Iron in PDB 8tsk: Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide

The structure of Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide, PDB code: 8tsk was solved by O.A.Esakova, D.M.Warui, S.S.Neti, J.N.Alumasa, S.J.Booker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.77 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.536, 69.025, 93.79, 90, 94.52, 90
R / Rfree (%)	17.8 / 21.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide (pdb code 8tsk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide, PDB code: 8tsk:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:26.3 occ:1.00 FE1 A:SF4401 0.0 26.3 1.0 S2 A:SF4401 2.3 27.5 1.0 S4 A:SF4401 2.3 25.6 1.0 SG A:CYS117 2.3 24.9 1.0 S3 A:SF4401 2.3 20.1 1.0 FE4 A:SF4401 2.7 27.5 1.0 FE3 A:SF4401 2.7 26.2 1.0 FE2 A:SF4401 2.8 29.2 1.0 CB A:CYS117 3.3 20.5 1.0 S1 A:SF4401 3.9 20.5 1.0 CA A:TYR353 4.0 18.8 1.0 O A:SER352 4.2 18.7 1.0 CB A:ASN113 4.2 28.1 1.0 N A:LYS354 4.4 16.5 1.0 C A:SER352 4.4 16.7 1.0 N A:TYR353 4.4 16.3 1.0 O A:ASN113 4.6 25.6 1.0 SG A:CYS111 4.6 27.8 1.0 CA A:CYS117 4.7 21.7 1.0 C A:ASN113 4.7 26.9 1.0 SG A:CYS106 4.8 25.0 1.0 C A:TYR353 4.8 15.9 1.0 OG A:SER352 4.8 24.2 1.0 CD1 A:TYR353 4.8 26.9 1.0 CB A:TYR353 4.9 22.4 1.0

Iron binding site 2 out of 16 in the Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:29.2 occ:1.00 FE2 A:SF4401 0.0 29.2 1.0 S1 A:SF4401 2.3 20.5 1.0 S3 A:SF4401 2.3 20.1 1.0 S4 A:SF4401 2.3 25.6 1.0 OG A:SER352 2.5 24.2 1.0 FE4 A:SF4401 2.7 27.5 1.0 FE3 A:SF4401 2.7 26.2 1.0 FE1 A:SF4401 2.8 26.3 1.0 CB A:SER352 3.3 14.8 1.0 OG1 A:THR129 3.6 24.8 1.0 O A:HOH514 3.8 35.4 1.0 S2 A:SF4401 3.9 27.5 1.0 C A:SER352 4.0 16.7 1.0 CA A:SER352 4.1 15.9 1.0 N A:TYR353 4.2 16.3 1.0 O A:SER352 4.3 18.7 1.0 N A:SER352 4.5 15.2 1.0 CB A:THR129 4.5 19.2 1.0 CA A:TYR353 4.7 18.8 1.0 SG A:CYS111 4.7 27.8 1.0 SG A:CYS106 4.8 25.0 1.0 O A:HOH596 4.9 39.5 1.0 CB A:ARG350 4.9 25.1 1.0 SG A:CYS117 5.0 24.9 1.0

Iron binding site 3 out of 16 in the Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:26.2 occ:1.00 FE3 A:SF4401 0.0 26.2 1.0 S1 A:SF4401 2.2 20.5 1.0 S4 A:SF4401 2.3 25.6 1.0 SG A:CYS106 2.3 25.0 1.0 S2 A:SF4401 2.3 27.5 1.0 FE4 A:SF4401 2.7 27.5 1.0 FE2 A:SF4401 2.7 29.2 1.0 FE1 A:SF4401 2.7 26.3 1.0 CB A:CYS106 3.2 35.0 1.0 CA A:CYS106 3.6 29.6 1.0 S3 A:SF4401 3.9 20.1 1.0 N A:CYS106 4.0 24.5 1.0 OG1 A:THR129 4.1 24.8 1.0 N A:THR129 4.4 22.4 1.0 CA A:ALA128 4.5 17.7 1.0 CB A:THR129 4.6 19.2 1.0 NE1 A:TRP118 4.6 28.6 1.0 SG A:CYS117 4.8 24.9 1.0 SG A:CYS111 4.8 27.8 1.0 C A:ALA128 4.8 21.6 1.0 OG A:SER352 4.8 24.2 1.0 CB A:CYS111 4.8 30.3 1.0 CB A:CYS117 4.9 20.5 1.0 C A:CYS106 5.0 40.9 1.0 O A:THR127 5.0 20.0 1.0

