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Iron in PDB 7lc7: Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Gmp From Thermotoga Maritima

Enzymatic activity of Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Gmp From Thermotoga Maritima

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

Protein crystallography data

The structure of Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Gmp From Thermotoga Maritima, PDB code: 7lc7 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) 47.53 / 1.58
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 53.335, 104.783, 73.741, 90, 90, 90
R / Rfree (%) 20 / 24.3

Other elements in 7lc7:

The structure of Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Gmp 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 in Complex with Gmp From Thermotoga Maritima (pdb code 7lc7). 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 in Complex with Gmp From Thermotoga Maritima, PDB code: 7lc7:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 7lc7

Go back to Iron Binding Sites List in 7lc7
Iron binding site 1 out of 5 in the Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Gmp 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 in Complex with Gmp From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:29.9
occ:1.00
 FE1 A:SF4301 0.0 29.9 1.0
S2 A:SF4301 2.3 25.8 1.0
S4 A:SF4301 2.3 27.7 1.0
S3 A:SF4301 2.3 33.4 1.0
SG A:CYS169 2.5 34.3 1.0
FE3 A:SF4301 2.6 27.1 1.0
FE2 A:SF4301 2.7 30.7 1.0
FE4 A:SF4301 2.7 31.9 1.0
CB A:CYS169 3.2 30.9 1.0
S1 A:SF4301 3.8 29.7 1.0
O A:HOH481 4.1 37.6 1.0
CA A:CYS169 4.5 30.5 1.0
C A:CYS169 4.5 29.8 1.0
OE1 A:GLU82 4.6 51.7 1.0
N A:GLY170 4.7 27.2 1.0
CE A:LYS120 4.8 39.6 1.0
SG A:CYS171 4.8 34.1 1.0
SG A:CYS87 4.9 33.2 1.0
SG A:CYS90 4.9 23.8 1.0
O A:CYS169 4.9 26.4 1.0
ND2 A:ASN32 4.9 25.2 1.0

Iron binding site 2 out of 5 in 7lc7

Go back to Iron Binding Sites List in 7lc7
Iron binding site 2 out of 5 in the Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Gmp 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 in Complex with Gmp From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:30.7
occ:1.00
 FE2 A:SF4301 0.0 30.7 1.0
S1 A:SF4301 2.3 29.7 1.0
S3 A:SF4301 2.3 33.4 1.0
S4 A:SF4301 2.3 27.7 1.0
SG A:CYS87 2.5 33.2 1.0
FE3 A:SF4301 2.7 27.1 1.0
FE1 A:SF4301 2.7 29.9 1.0
FE4 A:SF4301 2.7 31.9 1.0
CB A:CYS87 3.3 32.9 1.0
CA A:CYS87 3.6 30.2 1.0
S2 A:SF4301 3.9 25.8 1.0
NH2 A:ARG86 4.0 46.1 1.0
NE A:ARG86 4.0 42.2 1.0
N A:CYS87 4.2 29.7 1.0
CZ A:ARG86 4.5 44.9 1.0
CB A:CYS90 4.7 25.2 1.0
SG A:CYS90 4.8 23.8 1.0
C A:ARG86 4.8 30.3 1.0
SG A:CYS169 4.9 34.3 1.0
C A:CYS87 4.9 29.6 1.0
O A:ARG86 4.9 30.8 1.0
SG A:CYS171 5.0 34.1 1.0

Iron binding site 3 out of 5 in 7lc7

Go back to Iron Binding Sites List in 7lc7
Iron binding site 3 out of 5 in the Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Gmp 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 in Complex with Gmp From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:27.1
occ:1.00
 FE3 A:SF4301 0.0 27.1 1.0
S2 A:SF4301 2.3 25.8 1.0
S1 A:SF4301 2.3 29.7 1.0
S4 A:SF4301 2.3 27.7 1.0
SG A:CYS90 2.4 23.8 1.0
FE1 A:SF4301 2.6 29.9 1.0
FE4 A:SF4301 2.7 31.9 1.0
FE2 A:SF4301 2.7 30.7 1.0
CB A:CYS90 3.1 25.2 1.0
S3 A:SF4301 3.8 33.4 1.0
O A:HOH481 4.0 37.6 1.0
ND2 A:ASN32 4.3 25.2 1.0
CA A:CYS90 4.6 22.0 1.0
CZ2 A:TRP70 4.6 30.7 1.0
CB A:ASN32 4.7 24.3 1.0
CA A:CYS87 4.7 30.2 1.0
SG A:CYS171 4.8 34.1 1.0
NE1 A:TRP70 4.8 25.6 1.0
CG A:ASN32 4.9 22.8 1.0
SG A:CYS87 4.9 33.2 1.0
CB A:CYS171 5.0 30.9 1.0
SG A:CYS169 5.0 34.3 1.0

