Iron in PDB 5d08: Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase

All present enzymatic activity of Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase:
1.17.99.6;

The structure of Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase, PDB code: 5d08 was solved by D.P.Dowling, Z.D.Miles, C.Kohrer, V.Bandarian, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.41 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.301, 95.780, 111.175, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.6

The structure of Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase also contains other interesting chemical elements:

Cobalt	(Co)	2 atoms
Chlorine	(Cl)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase (pdb code 5d08). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase, PDB code: 5d08:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase


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 Selenomethionine-Labeled Epoxyqueuosine Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:23.9 occ:1.00 FE1 A:SF4501 0.0 23.9 1.0 SG A:CYS194 2.3 22.7 1.0 S2 A:SF4501 2.3 23.4 1.0 S3 A:SF4501 2.3 26.8 1.0 S4 A:SF4501 2.3 27.3 1.0 FE4 A:SF4501 2.7 27.3 1.0 FE2 A:SF4501 2.7 27.4 1.0 FE3 A:SF4501 2.7 25.3 1.0 CB A:CYS194 3.2 24.6 1.0 N A:CYS194 3.8 26.2 1.0 S1 A:SF4501 3.9 27.1 1.0 CA A:CYS194 4.1 25.3 1.0 CB A:LYS154 4.2 23.3 1.0 N A:ASN155 4.3 21.4 1.0 CB A:ASN155 4.5 16.9 1.0 ND2 A:ASN155 4.6 19.6 1.0 CG A:ASN155 4.6 18.7 1.0 N A:LYS193 4.7 29.5 1.0 SG A:CYS191 4.7 30.2 1.0 SG A:CYS188 4.8 25.4 1.0 C A:LYS154 4.8 23.4 1.0 SG A:CYS247 4.8 24.0 1.0 N A:LYS154 4.9 23.7 1.0 CA A:LYS154 4.9 24.2 1.0 C A:LYS193 4.9 26.4 1.0 CA A:ASN155 5.0 18.6 1.0

Iron binding site 2 out of 16 in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase


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 Selenomethionine-Labeled Epoxyqueuosine Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:27.4 occ:1.00 FE2 A:SF4501 0.0 27.4 1.0 SG A:CYS191 2.3 30.2 1.0 S4 A:SF4501 2.3 27.3 1.0 S3 A:SF4501 2.3 26.8 1.0 S1 A:SF4501 2.3 27.1 1.0 FE3 A:SF4501 2.7 25.3 1.0 FE1 A:SF4501 2.7 23.9 1.0 FE4 A:SF4501 2.7 27.3 1.0 CB A:CYS191 3.1 30.4 1.0 S2 A:SF4501 3.9 23.4 1.0 CD A:PRO248 4.0 27.6 1.0 C A:CYS191 4.2 29.6 1.0 N A:LYS193 4.2 29.5 1.0 CA A:CYS191 4.3 29.7 1.0 O A:CYS191 4.4 29.7 1.0 CB A:LYS193 4.5 27.5 1.0 N A:THR192 4.5 31.9 1.0 CG A:PRO248 4.7 30.7 1.0 SG A:CYS194 4.7 22.7 1.0 N A:CYS194 4.7 26.2 1.0 SG A:CYS247 4.8 24.0 1.0 SG A:CYS188 4.9 25.4 1.0 CA A:LYS193 4.9 29.5 1.0 O A:CYS188 4.9 37.2 1.0 CG A:LYS193 4.9 31.7 1.0 C A:THR192 5.0 27.4 1.0

Iron binding site 3 out of 16 in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase


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 Selenomethionine-Labeled Epoxyqueuosine Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:25.3 occ:1.00 FE3 A:SF4501 0.0 25.3 1.0 SG A:CYS247 2.3 24.0 1.0 S4 A:SF4501 2.3 27.3 1.0 S1 A:SF4501 2.3 27.1 1.0 S2 A:SF4501 2.3 23.4 1.0 FE4 A:SF4501 2.7 27.3 1.0 FE2 A:SF4501 2.7 27.4 1.0 FE1 A:SF4501 2.7 23.9 1.0 CB A:CYS247 3.2 21.6 1.0 CA A:CYS247 3.8 23.8 1.0 S3 A:SF4501 3.9 26.8 1.0 CD A:PRO248 3.9 27.6 1.0 O A:HOH777 4.3 22.6 1.0 N A:PRO248 4.4 26.8 1.0 C A:CYS247 4.5 23.6 1.0 CD1 A:LEU249 4.5 32.4 1.0 ND2 A:ASN155 4.5 19.6 1.0 CG A:LEU249 4.6 31.2 1.0 SG A:CYS188 4.7 25.4 1.0 SG A:CYS194 4.8 22.7 1.0 SG A:CYS191 4.8 30.2 1.0 N A:LEU249 4.9 28.9 1.0 N A:CYS247 5.0 22.3 1.0 CB A:LEU249 5.0 28.9 1.0

Iron binding site 4 out of 16 in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase


