Iron in PDB 5d6s: Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.

The structure of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus., PDB code: 5d6s was solved by K.A.P.Payne, K.Fisher, M.S.Dunstan, H.Sjuts, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	88.58 / 2.65
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.120, 106.120, 332.280, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 25.3

The structure of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. also contains other interesting chemical elements:

Cobalt

(Co)

5 atoms

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 Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. (pdb code 5d6s). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 40 binding sites of Iron where determined in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus., PDB code: 5d6s:
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 Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:73.6 occ:1.00 FE1 A:SF4401 0.0 73.6 1.0 S4 A:SF4401 2.1 76.8 1.0 S3 A:SF4401 2.1 65.7 1.0 S2 A:SF4401 2.1 74.2 1.0 SG A:CYS190 2.3 79.2 1.0 FE4 A:SF4401 2.5 69.9 1.0 FE3 A:SF4401 2.6 69.2 1.0 FE2 A:SF4401 2.6 73.3 1.0 CB A:CYS190 3.4 75.3 1.0 S1 A:SF4401 3.6 78.0 1.0 N A:CYS190 4.1 80.6 1.0 N A:ASN151 4.3 64.7 1.0 CB A:LYS150 4.4 88.7 1.0 CA A:CYS190 4.4 68.3 1.0 SG A:CYS184 4.5 95.5 1.0 N A:LYS150 4.5 71.7 1.0 CB A:ASN151 4.5 61.5 1.0 SG A:CYS187 4.6 79.6 1.0 SG A:CYS243 4.7 65.4 1.0 N A:ARG189 4.7 75.1 1.0 CG A:ASN151 4.7 62.0 1.0 ND2 A:ASN151 4.8 60.5 1.0 CA A:LYS150 4.8 75.0 1.0 C A:LYS150 4.9 70.3 1.0 CD A:LYS150 5.0 96.4 1.0

Iron binding site 2 out of 40 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:73.3 occ:1.00 FE2 A:SF4401 0.0 73.3 1.0 S4 A:SF4401 2.1 76.8 1.0 S3 A:SF4401 2.1 65.7 1.0 S1 A:SF4401 2.2 78.0 1.0 SG A:CYS187 2.4 79.6 1.0 FE4 A:SF4401 2.5 69.9 1.0 FE3 A:SF4401 2.5 69.2 1.0 FE1 A:SF4401 2.6 73.6 1.0 CB A:CYS187 3.1 90.9 1.0 S2 A:SF4401 3.5 74.2 1.0 CD A:PRO244 3.7 92.2 1.0 SG A:CYS243 4.3 65.4 1.0 CG A:PRO244 4.3 89.0 1.0 N A:ARG188 4.3 78.2 1.0 CA A:CYS187 4.4 96.9 1.0 N A:ARG189 4.4 75.1 1.0 C A:CYS187 4.4 92.8 1.0 SG A:CYS184 4.5 95.5 1.0 SG A:CYS190 4.6 79.2 1.0 CB A:ARG189 4.7 75.9 1.0 CA A:CYS243 5.0 75.8 1.0

Iron binding site 3 out of 40 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:69.2 occ:1.00 FE3 A:SF4401 0.0 69.2 1.0 S4 A:SF4401 2.1 76.8 1.0 S2 A:SF4401 2.1 74.2 1.0 S1 A:SF4401 2.1 78.0 1.0 SG A:CYS243 2.2 65.4 1.0 FE2 A:SF4401 2.5 73.3 1.0 FE1 A:SF4401 2.6 73.6 1.0 FE4 A:SF4401 2.6 69.9 1.0 CB A:CYS243 3.2 75.4 1.0 S3 A:SF4401 3.6 65.7 1.0 CA A:CYS243 3.8 75.8 1.0 CD A:PRO244 3.9 92.2 1.0 CD1 A:ILE155 4.4 83.7 1.0 ND2 A:ASN151 4.6 60.5 1.0 N A:PRO244 4.6 88.1 1.0 C A:CYS243 4.6 87.6 1.0 SG A:CYS190 4.7 79.2 1.0 SG A:CYS187 4.8 79.6 1.0 SG A:CYS184 4.8 95.5 1.0 CD1 A:TYR245 4.8 67.3 1.0 N A:CYS243 5.0 81.1 1.0

