Iron in PDB 9bt4: Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans

Enzymatic activity of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans

All present enzymatic activity of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans:
1.2.7.1;

Protein crystallography data

The structure of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans, PDB code: 9bt4 was solved by D.Catlin, S.J.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.92
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 79.121, 79.121, 496.524, 90, 90, 120
R / Rfree (%) 17.3 / 20

Other elements in 9bt4:

The structure of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron atom in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans (pdb code 9bt4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans, PDB code: 9bt4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 9bt4

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Iron binding site 1 out of 24 in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:15.7
occ:1.00
 FE1 C:SF4301 0.0 15.7 1.0
SG C:CYS17 2.3 16.6 1.0
S2 C:SF4301 2.3 14.6 1.0
S4 C:SF4301 2.3 14.9 1.0
S3 C:SF4301 2.3 14.8 1.0
FE2 C:SF4301 2.7 15.5 1.0
FE3 C:SF4301 2.7 14.3 1.0
FE4 C:SF4301 2.8 15.2 1.0
CB C:CYS17 3.2 16.1 1.0
N C:CYS17 3.8 15.6 1.0
OG1 C:THR212 3.9 16.4 1.0
S1 C:SF4301 3.9 13.8 1.0
CB C:THR212 4.1 15.8 1.0
CA C:CYS17 4.1 16.1 1.0
SG C:CYS210 4.6 14.9 1.0
SG C:CYS20 4.7 15.2 1.0
CG2 C:THR212 4.7 16.0 1.0
NH1 E:ARG42 4.8 24.1 1.0
SG C:CYS45 4.8 13.9 1.0

Iron binding site 2 out of 24 in 9bt4

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Iron binding site 2 out of 24 in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:15.5
occ:1.00
 FE2 C:SF4301 0.0 15.5 1.0
S3 C:SF4301 2.3 14.8 1.0
SG C:CYS20 2.3 15.2 1.0
S4 C:SF4301 2.3 14.9 1.0
S1 C:SF4301 2.3 13.8 1.0
FE1 C:SF4301 2.7 15.7 1.0
FE4 C:SF4301 2.8 15.2 1.0
FE3 C:SF4301 2.8 14.3 1.0
CB C:CYS20 3.4 14.6 1.0
CA C:CYS20 3.8 14.8 1.0
S2 C:SF4301 3.9 14.6 1.0
N C:CYS21 4.2 14.0 1.0
N C:CYS17 4.4 15.6 1.0
N C:ASP22 4.4 13.4 1.0
CB C:ASP22 4.4 13.0 1.0
SG C:CYS21 4.4 14.5 1.0
C C:CYS20 4.5 14.6 1.0
SG C:CYS17 4.6 16.6 1.0
CG C:ASP22 4.7 13.1 1.0
SD C:MET49 4.7 15.5 1.0
SG C:CYS45 4.7 13.9 1.0
CB C:CYS17 4.7 16.1 1.0
CB C:CYS45 4.8 12.8 1.0
CA C:GLY16 4.9 15.3 1.0
SG C:CYS210 4.9 14.9 1.0

Iron binding site 3 out of 24 in 9bt4

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Iron binding site 3 out of 24 in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:14.3
occ:1.00
 FE3 C:SF4301 0.0 14.3 1.0
S2 C:SF4301 2.3 14.6 1.0
SG C:CYS45 2.3 13.9 1.0
S1 C:SF4301 2.3 13.8 1.0
S4 C:SF4301 2.3 14.9 1.0
FE1 C:SF4301 2.7 15.7 1.0
FE4 C:SF4301 2.8 15.2 1.0
FE2 C:SF4301 2.8 15.5 1.0
CB C:CYS45 3.2 12.8 1.0
S3 C:SF4301 3.9 14.8 1.0
NH1 E:ARG42 4.0 24.1 1.0
CB C:MET130 4.0 15.2 1.0
CA C:CYS45 4.6 12.5 1.0
SG C:CYS210 4.7 14.9 1.0
CG C:MET130 4.8 15.2 1.0
SG C:CYS20 4.8 15.2 1.0
SG C:CYS17 4.8 16.6 1.0
OD2 C:ASP22 4.9 12.8 1.0

