Iron in PDB 7yyl: Nucleotide-Free Dccp:Dccp-R Complex

The structure of Nucleotide-Free Dccp:Dccp-R Complex, PDB code: 7yyl was solved by J.-H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.93 / 3.25
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	81.672, 83.332, 124.376, 99.72, 95.62, 94.02
R / Rfree (%)	24.6 / 30.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Iron atom in the Nucleotide-Free Dccp:Dccp-R Complex (pdb code 7yyl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 40 binding sites of Iron where determined in the Nucleotide-Free Dccp:Dccp-R Complex, PDB code: 7yyl:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 40 in the Nucleotide-Free Dccp:Dccp-R Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Nucleotide-Free Dccp:Dccp-R Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:36.5 occ:1.00 FE1 C:BJ8501 0.0 36.5 1.0 S4 C:BJ8501 2.2 39.7 1.0 S9 C:BJ8501 2.2 36.4 1.0 S3 C:BJ8501 2.3 30.3 1.0 S2 C:BJ8501 2.4 41.8 1.0 FE2 C:BJ8501 2.6 32.8 1.0 FE4 C:BJ8501 2.7 33.1 1.0 FE3 C:BJ8501 2.7 34.1 1.0 FE8 C:BJ8501 3.8 26.5 1.0 S1 C:BJ8501 3.8 33.3 1.0 CD2 C:LEU115 4.6 30.7 1.0 S7 C:BJ8501 4.6 25.9 1.0 S6 C:BJ8501 4.7 45.3 1.0 CE C:LYS146 4.7 34.8 1.0 NZ C:LYS146 4.7 35.0 1.0

Iron binding site 2 out of 40 in the Nucleotide-Free Dccp:Dccp-R Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Nucleotide-Free Dccp:Dccp-R Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:32.8 occ:1.00 FE2 C:BJ8501 0.0 32.8 1.0 S4 C:BJ8501 2.2 39.7 1.0 S3 C:BJ8501 2.3 30.3 1.0 S1 C:BJ8501 2.4 33.3 1.0 FE1 C:BJ8501 2.6 36.5 1.0 FE3 C:BJ8501 2.7 34.1 1.0 FE4 C:BJ8501 2.7 33.1 1.0 SG C:CYS113 2.8 38.4 1.0 CB C:CYS113 3.7 29.2 1.0 S2 C:BJ8501 3.9 41.8 1.0 SG C:CYS373 4.1 17.2 1.0 CB C:CYS373 4.3 39.6 1.0 S9 C:BJ8501 4.6 36.4 1.0 CB C:LEU115 5.0 28.2 1.0 CD2 C:LEU115 5.0 30.7 1.0

Iron binding site 3 out of 40 in the Nucleotide-Free Dccp:Dccp-R Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Nucleotide-Free Dccp:Dccp-R Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:34.1 occ:1.00 FE3 C:BJ8501 0.0 34.1 1.0 S1 C:BJ8501 2.2 33.3 1.0 S2 C:BJ8501 2.3 41.8 1.0 S4 C:BJ8501 2.3 39.7 1.0 FE4 C:BJ8501 2.6 33.1 1.0 FE1 C:BJ8501 2.7 36.5 1.0 FE2 C:BJ8501 2.7 32.8 1.0 SG C:CYS373 2.9 17.2 1.0 S3 C:BJ8501 3.9 30.3 1.0 CB C:CYS373 4.1 39.6 1.0 CD1 C:TYR376 4.4 34.9 1.0 SG C:CYS143 4.7 24.9 1.0 S9 C:BJ8501 4.7 36.4 1.0 CE1 C:TYR376 4.7 36.4 1.0 CB C:CYS143 4.7 30.1 1.0 CD C:PRO375 4.8 26.7 1.0 CA C:CYS373 4.8 35.6 1.0 CG C:PRO375 4.9 24.1 1.0

