
CD2 G:LEU63 3.7 87.2 1.0
CG G:LEU63 3.8 86.8 1.0
OH G:TYR129 3.9 68.2 1.0
C4 G:PCI1251 4.0 50.4 1.0
C2 G:PCI1251 4.0 49.5 1.0
CG2 G:ILE88 4.3 65.8 1.0
C3 G:PCI1251 4.5 50.9 1.0
O G:ILE88 4.5 65.9 1.0
CZ G:TYR129 4.7 67.0 1.0
CB G:LEU63 4.7 86.4 1.0
CA G:ALA92 4.7 70.4 1.0
N G:ALA92 4.8 70.2 1.0
O G:GLY91 4.8 69.1 1.0
C G:GLY91 4.8 69.5 1.0
CB G:ALA92 5.0 69.8 1.0

Reference:

M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, S.Iwata. Molecular Mechanism of Energy Conservation in Polysulfide Respiration. Nat.Struct.Mol.Biol. V. 15 730 2008.
ISSN: ISSN 1545-9993
PubMed: 18536726
DOI: 10.1038/NSMB.1434
Page generated: Sat Jul 20 12:06:57 2024

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