Iron binding site 4 out of 40 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:69.9 occ:1.00 FE4 A:SF4401 0.0 69.9 1.0 S1 A:SF4401 2.1 78.0 1.0 S2 A:SF4401 2.1 74.2 1.0 S3 A:SF4401 2.1 65.7 1.0 SG A:CYS184 2.3 95.5 1.0 FE2 A:SF4401 2.5 73.3 1.0 FE1 A:SF4401 2.5 73.6 1.0 FE3 A:SF4401 2.6 69.2 1.0 CB A:CYS184 3.5 91.8 1.0 S4 A:SF4401 3.5 76.8 1.0 N A:LYS150 4.0 71.7 1.0 CA A:CYS184 4.1 88.9 1.0 CA A:GLY149 4.4 62.4 1.0 CB A:CYS187 4.5 90.9 1.0 SG A:CYS243 4.6 65.4 1.0 CB A:LYS150 4.6 88.7 1.0 SG A:CYS187 4.6 79.6 1.0 CD A:LYS150 4.7 96.4 1.0 SG A:CYS190 4.7 79.2 1.0 C A:GLY149 4.8 66.2 1.0 CG A:LYS150 4.8 93.4 1.0 CE2 A:PHE147 4.9 55.4 1.0 CA A:LYS150 4.9 75.0 1.0

Iron binding site 5 out of 40 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:53.3 occ:1.00 FE1 A:SF4402 0.0 53.3 1.0 S2 A:SF4402 2.1 56.0 1.0 S4 A:SF4402 2.1 54.4 1.0 SG A:CYS210 2.1 57.5 1.0 S3 A:SF4402 2.1 57.8 1.0 FE2 A:SF4402 2.6 64.4 1.0 FE3 A:SF4402 2.6 60.9 1.0 FE4 A:SF4402 2.6 57.2 1.0 CB A:CYS210 3.5 51.0 1.0 S1 A:SF4402 3.6 60.0 1.0 CA A:CYS210 3.8 54.2 1.0 SG A:CYS198 3.8 59.0 1.0 N A:LEU211 4.0 52.0 1.0 CE A:MET205 4.3 57.4 1.0 C A:CYS210 4.3 55.3 1.0 SG A:CYS236 4.4 56.9 1.0 N A:SER212 4.5 54.4 1.0 SG A:CYS239 4.6 61.6 1.0 SG A:CYS194 4.6 60.0 1.0 C42 A:B12403 4.6 56.5 1.0 CB A:CYS236 4.6 54.3 1.0 N45 A:B12403 4.8 52.2 1.0 CB A:SER212 5.0 55.1 1.0

Iron binding site 6 out of 40 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:64.4 occ:1.00 FE2 A:SF4402 0.0 64.4 1.0 S3 A:SF4402 2.1 57.8 1.0 S1 A:SF4402 2.1 60.0 1.0 S4 A:SF4402 2.1 54.4 1.0 SG A:CYS236 2.3 56.9 1.0 FE1 A:SF4402 2.6 53.3 1.0 FE4 A:SF4402 2.6 57.2 1.0 FE3 A:SF4402 2.6 60.9 1.0 CB A:CYS236 3.3 54.3 1.0 S2 A:SF4402 3.6 56.0 1.0 CD A:PRO195 4.2 58.5 1.0 SG A:CYS210 4.3 57.5 1.0 SG A:CYS239 4.4 61.6 1.0 CB A:ILE238 4.4 58.9 1.0 SG A:CYS194 4.5 60.0 1.0 N A:ILE238 4.6 62.6 1.0 CA A:CYS236 4.6 50.6 1.0 C A:CYS236 4.7 52.0 1.0 CB A:LEU211 4.7 53.0 1.0 N A:CYS239 4.7 64.6 1.0 N A:LEU211 4.7 52.0 1.0 O A:CYS236 4.8 61.3 1.0 CG A:PRO195 5.0 55.4 1.0 CG A:LEU211 5.0 52.5 1.0 CA A:ILE238 5.0 60.4 1.0

Iron binding site 7 out of 40 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:60.9 occ:1.00 FE3 A:SF4402 0.0 60.9 1.0 S2 A:SF4402 2.1 56.0 1.0 S1 A:SF4402 2.1 60.0 1.0 S4 A:SF4402 2.1 54.4 1.0 SG A:CYS239 2.2 61.6 1.0 FE4 A:SF4402 2.6 57.2 1.0 FE1 A:SF4402 2.6 53.3 1.0 FE2 A:SF4402 2.6 64.4 1.0 CB A:CYS239 3.1 57.0 1.0 S3 A:SF4402 3.6 57.8 1.0 N A:CYS239 4.0 64.6 1.0 N45 A:B12403 4.1 52.2 1.0 CA A:CYS239 4.2 59.8 1.0 SG A:CYS236 4.4 56.9 1.0 SG A:CYS210 4.5 57.5 1.0 CD1 A:LEU199 4.5 57.1 1.0 SG A:CYS194 4.6 60.0 1.0 C42 A:B12403 4.9 56.5 1.0

