Iron in PDB 1y5n: 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;

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

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
Chlorine	(Cl)	5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Iron 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 Iron atom.
In total 21 binding sites of Iron where determined in the The Crystal Structure of the Narghi Mutant Nari-K86A in Complex with Pentachlorophenol, PDB code: 1y5n:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 21 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 Iron with other atoms in the Fe 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 A:Fe1801 b:39.6 occ:1.00 FE1 A:SF41801 0.0 39.6 1.0 S4 A:SF41801 2.3 34.2 1.0 S2 A:SF41801 2.3 37.5 1.0 S3 A:SF41801 2.3 43.4 1.0 SG A:CYS57 2.3 41.4 1.0 FE4 A:SF41801 2.7 47.5 1.0 FE3 A:SF41801 2.7 39.3 1.0 FE2 A:SF41801 2.7 46.6 1.0 CB A:CYS57 3.3 37.6 1.0 CA A:GLY55 3.8 41.8 1.0 S1 A:SF41801 3.9 39.5 1.0 N A:CYS57 3.9 45.8 1.0 C A:GLY55 4.0 44.1 1.0 CA A:GLY91 4.1 27.4 1.0 N A:SER56 4.2 42.8 1.0 CA A:CYS57 4.2 40.8 1.0 C A:GLY91 4.4 28.5 1.0 N A:GLY91 4.4 31.0 1.0 NE1 A:TRP59 4.4 44.2 1.0 ND1 A:HIS49 4.5 45.5 1.0 CG A:PRO262 4.5 27.4 1.0 O A:GLY55 4.6 40.9 1.0 SG A:CYS53 4.7 56.5 1.0 N A:CYS92 4.7 30.7 1.0 SG A:CYS92 4.8 39.7 1.0 C A:SER56 4.8 44.0 1.0 O A:GLY91 4.8 30.9 1.0 N A:GLY55 4.9 45.6 1.0 CB A:PRO262 4.9 20.8 1.0

Iron binding site 2 out of 21 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 Iron with other atoms in the Fe 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 A:Fe1801 b:46.6 occ:1.00 FE2 A:SF41801 0.0 46.6 1.0 SG A:CYS92 2.3 39.7 1.0 S4 A:SF41801 2.3 34.2 1.0 S3 A:SF41801 2.3 43.4 1.0 S1 A:SF41801 2.3 39.5 1.0 FE3 A:SF41801 2.7 39.3 1.0 FE4 A:SF41801 2.7 47.5 1.0 FE1 A:SF41801 2.7 39.6 1.0 CB A:CYS92 3.3 36.1 1.0 N A:GLY95 3.8 35.5 1.0 S2 A:SF41801 3.9 37.5 1.0 N A:CYS92 3.9 30.7 1.0 CA A:GLY95 4.0 32.9 1.0 CA A:CYS92 4.2 32.5 1.0 C A:GLY91 4.3 28.5 1.0 ND1 A:HIS49 4.5 45.5 1.0 C A:CYS92 4.7 32.6 1.0 SG A:CYS53 4.8 56.5 1.0 O A:CYS92 4.8 27.9 1.0 CA A:GLY91 4.8 27.4 1.0 O A:GLY91 4.8 30.9 1.0 SG A:CYS57 4.8 41.4 1.0 CB A:ARG94 4.9 38.7 1.0 C A:ARG94 5.0 37.2 1.0 CE1 A:HIS49 5.0 43.0 1.0

Iron binding site 3 out of 21 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 Iron with other atoms in the Fe 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 A:Fe1801 b:39.3 occ:1.00 FE3 A:SF41801 0.0 39.3 1.0 ND1 A:HIS49 2.0 45.5 1.0 S4 A:SF41801 2.2 34.2 1.0 S1 A:SF41801 2.3 39.5 1.0 S2 A:SF41801 2.3 37.5 1.0 FE2 A:SF41801 2.7 46.6 1.0 FE1 A:SF41801 2.7 39.6 1.0 FE4 A:SF41801 2.8 47.5 1.0 CE1 A:HIS49 2.9 43.0 1.0 CG A:HIS49 3.1 41.9 1.0 CB A:HIS49 3.5 33.0 1.0 CA A:GLY95 3.8 32.9 1.0 S3 A:SF41801 3.9 43.4 1.0 NE1 A:TRP59 3.9 44.2 1.0 NE2 A:HIS49 4.1 47.5 1.0 CD2 A:HIS49 4.2 44.5 1.0 N A:GLY95 4.5 35.5 1.0 OH A:TYR1101 4.6 39.5 1.0 SG A:CYS57 4.7 41.4 1.0 CE2 A:TRP59 4.7 31.9 1.0 CD1 A:TRP59 4.7 34.9 1.0 SG A:CYS92 4.7 39.7 1.0 CA A:HIS49 4.8 34.1 1.0 SG A:CYS53 4.8 56.5 1.0 N A:HIS49 4.8 33.3 1.0 CB A:CYS57 4.9 37.6 1.0 CZ2 A:TRP59 4.9 36.1 1.0 C A:GLY95 5.0 32.5 1.0

