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Iron in PDB 8q5w: Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus

Protein crystallography data

The structure of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus, PDB code: 8q5w was solved by N.Maslac, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.26 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 147.948, 156.729, 206.454, 90, 90, 90
R / Rfree (%) 22.1 / 24.2

Other elements in 8q5w:

The structure of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus also contains other interesting chemical elements:

Magnesium (Mg) 12 atoms
Chlorine (Cl) 4 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 Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus (pdb code 8q5w). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 24 binding sites of Iron where determined in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus, PDB code: 8q5w:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 8q5w

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Iron binding site 1 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:44.4
occ:1.00
 FE1 B:SF4301 0.0 44.4 1.0
S4 B:SF4301 2.3 53.6 1.0
S2 B:SF4301 2.3 53.1 1.0
S3 B:SF4301 2.3 52.0 1.0
SG B:CYS140 2.4 55.6 1.0
FE2 B:SF4301 2.6 50.5 1.0
FE3 B:SF4301 2.6 51.5 1.0
FE4 B:SF4301 2.7 50.3 1.0
CB B:CYS140 3.3 54.9 1.0
S1 B:SF4301 3.9 51.7 1.0
C B:CYS140 4.0 58.7 1.0
O B:CYS140 4.2 59.4 1.0
CA B:CYS140 4.2 58.3 1.0
N B:GLY141 4.2 60.6 1.0
N A:ALA106 4.4 51.7 1.0
SG A:CYS105 4.5 51.9 1.0
CG1 B:VAL138 4.5 53.1 1.0
CA A:CYS105 4.6 52.8 1.0
SG B:CYS105 4.7 55.8 1.0
CA B:GLY141 4.7 60.8 1.0
SG A:CYS140 4.7 52.3 1.0
CB A:CYS105 4.8 52.5 1.0
N B:CYS140 4.9 55.7 1.0
CG2 B:VAL138 4.9 57.3 1.0

Iron binding site 2 out of 24 in 8q5w

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Iron binding site 2 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:50.5
occ:1.00
 FE2 B:SF4301 0.0 50.5 1.0
S1 B:SF4301 2.3 51.7 1.0
S4 B:SF4301 2.3 53.6 1.0
S3 B:SF4301 2.3 52.0 1.0
SG A:CYS105 2.3 51.9 1.0
FE1 B:SF4301 2.6 44.4 1.0
FE3 B:SF4301 2.6 51.5 1.0
FE4 B:SF4301 2.6 50.3 1.0
CB A:CYS105 3.1 52.5 1.0
CA A:CYS105 3.7 52.8 1.0
S2 B:SF4301 3.9 53.1 1.0
CE L:MET233 4.2 55.4 1.0
N A:ALA106 4.3 51.7 1.0
C A:CYS105 4.4 50.6 1.0
SG B:CYS140 4.6 55.6 1.0
SG A:CYS140 4.8 52.3 1.0
CA A:GLY141 4.8 53.0 1.0
N A:GLY107 4.8 49.4 1.0
SG B:CYS105 4.9 55.8 1.0

Iron binding site 3 out of 24 in 8q5w

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Iron binding site 3 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:51.5
occ:1.00
 FE3 B:SF4301 0.0 51.5 1.0
S4 B:SF4301 2.3 53.6 1.0
SG B:CYS105 2.3 55.8 1.0
S2 B:SF4301 2.3 53.1 1.0
S1 B:SF4301 2.3 51.7 1.0
FE2 B:SF4301 2.6 50.5 1.0
FE1 B:SF4301 2.6 44.4 1.0
FE4 B:SF4301 2.7 50.3 1.0
CB B:CYS105 3.2 53.6 1.0
CA B:CYS105 3.8 53.2 1.0
S3 B:SF4301 3.9 52.0 1.0
CE L:MET233 4.2 55.4 1.0
N B:ALA106 4.2 55.0 1.0
C B:CYS105 4.3 55.2 1.0
CA B:GLY141 4.5 60.8 1.0
N B:GLY107 4.6 58.4 1.0
SG A:CYS140 4.6 52.3 1.0
N B:GLY141 4.8 60.6 1.0
SG A:CYS105 4.9 51.9 1.0
OD1 L:ASN231 4.9 60.8 1.0
SG B:CYS140 5.0 55.6 1.0