Iron binding site 4 out of 40 in the Nucleotide-Free Dccp:Dccp-R Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Nucleotide-Free Dccp:Dccp-R Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:33.1 occ:1.00 FE4 C:BJ8501 0.0 33.1 1.0 S1 C:BJ8501 2.2 33.3 1.0 S3 C:BJ8501 2.3 30.3 1.0 S2 C:BJ8501 2.3 41.8 1.0 FE3 C:BJ8501 2.6 34.1 1.0 FE1 C:BJ8501 2.7 36.5 1.0 FE2 C:BJ8501 2.7 32.8 1.0 SG C:CYS143 2.9 24.9 1.0 S4 C:BJ8501 3.8 39.7 1.0 CB C:CYS143 3.9 30.1 1.0 CE C:LYS146 4.2 34.8 1.0 CD1 C:ILE116 4.3 25.5 1.0 S9 C:BJ8501 4.6 36.4 1.0 SG C:CYS113 4.6 38.4 1.0 CB C:CYS113 4.7 29.2 1.0 CG1 C:ILE116 4.8 23.2 1.0 CG C:LYS146 4.9 27.9 1.0

Iron binding site 5 out of 40 in the Nucleotide-Free Dccp:Dccp-R Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Nucleotide-Free Dccp:Dccp-R Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:24.0 occ:1.00 FE5 C:BJ8501 0.0 24.0 1.0 S7 C:BJ8501 2.2 25.9 1.0 S6 C:BJ8501 2.3 45.3 1.0 S8 C:BJ8501 2.4 38.0 1.0 FE8 C:BJ8501 2.6 26.5 1.0 FE7 C:BJ8501 2.7 23.7 1.0 SG C:CYS340 2.9 30.6 1.0 FE6 C:BJ8501 2.9 30.5 1.0 OH C:TYR376 3.8 29.6 1.0 CB C:CYS340 3.9 31.7 1.0 S5 C:BJ8501 4.0 40.9 1.0 CE1 C:TYR376 4.4 36.4 1.0 CZ C:TYR376 4.6 32.0 1.0 SG C:CYS342 4.6 34.0 1.0 S9 C:BJ8501 4.7 36.4 1.0 S2 C:BJ8501 4.7 41.8 1.0 CG2 C:THR142 4.8 35.2 1.0 CA C:CYS340 4.9 33.3 1.0

Iron binding site 6 out of 40 in the Nucleotide-Free Dccp:Dccp-R Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Nucleotide-Free Dccp:Dccp-R Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:30.5 occ:1.00 FE6 C:BJ8501 0.0 30.5 1.0 S5 C:BJ8501 2.2 40.9 1.0 S8 C:BJ8501 2.3 38.0 1.0 S7 C:BJ8501 2.5 25.9 1.0 FE7 C:BJ8501 2.8 23.7 1.0 FE8 C:BJ8501 2.8 26.5 1.0 SG C:CYS75 2.9 48.6 1.0 FE5 C:BJ8501 2.9 24.0 1.0 CB C:CYS75 3.9 43.5 1.0 CA C:CYS75 3.9 40.2 1.0 N C:VAL76 4.1 40.0 1.0 S6 C:BJ8501 4.1 45.3 1.0 CG2 C:THR142 4.5 35.2 1.0 C C:CYS75 4.5 44.0 1.0 CG2 C:VAL76 4.5 37.5 1.0 CD1 C:TYR77 4.7 39.6 1.0 NZ C:LYS146 4.7 35.0 1.0 S9 C:BJ8501 4.8 36.4 1.0 O C:PHE74 4.9 48.4 1.0 SG C:CYS308 5.0 30.6 1.0

Iron binding site 7 out of 40 in the Nucleotide-Free Dccp:Dccp-R Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Nucleotide-Free Dccp:Dccp-R Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:23.7 occ:1.00 FE7 C:BJ8501 0.0 23.7 1.0 S6 C:BJ8501 2.3 45.3 1.0 S8 C:BJ8501 2.3 38.0 1.0 S5 C:BJ8501 2.4 40.9 1.0 FE5 C:BJ8501 2.7 24.0 1.0 FE8 C:BJ8501 2.7 26.5 1.0 FE6 C:BJ8501 2.8 30.5 1.0 SG C:CYS308 2.8 30.6 1.0 CB C:CYS308 3.2 28.1 1.0 S7 C:BJ8501 3.8 25.9 1.0 OH C:TYR376 4.5 29.6 1.0 NH2 C:ARG312 4.5 26.3 1.0 S9 C:BJ8501 4.6 36.4 1.0 CG2 C:VAL76 4.6 37.5 1.0 CA C:CYS308 4.7 27.6 1.0 CG C:PRO283 4.7 27.4 1.0 NE C:ARG312 4.8 27.5 1.0 CD C:PRO283 4.9 28.5 1.0 SG C:CYS340 5.0 30.6 1.0

