Iron in PDB 8ugo: Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine

All present enzymatic activity of Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine:
2.8.1.8;

The structure of Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine, PDB code: 8ugo 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)	38.06 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.681, 169.209, 183.183, 90, 90, 90
R / Rfree (%)	18.5 / 22.3

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 Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine (pdb code 8ugo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 21 binding sites of Iron where determined in the Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine, PDB code: 8ugo:
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 Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:25.0 occ:1.00 FE1 A:SF4402 0.0 25.0 1.0 SG A:CYS141 2.3 28.9 1.0 S3 A:SF4402 2.3 26.8 1.0 S2 A:SF4402 2.3 25.5 1.0 S4 A:SF4402 2.3 23.2 1.0 FE4 A:SF4402 2.7 31.5 1.0 FE3 A:SF4402 2.7 27.7 1.0 FE2 A:SF4402 2.7 28.0 1.0 CB A:CYS141 3.2 28.8 1.0 O A:HOH536 3.8 26.7 1.0 S1 A:SF4402 3.9 33.9 1.0 OXT A:MET406 4.1 24.6 1.0 N A:CYS141 4.2 31.4 1.0 CA A:CYS141 4.4 32.2 1.0 CB A:ARG139 4.4 31.9 1.0 CB A:CYS144 4.5 26.2 1.0 SG A:CYS144 4.7 30.4 1.0 SG A:CYS137 4.7 34.4 1.0 O A:HOH502 4.8 27.9 1.0 SD A:MET406 4.8 36.3 1.0 CZ A:PHE143 4.8 28.6 1.0

Iron binding site 2 out of 21 in the Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:28.0 occ:1.00 FE2 A:SF4402 0.0 28.0 1.0 S4 A:SF4402 2.3 23.2 1.0 S1 A:SF4402 2.3 33.9 1.0 S3 A:SF4402 2.3 26.8 1.0 SD A:MET406 2.3 36.3 1.0 OXT A:MET406 2.6 24.6 1.0 FE3 A:SF4402 2.7 27.7 1.0 FE1 A:SF4402 2.7 25.0 1.0 FE4 A:SF4402 2.8 31.5 1.0 N A:MET406 2.8 28.9 1.0 C A:MET406 3.4 30.2 1.0 CA A:MET406 3.5 36.5 1.0 CE A:MET406 3.6 25.9 1.0 CG A:MET406 3.6 30.7 1.0 S2 A:SF4402 3.9 25.5 1.0 CB A:MET406 4.1 30.6 1.0 OD1 A:ASP181 4.2 32.3 1.0 O A:HOH502 4.5 27.9 1.0 O A:MET406 4.5 35.9 1.0 O A:HOH536 4.7 26.7 1.0 SG A:CYS137 4.7 34.4 1.0 CG A:ASP181 4.8 29.6 1.0 O A:SER179 4.8 32.5 1.0 SG A:CYS144 4.8 30.4 1.0 SG A:CYS141 4.9 28.9 1.0

Iron binding site 3 out of 21 in the Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:27.7 occ:1.00 FE3 A:SF4402 0.0 27.7 1.0 SG A:CYS144 2.3 30.4 1.0 S1 A:SF4402 2.3 33.9 1.0 S4 A:SF4402 2.3 23.2 1.0 S2 A:SF4402 2.3 25.5 1.0 FE1 A:SF4402 2.7 25.0 1.0 FE2 A:SF4402 2.7 28.0 1.0 FE4 A:SF4402 2.7 31.5 1.0 CB A:CYS144 3.0 26.2 1.0 S3 A:SF4402 3.9 26.8 1.0 SD A:MET406 4.0 36.3 1.0 CB A:VAL146 4.2 29.7 1.0 CG2 A:VAL146 4.4 27.7 1.0 O A:HOH508 4.4 26.6 1.0 CA A:CYS144 4.5 30.3 1.0 CB A:CYS141 4.6 28.8 1.0 SG A:CYS141 4.6 28.9 1.0 CE A:MET406 4.6 25.9 1.0 SG A:CYS137 4.9 34.4 1.0 CG1 A:VAL146 5.0 29.9 1.0