Iron binding site 4 out of 16 in the Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:27.5 occ:1.00 FE4 A:SF4401 0.0 27.5 1.0 S3 A:SF4401 2.2 20.1 1.0 SG A:CYS111 2.3 27.8 1.0 S2 A:SF4401 2.3 27.5 1.0 S1 A:SF4401 2.3 20.5 1.0 FE2 A:SF4401 2.7 29.2 1.0 FE3 A:SF4401 2.7 26.2 1.0 FE1 A:SF4401 2.7 26.3 1.0 CB A:CYS111 3.0 30.3 1.0 S4 A:SF4401 3.8 25.6 1.0 CB A:ASN113 4.2 28.1 1.0 ND2 A:ASN113 4.4 20.7 1.0 CA A:CYS111 4.5 40.2 1.0 CA A:CYS106 4.5 29.6 1.0 SG A:CYS106 4.7 25.0 1.0 SG A:CYS117 4.7 24.9 1.0 N A:ASN113 4.8 36.5 1.0 CB A:CYS106 4.8 35.0 1.0 CG A:ASN113 4.8 30.8 1.0 CA A:ASN113 4.9 29.5 1.0 C A:ASN113 4.9 26.9 1.0 N A:ILE114 4.9 36.1 1.0 C A:CYS111 4.9 38.3 1.0

Iron binding site 5 out of 16 in the Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:12.4 occ:1.00 FE1 A:SF4402 0.0 12.4 1.0 S4 A:SF4402 2.3 14.3 1.0 S3 A:SF4402 2.3 15.9 1.0 S2 A:SF4402 2.3 12.1 1.0 SG A:CYS141 2.3 12.7 1.0 FE4 A:SF4402 2.7 12.0 1.0 FE2 A:SF4402 2.7 13.0 1.0 FE3 A:SF4402 2.8 11.3 1.0 CB A:CYS141 3.3 12.6 1.0 S1 A:SF4402 3.9 13.5 1.0 O A:HOH657 3.9 13.9 1.0 O A:HOH616 3.9 14.0 1.0 O A:MET403 4.0 12.3 1.0 N A:CYS141 4.2 12.6 1.0 CA A:CYS141 4.4 12.5 1.0 CB A:ARG139 4.5 18.2 1.0 CB A:CYS144 4.6 10.6 1.0 SG A:CYS144 4.7 14.1 1.0 SG A:CYS137 4.7 13.5 1.0 CZ A:PHE143 4.8 13.8 1.0 O A:HOH546 4.9 12.2 1.0

Iron binding site 6 out of 16 in the Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:13.0 occ:1.00 FE2 A:SF4402 0.0 13.0 1.0 SG A:CYS137 2.3 13.5 1.0 S3 A:SF4402 2.3 15.9 1.0 S1 A:SF4402 2.3 13.5 1.0 S4 A:SF4402 2.3 14.3 1.0 FE4 A:SF4402 2.7 12.0 1.0 FE1 A:SF4402 2.7 12.4 1.0 FE3 A:SF4402 2.8 11.3 1.0 CB A:CYS137 3.3 19.2 1.0 S2 A:SF4402 3.9 12.1 1.0 N A:MET403 4.1 11.1 1.0 CB A:ARG139 4.2 18.2 1.0 O A:ARG139 4.3 16.9 1.0 N A:ASP181 4.3 12.2 1.0 C A:ARG139 4.7 12.9 1.0 CA A:CYS137 4.7 14.0 1.0 CB A:ASP181 4.7 13.7 1.0 N A:ARG139 4.8 15.7 1.0 CA A:ARG139 4.8 16.3 1.0 SG A:CYS141 4.8 12.7 1.0 SG A:CYS144 4.8 14.1 1.0 O A:MET403 4.8 12.3 1.0 CG A:ASP181 4.8 16.1 1.0 OD1 A:ASP181 4.9 13.5 1.0 CA A:VAL180 5.0 13.1 1.0

Iron binding site 7 out of 16 in the Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:11.3 occ:1.00 FE3 A:SF4402 0.0 11.3 1.0 S1 A:SF4402 2.3 13.5 1.0 S2 A:SF4402 2.3 12.1 1.0 S4 A:SF4402 2.3 14.3 1.0 O A:MET403 2.4 12.3 1.0 N A:MET403 2.4 11.1 1.0 FE4 A:SF4402 2.8 12.0 1.0 FE2 A:SF4402 2.8 13.0 1.0 FE1 A:SF4402 2.8 12.4 1.0 SD A:MET403 2.8 11.9 1.0 C A:MET403 3.1 10.6 1.0 CA A:MET403 3.2 12.4 1.0 CG A:MET403 3.8 10.7 1.0 CE A:MET403 3.9 12.3 1.0 CB A:MET403 4.0 10.9 1.0 S3 A:SF4402 4.0 15.9 1.0 OXT A:MET403 4.3 12.3 1.0 OD1 A:ASP181 4.3 13.5 1.0 O A:HOH546 4.5 12.2 1.0 SG A:CYS137 4.7 13.5 1.0 O A:HOH657 4.8 13.9 1.0 CG A:ASP181 4.8 16.1 1.0 O A:SER179 4.9 11.2 1.0 SG A:CYS144 4.9 14.1 1.0 O A:HOH758 5.0 28.4 1.0

