Iron in PDB 3w1w: Protein-Drug Complex

All present enzymatic activity of Protein-Drug Complex:
4.99.1.1;

The structure of Protein-Drug Complex, PDB code: 3w1w was solved by R.Ishii, V.Gupta, Y.Yamaguchi, H.Handa, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.28 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.531, 93.627, 110.287, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22.9

The binding sites of Iron atom in the Protein-Drug Complex (pdb code 3w1w). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Protein-Drug Complex, PDB code: 3w1w:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Protein-Drug Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Protein-Drug Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1501 b:17.4 occ:1.00 FE1 A:FES1501 0.0 17.4 1.0 S1 A:FES1501 2.2 16.9 1.0 S2 A:FES1501 2.2 18.9 1.0 SG A:CYS196 2.4 20.1 1.0 SG A:CYS403 2.5 17.1 1.0 FE2 A:FES1501 2.7 18.3 1.0 CB A:CYS403 3.3 15.4 1.0 CB A:CYS196 3.4 18.6 1.0 O A:HOH1631 3.8 15.5 1.0 N A:CYS403 3.9 17.8 1.0 O A:HOH1787 4.0 20.6 1.0 O B:HOH695 4.2 28.9 1.0 CA A:CYS403 4.2 17.2 1.0 CB A:CYS406 4.5 15.5 1.0 SG A:CYS406 4.7 22.7 1.0 CA A:CYS196 4.7 19.7 1.0 SG A:CYS411 4.8 20.4 1.0 NH2 B:ARG298 5.0 25.8 1.0

Iron binding site 2 out of 4 in the Protein-Drug Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Protein-Drug Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1501 b:18.3 occ:1.00 FE2 A:FES1501 0.0 18.3 1.0 S2 A:FES1501 2.2 18.9 1.0 S1 A:FES1501 2.2 16.9 1.0 SG A:CYS411 2.4 20.4 1.0 SG A:CYS406 2.5 22.7 1.0 FE1 A:FES1501 2.7 17.4 1.0 CB A:CYS411 3.2 22.5 1.0 CB A:CYS406 3.3 15.5 1.0 O A:HOH1669 4.1 20.7 1.0 CA A:CYS406 4.2 16.4 1.0 C1 A:EDO1506 4.3 21.1 1.0 O A:HOH1787 4.4 20.6 1.0 CB A:ASN408 4.5 24.2 1.0 C2 A:EDO1506 4.5 22.7 1.0 O A:ASN408 4.6 23.2 1.0 CA A:CYS411 4.6 23.9 1.0 SG A:CYS196 4.7 20.1 1.0 SG A:CYS403 4.8 17.1 1.0 N A:CYS403 4.8 17.8 1.0 CB A:CYS403 4.8 15.4 1.0 N A:ASN408 4.9 22.6 1.0 CB A:CYS196 4.9 18.6 1.0 CB A:SER402 4.9 21.6 1.0

Iron binding site 3 out of 4 in the Protein-Drug Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Protein-Drug Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:17.6 occ:1.00 FE1 B:FES501 0.0 17.6 1.0 S1 B:FES501 2.2 15.6 1.0 S2 B:FES501 2.2 18.6 1.0 SG B:CYS403 2.4 16.0 1.0 SG B:CYS196 2.5 20.1 1.0 FE2 B:FES501 2.8 17.8 1.0 CB B:CYS403 3.4 17.2 1.0 CB B:CYS196 3.4 19.3 1.0 O B:HOH637 3.8 15.5 1.0 N B:CYS403 3.9 17.1 1.0 O B:HOH684 4.1 18.2 1.0 CA B:CYS403 4.2 16.8 1.0 O B:HOH607 4.3 28.3 1.0 CB B:CYS406 4.6 14.2 1.0 SG B:CYS406 4.7 19.7 1.0 CA B:CYS196 4.7 15.9 1.0 SG B:CYS411 4.8 20.2 1.0 NE B:ARG272 4.8 20.0 0.9 NH2 A:ARG298 4.9 27.6 1.0

Iron binding site 4 out of 4 in the Protein-Drug Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Protein-Drug Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:17.8 occ:1.00 FE2 B:FES501 0.0 17.8 1.0 S2 B:FES501 2.2 18.6 1.0 S1 B:FES501 2.2 15.6 1.0 SG B:CYS411 2.4 20.2 1.0 SG B:CYS406 2.5 19.7 1.0 FE1 B:FES501 2.8 17.6 1.0 CB B:CYS411 3.2 20.6 1.0 CB B:CYS406 3.4 14.2 1.0 O B:HOH708 4.2 23.2 1.0 CA B:CYS406 4.3 19.7 1.0 C1 B:EDO505 4.4 26.3 1.0 O B:HOH684 4.5 18.2 1.0 O B:ASN408 4.6 23.4 1.0 CB B:ASN408 4.6 20.1 1.0 C2 B:EDO505 4.6 25.2 1.0 CA B:CYS411 4.7 23.6 1.0 SG B:CYS196 4.8 20.1 1.0 N B:CYS403 4.8 17.1 1.0 SG B:CYS403 4.8 16.0 1.0 CB B:CYS403 4.8 17.2 1.0 CB B:CYS196 4.9 19.3 1.0 CB B:SER402 4.9 20.9 1.0 N B:ASN408 5.0 23.5 1.0

V.Gupta, S.Liu, H.Ando, R.Ishii, S.Tateno, Y.Kaneko, M.Yugami, S.Sakamoto, Y.Yamaguchi, O.Nureki, H.Handa. Salicylic Acid Induces Mitochondrial Injury By Inhibiting Ferrochelatase Heme Biosynthesis Activity Mol.Pharmacol. V. 84 824 2013.
ISSN: ISSN 0026-895X
PubMed: 24043703
DOI: 10.1124/MOL.113.087940