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 Selenomethionine-Labeled Epoxyqueuosine Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:27.3 occ:1.00 FE4 A:SF4501 0.0 27.3 1.0 S3 A:SF4501 2.3 26.8 1.0 S2 A:SF4501 2.3 23.4 1.0 SG A:CYS188 2.3 25.4 1.0 S1 A:SF4501 2.3 27.1 1.0 FE3 A:SF4501 2.7 25.3 1.0 FE1 A:SF4501 2.7 23.9 1.0 FE2 A:SF4501 2.7 27.4 1.0 CB A:CYS188 3.3 26.4 1.0 CA A:CYS188 3.9 28.9 1.0 S4 A:SF4501 3.9 27.3 1.0 N A:LYS154 4.3 23.7 1.0 CB A:LYS154 4.3 23.3 1.0 CG A:LYS154 4.4 26.4 1.0 CB A:ALA153 4.4 22.0 1.0 CD1 A:LEU249 4.6 32.4 1.0 SG A:CYS247 4.7 24.0 1.0 O A:CYS188 4.7 37.2 1.0 SG A:CYS194 4.8 22.7 1.0 SG A:CYS191 4.8 30.2 1.0 CB A:CYS191 4.8 30.4 1.0 CD A:LYS154 4.8 28.7 1.0 C A:CYS188 4.8 34.1 1.0 N A:CYS188 4.9 30.4 1.0 CA A:LYS154 4.9 24.2 1.0

Iron binding site 5 out of 16 in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:19.9 occ:1.00 FE1 A:SF4502 0.0 19.9 1.0 SG A:CYS198 2.3 22.3 1.0 S4 A:SF4502 2.3 21.4 1.0 S2 A:SF4502 2.3 18.0 1.0 S3 A:SF4502 2.3 20.1 1.0 FE4 A:SF4502 2.7 18.2 1.0 FE2 A:SF4502 2.7 18.4 1.0 FE3 A:SF4502 2.8 17.8 1.0 CB A:CYS198 3.3 17.0 1.0 CA A:CYS198 3.9 20.5 1.0 S1 A:SF4502 3.9 18.6 1.0 CD A:PRO199 3.9 26.1 1.0 CB A:ALA202 4.5 18.8 1.0 N A:PRO199 4.5 22.6 1.0 C A:CYS198 4.6 23.8 1.0 OG1 A:THR200 4.6 22.8 1.0 SG A:CYS243 4.8 19.4 1.0 SG A:CYS214 4.9 16.9 1.0 SG A:CYS240 4.9 19.2 1.0 CB A:CYS243 4.9 18.3 1.0 CG A:LEU203 4.9 19.3 1.0 CD1 A:LEU203 4.9 22.3 1.0

Iron binding site 6 out of 16 in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:18.4 occ:1.00 FE2 A:SF4502 0.0 18.4 1.0 S1 A:SF4502 2.3 18.6 1.0 SG A:CYS243 2.3 19.4 1.0 S3 A:SF4502 2.3 20.1 1.0 S4 A:SF4502 2.3 21.4 1.0 FE3 A:SF4502 2.7 17.8 1.0 FE1 A:SF4502 2.7 19.9 1.0 FE4 A:SF4502 2.8 18.2 1.0 CB A:CYS243 3.2 18.3 1.0 S2 A:SF4502 3.9 18.0 1.0 N45 A:B12503 3.9 19.3 1.0 N A:CYS243 3.9 20.4 1.0 CA A:CYS243 4.2 20.0 1.0 O A:HOH718 4.2 23.2 1.0 C42 A:B12503 4.7 17.8 1.0 SG A:CYS240 4.7 19.2 1.0 CD1 A:LEU203 4.8 22.3 1.0 C43 A:B12503 4.8 15.7 1.0 SG A:CYS214 4.8 16.9 1.0 SG A:CYS198 4.8 22.3 1.0 O A:CYS240 5.0 17.7 1.0

Iron binding site 7 out of 16 in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:17.8 occ:1.00 FE3 A:SF4502 0.0 17.8 1.0 S4 A:SF4502 2.3 21.4 1.0 SG A:CYS240 2.3 19.2 1.0 S2 A:SF4502 2.3 18.0 1.0 S1 A:SF4502 2.3 18.6 1.0 FE2 A:SF4502 2.7 18.4 1.0 FE4 A:SF4502 2.7 18.2 1.0 FE1 A:SF4502 2.8 19.9 1.0 CB A:CYS240 3.2 15.6 1.0 S3 A:SF4502 3.9 20.1 1.0 CD A:PRO199 4.3 26.1 1.0 C A:CYS240 4.4 17.4 1.0 CA A:CYS240 4.4 15.6 1.0 O A:CYS240 4.5 17.7 1.0 CB A:ILE215 4.5 21.0 1.0 CB A:THR242 4.5 20.7 1.0 N A:THR242 4.5 18.4 1.0 SG A:CYS243 4.7 19.4 1.0 SG A:CYS214 4.7 16.9 1.0 N A:ILE215 4.8 16.7 1.0 N A:CYS243 4.8 20.4 1.0 SG A:CYS198 4.8 22.3 1.0 CG1 A:ILE215 4.8 25.5 1.0 OG1 A:THR242 4.9 20.1 1.0 N A:ASP241 5.0 17.5 1.0 N A:SER216 5.0 14.4 1.0