Iron binding site 4 out of 24 in 9bt4

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Iron binding site 4 out of 24 in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:15.2
occ:1.00
 FE4 C:SF4301 0.0 15.2 1.0
S3 C:SF4301 2.3 14.8 1.0
SG C:CYS210 2.3 14.9 1.0
S1 C:SF4301 2.3 13.8 1.0
S2 C:SF4301 2.3 14.6 1.0
FE2 C:SF4301 2.8 15.5 1.0
FE3 C:SF4301 2.8 14.3 1.0
FE1 C:SF4301 2.8 15.7 1.0
CB C:CYS210 3.5 14.4 1.0
S4 C:SF4301 3.9 14.9 1.0
SG C:CYS21 4.0 14.5 1.0
CA C:CYS210 4.2 14.8 1.0
CG C:MET130 4.3 15.2 1.0
CB C:MET130 4.4 15.2 1.0
CB C:THR212 4.5 15.8 1.0
ND2 C:ASN126 4.7 12.7 1.0
CD C:PRO211 4.7 14.8 1.0
C C:CYS210 4.8 14.9 1.0
SG C:CYS45 4.8 13.9 1.0
SG C:CYS17 4.8 16.6 1.0
OG1 C:THR212 4.8 16.4 1.0
SG C:CYS20 4.9 15.2 1.0
N C:THR212 4.9 15.6 1.0
N C:PRO211 5.0 14.9 1.0
N C:GLY213 5.0 15.8 1.0

Iron binding site 5 out of 24 in 9bt4

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Iron binding site 5 out of 24 in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:15.4
occ:1.00
 FE1 D:SF4301 0.0 15.4 1.0
SG D:CYS17 2.3 16.6 1.0
S3 D:SF4301 2.3 14.6 1.0
S2 D:SF4301 2.3 14.6 1.0
S4 D:SF4301 2.3 14.3 1.0
FE2 D:SF4301 2.7 15.4 1.0
FE3 D:SF4301 2.7 14.3 1.0
FE4 D:SF4301 2.8 15.3 1.0
CB D:CYS17 3.2 16.0 1.0
OG1 D:THR212 3.8 16.1 1.0
N D:CYS17 3.9 15.7 1.0
S1 D:SF4301 3.9 14.0 1.0
CB D:THR212 4.1 15.5 1.0
CA D:CYS17 4.1 16.0 1.0
SG D:CYS210 4.6 14.6 1.0
SG D:CYS20 4.7 15.4 1.0
CG2 D:THR212 4.7 15.8 1.0
SG D:CYS45 4.8 13.8 1.0
NH1 F:ARG42 4.8 24.4 1.0
CD F:ARG42 5.0 25.6 1.0

Iron binding site 6 out of 24 in 9bt4

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Iron binding site 6 out of 24 in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:15.4
occ:1.00
 FE2 D:SF4301 0.0 15.4 1.0
S3 D:SF4301 2.3 14.6 1.0
SG D:CYS20 2.3 15.4 1.0
S4 D:SF4301 2.3 14.3 1.0
S1 D:SF4301 2.3 14.0 1.0
FE1 D:SF4301 2.7 15.4 1.0
FE4 D:SF4301 2.7 15.3 1.0
FE3 D:SF4301 2.8 14.3 1.0
CB D:CYS20 3.4 14.6 1.0
CA D:CYS20 3.8 14.7 1.0
S2 D:SF4301 3.9 14.6 1.0
N D:CYS21 4.2 14.2 1.0
N D:CYS17 4.4 15.7 1.0
N D:ASP22 4.4 14.0 1.0
C D:CYS20 4.4 14.5 1.0
SG D:CYS21 4.5 14.8 1.0
CB D:ASP22 4.5 13.7 1.0
SG D:CYS17 4.6 16.6 1.0
SG D:CYS45 4.7 13.8 1.0
SD D:MET49 4.7 14.9 1.0
CB D:CYS17 4.7 16.0 1.0
CG D:ASP22 4.7 13.8 1.0
CB D:CYS45 4.8 12.6 1.0
CA D:GLY16 4.9 15.6 1.0
SG D:CYS210 4.9 14.6 1.0

Iron binding site 7 out of 24 in 9bt4

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Iron binding site 7 out of 24 in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:14.3
occ:1.00
 FE3 D:SF4301 0.0 14.3 1.0
SG D:CYS45 2.3 13.8 1.0
S2 D:SF4301 2.3 14.6 1.0
S4 D:SF4301 2.3 14.3 1.0
S1 D:SF4301 2.3 14.0 1.0
FE1 D:SF4301 2.7 15.4 1.0
FE2 D:SF4301 2.8 15.4 1.0
FE4 D:SF4301 2.8 15.3 1.0
CB D:CYS45 3.2 12.6 1.0
S3 D:SF4301 3.9 14.6 1.0
NH1 F:ARG42 4.0 24.4 1.0
CB D:MET130 4.0 15.0 1.0
CA D:CYS45 4.6 12.2 1.0
SG D:CYS210 4.7 14.6 1.0
CG D:MET130 4.8 15.3 1.0
SG D:CYS20 4.8 15.4 1.0
SG D:CYS17 4.8 16.6 1.0
OD2 D:ASP22 4.9 13.7 1.0
C D:MET130 5.0 15.6 1.0

