Iron in PDB 8trw: Structure of Human Lias

The structure of Structure of Human Lias, PDB code: 8trw 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)	27.08 / 1.54
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.353, 88.789, 108.166, 90, 90, 90
R / Rfree (%)	15.2 / 18

The binding sites of Iron atom in the Structure of Human Lias (pdb code 8trw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of Human Lias, PDB code: 8trw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Structure of Human Lias


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:12.4 occ:1.00 FE1 A:SF4403 0.0 12.4 1.0 S4 A:SF4403 2.2 13.5 1.0 S2 A:SF4403 2.3 13.2 1.0 S3 A:SF4403 2.3 12.0 1.0 SG A:CYS141 2.4 13.3 1.0 FE4 A:SF4403 2.6 11.7 1.0 FE2 A:SF4403 2.7 11.7 1.0 FE3 A:SF4403 2.7 13.2 1.0 CB A:CYS141 3.2 10.2 1.0 S1 A:SF4403 3.8 11.8 1.0 CB A:ARG139 4.0 13.2 0.4 O A:HOH702 4.1 18.3 1.0 CB A:ARG139 4.1 12.8 0.6 N A:CYS141 4.2 11.1 1.0 CA A:CYS141 4.3 10.8 1.0 CB A:CYS144 4.5 10.4 1.0 SG A:CYS144 4.6 12.0 1.0 CG A:ARG139 4.7 18.3 0.4 CG A:ARG139 4.7 18.4 0.6 SG A:CYS137 4.8 11.9 1.0 O2 A:DTT401 4.8 17.8 0.6 S1 A:DTT401 4.8 12.7 0.6 S1 A:DTT401 4.8 16.3 0.4

Iron binding site 2 out of 8 in the Structure of Human Lias


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:11.7 occ:1.00 FE2 A:SF4403 0.0 11.7 1.0 S1 A:SF4403 2.3 11.8 1.0 S3 A:SF4403 2.3 12.0 1.0 S4 A:SF4403 2.3 13.5 1.0 SG A:CYS137 2.3 11.9 1.0 FE4 A:SF4403 2.7 11.7 1.0 FE1 A:SF4403 2.7 12.4 1.0 FE3 A:SF4403 2.7 13.2 1.0 CB A:CYS137 3.1 12.6 1.0 S2 A:SF4403 3.9 13.2 1.0 CB A:ARG139 4.0 13.2 0.4 CB A:ARG139 4.1 12.8 0.6 CG A:ARG139 4.1 18.4 0.6 CG A:ARG139 4.2 18.3 0.4 CB A:VAL180 4.3 12.1 1.0 N A:ASP181 4.5 14.4 1.0 S1 A:DTT401 4.5 12.7 0.6 N A:ARG139 4.6 12.6 1.0 CA A:CYS137 4.6 11.9 1.0 S1 A:DTT401 4.7 16.3 0.4 O A:HOH638 4.8 14.1 1.0 SG A:CYS144 4.8 12.0 1.0 SG A:CYS141 4.8 13.3 1.0 CA A:ARG139 4.8 13.1 0.4 CG1 A:VAL180 4.8 17.1 1.0 CA A:ARG139 4.9 13.2 0.6 O A:HOH577 4.9 13.4 1.0 CB A:ASP181 4.9 16.2 1.0 O2 A:DTT401 5.0 17.8 0.6

