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Iron in PDB 7lc5: Crystal Structure of Epoxyqueuosine Reductase Queh From Thermotoga Maritima

Enzymatic activity of Crystal Structure of Epoxyqueuosine Reductase Queh From Thermotoga Maritima

All present enzymatic activity of Crystal Structure of Epoxyqueuosine Reductase Queh From Thermotoga Maritima:
1.17.99.6;

Protein crystallography data

The structure of Crystal Structure of Epoxyqueuosine Reductase Queh From Thermotoga Maritima, PDB code: 7lc5 was solved by Q.Li, S.D.Bruner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.49 / 1.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 53.224, 105.181, 73.899, 90, 90, 90
R / Rfree (%) 19.6 / 21.1

Other elements in 7lc5:

The structure of Crystal Structure of Epoxyqueuosine Reductase Queh From Thermotoga Maritima also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Epoxyqueuosine Reductase Queh From Thermotoga Maritima (pdb code 7lc5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of Epoxyqueuosine Reductase Queh From Thermotoga Maritima, PDB code: 7lc5:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 7lc5

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Iron binding site 1 out of 5 in the Crystal Structure of Epoxyqueuosine Reductase Queh From Thermotoga Maritima


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 From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:28.5
occ:1.00
 FE1 A:SF4501 0.0 28.5 1.0
S2 A:SF4501 2.3 24.8 1.0
S4 A:SF4501 2.3 25.4 1.0
S3 A:SF4501 2.3 33.6 1.0
SG A:CYS169 2.5 32.1 1.0
FE2 A:SF4501 2.7 29.4 1.0
FE3 A:SF4501 2.7 25.3 1.0
FE4 A:SF4501 2.7 29.4 1.0
CB A:CYS169 3.3 28.8 1.0
S1 A:SF4501 3.8 28.5 1.0
O A:HOH687 4.3 32.0 1.0
CA A:CYS169 4.5 27.8 1.0
C A:CYS169 4.5 26.0 1.0
N A:GLY170 4.7 26.5 1.0
SG A:CYS87 4.8 30.1 1.0
CE A:LYS120 4.8 40.6 1.0
SG A:CYS90 4.9 22.9 1.0
SG A:CYS171 4.9 32.0 1.0
O A:CYS169 4.9 24.8 1.0
OE1 A:GLU82 4.9 53.0 1.0
ND2 A:ASN32 4.9 23.9 1.0

Iron binding site 2 out of 5 in 7lc5

Go back to Iron Binding Sites List in 7lc5
Iron binding site 2 out of 5 in the Crystal Structure of Epoxyqueuosine Reductase Queh From Thermotoga Maritima


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 From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:29.4
occ:1.00
 FE2 A:SF4501 0.0 29.4 1.0
S3 A:SF4501 2.3 33.6 1.0
S4 A:SF4501 2.3 25.4 1.0
S1 A:SF4501 2.3 28.5 1.0
SG A:CYS87 2.4 30.1 1.0
FE1 A:SF4501 2.7 28.5 1.0
FE3 A:SF4501 2.7 25.3 1.0
FE4 A:SF4501 2.7 29.4 1.0
CB A:CYS87 3.3 28.7 1.0
CA A:CYS87 3.6 26.9 1.0
S2 A:SF4501 3.9 24.8 1.0
NH2 A:ARG86 4.0 43.1 1.0
NE A:ARG86 4.1 38.1 1.0
N A:CYS87 4.2 28.9 1.0
CZ A:ARG86 4.6 41.5 1.0
CG A:GLU82 4.6 50.5 1.0
CB A:CYS90 4.7 23.3 1.0
SG A:CYS90 4.8 22.9 1.0
SG A:CYS169 4.8 32.1 1.0
C A:ARG86 4.9 29.3 1.0
C A:CYS87 4.9 28.3 1.0

Iron binding site 3 out of 5 in 7lc5

Go back to Iron Binding Sites List in 7lc5
Iron binding site 3 out of 5 in the Crystal Structure of Epoxyqueuosine Reductase Queh From Thermotoga Maritima


