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Chlorine in PDB 1y5n: The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol

Enzymatic activity of The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol

All present enzymatic activity of The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol:
1.7.99.4;

Protein crystallography data

The structure of The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol, PDB code: 1y5n was solved by M.G.Bertero, R.A.Rothery, N.Boroumand, M.Palak, F.Blasco, N.Ginet, J.H.Weiner, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.84 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 154.258, 241.957, 140.121, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.8

Other elements in 1y5n:

The structure of The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol also contains other interesting chemical elements:

Molybdenum (Mo) 1 atom
Iron (Fe) 21 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol (pdb code 1y5n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol, PDB code: 1y5n:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 1y5n

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Chlorine binding site 1 out of 5 in the The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl808

b:71.9
occ:1.00
 CL1 C:PCI808 0.0 71.9 1.0
C2 C:PCI808 1.4 72.6 1.0
C1 C:PCI808 2.4 71.3 1.0
C3 C:PCI808 2.5 76.2 1.0
O1 C:PCI808 2.8 59.6 1.0
CL2 C:PCI808 2.9 72.0 1.0
ND1 C:HIS66 3.0 56.7 1.0
O2D C:HEM807 3.0 84.2 1.0
CE1 C:HIS66 3.4 50.6 1.0
N C:HIS66 3.7 61.4 1.0
C C:GLY65 3.7 63.9 1.0
C6 C:PCI808 3.8 69.8 1.0
C4 C:PCI808 3.8 74.1 1.0
CGD C:HEM807 4.1 87.5 1.0
CG C:HIS66 4.1 48.1 1.0
CA C:GLY65 4.1 64.4 1.0
CA C:HIS66 4.1 55.9 1.0
O C:GLY65 4.1 60.9 1.0
O C:ILE62 4.3 64.2 1.0
C5 C:PCI808 4.3 69.5 1.0
CB C:ALA90 4.4 67.2 1.0
O1D C:HEM807 4.5 89.4 1.0
NE2 C:HIS66 4.5 50.0 1.0
CB C:HIS66 4.7 45.0 1.0
CA C:ALA90 4.8 68.6 1.0
CL5 C:PCI808 4.9 69.0 1.0
CD2 C:HIS66 4.9 46.6 1.0

Chlorine binding site 2 out of 5 in 1y5n

Go back to Chlorine Binding Sites List in 1y5n
Chlorine binding site 2 out of 5 in the The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl808

b:72.0
occ:1.00
 CL2 C:PCI808 0.0 72.0 1.0
C3 C:PCI808 1.4 76.2 1.0
C2 C:PCI808 2.5 72.6 1.0
C4 C:PCI808 2.5 74.1 1.0
CL3 C:PCI808 2.9 67.9 1.0
CL1 C:PCI808 2.9 71.9 1.0
CA C:GLY65 3.5 64.4 1.0
CA C:ALA90 3.6 68.6 1.0
C1 C:PCI808 3.8 71.3 1.0
C5 C:PCI808 3.9 69.5 1.0
CB C:ALA90 3.9 67.2 1.0
C C:GLY65 4.0 63.9 1.0
N C:ALA90 4.2 72.0 1.0
O C:GLY65 4.2 60.9 1.0
C6 C:PCI808 4.4 69.8 1.0
O2D C:HEM807 4.4 84.2 1.0
N C:GLY94 4.7 69.6 1.0
C C:MET89 4.7 75.9 1.0
N C:GLY65 4.7 65.7 1.0
C C:ALA90 4.7 67.7 1.0
CA C:GLY94 4.8 66.0 1.0
N C:HIS66 4.8 61.4 1.0
O C:ALA90 4.8 68.7 1.0
O C:MET89 4.8 76.4 1.0
O1 C:PCI808 5.0 59.6 1.0