Iron binding site 3 out of 8 in the Structure of Human Lias


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:13.2 occ:1.00 FE3 A:SF4403 0.0 13.2 1.0 S2 A:SF4403 2.3 13.2 1.0 S1 A:SF4403 2.3 11.8 1.0 S4 A:SF4403 2.3 13.5 1.0 S1 A:DTT401 2.3 12.7 0.6 S1 A:DTT401 2.4 16.3 0.4 O2 A:DTT401 2.6 17.8 0.6 FE4 A:SF4403 2.7 11.7 1.0 FE2 A:SF4403 2.7 11.7 1.0 FE1 A:SF4403 2.7 12.4 1.0 O2 A:DTT401 2.8 20.8 0.4 C1 A:DTT401 3.2 21.9 0.6 C2 A:DTT401 3.4 22.1 0.6 C1 A:DTT401 3.6 12.1 0.4 C2 A:DTT401 3.7 22.9 0.4 S3 A:SF4403 3.9 12.0 1.0 O A:HOH842 4.1 34.0 1.0 O A:HOH542 4.3 23.0 1.0 N A:ASP181 4.5 14.4 1.0 O A:HOH647 4.5 24.4 1.0 C3 A:DTT401 4.6 28.7 0.6 SG A:CYS137 4.7 11.9 1.0 SG A:CYS144 4.8 12.0 1.0 O A:HOH763 4.8 29.4 1.0 CA A:VAL180 4.9 13.6 1.0 CB A:ASP181 4.9 16.2 1.0 SG A:CYS141 4.9 13.3 1.0 C3 A:DTT401 5.0 18.1 0.4

Iron binding site 4 out of 8 in the Structure of Human Lias


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:11.7 occ:1.00 FE4 A:SF4403 0.0 11.7 1.0 S1 A:SF4403 2.2 11.8 1.0 S3 A:SF4403 2.3 12.0 1.0 S2 A:SF4403 2.3 13.2 1.0 SG A:CYS144 2.4 12.0 1.0 FE1 A:SF4403 2.6 12.4 1.0 FE2 A:SF4403 2.7 11.7 1.0 FE3 A:SF4403 2.7 13.2 1.0 CB A:CYS144 3.2 10.4 1.0 O2 A:DTT401 3.7 17.8 0.6 O A:HOH647 3.7 24.4 1.0 S4 A:SF4403 3.8 13.5 1.0 O2 A:DTT401 4.0 20.8 0.4 O A:HOH577 4.1 13.4 1.0 CG2 A:VAL146 4.4 13.3 1.0 CB A:VAL146 4.4 11.7 1.0 CA A:CYS144 4.6 9.7 1.0 CB A:CYS141 4.6 10.2 1.0 SG A:CYS141 4.6 13.3 1.0 SG A:CYS137 4.8 11.9 1.0 CB A:CYS137 4.8 12.6 1.0 C2 A:DTT401 4.9 22.1 0.6 S1 A:DTT401 5.0 12.7 0.6

Iron binding site 5 out of 8 in the Structure of Human Lias


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:13.5 occ:1.00 FE1 A:SF4404 0.0 13.5 1.0 OG A:SER352 2.1 13.8 1.0 S2 A:SF4404 2.3 11.0 1.0 S4 A:SF4404 2.3 11.8 1.0 S3 A:SF4404 2.3 14.6 1.0 FE3 A:SF4404 2.6 11.1 1.0 FE4 A:SF4404 2.7 11.4 1.0 FE2 A:SF4404 2.7 11.3 1.0 CB A:SER352 3.0 11.7 1.0 OG1 A:THR129 3.6 11.7 1.0 O A:HOH508 3.8 29.1 1.0 C A:SER352 3.8 10.2 1.0 S1 A:SF4404 3.9 11.4 1.0 CA A:SER352 4.0 9.2 1.0 CD A:ARG350 4.0 19.7 0.6 N A:TYR353 4.1 10.3 1.0 O A:SER352 4.1 11.3 1.0 NE A:ARG350 4.1 17.9 0.6 CG A:ARG350 4.2 19.1 0.6 CG A:ARG350 4.3 18.5 0.4 N A:SER352 4.5 13.5 1.0 CB A:THR129 4.5 11.2 1.0 CD A:ARG350 4.5 23.8 0.4 CA A:TYR353 4.6 8.2 1.0 SG A:CYS117 4.7 11.3 1.0 SG A:CYS111 4.9 13.1 1.0 SG A:CYS106 4.9 11.7 1.0 CZ A:ARG350 4.9 18.5 0.6

