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Iron in PDB 8a8o: Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A

Protein crystallography data

The structure of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A, PDB code: 8a8o was solved by M.Jespersen, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.04 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.714, 123.65, 88.842, 90, 104.44, 90
R / Rfree (%) 15.1 / 17.8

Other elements in 8a8o:

The structure of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A also contains other interesting chemical elements:

Sodium (Na) 3 atoms
Calcium (Ca) 2 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A (pdb code 8a8o). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A, PDB code: 8a8o:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 8a8o

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Iron binding site 1 out of 16 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:18.4
occ:1.00
 FE1 C:SF4201 0.0 18.4 1.0
S2 C:SF4201 2.3 17.0 1.0
SG C:CYS44 2.3 19.4 1.0
S4 C:SF4201 2.3 17.7 1.0
S3 C:SF4201 2.4 17.0 1.0
FE2 C:SF4201 2.7 17.4 1.0
FE4 C:SF4201 2.7 17.3 1.0
FE3 C:SF4201 2.8 17.7 1.0
CB C:CYS44 3.4 19.3 1.0
N C:CYS44 3.5 17.9 1.0
N C:ALA45 3.8 20.6 1.0
CA C:CYS44 3.8 18.7 1.0
S1 C:SF4201 3.9 16.8 1.0
C C:CYS44 4.1 18.3 1.0
N C:ALA46 4.1 20.4 1.0
CD C:PRO21 4.3 19.1 1.0
C C:ASP43 4.5 17.7 1.0
N C:ASP43 4.6 16.0 1.0
SG C:CYS41 4.6 17.0 1.0
SG C:CYS20 4.6 18.1 1.0
CG C:PRO21 4.7 19.5 1.0
CA C:ALA45 4.7 21.6 1.0
SG C:CYS47 4.7 19.2 1.0
CB C:ALA46 4.7 21.0 1.0
CA C:ASP43 4.8 16.1 1.0
C C:ALA45 4.9 22.2 1.0
N C:CYS47 4.9 21.5 1.0
CA C:ALA46 5.0 20.0 1.0

Iron binding site 2 out of 16 in 8a8o

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Iron binding site 2 out of 16 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:17.4
occ:1.00
 FE2 C:SF4201 0.0 17.4 1.0
S4 C:SF4201 2.3 17.7 1.0
S1 C:SF4201 2.3 16.8 1.0
SG C:CYS20 2.3 18.1 1.0
S3 C:SF4201 2.3 17.0 1.0
FE4 C:SF4201 2.7 17.3 1.0
FE1 C:SF4201 2.7 18.4 1.0
FE3 C:SF4201 2.7 17.7 1.0
CB C:CYS20 3.3 19.3 1.0
S2 C:SF4201 3.9 17.0 1.0
CA C:CYS20 4.0 19.5 1.0
CD C:PRO21 4.2 19.1 1.0
CD1 C:LEU24 4.3 16.3 1.0
SG C:CYS44 4.6 19.4 1.0
CB C:LEU24 4.6 16.7 1.0
CG C:LEU24 4.6 16.9 1.0
C C:CYS20 4.7 18.0 1.0
N C:PRO21 4.7 18.1 1.0
SG C:CYS47 4.8 19.2 1.0
SG C:CYS41 4.9 17.0 1.0
CG C:PRO21 5.0 19.5 1.0
CD1 C:LEU25 5.0 22.9 1.0

Iron binding site 3 out of 16 in 8a8o

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Iron binding site 3 out of 16 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:17.7
occ:1.00
 FE3 C:SF4201 0.0 17.7 1.0
S4 C:SF4201 2.2 17.7 1.0
SG C:CYS47 2.2 19.2 1.0
S1 C:SF4201 2.3 16.8 1.0
S2 C:SF4201 2.3 17.0 1.0
FE2 C:SF4201 2.7 17.4 1.0
FE4 C:SF4201 2.7 17.3 1.0
FE1 C:SF4201 2.8 18.4 1.0
CB C:CYS47 3.3 19.3 1.0
N C:CYS47 3.8 21.5 1.0
S3 C:SF4201 3.9 17.0 1.0
CA C:CYS47 4.2 20.4 1.0
CD1 C:LEU25 4.3 22.9 1.0
CG2 C:ILE3 4.4 18.0 1.0
CG1 C:ILE3 4.5 21.4 1.0
SG C:CYS41 4.6 17.0 1.0
N C:ALA46 4.7 20.4 1.0
SG C:CYS44 4.7 19.4 1.0
SG C:CYS20 4.8 18.1 1.0
N C:ALA45 4.9 20.6 1.0
N C:VAL48 5.0 20.1 1.0

