Iron in PDB 8cnr: Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution

Enzymatic activity of Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution

All present enzymatic activity of Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution:
1.7.99.1;

Protein crystallography data

The structure of Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution, PDB code: 8cnr was solved by O.N.Lemaire, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.06 / 1.45
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.557, 102.454, 58.896, 90, 90, 90
R / Rfree (%) 13.3 / 15.2

Other elements in 8cnr:

The structure of Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution (pdb code 8cnr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution, PDB code: 8cnr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8cnr

Go back to Iron Binding Sites List in 8cnr
Iron binding site 1 out of 8 in the Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe606

b:8.6
occ:1.00
 FE1 A:SF4606 0.0 8.6 1.0
S3 A:SF4606 2.3 8.4 1.0
SG A:CYS8 2.3 8.2 1.0
S4 A:SF4606 2.3 8.3 1.0
S2 A:SF4606 2.3 8.5 1.0
FE3 A:SF4606 2.7 8.5 1.0
FE2 A:SF4606 2.7 9.0 1.0
FE4 A:SF4606 2.8 8.7 1.0
CB A:CYS8 3.2 7.4 1.0
NZ A:LYS28 3.9 9.2 1.0
S1 A:SF4606 4.0 8.7 1.0
C A:CYS8 4.0 8.4 1.0
CG A:GLN10 4.1 7.7 1.0
O A:CYS8 4.1 9.2 1.0
CE A:LYS28 4.2 10.8 1.0
CA A:CYS8 4.2 7.3 1.0
N A:GLN10 4.3 7.8 1.0
N A:TYR9 4.4 7.3 1.0
NE2 A:GLN10 4.8 9.5 1.0
SG A:CYS20 4.8 9.1 1.0
N A:CYS11 4.8 8.5 1.0
SG A:CYS11 4.9 8.4 1.0
CA A:TYR9 4.9 8.7 1.0
SG A:CYS26 4.9 8.5 1.0
CD A:GLN10 5.0 13.1 1.0

Iron binding site 2 out of 8 in 8cnr

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Iron binding site 2 out of 8 in the Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe606

b:9.0
occ:1.00
 FE2 A:SF4606 0.0 9.0 1.0
S4 A:SF4606 2.2 8.3 1.0
SG A:CYS11 2.3 8.4 1.0
S1 A:SF4606 2.3 8.7 1.0
S3 A:SF4606 2.4 8.4 1.0
FE4 A:SF4606 2.7 8.7 1.0
FE3 A:SF4606 2.7 8.5 1.0
FE1 A:SF4606 2.7 8.6 1.0
CB A:CYS11 3.3 6.7 1.0
N A:CYS11 3.8 8.5 1.0
S2 A:SF4606 3.9 8.5 1.0
CA A:CYS11 4.0 8.1 1.0
OG1 A:THR73 4.4 7.7 1.0
CG2 A:THR73 4.5 8.4 1.0
C A:CYS11 4.5 7.9 1.0
N A:THR14 4.5 9.1 1.0
O A:CYS11 4.6 8.1 1.0
CA A:THR14 4.6 10.3 1.0
SG A:CYS26 4.7 8.5 1.0
O A:HOH841 4.7 10.3 1.0
CB A:THR14 4.8 10.6 1.0
SG A:CYS8 4.9 8.2 1.0
SG A:CYS20 4.9 9.1 1.0
CG A:GLN10 4.9 7.7 1.0
C A:GLN10 4.9 6.9 1.0
C A:GLU13 4.9 8.2 1.0
N A:GLN10 4.9 7.8 1.0
CB A:CYS26 5.0 7.8 1.0

Iron binding site 3 out of 8 in 8cnr

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Iron binding site 3 out of 8 in the Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe606

