Iron in PDB 3bk7: Structure of the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii

The structure of Structure of the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii, PDB code: 3bk7 was solved by A.Karcher, K.P.Hopfner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	63.200, 63.200, 319.380, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 27.5

The structure of Structure of the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the Structure of the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii (pdb code 3bk7). 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 the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii, PDB code: 3bk7:
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 the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii


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 Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe596 b:29.9 occ:1.00 FE1 A:SF4596 0.0 29.9 1.0 S2 A:SF4596 2.3 25.1 1.0 S4 A:SF4596 2.3 27.7 1.0 S3 A:SF4596 2.3 27.7 1.0 SG A:CYS29 2.6 38.1 1.0 FE3 A:SF4596 2.7 29.9 1.0 FE2 A:SF4596 2.7 30.5 1.0 FE4 A:SF4596 2.8 30.0 1.0 CB A:CYS29 3.7 42.3 1.0 CB A:ALA38 3.7 42.3 1.0 S1 A:SF4596 3.9 29.6 1.0 CD A:PRO30 4.1 44.7 1.0 CD1 A:ILE39 4.1 36.5 1.0 CA A:CYS29 4.2 43.4 1.0 CG1 A:ILE39 4.3 37.5 1.0 CG A:PRO30 4.4 43.7 1.0 CG2 A:VAL31 4.6 35.1 1.0 N A:PRO30 4.6 43.9 1.0 C A:CYS29 4.7 43.7 1.0 CB A:VAL31 4.7 39.2 1.0 N A:VAL31 4.8 42.7 1.0 CA A:CYS55 4.8 48.2 1.0 SG A:CYS58 4.9 42.4 1.0 SG A:CYS61 4.9 27.4 1.0

Iron binding site 2 out of 8 in the Structure of the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii


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 Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe596 b:30.5 occ:1.00 FE2 A:SF4596 0.0 30.5 1.0 S4 A:SF4596 2.2 27.7 1.0 S3 A:SF4596 2.2 27.7 1.0 S1 A:SF4596 2.3 29.6 1.0 SG A:CYS55 2.4 42.0 1.0 FE4 A:SF4596 2.7 30.0 1.0 FE1 A:SF4596 2.7 29.9 1.0 FE3 A:SF4596 2.8 29.9 1.0 CB A:CYS55 2.9 46.9 1.0 CA A:CYS55 3.1 48.2 1.0 C A:CYS55 3.7 48.3 1.0 N A:THR56 3.7 48.1 1.0 S2 A:SF4596 3.8 25.1 1.0 N A:GLY57 3.9 44.9 1.0 N A:CYS55 4.4 49.8 1.0 CB A:ALA38 4.5 42.3 1.0 CA A:GLY57 4.5 43.6 1.0 CD1 A:ILE72 4.7 22.9 1.0 O A:CYS55 4.7 47.1 1.0 N A:CYS58 4.8 42.4 1.0 CA A:THR56 4.9 47.1 1.0 SG A:CYS61 4.9 27.4 1.0 C A:THR56 4.9 45.9 1.0 CG2 A:ILE50 4.9 27.7 1.0 OG1 A:THR56 5.0 47.5 1.0

Iron binding site 3 out of 8 in the Structure of the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii


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 Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe596 b:29.9 occ:1.00 FE3 A:SF4596 0.0 29.9 1.0 S4 A:SF4596 2.2 27.7 1.0 S2 A:SF4596 2.2 25.1 1.0 S1 A:SF4596 2.3 29.6 1.0 SG A:CYS61 2.4 27.4 1.0 FE4 A:SF4596 2.7 30.0 1.0 FE1 A:SF4596 2.7 29.9 1.0 FE2 A:SF4596 2.8 30.5 1.0 CB A:CYS61 3.1 31.0 1.0 S3 A:SF4596 3.8 27.7 1.0 N A:CYS61 3.9 32.2 1.0 CD1 A:ILE39 4.1 36.5 1.0 CA A:CYS61 4.1 30.2 1.0 N A:ILE60 4.7 34.9 1.0 CG1 A:ILE39 4.7 37.5 1.0 SG A:CYS55 4.7 42.0 1.0 CG1 A:ILE72 4.8 22.9 1.0 SG A:CYS58 4.8 42.4 1.0 SG A:CYS29 4.8 38.1 1.0 N A:GLY59 4.9 40.5 1.0 CD1 A:ILE72 4.9 22.9 1.0 CA A:GLY59 5.0 38.2 1.0