Iron binding site 8 out of 40 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:57.2 occ:1.00 FE4 A:SF4402 0.0 57.2 1.0 S1 A:SF4402 2.1 60.0 1.0 S2 A:SF4402 2.1 56.0 1.0 S3 A:SF4402 2.2 57.8 1.0 SG A:CYS194 2.2 60.0 1.0 FE3 A:SF4402 2.6 60.9 1.0 FE2 A:SF4402 2.6 64.4 1.0 FE1 A:SF4402 2.6 53.3 1.0 CB A:CYS194 3.2 68.8 1.0 SG A:CYS198 3.5 59.0 1.0 S4 A:SF4402 3.6 54.4 1.0 CA A:CYS194 3.8 72.6 1.0 CD A:PRO195 4.1 58.5 1.0 CD1 A:LEU199 4.5 57.1 1.0 OG1 A:THR196 4.5 56.5 1.0 SG A:CYS239 4.5 61.6 1.0 C A:CYS194 4.6 70.8 1.0 SG A:CYS210 4.6 57.5 1.0 CG A:LEU199 4.7 59.3 1.0 N A:PRO195 4.7 58.2 1.0 CB A:CYS239 4.8 57.0 1.0 SG A:CYS236 4.8 56.9 1.0

Iron binding site 9 out of 40 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:68.0 occ:1.00 FE1 B:SF4401 0.0 68.0 1.0 S2 B:SF4401 2.1 69.0 1.0 S4 B:SF4401 2.1 76.8 1.0 S3 B:SF4401 2.1 63.0 1.0 SG B:CYS190 2.4 68.9 1.0 FE3 B:SF4401 2.5 64.1 1.0 FE4 B:SF4401 2.6 69.2 1.0 FE2 B:SF4401 2.6 71.3 1.0 CB B:CYS190 3.4 65.2 1.0 S1 B:SF4401 3.6 75.8 1.0 N B:CYS190 4.1 75.6 1.0 N B:ASN151 4.3 54.5 1.0 CA B:CYS190 4.4 63.5 1.0 CB B:LYS150 4.4 84.6 1.0 SG B:CYS184 4.5 77.3 1.0 CB B:ASN151 4.5 51.7 1.0 N B:LYS150 4.5 76.3 1.0 SG B:CYS243 4.6 57.3 1.0 CG B:ASN151 4.6 48.4 1.0 ND2 B:ASN151 4.7 49.4 1.0 SG B:CYS187 4.7 69.9 1.0 N B:ARG189 4.8 73.6 1.0 CA B:LYS150 4.9 72.6 1.0 C B:LYS150 4.9 68.9 1.0 CA B:ASN151 5.0 53.7 1.0

Iron binding site 10 out of 40 in the Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Epoxyqueuosine Reductase From Streptococcus Thermophilus. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:71.3 occ:1.00 FE2 B:SF4401 0.0 71.3 1.0 S3 B:SF4401 2.1 63.0 1.0 S4 B:SF4401 2.1 76.8 1.0 S1 B:SF4401 2.1 75.8 1.0 SG B:CYS187 2.3 69.9 1.0 FE4 B:SF4401 2.5 69.2 1.0 FE3 B:SF4401 2.6 64.1 1.0 FE1 B:SF4401 2.6 68.0 1.0 CB B:CYS187 2.9 92.2 1.0 S2 B:SF4401 3.6 69.0 1.0 CD B:PRO244 3.8 98.4 1.0 N B:ARG188 4.2 96.8 1.0 CA B:CYS187 4.2 99.3 1.0 N B:ARG189 4.3 73.6 1.0 C B:CYS187 4.3 0.3 1.0 CG B:PRO244 4.4 95.5 1.0 SG B:CYS184 4.5 77.3 1.0 SG B:CYS243 4.5 57.3 1.0 SG B:CYS190 4.6 68.9 1.0 CB B:ARG189 4.7 95.3 1.0 N B:CYS190 4.9 75.6 1.0 O B:CYS187 5.0 0.9 1.0 CB B:CYS184 5.0 95.3 1.0

K.A.Payne, K.Fisher, H.Sjuts, M.S.Dunstan, B.Bellina, L.Johannissen, P.Barran, S.Hay, S.E.Rigby, D.Leys. Epoxyqueuosine Reductase Structure Suggests A Mechanism For Cobalamin-Dependent Trna Modification. J.Biol.Chem. V. 290 27572 2015.
ISSN: ESSN 1083-351X
PubMed: 26378237
DOI: 10.1074/JBC.M115.685693