Iron in PDB 4fwi: Crystal Structure of the Nucleotide-Binding Domain of A Dipeptide Abc Transporter

The structure of Crystal Structure of the Nucleotide-Binding Domain of A Dipeptide Abc Transporter, PDB code: 4fwi was solved by X.Li, J.Ge, M.Yang, N.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.81 / 2.89
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.247, 64.247, 320.608, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 26.8

The structure of Crystal Structure of the Nucleotide-Binding Domain of A Dipeptide Abc Transporter also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Crystal Structure of the Nucleotide-Binding Domain of A Dipeptide Abc Transporter (pdb code 4fwi). 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 the Nucleotide-Binding Domain of A Dipeptide Abc Transporter, PDB code: 4fwi:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Nucleotide-Binding Domain of A Dipeptide Abc Transporter


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 the Nucleotide-Binding Domain of A Dipeptide Abc Transporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:81.4 occ:1.00 FE1 B:SF4401 0.0 81.4 1.0 S3 B:SF4401 2.2 55.7 1.0 S2 B:SF4401 2.2 58.8 1.0 S4 B:SF4401 2.2 64.0 1.0 SG B:CYS298 2.3 81.7 1.0 FE2 B:SF4401 2.9 70.9 1.0 CB B:CYS298 3.0 56.0 1.0 FE4 B:SF4401 3.0 74.1 1.0 FE3 B:SF4401 3.1 65.0 1.0 S1 B:SF4401 3.8 56.0 1.0 CA B:CYS298 4.1 68.2 1.0 CD2 B:HIS317 4.1 50.5 1.0 CE B:MET295 4.3 68.4 1.0 CB B:HIS317 4.4 53.6 1.0 O B:TYR293 4.6 62.6 1.0 N B:HIS317 4.6 54.9 1.0 CA B:ALA294 4.6 84.2 1.0 CG B:HIS317 4.6 59.6 1.0 CB B:CYS285 4.7 38.9 1.0 N B:MET295 4.7 82.5 1.0 SG B:CYS285 4.7 63.6 1.0 N B:CYS298 4.9 76.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Nucleotide-Binding Domain of A Dipeptide Abc Transporter


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 the Nucleotide-Binding Domain of A Dipeptide Abc Transporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:70.9 occ:1.00 FE2 B:SF4401 0.0 70.9 1.0 S4 B:SF4401 2.1 64.0 1.0 S3 B:SF4401 2.2 55.7 1.0 S1 B:SF4401 2.2 56.0 1.0 SG B:CYS285 2.3 63.6 1.0 FE1 B:SF4401 2.9 81.4 1.0 FE3 B:SF4401 2.9 65.0 1.0 FE4 B:SF4401 3.0 74.1 1.0 CB B:CYS285 3.2 38.9 1.0 S2 B:SF4401 3.6 58.8 1.0 CE1 B:HIS248 4.1 50.3 1.0 NE2 B:HIS248 4.2 45.2 1.0 N B:HIS288 4.3 64.0 1.0 CB B:PHE287 4.4 46.4 1.0 CA B:CYS285 4.5 57.8 1.0 C B:PHE287 4.6 60.1 1.0 CD2 B:PHE287 4.6 46.3 1.0 CA B:HIS288 4.6 62.6 1.0 O B:CYS285 4.7 58.6 1.0 CB B:CYS298 4.7 56.0 1.0 CB B:CYS291 4.7 40.1 1.0 CB B:HIS288 4.8 67.1 1.0 CA B:PHE287 4.8 58.4 1.0 C B:CYS285 4.8 59.2 1.0 SG B:CYS291 4.8 46.6 1.0 N B:PHE287 4.9 65.8 1.0 CG B:PRO303 4.9 55.2 1.0 SG B:CYS298 4.9 81.7 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Nucleotide-Binding Domain of A Dipeptide Abc Transporter


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 the Nucleotide-Binding Domain of A Dipeptide Abc Transporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:65.0 occ:1.00 FE3 B:SF4401 0.0 65.0 1.0 S1 B:SF4401 2.2 56.0 1.0 S4 B:SF4401 2.2 64.0 1.0 S2 B:SF4401 2.2 58.8 1.0 SG B:CYS291 2.2 46.6 1.0 FE2 B:SF4401 2.9 70.9 1.0 CB B:CYS291 3.0 40.1 1.0 FE4 B:SF4401 3.0 74.1 1.0 FE1 B:SF4401 3.1 81.4 1.0 S3 B:SF4401 3.8 55.7 1.0 CG B:PRO249 3.9 43.7 1.0 N B:ALA294 4.1 83.4 1.0 C B:TYR293 4.2 68.9 1.0 CA B:ALA294 4.3 84.2 1.0 CB B:PRO249 4.4 42.3 1.0 O B:TYR293 4.4 62.6 1.0 CA B:CYS291 4.4 46.9 1.0 CD2 B:PHE287 4.4 46.3 1.0 CB B:TYR293 4.5 56.9 1.0 N B:TYR293 4.7 63.2 1.0 CA B:TYR293 4.7 58.7 1.0 CD B:PRO249 4.8 40.5 1.0 C B:CYS291 4.8 54.5 1.0 SG B:CYS298 4.9 81.7 1.0 CE2 B:PHE287 4.9 46.0 1.0 CB B:ALA294 5.0 80.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Nucleotide-Binding Domain of A Dipeptide Abc Transporter


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 the Nucleotide-Binding Domain of A Dipeptide Abc Transporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:74.1 occ:1.00 FE4 B:SF4401 0.0 74.1 1.0 S2 B:SF4401 2.1 58.8 1.0 S1 B:SF4401 2.2 56.0 1.0 S3 B:SF4401 2.2 55.7 1.0 SG B:CYS316 2.3 52.8 1.0 FE2 B:SF4401 3.0 70.9 1.0 FE1 B:SF4401 3.0 81.4 1.0 FE3 B:SF4401 3.0 65.0 1.0 CB B:CYS316 3.5 46.0 1.0 CA B:CYS316 3.7 54.3 1.0 S4 B:SF4401 3.8 64.0 1.0 N B:HIS317 3.9 54.9 1.0 CD B:PRO249 4.0 40.5 1.0 CG B:PRO249 4.1 43.7 1.0 C B:CYS316 4.2 50.8 1.0 CE1 B:HIS248 4.2 50.3 1.0 CG B:LEU318 4.5 52.9 1.0 N B:LEU318 4.6 66.1 1.0 NE2 B:HIS248 4.6 45.2 1.0 ND1 B:HIS248 4.6 53.8 1.0 SG B:CYS285 4.9 63.6 1.0 CA B:HIS317 5.0 62.3 1.0 CB B:LEU318 5.0 51.6 1.0 O B:ALA315 5.0 45.3 1.0 SG B:CYS291 5.0 46.6 1.0

X.Li, W.Zhuo, J.Yu, J.Ge, J.Gu, Y.Feng, M.Yang, L.Wang, N.Wang. Structure of the Nucleotide-Binding Domain of A Dipeptide Abc Transporter Reveals A Novel Iron-Sulfur Cluster-Binding Domain Acta Crystallogr.,Sect.D V. 69 256 2013.
ISSN: ISSN 0907-4449
PubMed: 23385461
DOI: 10.1107/S0907444912045180