Iron binding site 4 out of 21 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 Iron with other atoms in the Fe 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 A:Fe1801 b:47.5 occ:1.00 FE4 A:SF41801 0.0 47.5 1.0 S3 A:SF41801 2.3 43.4 1.0 SG A:CYS53 2.3 56.5 1.0 S2 A:SF41801 2.3 37.5 1.0 S1 A:SF41801 2.3 39.5 1.0 FE1 A:SF41801 2.7 39.6 1.0 FE2 A:SF41801 2.7 46.6 1.0 FE3 A:SF41801 2.8 39.3 1.0 CB A:CYS53 3.4 52.6 1.0 S4 A:SF41801 3.8 34.2 1.0 CA A:GLY55 3.9 41.8 1.0 N A:GLY55 4.1 45.6 1.0 CG1 A:VAL51 4.3 36.2 1.0 N A:SER56 4.3 42.8 1.0 C A:GLY55 4.5 44.1 1.0 ND1 A:HIS49 4.6 45.5 1.0 CA A:CYS53 4.7 53.5 1.0 SG A:CYS57 4.7 41.4 1.0 SG A:CYS92 4.8 39.7 1.0 CB A:HIS49 4.9 33.0 1.0 C A:CYS53 4.9 53.1 1.0

Iron binding site 5 out of 21 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 Iron with other atoms in the Fe 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 B:Fe1802 b:38.0 occ:1.00 FE1 B:SF41802 0.0 38.0 1.0 S4 B:SF41802 2.3 44.4 1.0 S3 B:SF41802 2.3 42.7 1.0 SG B:CYS263 2.3 40.6 1.0 S2 B:SF41802 2.3 39.7 1.0 FE2 B:SF41802 2.7 41.2 1.0 FE3 B:SF41802 2.8 43.1 1.0 FE4 B:SF41802 2.8 37.8 1.0 CB B:CYS263 3.5 28.8 1.0 CA B:CYS263 3.8 26.1 1.0 S1 B:SF41802 3.9 40.9 1.0 N B:GLY265 4.0 29.6 1.0 CG1 B:ILE267 4.1 28.8 1.0 N B:VAL264 4.2 26.0 1.0 C B:CYS263 4.2 27.2 1.0 CD1 B:ILE267 4.3 19.3 1.0 CA B:GLY265 4.5 25.8 1.0 NE B:ARG268 4.6 34.8 1.0 SG B:CYS22 4.8 35.7 1.0 CG2 B:ILE267 4.8 33.0 1.0 SG B:CYS19 4.8 40.5 1.0 SG B:CYS16 4.9 37.1 1.0 NH2 B:ARG268 4.9 27.3 1.0 O B:CYS263 5.0 27.1 1.0

Iron binding site 6 out of 21 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 Iron with other atoms in the Fe binding site number 6 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 B:Fe1802 b:41.2 occ:1.00 FE2 B:SF41802 0.0 41.2 1.0 S3 B:SF41802 2.2 42.7 1.0 S4 B:SF41802 2.3 44.4 1.0 S1 B:SF41802 2.3 40.9 1.0 SG B:CYS22 2.3 35.7 1.0 FE1 B:SF41802 2.7 38.0 1.0 FE3 B:SF41802 2.8 43.1 1.0 FE4 B:SF41802 2.8 37.8 1.0 CB B:CYS22 3.3 32.7 1.0 NH2 B:ARG268 3.6 27.3 1.0 S2 B:SF41802 3.9 39.7 1.0 N B:CYS22 4.1 30.1 1.0 CA B:CYS22 4.3 32.8 1.0 CG2 B:VAL44 4.5 20.2 1.0 N B:HIS20 4.5 34.5 1.0 CB B:PRO181 4.5 24.8 1.0 CZ B:ARG268 4.6 36.2 1.0 NE B:ARG268 4.6 34.8 1.0 CA B:HIS20 4.7 33.6 1.0 N B:THR21 4.7 31.6 1.0 SG B:CYS19 4.7 40.5 1.0 SG B:CYS263 4.8 40.6 1.0 C B:HIS20 4.8 34.4 1.0 SG B:CYS16 4.9 37.1 1.0

Iron binding site 7 out of 21 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 Iron with other atoms in the Fe binding site number 7 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 B:Fe1802 b:43.1 occ:1.00 FE3 B:SF41802 0.0 43.1 1.0 S4 B:SF41802 2.3 44.4 1.0 S2 B:SF41802 2.3 39.7 1.0 S1 B:SF41802 2.3 40.9 1.0 SG B:CYS19 2.3 40.5 1.0 FE4 B:SF41802 2.7 37.8 1.0 FE2 B:SF41802 2.8 41.2 1.0 FE1 B:SF41802 2.8 38.0 1.0 CB B:CYS19 3.7 36.3 1.0 N B:CYS19 3.7 39.6 1.0 N B:HIS20 3.9 34.5 1.0 S3 B:SF41802 3.9 42.7 1.0 CA B:CYS19 4.1 36.7 1.0 CG1 B:ILE17 4.1 41.7 1.0 C B:CYS19 4.3 40.0 1.0 N B:THR21 4.4 31.6 1.0 CD1 B:ILE17 4.7 36.2 1.0 N B:GLY265 4.7 29.6 1.0 N B:VAL264 4.7 26.0 1.0 SG B:CYS22 4.8 35.7 1.0 OG1 B:THR21 4.8 37.9 1.0 SG B:CYS16 4.8 37.1 1.0 CA B:HIS20 4.8 33.6 1.0 SG B:CYS263 4.8 40.6 1.0 CB B:THR21 4.8 27.9 1.0 N B:GLY18 4.9 45.9 1.0 C B:GLY18 4.9 39.5 1.0 N B:ILE17 4.9 38.9 1.0 CB B:VAL264 5.0 22.2 1.0