Iron binding site 8 out of 24 in 9bt4

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Iron binding site 8 out of 24 in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:15.3
occ:1.00
 FE4 D:SF4301 0.0 15.3 1.0
S3 D:SF4301 2.3 14.6 1.0
SG D:CYS210 2.3 14.6 1.0
S1 D:SF4301 2.3 14.0 1.0
S2 D:SF4301 2.3 14.6 1.0
FE2 D:SF4301 2.7 15.4 1.0
FE3 D:SF4301 2.8 14.3 1.0
FE1 D:SF4301 2.8 15.4 1.0
CB D:CYS210 3.5 14.1 1.0
S4 D:SF4301 3.9 14.3 1.0
SG D:CYS21 4.0 14.8 1.0
CA D:CYS210 4.2 14.6 1.0
CG D:MET130 4.3 15.3 1.0
CB D:MET130 4.4 15.0 1.0
CB D:THR212 4.5 15.5 1.0
CD D:PRO211 4.7 14.9 1.0
ND2 D:ASN126 4.7 12.4 1.0
C D:CYS210 4.8 14.5 1.0
SG D:CYS45 4.8 13.8 1.0
OG1 D:THR212 4.8 16.1 1.0
SG D:CYS17 4.8 16.6 1.0
SG D:CYS20 4.8 15.4 1.0
N D:THR212 4.8 15.0 1.0
N D:PRO211 4.9 14.8 1.0
N D:GLY213 5.0 15.1 1.0

Iron binding site 9 out of 24 in 9bt4

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Iron binding site 9 out of 24 in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe900

b:16.9
occ:1.00
 FE1 G:SF4900 0.0 16.9 1.0
SG G:CYS37 2.2 16.3 1.0
S4 G:SF4900 2.3 16.1 1.0
S2 G:SF4900 2.3 16.6 1.0
S3 G:SF4900 2.3 17.0 1.0
FE3 G:SF4900 2.7 17.1 1.0
FE4 G:SF4900 2.7 17.4 1.0
FE2 G:SF4900 2.7 17.3 1.0
CB G:CYS37 3.3 16.4 1.0
CA G:CYS37 3.8 17.1 1.0
S1 G:SF4900 3.9 16.9 1.0
CD G:PRO38 4.0 16.8 1.0
CB G:SER41 4.5 17.8 1.0
C G:CYS37 4.5 16.9 1.0
N G:PRO38 4.5 16.9 1.0
SG G:CYS60 4.6 18.1 1.0
CG2 G:VAL42 4.7 18.2 1.0
N G:ASP39 4.8 16.7 1.0
SG G:CYS57 4.8 17.6 1.0
SG G:CYS63 4.8 19.1 1.0
CB G:ASP39 5.0 17.6 1.0
N G:SER41 5.0 18.0 1.0

Iron binding site 10 out of 24 in 9bt4

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Iron binding site 10 out of 24 in the Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Pyruvate:Ferredoxin Oxidoreductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe900

b:17.3
occ:1.00
 FE2 G:SF4900 0.0 17.3 1.0
S3 G:SF4900 2.3 17.0 1.0
SG G:CYS63 2.3 19.1 1.0
S1 G:SF4900 2.3 16.9 1.0
S4 G:SF4900 2.3 16.1 1.0
FE4 G:SF4900 2.7 17.4 1.0
FE1 G:SF4900 2.7 16.9 1.0
FE3 G:SF4900 2.8 17.1 1.0
CB G:CYS63 3.4 18.6 1.0
S2 G:SF4900 3.9 16.6 1.0
N G:CYS63 4.0 18.2 1.0
CE1 G:TYR52 4.1 18.7 1.0
CG G:PRO20 4.2 20.8 1.0
CA G:CYS63 4.3 19.0 1.0
CB G:PRO20 4.5 21.1 1.0
SG G:CYS57 4.7 17.6 1.0
OH G:TYR52 4.7 19.6 1.0
SG G:CYS60 4.7 18.1 1.0
SG G:CYS37 4.8 16.3 1.0
N G:GLY61 4.8 18.7 1.0
CZ G:TYR52 4.8 19.3 1.0
N G:ILE62 4.8 17.8 1.0
CD1 G:TYR52 4.9 19.3 1.0
CG2 G:VAL42 4.9 18.2 1.0

Reference:

M.Cossu, D.Catlin, S.J.Elliott, W.W.Metcalf, S.K.Nair. Structural Organization of Pyruvate: Ferredoxin Oxidoreductase From the Methanogenic Archaeon Methanosarcina Acetivorans. Structure 2024.
ISSN: ISSN 0969-2126
PubMed: 39265575
DOI: 10.1016/J.STR.2024.08.011
Page generated: Thu Oct 31 20:52:18 2024

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