Iron binding site 8 out of 16 in the Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:12.0 occ:1.00 FE4 A:SF4402 0.0 12.0 1.0 S1 A:SF4402 2.3 13.5 1.0 S3 A:SF4402 2.3 15.9 1.0 S2 A:SF4402 2.3 12.1 1.0 SG A:CYS144 2.3 14.1 1.0 FE2 A:SF4402 2.7 13.0 1.0 FE1 A:SF4402 2.7 12.4 1.0 FE3 A:SF4402 2.8 11.3 1.0 CB A:CYS144 3.1 10.6 1.0 S4 A:SF4402 3.8 14.3 1.0 O A:HOH758 4.0 28.4 1.0 CB A:VAL146 4.3 16.1 1.0 SD A:MET403 4.3 11.9 1.0 CG2 A:VAL146 4.3 14.8 1.0 CA A:CYS144 4.6 12.2 1.0 SG A:CYS141 4.7 12.7 1.0 CB A:CYS141 4.7 12.6 1.0 NH2 B:ARG315 4.8 20.1 1.0 SG A:CYS137 4.8 13.5 1.0 O A:MET403 4.9 12.3 1.0 CE A:MET403 4.9 12.3 1.0 N A:MET403 4.9 11.1 1.0

Iron binding site 9 out of 16 in the Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:12.9 occ:1.00 FE1 B:SF4401 0.0 12.9 1.0 OG B:SER352 2.2 15.1 1.0 S4 B:SF4401 2.3 11.6 1.0 S2 B:SF4401 2.3 10.6 1.0 S3 B:SF4401 2.3 8.6 1.0 FE2 B:SF4401 2.7 9.3 1.0 FE4 B:SF4401 2.7 9.0 1.0 FE3 B:SF4401 2.7 10.2 1.0 CB B:SER352 3.3 10.4 1.0 S1 B:SF4401 3.9 11.2 1.0 C B:SER352 3.9 9.5 1.0 C7 B:OCA404 4.0 33.0 1.0 N B:TYR353 4.0 9.1 1.0 CA B:SER352 4.1 9.9 1.0 OG1 B:THR129 4.1 10.7 1.0 O B:SER352 4.3 10.5 1.0 C8 B:OCA404 4.3 25.6 1.0 N B:SER352 4.4 8.2 1.0 CA B:TYR353 4.5 9.5 1.0 C6 B:OCA404 4.5 31.3 1.0 C5 B:OCA404 4.5 24.4 1.0 SG B:CYS106 4.7 9.8 1.0 CB B:ARG350 4.7 12.6 1.0 CB B:THR129 4.8 9.2 1.0 SG B:CYS111 4.8 9.8 1.0 SG B:CYS117 4.9 11.3 1.0

Iron binding site 10 out of 16 in the Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Human Lias in the Presence of 5'-Deoxyadenosine and Octanoyl-Modified Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:9.3 occ:1.00 FE2 B:SF4401 0.0 9.3 1.0 S3 B:SF4401 2.3 8.6 1.0 SG B:CYS106 2.3 9.8 1.0 S4 B:SF4401 2.3 11.6 1.0 S1 B:SF4401 2.3 11.2 1.0 FE1 B:SF4401 2.7 12.9 1.0 FE4 B:SF4401 2.7 9.0 1.0 FE3 B:SF4401 2.7 10.2 1.0 CB B:CYS106 3.2 9.6 1.0 CA B:CYS106 3.7 10.1 1.0 S2 B:SF4401 3.9 10.6 1.0 N B:CYS106 4.2 8.7 1.0 OG1 B:THR129 4.3 10.7 1.0 OG B:SER352 4.4 15.1 1.0 CB B:THR129 4.5 9.2 1.0 NE1 B:TRP118 4.5 13.4 1.0 N B:THR129 4.6 10.3 1.0 SG B:CYS111 4.8 9.8 1.0 CB B:CYS111 4.8 8.6 1.0 SG B:CYS117 4.8 11.3 1.0 CB B:CYS117 4.8 12.9 1.0 CG1 B:VAL105 4.9 8.1 1.0

O.A.Esakova, D.M.Warui, S.S.Neti, J.N.Alumasa, S.J.Booker. Structural Basis For the Mechanism of the Human Lipoyl Synthase (Lias) and Its Complex with the H-Protein To Be Published.