Iron binding site 4 out of 24 in 8q5w

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Iron binding site 4 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:50.3
occ:1.00
 FE4 B:SF4301 0.0 50.3 1.0
S3 B:SF4301 2.3 52.0 1.0
SG A:CYS140 2.3 52.3 1.0
S1 B:SF4301 2.3 51.7 1.0
S2 B:SF4301 2.3 53.1 1.0
FE2 B:SF4301 2.6 50.5 1.0
FE1 B:SF4301 2.7 44.4 1.0
FE3 B:SF4301 2.7 51.5 1.0
CB A:CYS140 3.3 52.7 1.0
S4 B:SF4301 3.9 53.6 1.0
C A:CYS140 4.1 51.8 1.0
O A:CYS140 4.2 51.9 1.0
N B:ALA106 4.3 55.0 1.0
CA A:CYS140 4.3 52.0 1.0
SG B:CYS105 4.5 55.8 1.0
N A:GLY141 4.5 52.4 1.0
SG A:CYS105 4.6 51.9 1.0
CA B:CYS105 4.7 53.2 1.0
CG2 A:VAL138 4.7 58.8 1.0
SG B:CYS140 4.8 55.6 1.0
CB B:ALA106 4.9 54.5 1.0
CB B:CYS105 4.9 53.6 1.0
CA A:GLY141 5.0 53.0 1.0
C B:CYS105 5.0 55.2 1.0

Iron binding site 5 out of 24 in 8q5w

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Iron binding site 5 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:57.9
occ:1.00
 FE1 C:SF4301 0.0 57.9 1.0
S2 C:SF4301 2.3 60.8 1.0
S4 C:SF4301 2.3 62.6 1.0
S3 C:SF4301 2.3 57.9 1.0
SG D:CYS140 2.4 65.5 1.0
FE3 C:SF4301 2.6 59.4 1.0
FE2 C:SF4301 2.7 57.4 1.0
FE4 C:SF4301 2.7 56.7 1.0
CB D:CYS140 3.3 68.6 1.0
S1 C:SF4301 3.9 58.5 1.0
C D:CYS140 4.1 78.9 1.0
N C:ALA106 4.2 57.2 1.0
O D:CYS140 4.3 84.3 1.0
CA D:CYS140 4.3 74.8 1.0
N D:GLY141 4.3 76.9 1.0
SG C:CYS105 4.5 60.5 1.0
CA C:CYS105 4.5 60.0 1.0
SG D:CYS105 4.6 63.2 1.0
CG2 D:VAL138 4.8 62.3 1.0
CB C:ALA106 4.8 54.7 1.0
CA D:GLY141 4.8 76.7 1.0
SG C:CYS140 4.9 63.5 1.0
CB C:CYS105 4.9 58.8 1.0
C C:CYS105 4.9 59.1 1.0
N D:CYS140 5.0 86.2 1.0

Iron binding site 6 out of 24 in 8q5w

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Iron binding site 6 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:57.4
occ:1.00
 FE2 C:SF4301 0.0 57.4 1.0
SG C:CYS105 2.2 60.5 1.0
S1 C:SF4301 2.3 58.5 1.0
S4 C:SF4301 2.3 62.6 1.0
S3 C:SF4301 2.3 57.9 1.0
FE3 C:SF4301 2.6 59.4 1.0
FE1 C:SF4301 2.7 57.9 1.0
FE4 C:SF4301 2.7 56.7 1.0
CB C:CYS105 3.1 58.8 1.0
CA C:CYS105 3.6 60.0 1.0
S2 C:SF4301 3.9 60.8 1.0
N C:ALA106 4.1 57.2 1.0
C C:CYS105 4.2 59.1 1.0
N C:GLY107 4.7 62.2 1.0
SG D:CYS140 4.7 65.5 1.0
SG D:CYS105 4.7 63.2 1.0
CA C:GLY141 4.8 57.6 1.0
SG C:CYS140 4.9 63.5 1.0
N C:CYS105 5.0 62.6 1.0

Iron binding site 7 out of 24 in 8q5w

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Iron binding site 7 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:59.4
occ:1.00
 FE3 C:SF4301 0.0 59.4 1.0
SG D:CYS105 2.2 63.2 1.0
S4 C:SF4301 2.3 62.6 1.0
S2 C:SF4301 2.3 60.8 1.0
S1 C:SF4301 2.3 58.5 1.0
FE1 C:SF4301 2.6 57.9 1.0
FE2 C:SF4301 2.6 57.4 1.0
FE4 C:SF4301 2.7 56.7 1.0
CB D:CYS105 3.2 60.1 1.0
CA D:CYS105 3.7 60.8 1.0
S3 C:SF4301 3.9 57.9 1.0
N D:ALA106 4.1 62.6 1.0
C D:CYS105 4.3 62.2 1.0
N D:GLY107 4.6 76.0 1.0
CA D:GLY141 4.7 76.7 1.0
SG C:CYS140 4.7 63.5 1.0
SG C:CYS105 4.8 60.5 1.0
SG D:CYS140 4.9 65.5 1.0
N D:GLY141 4.9 76.9 1.0
CE A:MET233 5.0 61.5 1.0