Iron binding site 8 out of 21 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 Iron with other atoms in the Fe binding site number 8 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 B:Fe1802 b:37.8 occ:1.00 FE4 B:SF41802 0.0 37.8 1.0 S1 B:SF41802 2.3 40.9 1.0 S2 B:SF41802 2.3 39.7 1.0 S3 B:SF41802 2.3 42.7 1.0 SG B:CYS16 2.3 37.1 1.0 FE3 B:SF41802 2.7 43.1 1.0 FE2 B:SF41802 2.8 41.2 1.0 FE1 B:SF41802 2.8 38.0 1.0 CB B:CYS16 3.6 35.7 1.0 S4 B:SF41802 3.9 44.4 1.0 CA B:CYS16 4.0 36.1 1.0 N B:ILE17 4.1 38.9 1.0 CD1 B:ILE267 4.2 19.3 1.0 N B:GLY18 4.3 45.9 1.0 C B:CYS16 4.4 35.0 1.0 CG B:PRO181 4.5 25.0 1.0 CB B:PRO181 4.6 24.8 1.0 N B:CYS19 4.7 39.6 1.0 CG1 B:ILE267 4.8 28.8 1.0 CA B:GLY18 4.8 39.1 1.0 SG B:CYS263 4.9 40.6 1.0 SG B:CYS22 4.9 35.7 1.0 SG B:CYS19 4.9 40.5 1.0

Iron binding site 9 out of 21 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 Iron with other atoms in the Fe binding site number 9 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 B:Fe1803 b:33.0 occ:1.00 FE1 B:SF41803 0.0 33.0 1.0 S4 B:SF41803 2.3 30.4 1.0 S2 B:SF41803 2.3 22.9 1.0 S3 B:SF41803 2.3 29.0 1.0 SG B:CYS247 2.3 29.2 1.0 FE3 B:SF41803 2.6 27.1 1.0 FE4 B:SF41803 2.7 27.4 1.0 FE2 B:SF41803 2.7 29.0 1.0 CB B:CYS247 3.5 32.2 1.0 N B:CYS247 3.6 37.1 1.0 S1 B:SF41803 3.8 25.0 1.0 CA B:CYS247 4.0 35.0 1.0 NE1 B:TRP30 4.1 27.9 1.0 CB B:THR257 4.1 29.4 1.0 C B:PHE246 4.2 28.4 1.0 N B:VAL258 4.4 30.1 1.0 CA B:PHE246 4.4 33.1 1.0 CD1 B:TRP30 4.5 32.5 1.0 SG B:CYS259 4.6 34.5 1.0 OG1 B:THR257 4.6 31.6 1.0 N B:PHE246 4.7 30.5 1.0 SG B:CYS26 4.8 27.2 1.0 SG B:CYS244 4.8 26.5 1.0 N B:CYS259 4.8 35.3 1.0 CG2 B:THR257 4.9 21.1 1.0 CB B:VAL258 4.9 23.7 1.0 O B:PHE246 5.0 32.1 1.0 CA B:THR257 5.0 31.2 1.0

Iron binding site 10 out of 21 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 Iron with other atoms in the Fe binding site number 10 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 B:Fe1803 b:29.0 occ:1.00 FE2 B:SF41803 0.0 29.0 1.0 S1 B:SF41803 2.2 25.0 1.0 S3 B:SF41803 2.3 29.0 1.0 S4 B:SF41803 2.3 30.4 1.0 SG B:CYS244 2.3 26.5 1.0 FE4 B:SF41803 2.6 27.4 1.0 FE3 B:SF41803 2.7 27.1 1.0 FE1 B:SF41803 2.7 33.0 1.0 CB B:CYS244 3.3 34.8 1.0 S2 B:SF41803 3.8 22.9 1.0 N B:PHE246 3.9 30.5 1.0 CA B:CYS244 4.0 28.1 1.0 CA B:PHE246 4.1 33.1 1.0 N B:ILE245 4.3 29.7 1.0 C B:CYS244 4.4 29.9 1.0 N B:CYS247 4.5 37.1 1.0 SG B:CYS26 4.7 27.2 1.0 C B:PHE246 4.7 28.4 1.0 CB B:LEU183 4.7 28.3 1.0 CD1 B:LEU183 4.7 20.4 1.0 SG B:CYS259 4.8 34.5 1.0 CB B:PHE41 4.8 21.9 1.0 SG B:CYS247 4.9 29.2 1.0 C B:ILE245 5.0 27.4 1.0

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