Iron binding site 4 out of 21 in the Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:31.5 occ:1.00 FE4 A:SF4402 0.0 31.5 1.0 SG A:CYS137 2.3 34.4 1.0 S3 A:SF4402 2.3 26.8 1.0 S2 A:SF4402 2.3 25.5 1.0 S1 A:SF4402 2.3 33.9 1.0 FE1 A:SF4402 2.7 25.0 1.0 FE3 A:SF4402 2.7 27.7 1.0 FE2 A:SF4402 2.8 28.0 1.0 CB A:CYS137 3.3 32.5 1.0 S4 A:SF4402 3.9 23.2 1.0 O A:HOH508 4.1 26.6 1.0 CB A:ARG139 4.2 31.9 1.0 N A:ASP181 4.3 31.8 1.0 N A:MET406 4.4 28.9 1.0 O A:ARG139 4.4 32.5 1.0 OD1 A:ASP181 4.6 32.3 1.0 CG A:ASP181 4.7 29.6 1.0 CA A:CYS137 4.7 33.7 1.0 CB A:ASP181 4.7 27.3 1.0 SG A:CYS144 4.8 30.4 1.0 C A:ARG139 4.8 33.5 1.0 SG A:CYS141 4.8 28.9 1.0 N A:ARG139 4.8 33.8 1.0 CA A:VAL180 4.8 30.9 1.0 SD A:MET406 4.8 36.3 1.0 CA A:ARG139 4.9 32.3 1.0 OXT A:MET406 4.9 24.6 1.0 CG A:ARG139 4.9 32.9 1.0

Iron binding site 5 out of 21 in the Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:27.1 occ:1.00 FE1 A:F3S403 0.0 27.1 1.0 SG A:CYS117 2.3 31.0 1.0 S3 A:F3S403 2.3 28.2 1.0 S2 A:F3S403 2.3 27.3 1.0 S1 A:F3S403 2.3 34.5 1.0 FE3 A:F3S403 2.7 31.6 1.0 FE4 A:F3S403 2.7 27.9 1.0 CB A:CYS117 3.2 26.6 1.0 S6 E:YVI201 4.2 30.8 1.0 CB A:ASN113 4.2 30.5 1.0 O A:ASN113 4.6 30.1 1.0 CA A:TYR353 4.7 28.7 1.0 CA A:CYS117 4.7 31.8 1.0 SG A:CYS111 4.7 30.1 1.0 CD1 A:TYR353 4.7 28.7 1.0 SG A:CYS106 4.8 32.6 1.0 C A:ASN113 4.8 31.9 1.0 N A:TYR353 5.0 30.1 1.0

Iron binding site 6 out of 21 in the Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:31.6 occ:1.00 FE3 A:F3S403 0.0 31.6 1.0 SG A:CYS111 2.3 30.1 1.0 S6 E:YVI201 2.3 30.8 1.0 S3 A:F3S403 2.3 28.2 1.0 S1 A:F3S403 2.3 34.5 1.0 FE4 A:F3S403 2.7 27.9 1.0 FE1 A:F3S403 2.7 27.1 1.0 CB A:CYS111 3.2 28.5 1.0 C6 E:YVI201 3.5 31.4 1.0 C5 E:YVI201 3.7 28.2 1.0 S2 A:F3S403 3.8 27.3 1.0 C7 E:YVI201 3.9 30.2 1.0 CB A:ASN113 4.1 30.5 1.0 C4 E:YVI201 4.2 30.6 1.0 ND2 A:ASN113 4.5 24.1 1.0 CG A:ARG350 4.6 25.3 1.0 CA A:CYS111 4.6 29.9 1.0 SG A:CYS117 4.6 31.0 1.0 SG A:CYS106 4.7 32.6 1.0 CB A:CYS106 4.8 32.8 1.0 CB A:ARG350 4.8 26.9 1.0 C3 E:YVI201 4.8 28.4 1.0 CA A:CYS106 4.8 31.4 1.0 N A:ASN113 4.8 33.1 1.0 CA A:ASN113 4.8 35.9 1.0 CG A:ASN113 4.9 28.8 1.0 C A:ASN113 5.0 31.9 1.0