Iron binding site 8 out of 24 in 8q5w

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Iron binding site 8 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:56.7
occ:1.00
 FE4 C:SF4301 0.0 56.7 1.0
S3 C:SF4301 2.3 57.9 1.0
S2 C:SF4301 2.3 60.8 1.0
S1 C:SF4301 2.3 58.5 1.0
SG C:CYS140 2.4 63.5 1.0
FE3 C:SF4301 2.7 59.4 1.0
FE1 C:SF4301 2.7 57.9 1.0
FE2 C:SF4301 2.7 57.4 1.0
CB C:CYS140 3.3 58.4 1.0
S4 C:SF4301 3.9 62.6 1.0
C C:CYS140 4.2 57.5 1.0
N D:ALA106 4.3 62.6 1.0
CA C:CYS140 4.4 57.6 1.0
O C:CYS140 4.4 57.6 1.0
SG D:CYS105 4.5 63.2 1.0
N C:GLY141 4.5 59.3 1.0
SG C:CYS105 4.6 60.5 1.0
CG2 C:VAL138 4.6 58.1 1.0
CA D:CYS105 4.7 60.8 1.0
SG D:CYS140 4.8 65.5 1.0
CB D:ALA106 4.9 61.7 1.0

Iron binding site 9 out of 24 in 8q5w

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Iron binding site 9 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe302

b:73.8
occ:1.00
 FE1 E:SF4302 0.0 73.8 1.0
S4 E:SF4302 2.3 86.2 1.0
S2 E:SF4302 2.3 73.6 1.0
S3 E:SF4302 2.3 68.0 1.0
SG F:CYS140 2.3 63.8 1.0
FE4 E:SF4302 2.6 65.1 1.0
FE2 E:SF4302 2.6 70.2 1.0
FE3 E:SF4302 2.7 74.7 1.0
CB F:CYS140 3.3 63.3 1.0
S1 E:SF4302 3.9 71.4 1.0
C F:CYS140 4.2 64.1 1.0
O F:CYS140 4.3 62.5 1.0
N E:ALA106 4.3 65.8 1.0
CA F:CYS140 4.4 62.4 1.0
SG E:CYS105 4.5 69.5 1.0
N F:GLY141 4.5 70.3 1.0
SG F:CYS105 4.6 68.2 1.0
CA E:CYS105 4.6 66.7 1.0
CG2 F:VAL138 4.7 59.2 1.0
SG E:CYS140 4.9 70.9 1.0
CB E:ALA106 4.9 63.2 1.0
CB E:CYS105 4.9 67.2 1.0
C E:CYS105 5.0 66.6 1.0

Iron binding site 10 out of 24 in 8q5w

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Iron binding site 10 out of 24 in the Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Mgadp-Bound Fe Protein of the Molybdenum Nitrogenase From Methanocaldococcus Infernus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe302

b:70.2
occ:1.00
 FE2 E:SF4302 0.0 70.2 1.0
SG E:CYS105 2.2 69.5 1.0
S3 E:SF4302 2.3 68.0 1.0
S1 E:SF4302 2.3 71.4 1.0
S4 E:SF4302 2.3 86.2 1.0
FE4 E:SF4302 2.6 65.1 1.0
FE1 E:SF4302 2.6 73.8 1.0
FE3 E:SF4302 2.7 74.7 1.0
CB E:CYS105 3.1 67.2 1.0
CA E:CYS105 3.7 66.7 1.0
S2 E:SF4302 3.9 73.6 1.0
N E:ALA106 4.2 65.8 1.0
C E:CYS105 4.3 66.6 1.0
SG F:CYS140 4.6 63.8 1.0
N E:GLY107 4.7 69.0 1.0
ND2 C:ASN231 4.7 84.5 1.0
CA E:GLY141 4.7 90.1 1.0
SG E:CYS140 4.9 70.9 1.0
SG F:CYS105 4.9 68.2 1.0
N E:GLY141 5.0 89.3 1.0
N E:CYS105 5.0 66.9 1.0

Reference:

N.Maslac, C.Cadoux, P.Bolte, F.Murken, W.Gu, R.D.Milton, T.Wagner. Structural Comparison of (Hyper-)Thermophilic Nitrogenase Reductases From Three Marine Methanococcales. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 38696373
DOI: 10.1111/FEBS.17148
Page generated: Sat Aug 10 15:16:58 2024

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