b:8.5
occ:1.00
 FE3 A:SF4606 0.0 8.5 1.0
S1 A:SF4606 2.3 8.7 1.0
S2 A:SF4606 2.3 8.5 1.0
S4 A:SF4606 2.3 8.3 1.0
SG A:CYS20 2.4 9.1 1.0
FE2 A:SF4606 2.7 9.0 1.0
FE4 A:SF4606 2.7 8.7 1.0
FE1 A:SF4606 2.7 8.6 1.0
CB A:CYS20 3.3 9.5 1.0
S3 A:SF4606 3.9 8.4 1.0
N A:VAL25 4.0 9.5 1.0
OG1 A:THR14 4.1 9.1 1.0
CA A:GLY24 4.1 9.4 1.0
O A:CYS8 4.1 9.2 1.0
CA A:THR14 4.1 10.3 1.0
CB A:THR14 4.4 10.6 1.0
CA A:CYS20 4.6 8.7 1.0
C A:GLY24 4.6 10.6 1.0
SG A:CYS11 4.6 8.4 1.0
SG A:CYS8 4.7 8.2 1.0
N A:CYS20 4.7 9.7 1.0
CB A:CYS8 4.7 7.4 1.0
C A:CYS8 4.7 8.4 1.0
SG A:CYS26 4.7 8.5 1.0
N A:THR14 4.8 9.1 1.0
CB A:VAL25 4.8 9.6 1.0
N A:ALA15 4.9 8.4 1.0
N A:CYS26 4.9 8.9 1.0

Iron binding site 4 out of 8 in 8cnr

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Iron binding site 4 out of 8 in the Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe606

b:8.7
occ:1.00
 FE4 A:SF4606 0.0 8.7 1.0
S2 A:SF4606 2.2 8.5 1.0
SG A:CYS26 2.3 8.5 1.0
S1 A:SF4606 2.3 8.7 1.0
S3 A:SF4606 2.4 8.4 1.0
FE2 A:SF4606 2.7 9.0 1.0
FE3 A:SF4606 2.7 8.5 1.0
FE1 A:SF4606 2.8 8.6 1.0
CB A:CYS26 3.4 7.8 1.0
S4 A:SF4606 3.9 8.3 1.0
N A:CYS26 3.9 8.9 1.0
CA A:GLY24 4.2 9.4 1.0
O A:HOH1107 4.2 11.2 1.0
CA A:CYS26 4.3 7.7 1.0
CE A:LYS28 4.3 10.8 1.0
N A:VAL25 4.5 9.5 1.0
CB A:LYS28 4.5 10.9 1.0
SG A:CYS11 4.6 8.4 1.0
C A:GLY24 4.6 10.6 1.0
SG A:CYS20 4.8 9.1 1.0
NZ A:LYS28 4.8 9.2 1.0
SG A:CYS8 4.8 8.2 1.0
CG2 A:THR73 4.9 8.4 1.0
O A:HOH841 5.0 10.3 1.0

Iron binding site 5 out of 8 in 8cnr

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Iron binding site 5 out of 8 in the Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe614

b:8.9
occ:1.00
 FE1 A:SF3614 0.0 8.9 1.0
S1 A:SF3614 2.3 10.8 1.0
S3 A:SF3614 2.3 9.7 1.0
S2 A:SF3614 2.3 9.2 1.0
SG A:CYS430 2.3 8.6 1.0
FE3 A:SF3614 2.7 11.0 1.0
FE4 A:SF3614 2.8 10.2 1.0
CB A:CYS430 3.5 6.8 1.0
FE7 A:SF3614 3.9 9.3 1.0
CG A:GLU267 4.0 8.4 1.0
CD1 A:TRP291 4.0 9.3 1.0
O A:HOH724 4.1 19.9 1.0
N A:CYS430 4.2 7.1 1.0
OE2 A:GLU490 4.3 12.9 1.0
CA A:CYS430 4.5 8.2 1.0
NE1 A:TRP291 4.5 9.3 1.0
CA A:CYS402 4.6 7.2 1.0
SG A:CYS402 4.6 10.0 1.0
CB A:CYS402 4.6 8.8 1.0
CD A:GLU267 4.7 8.2 1.0
OE2 A:GLU267 4.8 8.9 1.0
N A:ASP403 4.8 8.1 1.0
SG A:CYS311 5.0 9.2 1.0

