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Iron in PDB 5d0b: Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop

Enzymatic activity of Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop

All present enzymatic activity of Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop:
1.17.99.6;

Protein crystallography data

The structure of Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop, PDB code: 5d0b 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) 32.05 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.644, 110.754, 99.223, 90.00, 95.16, 90.00
R / Rfree (%) 19.2 / 22.1

Other elements in 5d0b:

The structure of Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop (pdb code 5d0b). 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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop, PDB code: 5d0b:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 5d0b

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Iron binding site 1 out of 16 in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop


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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:21.9
occ:1.00
 FE1 A:SF4501 0.0 21.9 1.0
S3 A:SF4501 2.3 26.1 1.0
S2 A:SF4501 2.3 20.9 1.0
S4 A:SF4501 2.3 25.6 1.0
SG A:CYS194 2.3 25.0 1.0
FE2 A:SF4501 2.7 31.0 1.0
FE3 A:SF4501 2.7 21.6 1.0
FE4 A:SF4501 2.7 24.5 1.0
CB A:CYS194 3.2 24.7 1.0
N A:CYS194 3.9 26.8 1.0
S1 A:SF4501 3.9 25.0 1.0
CB A:LYS154 4.1 23.6 1.0
CA A:CYS194 4.2 24.6 1.0
N A:ASN155 4.5 24.1 1.0
CG A:ASN155 4.7 24.7 1.0
CB A:ASN155 4.7 22.8 1.0
N A:LYS193 4.7 28.1 1.0
SG A:CYS188 4.7 25.7 1.0
SG A:CYS191 4.8 28.7 1.0
N A:LYS154 4.8 23.8 1.0
CA A:LYS154 4.8 25.1 1.0
ND2 A:ASN155 4.8 23.3 1.0
C A:LYS154 4.8 26.7 1.0
SG A:CYS247 4.8 26.9 1.0
CG A:LYS154 5.0 23.7 1.0

Iron binding site 2 out of 16 in 5d0b

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Iron binding site 2 out of 16 in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop


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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:31.0
occ:1.00
 FE2 A:SF4501 0.0 31.0 1.0
S3 A:SF4501 2.3 26.1 1.0
S4 A:SF4501 2.3 25.6 1.0
SG A:CYS191 2.3 28.7 1.0
S1 A:SF4501 2.3 25.0 1.0
FE1 A:SF4501 2.7 21.9 1.0
FE3 A:SF4501 2.7 21.6 1.0
FE4 A:SF4501 2.7 24.5 1.0
CB A:CYS191 3.2 28.9 1.0
S2 A:SF4501 3.9 20.9 1.0
CD A:PRO248 4.0 29.1 1.0
C A:CYS191 4.1 29.9 1.0
N A:LYS193 4.2 28.1 1.0
CA A:CYS191 4.3 29.2 1.0
O A:CYS191 4.3 29.7 1.0
N A:THR192 4.3 29.6 1.0
CB A:LYS193 4.6 24.5 1.0
CG A:PRO248 4.6 30.4 1.0
SG A:CYS194 4.7 25.0 1.0
SG A:CYS247 4.8 26.9 1.0
N A:CYS194 4.8 26.8 1.0
SG A:CYS188 4.8 25.7 1.0
CA A:THR192 4.9 27.1 1.0
CA A:LYS193 4.9 26.0 1.0
C A:THR192 4.9 28.4 1.0
O A:CYS188 4.9 31.5 1.0

Iron binding site 3 out of 16 in 5d0b

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Iron binding site 3 out of 16 in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop


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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:21.6
occ:1.00
 FE3 A:SF4501 0.0 21.6 1.0
S2 A:SF4501 2.3 20.9 1.0
S4 A:SF4501 2.3 25.6 1.0
S1 A:SF4501 2.3 25.0 1.0
SG A:CYS247 2.3 26.9 1.0
FE4 A:SF4501 2.7 24.5 1.0
FE1 A:SF4501 2.7 21.9 1.0
FE2 A:SF4501 2.7 31.0 1.0
CB A:CYS247 3.2 25.8 1.0
CA A:CYS247 3.7 26.0 1.0
CD A:PRO248 3.8 29.1 1.0
S3 A:SF4501 3.9 26.1 1.0
N A:PRO248 4.4 29.9 1.0
C A:CYS247 4.4 28.2 1.0
CG A:LEU249 4.6 25.6 1.0
CD1 A:LEU249 4.7 24.5 1.0
ND2 A:ASN155 4.7 23.3 1.0
SG A:CYS194 4.8 25.0 1.0
SG A:CYS188 4.8 25.7 1.0
SG A:CYS191 4.8 28.7 1.0
N A:CYS247 4.9 24.8 1.0
N A:LEU249 4.9 27.8 1.0

Iron binding site 4 out of 16 in 5d0b

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Iron binding site 4 out of 16 in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop


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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:24.5
occ:1.00
 FE4 A:SF4501 0.0 24.5 1.0
SG A:CYS188 2.3 25.7 1.0
S1 A:SF4501 2.3 25.0 1.0
S2 A:SF4501 2.3 20.9 1.0
S3 A:SF4501 2.3 26.1 1.0
FE3 A:SF4501 2.7 21.6 1.0
FE1 A:SF4501 2.7 21.9 1.0
FE2 A:SF4501 2.7 31.0 1.0
CB A:CYS188 3.3 29.4 1.0
CA A:CYS188 3.9 30.1 1.0
S4 A:SF4501 3.9 25.6 1.0
N A:LYS154 4.3 23.8 1.0
CB A:LYS154 4.3 23.6 1.0
CB A:ALA153 4.6 25.4 1.0
CG A:LYS154 4.6 23.7 1.0
CD1 A:LEU249 4.6 24.5 1.0
SG A:CYS247 4.7 26.9 1.0
SG A:CYS191 4.7 28.7 1.0
CD A:LYS154 4.8 25.7 1.0
C A:CYS188 4.8 30.6 1.0
O A:CYS188 4.8 31.5 1.0
SG A:CYS194 4.8 25.0 1.0
N A:CYS188 4.9 31.4 1.0
CB A:CYS191 4.9 28.9 1.0
CA A:LYS154 4.9 25.1 1.0

Iron binding site 5 out of 16 in 5d0b

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Iron binding site 5 out of 16 in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop


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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:20.9
occ:1.00
 FE1 A:SF4502 0.0 20.9 1.0
S4 A:SF4502 2.3 22.6 1.0
S3 A:SF4502 2.3 20.7 1.0
S2 A:SF4502 2.3 26.5 1.0
SG A:CYS198 2.3 23.4 1.0
FE2 A:SF4502 2.7 21.6 1.0
FE4 A:SF4502 2.7 19.7 1.0
FE3 A:SF4502 2.7 24.1 1.0
CB A:CYS198 3.4 21.1 1.0
S1 A:SF4502 3.9 23.0 1.0
CA A:CYS198 4.0 19.9 1.0
CD A:PRO199 4.1 22.7 1.0
CB A:ALA202 4.2 23.8 1.0
C A:CYS198 4.6 23.4 1.0
N A:PRO199 4.7 24.8 1.0
OG1 A:THR200 4.7 26.5 1.0
SG A:CYS243 4.8 20.7 1.0
SG A:CYS214 4.8 21.2 1.0
N A:ALA202 4.8 25.5 1.0
SG A:CYS240 4.9 18.9 1.0
CG A:LEU203 4.9 21.2 1.0

Iron binding site 6 out of 16 in 5d0b

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Iron binding site 6 out of 16 in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop


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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:21.6
occ:1.00
 FE2 A:SF4502 0.0 21.6 1.0
SG A:CYS243 2.3 20.7 1.0
S4 A:SF4502 2.3 22.6 1.0
S1 A:SF4502 2.3 23.0 1.0
S3 A:SF4502 2.3 20.7 1.0
FE3 A:SF4502 2.7 24.1 1.0
FE1 A:SF4502 2.7 20.9 1.0
FE4 A:SF4502 2.7 19.7 1.0
CB A:CYS243 3.3 21.9 1.0
S2 A:SF4502 3.9 26.5 1.0
N A:CYS243 4.1 19.2 1.0
N45 A:B12503 4.1 23.1 1.0
CA A:CYS243 4.3 19.1 1.0
C42 A:B12503 4.6 20.6 1.0
SG A:CYS240 4.7 18.9 1.0
SG A:CYS198 4.8 23.4 1.0
SG A:CYS214 4.8 21.2 1.0
C43 A:B12503 4.8 22.9 1.0
CD1 A:LEU203 4.9 20.4 1.0

Iron binding site 7 out of 16 in 5d0b

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Iron binding site 7 out of 16 in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop


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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:24.1
occ:1.00
 FE3 A:SF4502 0.0 24.1 1.0
S1 A:SF4502 2.3 23.0 1.0
S2 A:SF4502 2.3 26.5 1.0
S4 A:SF4502 2.3 22.6 1.0
SG A:CYS240 2.3 18.9 1.0
FE2 A:SF4502 2.7 21.6 1.0
FE4 A:SF4502 2.7 19.7 1.0
FE1 A:SF4502 2.7 20.9 1.0
CB A:CYS240 3.2 21.0 1.0
S3 A:SF4502 3.9 20.7 1.0
CA A:CYS240 4.4 20.8 1.0
CB A:ILE215 4.4 25.2 1.0
CB A:THR242 4.4 18.0 1.0
CD A:PRO199 4.5 22.7 1.0
C A:CYS240 4.5 20.8 1.0
N A:THR242 4.6 19.3 1.0
SG A:CYS243 4.6 20.7 1.0
CG1 A:ILE215 4.6 24.7 1.0
O A:CYS240 4.6 19.9 1.0
SG A:CYS214 4.7 21.2 1.0
OG1 A:THR242 4.8 16.2 1.0
N A:ILE215 4.8 24.7 1.0
N A:CYS243 4.8 19.2 1.0
SG A:CYS198 4.8 23.4 1.0
N A:ASP241 5.0 20.5 1.0