Iron binding site 4 out of 16 in 8a8o

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Iron binding site 4 out of 16 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:17.3
occ:1.00
 FE4 C:SF4201 0.0 17.3 1.0
S3 C:SF4201 2.2 17.0 1.0
SG C:CYS41 2.2 17.0 1.0
S1 C:SF4201 2.3 16.8 1.0
S2 C:SF4201 2.4 17.0 1.0
FE2 C:SF4201 2.7 17.4 1.0
FE3 C:SF4201 2.7 17.7 1.0
FE1 C:SF4201 2.7 18.4 1.0
CB C:CYS41 3.4 16.4 1.0
CA C:CYS41 3.8 15.5 1.0
S4 C:SF4201 3.9 17.7 1.0
N C:TRP42 3.9 16.1 1.0
N C:ASP43 4.0 16.0 1.0
C C:CYS41 4.3 15.8 1.0
CD1 C:LEU24 4.5 16.3 1.0
CA C:ASP43 4.6 16.1 1.0
CG1 C:ILE3 4.6 21.4 1.0
CG2 C:ILE3 4.6 18.0 1.0
N C:CYS44 4.7 17.9 1.0
SG C:CYS47 4.7 19.2 1.0
SG C:CYS20 4.8 18.1 1.0
C C:TRP42 4.9 15.1 1.0
CA C:TRP42 4.9 14.5 1.0
SG C:CYS44 5.0 19.4 1.0

Iron binding site 5 out of 16 in 8a8o

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Iron binding site 5 out of 16 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:23.9
occ:1.00
 FE1 C:SF4202 0.0 23.9 1.0
S2 C:SF4202 2.2 24.6 1.0
S4 C:SF4202 2.2 23.9 1.0
SG C:CYS16 2.3 23.8 1.0
S3 C:SF4202 2.3 23.4 1.0
FE2 C:SF4202 2.7 23.6 1.0
FE4 C:SF4202 2.7 24.9 1.0
FE3 C:SF4202 2.7 26.1 1.0
CB C:CYS16 3.2 24.3 1.0
CB C:SER33 3.8 24.2 1.0
S1 C:SF4202 3.9 24.4 1.0
N C:CYS16 3.9 23.9 1.0
CA C:CYS16 4.2 22.5 1.0
OG C:SER33 4.3 28.4 1.0
CD1 C:ILE56 4.3 24.3 1.0
SG C:CYS13 4.6 30.2 1.0
SG C:CYS10 4.7 24.7 1.0
SG C:CYS51 4.8 26.9 1.0
N C:LEU15 4.8 27.6 1.0
CG1 C:ILE56 4.8 23.1 1.0
N C:GLY14 4.8 26.3 1.0
CB C:CYS51 5.0 27.0 1.0
C C:GLY14 5.0 25.6 1.0

Iron binding site 6 out of 16 in 8a8o

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Iron binding site 6 out of 16 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:23.6
occ:1.00
 FE2 C:SF4202 0.0 23.6 1.0
S3 C:SF4202 2.2 23.4 1.0
SG C:CYS10 2.3 24.7 1.0
S4 C:SF4202 2.3 23.9 1.0
S1 C:SF4202 2.3 24.4 1.0
FE1 C:SF4202 2.7 23.9 1.0
FE4 C:SF4202 2.7 24.9 1.0
FE3 C:SF4202 2.7 26.1 1.0
CB C:CYS10 3.3 24.9 1.0
CA C:CYS10 3.7 26.6 1.0
S2 C:SF4202 3.9 24.6 1.0
N C:GLY12 3.9 27.7 1.0
N C:ILE11 4.0 29.4 1.0
C C:CYS10 4.2 29.6 1.0
CB C:SER33 4.4 24.2 1.0
CA C:GLY12 4.5 31.2 1.0
N C:CYS13 4.6 30.2 1.0
CB C:ALA55 4.6 25.5 1.0
SG C:CYS16 4.7 23.8 1.0
N C:SER33 4.7 21.8 1.0
SG C:CYS51 4.8 26.9 1.0
C C:ILE11 4.9 28.2 1.0
SG C:CYS13 4.9 30.2 1.0
N C:CYS10 5.0 27.4 1.0

Iron binding site 7 out of 16 in 8a8o

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Iron binding site 7 out of 16 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:26.1
occ:1.00
 FE3 C:SF4202 0.0 26.1 1.0
SG C:CYS13 2.3 30.2 1.0
S2 C:SF4202 2.3 24.6 1.0
S1 C:SF4202 2.3 24.4 1.0
S4 C:SF4202 2.4 23.9 1.0
FE4 C:SF4202 2.7 24.9 1.0
FE1 C:SF4202 2.7 23.9 1.0
FE2 C:SF4202 2.7 23.6 1.0
N C:CYS13 3.5 30.2 1.0
CB C:CYS13 3.5 32.6 1.0
N C:GLY14 3.8 26.3 1.0
CA C:CYS13 3.9 34.2 1.0
S3 C:SF4202 3.9 23.4 1.0
CD C:PRO52 4.2 34.6 1.0
C C:CYS13 4.2 30.2 1.0
N C:LEU15 4.2 27.6 1.0
N C:GLY12 4.5 27.7 1.0
C C:GLY12 4.5 30.8 1.0
SG C:CYS51 4.6 26.9 1.0
SG C:CYS16 4.7 23.8 1.0
SG C:CYS10 4.7 24.7 1.0
CA C:GLY14 4.7 25.3 1.0
CG1 C:ILE11 4.8 30.0 1.0
N C:CYS16 4.8 23.9 1.0
CA C:GLY12 4.8 31.2 1.0
CG C:PRO52 4.9 37.4 1.0
C C:GLY14 4.9 25.6 1.0
CB C:LEU15 4.9 29.9 1.0