Iron binding site 4 out of 8 in the Structure of the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii


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 Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe596 b:30.0 occ:1.00 FE4 A:SF4596 0.0 30.0 1.0 S3 A:SF4596 2.1 27.7 1.0 S1 A:SF4596 2.1 29.6 1.0 S2 A:SF4596 2.2 25.1 1.0 SG A:CYS58 2.5 42.4 1.0 FE3 A:SF4596 2.7 29.9 1.0 FE2 A:SF4596 2.7 30.5 1.0 FE1 A:SF4596 2.8 29.9 1.0 N A:GLY59 3.6 40.5 1.0 N A:CYS58 3.7 42.4 1.0 CB A:CYS58 3.7 42.4 1.0 S4 A:SF4596 3.8 27.7 1.0 CA A:CYS58 4.0 41.8 1.0 N A:ILE60 4.1 34.9 1.0 C A:CYS58 4.2 41.6 1.0 OG1 A:THR56 4.2 47.5 1.0 CG A:PRO30 4.2 43.7 1.0 CD A:PRO30 4.3 44.7 1.0 N A:GLY57 4.4 44.9 1.0 CA A:GLY59 4.4 38.2 1.0 C A:GLY57 4.5 42.6 1.0 SG A:CYS55 4.7 42.0 1.0 C A:GLY59 4.7 36.7 1.0 SG A:CYS61 4.8 27.4 1.0 N A:THR56 4.8 48.1 1.0 N A:CYS61 4.8 32.2 1.0 CA A:GLY57 4.8 43.6 1.0 CB A:ILE60 4.9 34.3 1.0

Iron binding site 5 out of 8 in the Structure of the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii


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 Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe597 b:22.7 occ:1.00 FE1 A:SF4597 0.0 22.7 1.0 S4 A:SF4597 2.3 20.4 1.0 S2 A:SF4597 2.3 20.2 1.0 S3 A:SF4597 2.3 21.1 1.0 SG A:CYS25 2.3 40.2 1.0 FE3 A:SF4597 2.7 23.3 1.0 FE2 A:SF4597 2.7 23.3 1.0 FE4 A:SF4597 2.8 22.6 1.0 CB A:CYS25 3.8 43.2 1.0 S1 A:SF4597 3.9 21.6 1.0 N A:CYS25 4.1 43.0 1.0 CD1 A:ILE70 4.3 24.3 1.0 CG A:PRO48 4.4 31.1 1.0 CA A:CYS25 4.5 42.8 1.0 N A:LEU24 4.5 45.8 1.0 CB A:PRO48 4.7 29.5 1.0 SG A:CYS20 4.7 42.2 1.0 CA A:PHE23 4.7 46.6 1.0 C A:PHE23 4.8 46.6 1.0 SG A:CYS15 5.0 34.3 1.0

Iron binding site 6 out of 8 in the Structure of the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii


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 Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe597 b:23.3 occ:1.00 FE2 A:SF4597 0.0 23.3 1.0 S4 A:SF4597 2.2 20.4 1.0 S3 A:SF4597 2.2 21.1 1.0 S1 A:SF4597 2.3 21.6 1.0 SG A:CYS20 2.4 42.2 1.0 FE4 A:SF4597 2.7 22.6 1.0 FE1 A:SF4597 2.7 22.7 1.0 FE3 A:SF4597 2.8 23.3 1.0 CB A:CYS20 3.4 49.8 1.0 S2 A:SF4597 3.8 20.2 1.0 N A:LEU24 4.2 45.8 1.0 CA A:PRO17 4.3 48.3 1.0 O A:ASN16 4.4 47.8 1.0 N A:PRO17 4.5 47.9 1.0 C A:ASN16 4.6 47.4 1.0 CA A:PHE23 4.6 46.6 1.0 CB A:LEU24 4.6 43.8 1.0 SG A:CYS15 4.7 34.3 1.0 CA A:CYS20 4.8 51.3 1.0 CD A:PRO66 4.8 33.9 1.0 N A:ASN16 4.8 44.3 1.0 CG A:PRO66 4.8 36.0 1.0 C A:PHE23 4.9 46.6 1.0 SG A:CYS25 4.9 40.2 1.0

Iron binding site 7 out of 8 in the Structure of the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii


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 Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe597 b:23.3 occ:1.00 FE3 A:SF4597 0.0 23.3 1.0 S2 A:SF4597 2.2 20.2 1.0 S4 A:SF4597 2.2 20.4 1.0 S1 A:SF4597 2.3 21.6 1.0 SG A:CYS65 2.6 29.3 1.0 FE4 A:SF4597 2.6 22.6 1.0 FE1 A:SF4597 2.7 22.7 1.0 FE2 A:SF4597 2.8 23.3 1.0 CB A:CYS65 3.6 31.3 1.0 S3 A:SF4597 3.8 21.1 1.0 CA A:CYS65 4.1 31.5 1.0 CB A:ALA69 4.4 35.0 1.0 CD A:PRO66 4.4 33.9 1.0 CD1 A:ILE70 4.5 24.3 1.0 SG A:CYS25 4.6 40.2 1.0 CG1 A:ILE70 4.7 26.6 1.0 C A:CYS65 4.8 32.8 1.0 CG A:PRO66 4.9 36.0 1.0 CB A:CYS15 4.9 39.6 1.0 N A:PRO66 4.9 34.4 1.0 SG A:CYS15 5.0 34.3 1.0

Iron binding site 8 out of 8 in the Structure of the Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii


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 Complete ABCE1/Rnaase-L Inhibitor Protein From Pyrococcus Abysii within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe597 b:22.6 occ:1.00 FE4 A:SF4597 0.0 22.6 1.0 S3 A:SF4597 2.1 21.1 1.0 S1 A:SF4597 2.1 21.6 1.0 S2 A:SF4597 2.1 20.2 1.0 SG A:CYS15 2.4 34.3 1.0 FE3 A:SF4597 2.6 23.3 1.0 FE2 A:SF4597 2.7 23.3 1.0 FE1 A:SF4597 2.8 22.7 1.0 CB A:CYS15 3.0 39.6 1.0 CA A:CYS15 3.7 41.9 1.0 S4 A:SF4597 3.8 20.4 1.0 N A:ASN16 3.9 44.3 1.0 C A:CYS15 4.2 43.0 1.0 CG A:PRO48 4.3 31.1 1.0 CD A:PRO48 4.5 33.5 1.0 N A:PRO17 4.6 47.9 1.0 CD A:PRO17 4.8 47.0 1.0 C A:ASN16 4.8 47.4 1.0 CG A:PRO17 4.8 46.8 1.0 CB A:ALA69 4.8 35.0 1.0 N A:CYS15 4.9 41.7 1.0 SG A:CYS65 5.0 29.3 1.0 SG A:CYS25 5.0 40.2 1.0 CA A:ASN16 5.0 46.6 1.0

A.Karcher, A.Schele, K.P.Hopfner. X-Ray Structure of the Complete Abc Enzyme ABCE1 From Pyrococcus Abyssi J.Biol.Chem. V. 283 7962 2008.
ISSN: ISSN 0021-9258
PubMed: 18160405
DOI: 10.1074/JBC.M707347200