Iron binding site 8 out of 40 in the Nucleotide-Free Dccp:Dccp-R Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Nucleotide-Free Dccp:Dccp-R Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:26.5 occ:1.00 FE8 C:BJ8501 0.0 26.5 1.0 S9 C:BJ8501 2.2 36.4 1.0 S7 C:BJ8501 2.2 25.9 1.0 S6 C:BJ8501 2.3 45.3 1.0 S5 C:BJ8501 2.4 40.9 1.0 FE5 C:BJ8501 2.6 24.0 1.0 FE7 C:BJ8501 2.7 23.7 1.0 FE6 C:BJ8501 2.8 30.5 1.0 FE1 C:BJ8501 3.8 36.5 1.0 S8 C:BJ8501 3.8 38.0 1.0 S2 C:BJ8501 4.1 41.8 1.0 NZ C:LYS146 4.3 35.0 1.0 CG C:PRO283 4.4 27.4 1.0 CD C:PRO283 4.7 28.5 1.0

Iron binding site 9 out of 40 in the Nucleotide-Free Dccp:Dccp-R Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Nucleotide-Free Dccp:Dccp-R Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:34.8 occ:1.00 FE1 D:BJ8501 0.0 34.8 1.0 S4 D:BJ8501 2.2 21.9 1.0 S9 D:BJ8501 2.2 32.2 1.0 S3 D:BJ8501 2.2 49.7 1.0 S2 D:BJ8501 2.4 44.5 1.0 FE2 D:BJ8501 2.6 39.5 1.0 FE3 D:BJ8501 2.7 31.8 1.0 FE4 D:BJ8501 2.7 27.0 1.0 S1 D:BJ8501 3.8 54.3 1.0 FE8 D:BJ8501 4.0 38.2 1.0 NZ D:LYS146 4.3 33.7 1.0 S7 D:BJ8501 5.0 57.4 1.0

Iron binding site 10 out of 40 in the Nucleotide-Free Dccp:Dccp-R Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Nucleotide-Free Dccp:Dccp-R Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:39.5 occ:1.00 FE2 D:BJ8501 0.0 39.5 1.0 S4 D:BJ8501 2.2 21.9 1.0 S3 D:BJ8501 2.2 49.7 1.0 S1 D:BJ8501 2.4 54.3 1.0 FE1 D:BJ8501 2.6 34.8 1.0 FE3 D:BJ8501 2.7 31.8 1.0 FE4 D:BJ8501 2.7 27.0 1.0 SG D:CYS113 2.8 35.8 1.0 CB D:CYS113 3.4 34.4 1.0 S2 D:BJ8501 3.9 44.5 1.0 CB D:LEU115 4.6 42.5 1.0 S9 D:BJ8501 4.6 32.2 1.0 CD1 D:ILE116 4.7 35.0 1.0 CG1 D:ILE116 4.7 38.9 1.0 CA D:CYS113 4.9 39.4 1.0 CB D:CYS373 5.0 37.7 1.0 SG D:CYS373 5.0 31.9 1.0 CD1 D:LEU370 5.0 33.3 1.0

J.H.Jeoung, S.Nicklisch, H.Dobbek. Structural Basis For Coupled Atp-Driven Electron Transfer in the Double-Cubane Cluster Protein. Proc.Natl.Acad.Sci.Usa V. 119 76119 2022.
ISSN: ESSN 1091-6490
PubMed: 35905315
DOI: 10.1073/PNAS.2203576119