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Chlorine in PDB 1y4z: The Crystal Structure of Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor Pentachlorophenol

Enzymatic activity of The Crystal Structure of Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor Pentachlorophenol

All present enzymatic activity of The Crystal Structure of Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor Pentachlorophenol:
1.7.99.4;

Protein crystallography data

The structure of The Crystal Structure of Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor Pentachlorophenol, PDB code: 1y4z 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) 29.75 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 154.456, 241.342, 140.014, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 23.3

Other elements in 1y4z:

The structure of The Crystal Structure of Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor Pentachlorophenol also contains other interesting chemical elements:

Molybdenum (Mo) 1 atom
Iron (Fe) 20 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Crystal Structure of Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor Pentachlorophenol (pdb code 1y4z). 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 Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor Pentachlorophenol, PDB code: 1y4z:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 1y4z

Go back to Chlorine Binding Sites List in 1y4z
Chlorine binding site 1 out of 5 in the The Crystal Structure of Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor 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 Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1808

b:33.8
occ:1.00
 CL1 C:PCI1808 0.0 33.8 1.0
C2 C:PCI1808 1.4 38.7 1.0
C1 C:PCI1808 2.5 38.8 1.0
C3 C:PCI1808 2.6 40.1 1.0
O1 C:PCI1808 2.8 38.7 1.0
CL2 C:PCI1808 3.0 36.1 1.0
CA C:GLY65 3.5 43.5 1.0
CA C:ALA90 3.6 42.5 1.0
C6 C:PCI1808 3.9 38.0 1.0
C4 C:PCI1808 3.9 40.4 1.0
O2D C:HEM807 3.9 43.5 1.0
CB C:ALA90 4.0 40.7 1.0
C C:GLY65 4.1 44.7 1.0
CA C:GLY94 4.2 38.0 1.0
N C:ALA90 4.2 44.0 1.0
N C:GLY94 4.3 39.4 1.0
O C:ALA90 4.4 40.5 1.0
C5 C:PCI1808 4.4 39.3 1.0
C C:ALA90 4.5 41.3 1.0
O C:GLY65 4.5 45.0 1.0
O C:MET89 4.6 44.2 1.0
N C:HIS66 4.7 44.7 1.0
C C:MET89 4.7 46.4 1.0
N C:GLY65 4.7 42.8 1.0
CGD C:HEM807 4.8 42.8 1.0
CL5 C:PCI1808 5.0 33.5 1.0
O1D C:HEM807 5.0 42.8 1.0

Chlorine binding site 2 out of 5 in 1y4z

Go back to Chlorine Binding Sites List in 1y4z
Chlorine binding site 2 out of 5 in the The Crystal Structure of Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor 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 Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1808

b:36.1
occ:1.00
 CL2 C:PCI1808 0.0 36.1 1.0
C3 C:PCI1808 1.4 40.1 1.0
C2 C:PCI1808 2.5 38.7 1.0
C4 C:PCI1808 2.6 40.4 1.0
CL3 C:PCI1808 3.0 37.0 1.0
CL1 C:PCI1808 3.0 33.8 1.0
O C:LYS86 3.6 52.1 1.0
N C:ALA90 3.8 44.0 1.0
C1 C:PCI1808 3.8 38.8 1.0
C5 C:PCI1808 3.9 39.3 1.0
CB C:MET89 4.0 52.2 1.0
CA C:ALA90 4.0 42.5 1.0
CB C:ALA90 4.1 40.7 1.0
C C:MET89 4.4 46.4 1.0
C6 C:PCI1808 4.4 38.0 1.0
C C:LYS86 4.5 51.3 1.0
CA C:LYS86 4.7 50.9 1.0
O C:GLY65 4.7 45.0 1.0
CA C:MET89 4.8 48.7 1.0
CB C:LYS86 4.8 49.3 1.0
CA C:GLY65 4.8 43.5 1.0
SD C:MET89 4.9 62.1 1.0
O1 C:PCI1808 5.0 38.7 1.0
CE C:MET89 5.0 59.9 1.0
O C:MET89 5.0 44.2 1.0