Iron binding site 8 out of 16 in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:18.2 occ:1.00 FE4 A:SF4502 0.0 18.2 1.0 S3 A:SF4502 2.3 20.1 1.0 S1 A:SF4502 2.3 18.6 1.0 S2 A:SF4502 2.3 18.0 1.0 SG A:CYS214 2.3 16.9 1.0 FE1 A:SF4502 2.7 19.9 1.0 FE3 A:SF4502 2.7 17.8 1.0 FE2 A:SF4502 2.8 18.4 1.0 CB A:CYS214 3.5 16.9 1.0 CA A:CYS214 3.8 15.9 1.0 S4 A:SF4502 3.9 21.4 1.0 N A:ILE215 4.0 16.7 1.0 C A:CYS214 4.2 16.6 1.0 N A:SER216 4.4 14.4 1.0 CD1 A:LEU209 4.5 19.3 1.0 C42 A:B12503 4.5 17.8 1.0 SG A:CYS198 4.7 22.3 1.0 CB A:ALA202 4.7 18.8 1.0 SG A:CYS240 4.7 19.2 1.0 CB A:SER216 4.8 14.4 1.0 N45 A:B12503 4.8 19.3 1.0 CB A:CYS240 4.9 15.6 1.0 SG A:CYS243 4.9 19.4 1.0 CA A:ILE215 4.9 17.3 1.0

Iron binding site 9 out of 16 in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:25.7 occ:1.00 FE1 B:SF4501 0.0 25.7 1.0 SG B:CYS194 2.3 24.5 1.0 S3 B:SF4501 2.3 27.9 1.0 S2 B:SF4501 2.3 25.2 1.0 S4 B:SF4501 2.3 28.9 1.0 FE4 B:SF4501 2.7 27.2 1.0 FE2 B:SF4501 2.7 30.5 1.0 FE3 B:SF4501 2.7 25.7 1.0 CB B:CYS194 3.3 21.0 1.0 N B:CYS194 3.8 25.4 1.0 S1 B:SF4501 3.9 29.0 1.0 CA B:CYS194 4.2 23.6 1.0 CB B:LYS154 4.2 24.8 1.0 N B:ASN155 4.3 23.9 1.0 CB B:ASN155 4.5 18.6 1.0 CG B:ASN155 4.6 23.1 1.0 ND2 B:ASN155 4.6 22.4 1.0 N B:LYS193 4.7 29.8 1.0 SG B:CYS188 4.7 28.7 1.0 SG B:CYS191 4.7 34.7 1.0 C B:LYS154 4.8 23.4 1.0 N B:LYS154 4.8 22.5 1.0 CA B:LYS154 4.8 22.6 1.0 SG B:CYS247 4.8 25.4 1.0 CA B:ASN155 5.0 20.0 1.0 C B:LYS193 5.0 26.4 1.0

Iron binding site 10 out of 16 in the Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Selenomethionine-Labeled Epoxyqueuosine Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:30.5 occ:1.00 FE2 B:SF4501 0.0 30.5 1.0 S4 B:SF4501 2.3 28.9 1.0 SG B:CYS191 2.3 34.7 1.0 S1 B:SF4501 2.3 29.0 1.0 S3 B:SF4501 2.3 27.9 1.0 FE3 B:SF4501 2.7 25.7 1.0 FE1 B:SF4501 2.7 25.7 1.0 FE4 B:SF4501 2.7 27.2 1.0 CB B:CYS191 3.2 32.0 1.0 S2 B:SF4501 3.9 25.2 1.0 CD B:PRO248 4.1 27.4 1.0 C B:CYS191 4.2 32.7 1.0 N B:LYS193 4.2 29.8 1.0 CA B:CYS191 4.3 32.3 1.0 O B:CYS191 4.4 32.2 1.0 N B:THR192 4.4 35.1 1.0 CB B:LYS193 4.5 29.2 1.0 SG B:CYS194 4.7 24.5 1.0 SG B:CYS247 4.8 25.4 1.0 CG B:PRO248 4.8 30.1 1.0 N B:CYS194 4.8 25.4 1.0 SG B:CYS188 4.8 28.7 1.0 O B:CYS188 4.8 33.5 1.0 CA B:LYS193 4.9 30.4 1.0 CA B:THR192 5.0 33.9 1.0 C B:THR192 5.0 33.1 1.0

D.P.Dowling, Z.D.Miles, C.Kohrer, S.J.Maiocco, S.J.Elliott, V.Bandarian, C.L.Drennan. Molecular Basis of Cobalamin-Dependent Rna Modification. Nucleic Acids Res. V. 44 9965 2016.
ISSN: ESSN 1362-4962
PubMed: 27638883
DOI: 10.1093/NAR/GKW806