Iron binding site 8 out of 16 in 8a8o

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Iron binding site 8 out of 16 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:24.9
occ:1.00
 FE4 C:SF4202 0.0 24.9 1.0
S1 C:SF4202 2.3 24.4 1.0
SG C:CYS51 2.3 26.9 1.0
S3 C:SF4202 2.3 23.4 1.0
S2 C:SF4202 2.3 24.6 1.0
FE3 C:SF4202 2.7 26.1 1.0
FE2 C:SF4202 2.7 23.6 1.0
FE1 C:SF4202 2.7 23.9 1.0
CB C:CYS51 3.2 27.0 1.0
CA C:CYS51 3.8 29.2 1.0
S4 C:SF4202 3.9 23.9 1.0
CD C:PRO52 4.1 34.6 1.0
CB C:ALA55 4.1 25.5 1.0
CG2 C:VAL53 4.4 35.1 1.0
CG1 C:ILE56 4.4 23.1 1.0
SG C:CYS13 4.6 30.2 1.0
C C:CYS51 4.6 32.6 1.0
N C:PRO52 4.6 31.5 1.0
CD1 C:ILE56 4.7 24.3 1.0
SG C:CYS16 4.7 23.8 1.0
N C:ALA55 4.8 32.2 1.0
SG C:CYS10 4.8 24.7 1.0
CA C:ALA55 4.9 29.0 1.0
CB C:CYS16 5.0 24.3 1.0

Iron binding site 9 out of 16 in 8a8o

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Iron binding site 9 out of 16 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe902

b:12.1
occ:1.00
 FE1 D:SF4902 0.0 12.1 1.0
SG D:CYS41 2.3 11.2 1.0
S2 D:SF4902 2.3 12.2 1.0
S3 D:SF4902 2.3 11.4 1.0
S4 D:SF4902 2.3 12.1 1.0
FE3 D:SF4902 2.7 12.5 1.0
FE4 D:SF4902 2.7 12.3 1.0
FE2 D:SF4902 2.8 12.6 1.0
CB D:CYS41 3.4 10.8 1.0
CA D:CYS41 3.8 11.2 1.0
S1 D:SF4902 3.9 12.2 1.0
N D:TRP42 3.9 10.5 1.0
N D:ASP43 4.0 10.7 1.0
C D:CYS41 4.3 10.7 1.0
CD1 D:LEU24 4.5 13.6 1.0
CG1 D:ILE3 4.6 14.8 1.0
CA D:ASP43 4.7 10.9 1.0
CG2 D:ILE3 4.7 14.2 1.0
SG D:CYS47 4.7 13.0 1.0
N D:CYS44 4.7 9.9 1.0
SG D:CYS20 4.8 12.4 1.0
C D:TRP42 4.9 9.7 1.0
CA D:TRP42 4.9 9.7 1.0
SG D:CYS44 5.0 11.7 1.0

Iron binding site 10 out of 16 in 8a8o

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Iron binding site 10 out of 16 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe902

b:12.6
occ:1.00
 FE2 D:SF4902 0.0 12.6 1.0
S4 D:SF4902 2.3 12.1 1.0
SG D:CYS44 2.3 11.7 1.0
S1 D:SF4902 2.4 12.2 1.0
S3 D:SF4902 2.4 11.4 1.0
FE4 D:SF4902 2.8 12.3 1.0
FE3 D:SF4902 2.8 12.5 1.0
FE1 D:SF4902 2.8 12.1 1.0
CB D:CYS44 3.5 11.4 1.0
N D:CYS44 3.5 9.9 1.0
N D:ALA45 3.8 11.2 1.0
CA D:CYS44 3.9 10.4 1.0
S2 D:SF4902 3.9 12.2 1.0
N D:ALA46 4.1 10.5 1.0
C D:CYS44 4.1 11.1 1.0
CD D:PRO21 4.2 12.9 1.0
N D:ASP43 4.6 10.7 1.0
C D:ASP43 4.6 10.7 1.0
SG D:CYS41 4.7 11.2 1.0
SG D:CYS20 4.7 12.4 1.0
CA D:ALA45 4.7 11.8 1.0
CB D:ALA46 4.7 13.1 1.0
SG D:CYS47 4.7 13.0 1.0
CG D:PRO21 4.7 12.5 1.0
C D:ALA45 4.9 11.9 1.0
N D:CYS47 4.9 12.6 1.0
CA D:ASP43 4.9 10.9 1.0
CA D:ALA46 5.0 11.5 1.0

Reference:

M.Jespersen, T.Wagner. How A Methanogen Assimilates Sulfate: Structural and Functional Elucidation of the Complete Sulfate-Reduction Pathway. To Be Published.
Page generated: Fri Aug 9 16:13:05 2024

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