Iron binding site 7 out of 21 in the Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:27.9 occ:1.00 FE4 A:F3S403 0.0 27.9 1.0 SG A:CYS106 2.3 32.6 1.0 S2 A:F3S403 2.3 27.3 1.0 S3 A:F3S403 2.3 28.2 1.0 S6 E:YVI201 2.5 30.8 1.0 FE3 A:F3S403 2.7 31.6 1.0 FE1 A:F3S403 2.7 27.1 1.0 CB A:CYS106 3.1 32.8 1.0 CA A:CYS106 3.7 31.4 1.0 S1 A:F3S403 3.9 34.5 1.0 C6 E:YVI201 4.0 31.4 1.0 N A:CYS106 4.2 30.3 1.0 C7 E:YVI201 4.2 30.2 1.0 OG1 A:THR129 4.3 30.0 1.0 NE1 A:TRP118 4.5 34.7 1.0 N A:THR129 4.5 28.2 1.0 CB A:THR129 4.5 31.8 1.0 SG A:CYS111 4.7 30.1 1.0 CB A:CYS111 4.7 28.5 1.0 SG A:CYS117 4.7 31.0 1.0 CG1 A:VAL105 4.8 33.9 1.0 CB A:CYS117 4.9 26.6 1.0 CD1 A:TRP118 4.9 34.2 1.0

Iron binding site 8 out of 21 in the Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:18.4 occ:1.00 FE1 B:SF4402 0.0 18.4 1.0 SG B:CYS141 2.3 27.0 1.0 S3 B:SF4402 2.3 15.1 1.0 S2 B:SF4402 2.3 18.8 1.0 S4 B:SF4402 2.3 22.7 1.0 FE4 B:SF4402 2.7 26.9 1.0 FE2 B:SF4402 2.7 19.7 1.0 FE3 B:SF4402 2.7 22.9 1.0 CB B:CYS141 3.3 22.2 1.0 S1 B:SF4402 3.9 22.8 1.0 O B:HOH547 4.1 25.8 1.0 OXT B:MET406 4.1 34.1 1.0 N B:CYS141 4.2 24.9 1.0 CA B:CYS141 4.3 24.2 1.0 CB B:ARG139 4.5 30.5 1.0 CB B:CYS144 4.7 22.3 1.0 SG B:CYS144 4.7 27.3 1.0 SG B:CYS137 4.7 22.5 1.0 CZ B:PHE143 4.8 19.8 1.0 CE1 B:PHE143 5.0 21.4 1.0

Iron binding site 9 out of 21 in the Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:19.7 occ:1.00 FE2 B:SF4402 0.0 19.7 1.0 S1 B:SF4402 2.3 22.8 1.0 S4 B:SF4402 2.3 22.7 1.0 SG B:CYS144 2.3 27.3 1.0 S3 B:SF4402 2.3 15.1 1.0 FE1 B:SF4402 2.7 18.4 1.0 FE3 B:SF4402 2.7 22.9 1.0 FE4 B:SF4402 2.8 26.9 1.0 CB B:CYS144 3.1 22.3 1.0 S2 B:SF4402 3.9 18.8 1.0 CB B:VAL146 4.4 24.9 1.0 CG2 B:VAL146 4.6 23.3 1.0 CG B:MET406 4.6 34.1 1.0 SG B:CYS141 4.6 27.0 1.0 CA B:CYS144 4.6 20.8 1.0 SD B:MET406 4.6 47.8 1.0 CB B:CYS141 4.6 22.2 1.0 CE B:MET406 4.8 37.1 1.0 SG B:CYS137 4.9 22.5 1.0

Iron binding site 10 out of 21 in the Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of the Complex Between Human Lias and H-Protein in the Presence of 5'-Deoxyadenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:22.9 occ:1.00 FE3 B:SF4402 0.0 22.9 1.0 SG B:CYS137 2.3 22.5 1.0 S1 B:SF4402 2.3 22.8 1.0 S4 B:SF4402 2.3 22.7 1.0 S2 B:SF4402 2.3 18.8 1.0 FE4 B:SF4402 2.7 26.9 1.0 FE2 B:SF4402 2.7 19.7 1.0 FE1 B:SF4402 2.7 18.4 1.0 CB B:CYS137 3.2 25.7 1.0 S3 B:SF4402 3.9 15.1 1.0 O B:ARG139 4.2 38.1 1.0 CB B:ARG139 4.2 30.5 1.0 N B:ASP181 4.4 24.3 1.0 C B:ARG139 4.6 35.1 1.0 CA B:CYS137 4.7 26.1 1.0 OD1 B:ASP181 4.7 28.7 1.0 CB B:ASP181 4.7 24.9 1.0 N B:ARG139 4.7 32.0 1.0 SG B:CYS141 4.8 27.0 1.0 SG B:CYS144 4.8 27.3 1.0 CA B:ARG139 4.8 31.1 1.0 N B:MET406 4.8 32.3 1.0 CG B:ASP181 4.8 30.0 1.0 CG B:ARG139 5.0 33.1 1.0 CA B:VAL180 5.0 23.2 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.