Chlorine binding site 3 out of 5 in 1y5n

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Chlorine binding site 3 out of 5 in the The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl808

b:67.9
occ:1.00
 CL3 C:PCI808 0.0 67.9 1.0
C4 C:PCI808 1.4 74.1 1.0
C3 C:PCI808 2.5 76.2 1.0
C5 C:PCI808 2.5 69.5 1.0
CL2 C:PCI808 2.9 72.0 1.0
CL4 C:PCI808 2.9 62.5 1.0
O C:ALA86 3.8 74.2 1.0
C2 C:PCI808 3.9 72.6 1.0
C6 C:PCI808 3.9 69.8 1.0
N C:ALA90 4.2 72.0 1.0
CB C:ALA90 4.3 67.2 1.0
C1 C:PCI808 4.4 71.3 1.0
CB C:MET89 4.4 81.5 1.0
CA C:ALA90 4.4 68.6 1.0
C C:ALA86 4.5 71.5 1.0
O C:GLY65 4.6 60.9 1.0
CB C:ALA86 4.6 67.5 1.0
CA C:ALA86 4.7 72.8 1.0
C C:MET89 4.9 75.9 1.0
CA C:GLY69 4.9 72.4 1.0
CA C:GLY65 4.9 64.4 1.0

Chlorine binding site 4 out of 5 in 1y5n

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Chlorine binding site 4 out of 5 in the The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl808

b:62.5
occ:1.00
 CL4 C:PCI808 0.0 62.5 1.0
C5 C:PCI808 1.4 69.5 1.0
C6 C:PCI808 2.5 69.8 1.0
C4 C:PCI808 2.5 74.1 1.0
CL3 C:PCI808 2.9 67.9 1.0
CL5 C:PCI808 2.9 69.0 1.0
CA C:GLY69 3.5 72.4 1.0
CE C:MET156 3.7 80.0 1.0
C1 C:PCI808 3.8 71.3 1.0
CB C:ALA86 3.8 67.5 1.0
C3 C:PCI808 3.9 76.2 1.0
O C:GLY69 3.9 74.8 1.0
SD C:MET156 4.0 88.1 1.0
C C:GLY69 4.1 74.3 1.0
C2 C:PCI808 4.4 72.6 1.0
O C:ALA86 4.6 74.2 1.0
C C:ALA86 4.7 71.5 1.0
CA C:ALA86 4.7 72.8 1.0
N C:GLY69 4.7 74.6 1.0
O C:GLY65 4.8 60.9 1.0
O1 C:PCI808 5.0 59.6 1.0

Chlorine binding site 5 out of 5 in 1y5n

Go back to Chlorine Binding Sites List in 1y5n
Chlorine binding site 5 out of 5 in the The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl808

b:69.0
occ:1.00
 CL5 C:PCI808 0.0 69.0 1.0
C6 C:PCI808 1.4 69.8 1.0
C1 C:PCI808 2.4 71.3 1.0
C5 C:PCI808 2.5 69.5 1.0
O1 C:PCI808 2.8 59.6 1.0
CL4 C:PCI808 2.9 62.5 1.0
CE C:MET156 3.6 80.0 1.0
C C:GLY69 3.7 74.3 1.0
CG C:MET70 3.7 80.8 1.0
O C:GLY69 3.8 74.8 1.0
C2 C:PCI808 3.8 72.6 1.0
CA C:GLY69 3.8 72.4 1.0
C4 C:PCI808 3.9 74.1 1.0
CG2 C:VAL160 4.0 56.0 1.0
N C:MET70 4.2 75.7 1.0
C3 C:PCI808 4.4 76.2 1.0
SD C:MET156 4.4 88.1 1.0
CG C:MET156 4.5 77.4 1.0
CBA C:HEM807 4.6 85.3 1.0
O C:GLY65 4.7 60.9 1.0
CA C:MET70 4.8 76.3 1.0
CB C:MET70 4.8 76.9 1.0
SD C:MET70 4.8 92.6 1.0
CL1 C:PCI808 4.9 71.9 1.0
O1A C:HEM807 5.0 92.8 1.0

Reference:

M.G.Bertero, R.A.Rothery, N.Boroumand, M.Palak, F.Blasco, N.Ginet, J.H.Weiner, N.C.J.Strynadka. Structural and Biochemical Characterization of A Quinol Binding Site of Escherichia Coli Nitrate Reductase A J.Biol.Chem. V. 280 14836 2005.
ISSN: ISSN 0021-9258
PubMed: 15615728
DOI: 10.1074/JBC.M410457200
Page generated: Thu Jul 10 20:32:28 2025

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