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Iron in PDB 9deu: Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Queuosine

Enzymatic activity of Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Queuosine

All present enzymatic activity of Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Queuosine:
1.17.99.6;

Protein crystallography data

The structure of Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Queuosine, PDB code: 9deu was solved by Y.Hu, S.D.Bruner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.90 / 1.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 53.647, 105.194, 73.792, 90, 90, 90
R / Rfree (%) 21.9 / 22.9

Other elements in 9deu:

The structure of Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Queuosine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Queuosine (pdb code 9deu). 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 Epoxyqueuosine Reductase Queh in Complex with Queuosine, PDB code: 9deu:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 9deu

Go back to Iron Binding Sites List in 9deu
Iron binding site 1 out of 4 in the Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Queuosine


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 Queh in Complex with Queuosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:144.2
occ:1.00
 FE1 A:SF4202 0.0 144.2 1.0
S3 A:SF4202 2.3 106.8 1.0
SG A:CYS169 2.3 100.7 1.0
S4 A:SF4202 2.3 80.7 1.0
S2 A:SF4202 2.3 74.7 1.0
FE2 A:SF4202 2.8 113.2 1.0
FE4 A:SF4202 2.8 114.5 1.0
FE3 A:SF4202 2.8 95.3 1.0
CB A:CYS169 3.2 83.0 1.0
S1 A:SF4202 3.9 84.6 1.0
CA A:CYS169 4.4 74.5 1.0
C A:CYS169 4.6 71.0 1.0
SG A:CYS87 4.8 69.3 1.0
O A:CYS169 4.8 67.0 1.0
SG A:CYS171 4.8 83.2 1.0
ND2 A:ASN32 4.9 39.3 1.0
SG A:CYS90 4.9 39.6 1.0
CE A:LYS120 4.9 61.8 1.0

Iron binding site 2 out of 4 in 9deu

Go back to Iron Binding Sites List in 9deu
Iron binding site 2 out of 4 in the Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Queuosine


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 Queh in Complex with Queuosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:113.2
occ:1.00
 FE2 A:SF4202 0.0 113.2 1.0
S4 A:SF4202 2.3 80.7 1.0
S3 A:SF4202 2.3 106.8 1.0
S1 A:SF4202 2.3 84.6 1.0
SG A:CYS87 2.3 69.3 1.0
FE1 A:SF4202 2.8 144.2 1.0
FE3 A:SF4202 2.8 95.3 1.0
FE4 A:SF4202 2.8 114.5 1.0
CB A:CYS87 3.1 57.3 1.0
CA A:CYS87 3.5 51.1 1.0
S2 A:SF4202 3.9 74.7 1.0
N A:CYS87 4.1 50.3 1.0
NH2 A:ARG86 4.1 80.3 1.0
NE A:ARG86 4.3 72.2 1.0
CB A:CYS90 4.6 41.6 1.0
CZ A:ARG86 4.7 78.1 1.0
SG A:CYS169 4.7 100.7 1.0
C A:CYS87 4.8 44.0 1.0
C A:ARG86 4.8 50.1 1.0
O A:ARG86 4.9 46.1 1.0
SG A:CYS90 4.9 39.6 1.0
SG A:CYS171 5.0 83.2 1.0

Iron binding site 3 out of 4 in 9deu

Go back to Iron Binding Sites List in 9deu
Iron binding site 3 out of 4 in the Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Queuosine


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 Queh in Complex with Queuosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:95.3
occ:1.00
 FE3 A:SF4202 0.0 95.3 1.0
S1 A:SF4202 2.3 84.6 1.0
S4 A:SF4202 2.3 80.7 1.0
S2 A:SF4202 2.3 74.7 1.0
SG A:CYS90 2.4 39.6 1.0
FE4 A:SF4202 2.8 114.5 1.0
FE1 A:SF4202 2.8 144.2 1.0
FE2 A:SF4202 2.8 113.2 1.0
CB A:CYS90 2.9 41.6 1.0
S3 A:SF4202 3.9 106.8 1.0
ND2 A:ASN32 4.3 39.3 1.0
CA A:CYS90 4.4 36.9 1.0
CA A:CYS87 4.6 51.1 1.0
SG A:CYS171 4.8 83.2 1.0
CB A:ASN32 4.8 31.7 1.0
SG A:CYS87 4.8 69.3 1.0
CZ2 A:TRP70 4.9 43.1 1.0
CB A:CYS87 4.9 57.3 1.0
SG A:CYS169 4.9 100.7 1.0
C A:CYS90 5.0 34.6 1.0
CG A:ASN32 5.0 32.2 1.0
CB A:CYS171 5.0 64.7 1.0
O A:ARG86 5.0 46.1 1.0

Iron binding site 4 out of 4 in 9deu

Go back to Iron Binding Sites List in 9deu
Iron binding site 4 out of 4 in the Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Queuosine


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 Queh in Complex with Queuosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:114.5
occ:1.00
 FE4 A:SF4202 0.0 114.5 1.0
S2 A:SF4202 2.3 74.7 1.0
S1 A:SF4202 2.3 84.6 1.0
S3 A:SF4202 2.3 106.8 1.0
SG A:CYS171 2.3 83.2 1.0
FE1 A:SF4202 2.8 144.2 1.0
FE3 A:SF4202 2.8 95.3 1.0
FE2 A:SF4202 2.8 113.2 1.0
CB A:CYS171 3.3 64.7 1.0
S4 A:SF4202 3.9 80.7 1.0
NH2 A:ARG86 4.0 80.3 1.0
NE A:ARG86 4.2 72.2 1.0
N A:CYS171 4.4 62.3 1.0
CA A:CYS171 4.4 63.4 1.0
CZ A:ARG86 4.6 78.1 1.0
CB A:CYS169 4.7 83.0 1.0
SG A:CYS169 4.7 100.7 1.0
SG A:CYS90 4.8 39.6 1.0
SG A:CYS87 4.9 69.3 1.0

Reference:

Y.Hu, M.Jaroch, G.Sun, P.C.Dedon, V.De Crecy-Lagard, S.D.Bruner. Mechanism of Catalysis and Substrate Binding of Epoxyqueuosine Reductase in the Biosynthetic Pathway to Queuosine-Modified Trna. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 39644232
DOI: 10.1021/ACS.BIOCHEM.4C00524
Page generated: Sat Feb 8 18:53:35 2025

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