Iron binding site 4 out of 5 in 7lc7

Go back to Iron Binding Sites List in 7lc7
Iron binding site 4 out of 5 in the Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Gmp 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 in Complex with Gmp From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:31.9
occ:1.00
 FE4 A:SF4301 0.0 31.9 1.0
S1 A:SF4301 2.3 29.7 1.0
S3 A:SF4301 2.3 33.4 1.0
S2 A:SF4301 2.3 25.8 1.0
SG A:CYS171 2.4 34.1 1.0
FE3 A:SF4301 2.7 27.1 1.0
FE1 A:SF4301 2.7 29.9 1.0
FE2 A:SF4301 2.7 30.7 1.0
CB A:CYS171 3.3 30.9 1.0
S4 A:SF4301 3.9 27.7 1.0
NH2 A:ARG86 4.1 46.1 1.0
NE A:ARG86 4.2 42.2 1.0
N A:CYS171 4.2 27.5 1.0
CA A:CYS171 4.4 30.0 1.0
CB A:SER174 4.5 35.0 1.0
CZ A:ARG86 4.5 44.9 1.0
OG A:SER174 4.5 33.8 1.0
CZ2 A:TRP70 4.7 30.7 1.0
CB A:CYS169 4.8 30.9 1.0
SG A:CYS90 4.8 23.8 1.0
SG A:CYS169 4.9 34.3 1.0
N A:SER174 4.9 37.1 1.0
CD2 A:PHE173 5.0 39.8 1.0

Iron binding site 5 out of 5 in 7lc7

Go back to Iron Binding Sites List in 7lc7
Iron binding site 5 out of 5 in the Crystal Structure of Epoxyqueuosine Reductase Queh in Complex with Gmp 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 in Complex with Gmp From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:15.4
occ:1.00
 OD2 A:ASP13 1.9 18.6 1.0
CL A:CL304 2.2 28.2 1.0
SG A:CYS9 2.3 16.6 1.0
SG A:CYS10 2.3 16.6 1.0
CG A:ASP13 2.9 20.8 1.0
CB A:CYS9 3.2 15.8 1.0
CB A:CYS10 3.4 16.2 1.0
CB A:ASP13 3.4 15.1 1.0
N A:CYS10 3.5 15.2 1.0
C A:CYS9 3.9 17.0 1.0
CA A:CYS10 4.0 13.6 1.0
OD1 A:ASP13 4.0 19.6 1.0
C8 A:5GP302 4.1 29.1 0.5
CA A:CYS9 4.1 15.1 1.0
NE2 A:GLN166 4.2 27.2 1.0
N7 A:5GP302 4.3 28.7 0.5
N9 A:5GP302 4.4 32.5 0.5
O A:CYS10 4.5 15.5 1.0
O A:CYS9 4.6 16.7 1.0
N A:ASP13 4.6 15.3 1.0
C A:CYS10 4.6 16.2 1.0
CA A:ASP13 4.6 13.7 1.0
C5 A:5GP302 4.7 28.4 0.5
O A:HOH422 4.7 24.8 1.0
O A:HOH470 4.7 34.2 1.0
C4 A:5GP302 4.7 31.2 0.5
N A:CYS9 4.8 13.5 1.0
CD2 A:LEU114 4.8 19.5 1.0
CB A:SER117 4.8 28.3 1.0
C1' A:5GP302 4.9 33.5 0.5
OG1 A:THR113 4.9 14.3 1.0

Reference:

Q.Li, S.D.Bruner. The Epoxyqueuosine Reductase Queh in the Biosynthesis of Trna Queuosine Is A Unique Metalloenzyme To Be Published.
Page generated: Thu Aug 8 06:57:16 2024

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