Iron binding site 6 out of 8 in the Structure of Human Lias


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:11.3 occ:1.00 FE2 A:SF4404 0.0 11.3 1.0 S4 A:SF4404 2.3 11.8 1.0 S3 A:SF4404 2.3 14.6 1.0 S1 A:SF4404 2.3 11.4 1.0 SG A:CYS106 2.3 11.7 1.0 FE3 A:SF4404 2.7 11.1 1.0 FE4 A:SF4404 2.7 11.4 1.0 FE1 A:SF4404 2.7 13.5 1.0 CB A:CYS106 3.2 10.6 1.0 CA A:CYS106 3.6 12.7 1.0 S2 A:SF4404 3.9 11.0 1.0 N A:CYS106 4.0 13.9 1.0 OG1 A:THR129 4.2 11.7 1.0 N A:THR129 4.3 9.7 1.0 CB A:THR129 4.5 11.2 1.0 OG A:SER352 4.5 13.8 1.0 CA A:ALA128 4.5 11.1 1.0 NE1 A:TRP118 4.6 13.8 1.0 SG A:CYS111 4.8 13.1 1.0 C A:ALA128 4.8 11.7 1.0 SG A:CYS117 4.8 11.3 1.0 CB A:CYS111 4.8 14.7 1.0 CB A:CYS117 4.9 11.0 1.0 O A:THR127 4.9 10.9 1.0

Iron binding site 7 out of 8 in the Structure of Human Lias


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:11.1 occ:1.00 FE3 A:SF4404 0.0 11.1 1.0 S1 A:SF4404 2.3 11.4 1.0 S4 A:SF4404 2.3 11.8 1.0 S2 A:SF4404 2.3 11.0 1.0 SG A:CYS117 2.3 11.3 1.0 FE1 A:SF4404 2.6 13.5 1.0 FE4 A:SF4404 2.7 11.4 1.0 FE2 A:SF4404 2.7 11.3 1.0 CB A:CYS117 3.1 11.0 1.0 S3 A:SF4404 3.8 14.6 1.0 CB A:ASN113 4.1 12.2 1.0 CA A:TYR353 4.3 8.2 1.0 O A:SER352 4.4 11.3 1.0 OG A:SER352 4.4 13.8 1.0 CA A:CYS117 4.6 11.8 1.0 C A:SER352 4.6 10.2 1.0 O A:ASN113 4.6 11.2 1.0 N A:LYS354 4.7 10.4 1.0 SG A:CYS111 4.7 13.1 1.0 N A:TYR353 4.7 10.3 1.0 SG A:CYS106 4.7 11.7 1.0 C A:ASN113 4.7 12.8 1.0 O A:THR127 4.9 10.9 1.0 CB A:SER352 4.9 11.7 1.0 CD1 A:TYR353 5.0 14.1 1.0

Iron binding site 8 out of 8 in the Structure of Human Lias


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:11.4 occ:1.00 FE4 A:SF4404 0.0 11.4 1.0 S2 A:SF4404 2.3 11.0 1.0 S3 A:SF4404 2.3 14.6 1.0 SG A:CYS111 2.3 13.1 1.0 S1 A:SF4404 2.3 11.4 1.0 FE3 A:SF4404 2.7 11.1 1.0 FE2 A:SF4404 2.7 11.3 1.0 FE1 A:SF4404 2.7 13.5 1.0 CB A:CYS111 3.2 14.7 1.0 S4 A:SF4404 3.9 11.8 1.0 CD A:ARG350 4.0 19.7 0.6 CB A:ASN113 4.1 12.2 1.0 ND2 A:ASN113 4.3 11.6 1.0 CD A:ARG350 4.3 23.8 0.4 CA A:CYS111 4.6 15.0 1.0 NE A:ARG350 4.6 17.9 0.6 OG A:SER352 4.6 13.8 1.0 CA A:CYS106 4.7 12.7 1.0 SG A:CYS117 4.7 11.3 1.0 CG A:ARG350 4.7 19.1 0.6 CG A:ASN113 4.7 13.0 1.0 N A:ASN113 4.8 12.7 1.0 SG A:CYS106 4.8 11.7 1.0 NH1 A:ARG350 4.8 15.2 0.4 CG A:ARG350 4.8 18.5 0.4 NE A:ARG350 4.8 22.9 0.4 CA A:ASN113 4.9 13.6 1.0 CB A:CYS106 4.9 10.6 1.0 NH2 A:ARG350 5.0 18.4 0.6 C A:ASN113 5.0 12.8 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.