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 From Thermotoga Maritima 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
S2 A:SF4501 2.3 24.8 1.0
S1 A:SF4501 2.3 28.5 1.0
S4 A:SF4501 2.3 25.4 1.0
SG A:CYS90 2.4 22.9 1.0
FE1 A:SF4501 2.7 28.5 1.0
FE4 A:SF4501 2.7 29.4 1.0
FE2 A:SF4501 2.7 29.4 1.0
CB A:CYS90 3.1 23.3 1.0
S3 A:SF4501 3.8 33.6 1.0
O A:HOH687 4.0 32.0 1.0
ND2 A:ASN32 4.3 23.9 1.0
CZ2 A:TRP70 4.6 28.1 1.0
CA A:CYS90 4.6 21.7 1.0
CB A:ASN32 4.6 24.2 1.0
CA A:CYS87 4.7 26.9 1.0
NE1 A:TRP70 4.8 24.7 1.0
SG A:CYS171 4.8 32.0 1.0
SG A:CYS87 4.9 30.1 1.0
CG A:ASN32 4.9 21.8 1.0
CB A:CYS87 5.0 28.7 1.0
CB A:CYS171 5.0 28.9 1.0
SG A:CYS169 5.0 32.1 1.0

Iron binding site 4 out of 5 in 7lc5

Go back to Iron Binding Sites List in 7lc5
Iron binding site 4 out of 5 in the Crystal Structure of Epoxyqueuosine Reductase Queh From Thermotoga Maritima


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 From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:29.4
occ:1.00
 FE4 A:SF4501 0.0 29.4 1.0
S1 A:SF4501 2.2 28.5 1.0
S3 A:SF4501 2.3 33.6 1.0
S2 A:SF4501 2.3 24.8 1.0
SG A:CYS171 2.4 32.0 1.0
FE3 A:SF4501 2.7 25.3 1.0
FE1 A:SF4501 2.7 28.5 1.0
FE2 A:SF4501 2.7 29.4 1.0
CB A:CYS171 3.3 28.9 1.0
S4 A:SF4501 3.9 25.4 1.0
NH2 A:ARG86 4.1 43.1 1.0
N A:CYS171 4.2 25.5 1.0
NE A:ARG86 4.2 38.1 1.0
CA A:CYS171 4.3 28.1 1.0
CB A:SER174 4.4 33.5 1.0
CZ A:ARG86 4.5 41.5 1.0
OG A:SER174 4.6 29.5 1.0
CZ2 A:TRP70 4.7 28.1 1.0
SG A:CYS90 4.8 22.9 1.0
CB A:CYS169 4.8 28.8 1.0
SG A:CYS169 4.9 32.1 1.0
N A:SER174 4.9 33.7 1.0
SG A:CYS87 5.0 30.1 1.0

Iron binding site 5 out of 5 in 7lc5

Go back to Iron Binding Sites List in 7lc5
Iron binding site 5 out of 5 in the Crystal Structure of Epoxyqueuosine Reductase Queh From Thermotoga Maritima


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 Queh From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:15.6
occ:1.00
 OD2 A:ASP13 2.0 19.1 1.0
CL A:CL503 2.2 26.3 1.0
SG A:CYS9 2.3 16.4 1.0
SG A:CYS10 2.4 16.9 1.0
CG A:ASP13 2.9 18.2 1.0
CB A:CYS9 3.3 18.4 1.0
CB A:CYS10 3.4 15.9 1.0
CB A:ASP13 3.4 17.1 1.0
N A:CYS10 3.6 15.1 1.0
C A:CYS9 3.9 15.9 1.0
O A:HOH611 3.9 37.9 1.0
CA A:CYS10 4.0 14.9 1.0
OD1 A:ASP13 4.0 20.4 1.0
CA A:CYS9 4.2 15.7 1.0
NE2 A:GLN166 4.2 25.8 1.0
O A:CYS10 4.5 15.7 1.0
O A:CYS9 4.6 17.8 1.0
N A:ASP13 4.6 16.7 1.0
C A:CYS10 4.6 15.2 1.0
CA A:ASP13 4.6 14.9 1.0
O A:HOH676 4.7 29.0 1.0
O A:HOH626 4.7 24.4 1.0
O A:HOH646 4.8 36.9 1.0
CB A:SER117 4.8 25.5 1.0
N A:CYS9 4.8 15.4 1.0
CD2 A:LEU114 4.9 21.5 1.0
OG1 A:THR113 5.0 14.3 1.0

Reference:

Q.Li, R.Zallot, B.S.Mactavish, A.Montoya, D.J.Payan, Y.Hu, J.A.Gerlt, A.Angerhofer, V.De Crecy-Lagard, S.D.Bruner. Epoxyqueuosine Reductase Queh in the Biosynthetic Pathway to Trna Queuosine Is A Unique Metalloenzyme. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 34652139
DOI: 10.1021/ACS.BIOCHEM.1C00164
Page generated: Thu Aug 8 06:57:15 2024

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