Iron binding site 6 out of 8 in 8cnr

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Iron binding site 6 out of 8 in the Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe614

b:11.0
occ:1.00
 FE3 A:SF3614 0.0 11.0 1.0
S1 A:SF3614 2.2 10.8 1.0
SG A:CYS311 2.3 9.2 1.0
S3 A:SF3614 2.3 9.7 1.0
FE1 A:SF3614 2.7 8.9 1.0
CB A:CYS311 3.2 9.2 1.0
CD1 A:TRP291 3.4 9.3 1.0
ND2 A:ASN310 3.6 21.7 1.0
NE1 A:TRP291 3.8 9.3 1.0
FE4 A:SF3614 3.8 10.2 1.0
N A:CYS311 3.8 7.4 1.0
CG A:TRP291 3.9 9.9 1.0
CA A:CYS311 4.1 8.3 1.0
CG A:GLU490 4.2 9.4 1.0
OE2 A:GLU490 4.2 12.9 1.0
CE2 A:TRP291 4.4 7.8 1.0
SG A:CYS430 4.4 8.6 1.0
CB A:TRP291 4.4 10.6 1.0
CD2 A:TRP291 4.5 7.1 1.0
O A:HOH724 4.5 19.9 1.0
C A:ASN310 4.5 8.4 1.0
S2 A:SF3614 4.5 9.2 1.0
CD A:GLU490 4.6 13.8 1.0
CG A:ASN310 4.6 16.4 1.0
CD2 A:TYR489 4.7 8.2 1.0
CB A:ASN310 4.8 9.6 1.0
O A:ASN310 4.9 9.1 1.0

Iron binding site 7 out of 8 in 8cnr

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Iron binding site 7 out of 8 in the Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe614

b:10.2
occ:1.00
 FE4 A:SF3614 0.0 10.2 1.0
OE2 A:GLU490 2.1 12.9 1.0
S3 A:SF3614 2.3 9.7 1.0
S2 A:SF3614 2.3 9.2 1.0
SG A:CYS402 2.4 10.0 1.0
FE1 A:SF3614 2.8 8.9 1.0
CD A:GLU490 3.1 13.8 1.0
O A:HOH724 3.3 19.9 1.0
CB A:CYS402 3.4 8.8 1.0
CG A:GLU490 3.4 9.4 1.0
FE3 A:SF3614 3.8 11.0 1.0
CA A:CYS402 3.9 7.2 1.0
FE7 A:SF3614 4.0 9.3 1.0
OE1 A:GLU490 4.2 11.0 1.0
S1 A:SF3614 4.4 10.8 1.0
SG A:CYS430 4.5 8.6 1.0
N A:CYS402 4.7 8.9 1.0
N A:GLU490 4.7 8.5 1.0
CB A:GLU490 4.9 9.9 1.0
ND2 A:ASN310 4.9 21.7 1.0
O A:GLY401 5.0 8.2 1.0

Iron binding site 8 out of 8 in 8cnr

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Iron binding site 8 out of 8 in the Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Hybrid Cluster Protein From the Thermophilic Methanogen Methanothermococcus Thermolithotrophicus As Isolated in A Reduced State at 1.45-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe614

b:9.3
occ:1.00
 FE7 A:SF3614 0.0 9.3 1.0
OE2 A:GLU267 2.2 8.9 1.0
NE2 A:HIS243 2.2 9.0 1.0
S2 A:SF3614 2.3 9.2 1.0
SG A:CYS455 2.4 9.2 1.0
O A:HOH724 2.4 19.9 1.0
CD A:GLU267 3.1 8.2 1.0
CE1 A:HIS243 3.2 8.2 1.0
CD2 A:HIS243 3.2 8.5 1.0
CB A:CYS455 3.3 7.0 1.0
CG A:GLU267 3.3 8.4 1.0
N A:CYS455 3.9 7.8 1.0
FE1 A:SF3614 3.9 8.9 1.0
FE4 A:SF3614 4.0 10.2 1.0
CB A:GLU267 4.2 7.6 1.0
CA A:CYS455 4.2 7.9 1.0
OE1 A:GLU267 4.2 9.9 1.0
ND1 A:HIS243 4.3 8.3 1.0
OE2 A:GLU490 4.3 12.9 1.0
CG A:HIS243 4.3 7.6 1.0
S1 A:SF3614 4.4 10.8 1.0
NZ A:LYS492 4.5 11.9 1.0
CA A:GLY429 4.8 7.3 1.0

Reference:

O.N.Lemaire, M.Belhamri, T.Wagner. Structural and Biochemical Elucidation of Class I Hybrid Cluster Protein Natively Extracted From A Marine Methanogenic Archaeon To Be Published.
Page generated: Tue Apr 25 20:46:17 2023

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