Chlorine binding site 3 out of 5 in 1y4z

Go back to Chlorine Binding Sites List in 1y4z
Chlorine binding site 3 out of 5 in the The Crystal Structure of Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor 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 Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1808

b:37.0
occ:1.00
 CL3 C:PCI1808 0.0 37.0 1.0
C4 C:PCI1808 1.4 40.4 1.0
C5 C:PCI1808 2.5 39.3 1.0
C3 C:PCI1808 2.5 40.1 1.0
CL2 C:PCI1808 3.0 36.1 1.0
CL4 C:PCI1808 3.0 38.6 1.0
CA C:GLY69 3.4 53.0 1.0
CB C:LYS86 3.6 49.3 1.0
CE C:MET156 3.6 48.1 1.0
C6 C:PCI1808 3.9 38.0 1.0
C2 C:PCI1808 3.9 38.7 1.0
O C:LYS86 3.9 52.1 1.0
CD C:LYS86 4.1 54.0 1.0
C C:GLY69 4.1 54.6 1.0
CG C:LYS86 4.1 50.2 1.0
SD C:MET156 4.2 46.2 1.0
O C:GLY69 4.2 56.1 1.0
C C:LYS86 4.2 51.3 1.0
CA C:LYS86 4.3 50.9 1.0
C1 C:PCI1808 4.4 38.8 1.0
N C:GLY69 4.6 52.5 1.0
CB C:ALA90 4.7 40.7 1.0
O C:GLY65 4.9 45.0 1.0

Chlorine binding site 4 out of 5 in 1y4z

Go back to Chlorine Binding Sites List in 1y4z
Chlorine binding site 4 out of 5 in the The Crystal Structure of Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor 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 Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1808

b:38.6
occ:1.00
 CL4 C:PCI1808 0.0 38.6 1.0
C5 C:PCI1808 1.4 39.3 1.0
C6 C:PCI1808 2.5 38.0 1.0
C4 C:PCI1808 2.6 40.4 1.0
CL5 C:PCI1808 3.0 33.5 1.0
CL3 C:PCI1808 3.0 37.0 1.0
CE C:MET156 3.4 48.1 1.0
C C:GLY69 3.6 54.6 1.0
CA C:GLY69 3.7 53.0 1.0
CG C:MET70 3.8 59.0 1.0
N C:MET70 3.9 55.2 1.0
C1 C:PCI1808 3.9 38.8 1.0
C3 C:PCI1808 3.9 40.1 1.0
O C:GLY69 4.0 56.1 1.0
SD C:MET156 4.4 46.2 1.0
CG2 C:VAL160 4.4 34.1 1.0
C2 C:PCI1808 4.4 38.7 1.0
CA C:MET70 4.5 55.0 1.0
CBA C:HEM807 4.6 45.6 1.0
CG C:MET156 4.6 40.5 1.0
CB C:MET70 4.8 56.6 1.0
O C:GLY65 4.8 45.0 1.0
N C:GLY69 4.8 52.5 1.0
O C:HIS66 5.0 44.8 1.0

Chlorine binding site 5 out of 5 in 1y4z

Go back to Chlorine Binding Sites List in 1y4z
Chlorine binding site 5 out of 5 in the The Crystal Structure of Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor 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 Nitrate Reductase A, Narghi, in Complex with the Q-Site Inhibitor Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1808

b:33.5
occ:1.00
 CL5 C:PCI1808 0.0 33.5 1.0
C6 C:PCI1808 1.4 38.0 1.0
C1 C:PCI1808 2.5 38.8 1.0
C5 C:PCI1808 2.5 39.3 1.0
O1 C:PCI1808 2.8 38.7 1.0
CL4 C:PCI1808 3.0 38.6 1.0
ND1 C:HIS66 3.1 38.3 1.0
CE1 C:HIS66 3.6 39.1 1.0
CG C:HIS66 3.7 39.0 1.0
CA C:HIS66 3.7 43.1 1.0
C2 C:PCI1808 3.8 38.7 1.0
CBA C:HEM807 3.9 45.6 1.0
C4 C:PCI1808 3.9 40.4 1.0
O1D C:HEM807 4.0 42.8 1.0
N C:HIS66 4.1 44.7 1.0
C2A C:HEM807 4.2 43.1 1.0
NE2 C:HIS66 4.2 35.3 1.0
CB C:HIS66 4.2 38.8 1.0
C1A C:HEM807 4.3 38.9 1.0
CD2 C:HIS66 4.3 36.6 1.0
C3A C:HEM807 4.4 42.5 1.0
CE C:MET70 4.4 62.6 1.0
C3 C:PCI1808 4.4 40.1 1.0
NA C:HEM807 4.5 41.2 1.0
CG C:MET70 4.5 59.0 1.0
C4A C:HEM807 4.5 42.0 1.0
C C:GLY65 4.6 44.7 1.0
O C:GLY65 4.6 45.0 1.0
CAA C:HEM807 4.7 43.1 1.0
O2D C:HEM807 4.7 43.5 1.0
CHA C:HEM807 4.7 35.9 1.0
C C:HIS66 4.7 44.7 1.0
CGD C:HEM807 4.7 42.8 1.0
O C:HIS66 4.8 44.8 1.0
SD C:MET70 4.9 61.8 1.0
CL1 C:PCI1808 5.0 33.8 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: Sat Dec 12 08:55:09 2020

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