Iron binding site 8 out of 16 in 5d0b

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Iron binding site 8 out of 16 in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop


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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:19.7
occ:1.00
 FE4 A:SF4502 0.0 19.7 1.0
S1 A:SF4502 2.3 23.0 1.0
S2 A:SF4502 2.3 26.5 1.0
SG A:CYS214 2.3 21.2 1.0
S3 A:SF4502 2.3 20.7 1.0
FE3 A:SF4502 2.7 24.1 1.0
FE1 A:SF4502 2.7 20.9 1.0
FE2 A:SF4502 2.7 21.6 1.0
CB A:CYS214 3.5 20.3 1.0
CA A:CYS214 3.8 24.4 1.0
S4 A:SF4502 3.9 22.6 1.0
N A:ILE215 4.0 24.7 1.0
C A:CYS214 4.2 25.5 1.0
N A:SER216 4.5 22.0 1.0
C42 A:B12503 4.5 20.6 1.0
CD1 A:LEU209 4.5 23.8 1.0
CB A:ALA202 4.5 23.8 1.0
CB A:SER216 4.7 23.1 1.0
SG A:CYS240 4.7 18.9 1.0
SG A:CYS198 4.7 23.4 1.0
CB A:CYS240 4.8 21.0 1.0
SG A:CYS243 4.9 20.7 1.0
CA A:ILE215 5.0 23.8 1.0
N45 A:B12503 5.0 23.1 1.0

Iron binding site 9 out of 16 in 5d0b

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Iron binding site 9 out of 16 in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop


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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:29.1
occ:1.00
 FE1 B:SF4501 0.0 29.1 1.0
SG B:CYS194 2.3 26.4 1.0
S3 B:SF4501 2.3 29.3 1.0
S2 B:SF4501 2.3 21.7 1.0
S4 B:SF4501 2.3 29.3 1.0
FE2 B:SF4501 2.7 35.7 1.0
FE3 B:SF4501 2.7 26.4 1.0
FE4 B:SF4501 2.7 26.2 1.0
CB B:CYS194 3.2 25.3 1.0
N B:CYS194 3.8 26.9 1.0
S1 B:SF4501 3.9 27.2 1.0
CB B:LYS154 4.1 24.5 1.0
CA B:CYS194 4.2 25.4 1.0
N B:ASN155 4.5 23.9 1.0
CB B:ASN155 4.7 23.4 1.0
CG B:ASN155 4.7 25.9 1.0
N B:LYS193 4.7 28.6 1.0
SG B:CYS188 4.7 27.4 1.0
SG B:CYS191 4.8 30.7 1.0
SG B:CYS247 4.8 27.4 1.0
ND2 B:ASN155 4.8 24.4 1.0
N B:LYS154 4.8 24.1 1.0
CA B:LYS154 4.8 26.0 1.0
C B:LYS154 4.9 26.6 1.0
C B:LYS193 5.0 26.8 1.0

Iron binding site 10 out of 16 in 5d0b

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Iron binding site 10 out of 16 in the Crystal Structure of Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop


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 Epoxyqueuosine Reductase with A Trna-Tyr Epoxyqueuosine-Modified Trna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:35.7
occ:1.00
 FE2 B:SF4501 0.0 35.7 1.0
S3 B:SF4501 2.3 29.3 1.0
SG B:CYS191 2.3 30.7 1.0
S1 B:SF4501 2.3 27.2 1.0
S4 B:SF4501 2.3 29.3 1.0
FE1 B:SF4501 2.7 29.1 1.0
FE3 B:SF4501 2.7 26.4 1.0
FE4 B:SF4501 2.7 26.2 1.0
CB B:CYS191 3.2 28.7 1.0
S2 B:SF4501 3.9 21.7 1.0
C B:CYS191 4.0 30.3 1.0
CD B:PRO248 4.1 30.1 1.0
N B:LYS193 4.2 28.6 1.0
CA B:CYS191 4.2 29.0 1.0
O B:CYS191 4.3 30.0 1.0
N B:THR192 4.3 30.1 1.0
CB B:LYS193 4.6 24.8 1.0
SG B:CYS194 4.7 26.4 1.0
CG B:PRO248 4.8 30.8 1.0
N B:CYS194 4.8 26.9 1.0
SG B:CYS247 4.8 27.4 1.0
SG B:CYS188 4.8 27.4 1.0
CA B:THR192 4.8 27.6 1.0
C B:THR192 4.9 28.5 1.0
CA B:LYS193 4.9 26.7 1.0
O B:CYS188 5.0 33.2 1.0

Reference:

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
Page generated: Mon Aug 5 21:40:13 2024

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