Iron in PDB 4cei: Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate

All present enzymatic activity of Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate:
3.6.4.12;

The structure of Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate, PDB code: 4cei was solved by W.W.Krajewski, M.Wilkinson, X.Fu, N.B.Cronin, D.Wigley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.949 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.944, 151.335, 124.560, 90.00, 95.95, 90.00
R / Rfree (%)	19.53 / 23.98

The structure of Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate (pdb code 4cei). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate, PDB code: 4cei:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe2160 b:51.3 occ:1.00 FE1 B:SF42160 0.0 51.3 1.0 S3 B:SF42160 2.2 24.0 1.0 S2 B:SF42160 2.2 28.9 1.0 S4 B:SF42160 2.2 25.0 1.0 SG B:CYS801 2.3 44.1 1.0 FE2 B:SF42160 3.1 47.4 1.0 FE4 B:SF42160 3.1 41.8 1.0 FE3 B:SF42160 3.1 42.5 1.0 CB B:CYS801 3.2 26.4 1.0 S1 B:SF42160 3.8 36.9 1.0 CB B:SER804 4.2 30.3 1.0 N B:SER804 4.3 30.7 1.0 CG B:PRO1112 4.3 40.6 1.0 CG2 B:ILE1110 4.5 26.1 1.0 OG B:SER804 4.6 42.0 1.0 CA B:CYS801 4.6 28.6 1.0 CB B:PHE803 4.7 25.9 1.0 CB B:PRO1112 4.7 34.6 1.0 CA B:SER804 4.7 29.4 1.0 N B:PRO1112 4.9 44.9 1.0 CD B:PRO1112 4.9 41.8 1.0 CA B:PRO1112 4.9 33.5 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe2160 b:47.4 occ:1.00 FE2 B:SF42160 0.0 47.4 1.0 S3 B:SF42160 2.2 24.0 1.0 S1 B:SF42160 2.2 36.9 1.0 S4 B:SF42160 2.2 25.0 1.0 SG B:CYS1121 2.3 53.9 1.0 FE4 B:SF42160 3.1 41.8 1.0 FE1 B:SF42160 3.1 51.3 1.0 FE3 B:SF42160 3.1 42.5 1.0 CB B:CYS1121 3.1 33.2 1.0 CA B:CYS1121 3.4 42.8 1.0 S2 B:SF42160 3.8 28.9 1.0 N B:CYS1121 3.9 41.0 1.0 CB B:PRO1112 4.1 34.6 1.0 CG B:PRO1112 4.1 40.6 1.0 C B:PRO1120 4.7 40.1 1.0 C B:CYS1121 4.8 55.8 1.0 CG B:PRO1120 4.8 35.0 1.0 CB B:CYS1124 4.9 37.0 1.0 SG B:CYS1130 5.0 40.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe2160 b:42.5 occ:1.00 FE3 B:SF42160 0.0 42.5 1.0 S4 B:SF42160 2.2 25.0 1.0 S2 B:SF42160 2.2 28.9 1.0 S1 B:SF42160 2.2 36.9 1.0 SG B:CYS1130 2.3 40.3 1.0 CB B:CYS1130 2.9 33.5 1.0 FE4 B:SF42160 3.1 41.8 1.0 FE1 B:SF42160 3.1 51.3 1.0 FE2 B:SF42160 3.1 47.4 1.0 S3 B:SF42160 3.8 24.0 1.0 O B:PHE1126 3.9 32.7 1.0 CA B:LYS1127 4.2 28.2 1.0 CA B:CYS1130 4.3 28.0 1.0 C B:PHE1126 4.4 37.6 1.0 CB B:PHE1132 4.5 23.8 1.0 N B:LYS1127 4.5 42.7 1.0 N B:CYS1130 4.7 20.0 1.0 CG2 B:ILE1110 4.8 26.1 1.0 O B:LYS1127 4.8 33.6 1.0 C B:LYS1127 4.9 28.4 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Adpnp-Bound Addab with A Forked Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe2160 b:41.8 occ:1.00 FE4 B:SF42160 0.0 41.8 1.0 S2 B:SF42160 2.2 28.9 1.0 S1 B:SF42160 2.2 36.9 1.0 S3 B:SF42160 2.2 24.0 1.0 SG B:CYS1124 2.3 50.8 1.0 CB B:CYS1124 3.0 37.0 1.0 FE2 B:SF42160 3.1 47.4 1.0 FE3 B:SF42160 3.1 42.5 1.0 FE1 B:SF42160 3.1 51.3 1.0 S4 B:SF42160 3.8 25.0 1.0 CB B:SER804 4.0 30.3 1.0 CA B:CYS1124 4.4 37.0 1.0 CA B:CYS1121 4.6 42.8 1.0 CB B:PHE1126 4.6 29.9 1.0 C B:PHE1126 4.6 37.6 1.0 N B:PHE1126 4.8 24.1 1.0 N B:LYS1127 4.8 42.7 1.0 CA B:SER804 4.8 29.4 1.0 C B:CYS1124 4.8 31.0 1.0 O B:PHE1126 4.8 32.7 1.0 CA B:PHE1126 4.9 33.7 1.0 OG B:SER804 4.9 42.0 1.0

W.W.Krajewski, X.Fu, M.Wilkinson, N.B.Cronin, M.S.Dillingham, D.B.Wigley. Structural Basis For Translocation By Addab Helicase-Nuclease and Its Arrest at Chi Sites. Nature V. 508 416 2014.
ISSN: ISSN 0028-0836
PubMed: 24670664
DOI: 10.1038/NATURE13037