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Iron in PDB 6vw7: Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound

Enzymatic activity of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound

All present enzymatic activity of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound:
1.2.1.2;

Protein crystallography data

The structure of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound, PDB code: 6vw7 was solved by T.Young, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.53 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 132.656, 127.050, 99.840, 90.00, 123.50, 90.00
R / Rfree (%) 15.9 / 19.9

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound (pdb code 6vw7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound, PDB code: 6vw7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 6vw7

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Iron binding site 1 out of 12 in the Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:26.9
occ:1.00
 FE1 A:FES301 0.0 26.9 1.0
S2 A:FES301 2.2 24.6 1.0
S1 A:FES301 2.2 26.4 1.0
SG A:CYS86 2.4 25.1 1.0
SG A:CYS91 2.5 26.2 1.0
FE2 A:FES301 2.7 40.1 1.0
CB A:CYS91 3.3 29.6 1.0
CB A:CYS86 3.3 27.6 1.0
N A:CYS91 3.8 29.1 1.0
CA A:CYS127 4.0 24.8 1.0
CA A:CYS91 4.2 28.8 1.0
N A:LEU128 4.3 25.9 1.0
N A:CYS127 4.5 27.2 1.0
CB A:ALA136 4.5 25.1 1.0
O A:HOH441 4.6 28.1 1.0
CB A:CYS127 4.7 23.1 1.0
CA A:CYS86 4.7 30.0 1.0
C A:CYS127 4.7 24.9 1.0
CB A:ALA88 4.7 25.8 1.0
O A:ALA88 4.8 28.9 1.0
SG A:CYS127 4.8 22.0 1.0
CA A:CYS131 4.9 21.8 1.0
N A:ALA88 4.9 24.4 1.0
C A:ALA90 4.9 28.4 1.0

Iron binding site 2 out of 12 in 6vw7

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Iron binding site 2 out of 12 in the Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:40.1
occ:1.00
 FE2 A:FES301 0.0 40.1 1.0
S1 A:FES301 2.2 26.4 1.0
S2 A:FES301 2.2 24.6 1.0
SG A:CYS131 2.5 22.9 1.0
SG A:CYS127 2.6 22.0 1.0
FE1 A:FES301 2.7 26.9 1.0
CB A:CYS131 3.4 21.6 1.0
CB A:CYS127 3.4 23.1 1.0
CA A:CYS127 3.5 24.8 1.0
CA A:CYS131 3.6 21.8 1.0
N A:CYS131 3.8 18.9 1.0
N A:LEU128 3.9 25.9 1.0
N A:GLY129 4.1 21.9 1.0
C A:CYS127 4.2 24.9 1.0
N A:GLN130 4.2 21.0 1.0
N B:GLY189 4.3 25.6 1.0
CA B:SER188 4.4 27.1 1.0
SG A:CYS86 4.5 25.1 1.0
C A:GLN130 4.5 21.8 1.0
CB A:ALA90 4.6 23.3 1.0
CA A:GLY129 4.6 17.8 1.0
N A:CYS127 4.7 27.2 1.0
SG A:CYS91 4.7 26.2 1.0
C A:GLY129 4.8 19.7 1.0
CB B:SER188 4.8 24.6 1.0
C A:LEU128 4.9 22.4 1.0
CA A:GLN130 4.9 20.6 1.0
CA A:LEU128 5.0 25.2 1.0
C B:SER188 5.0 26.4 1.0

Iron binding site 3 out of 12 in 6vw7

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Iron binding site 3 out of 12 in the Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:28.5
occ:1.00
 FE1 B:SF4601 0.0 28.5 1.0
S3 B:SF4601 2.3 31.8 1.0
S4 B:SF4601 2.3 34.4 1.0
S2 B:SF4601 2.3 30.1 1.0
SG B:CYS489 2.4 32.4 1.0
FE4 B:SF4601 2.7 29.6 1.0
FE2 B:SF4601 2.7 33.3 1.0
FE3 B:SF4601 2.7 30.9 1.0
CB B:CYS489 3.4 28.4 1.0
N B:CYS489 3.6 34.6 1.0
CA B:CYS489 3.9 30.4 1.0
S1 B:SF4601 3.9 34.1 1.0
CG2 B:VAL289 4.1 27.1 1.0
CB B:MET491 4.1 30.5 1.0
C B:CYS489 4.1 32.1 1.0
O B:CYS489 4.1 33.2 1.0
N B:GLY492 4.5 31.1 1.0
C B:LEU488 4.5 38.9 1.0
N B:MET491 4.6 31.4 1.0
CB B:VAL289 4.8 30.9 1.0
N B:LEU488 4.8 37.3 1.0
SG B:CYS443 4.8 29.7 1.0
CA B:MET491 4.9 31.7 1.0
N B:ALA490 4.9 32.9 1.0
CG B:MET491 4.9 33.0 1.0
SG B:CYS446 4.9 36.4 1.0
SG B:CYS449 5.0 32.0 1.0

Iron binding site 4 out of 12 in 6vw7

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Iron binding site 4 out of 12 in the Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:33.3
occ:1.00
 FE2 B:SF4601 0.0 33.3 1.0
S4 B:SF4601 2.2 34.4 1.0
S1 B:SF4601 2.3 34.1 1.0
S3 B:SF4601 2.3 31.8 1.0
SG B:CYS446 2.4 36.4 1.0
FE4 B:SF4601 2.7 29.6 1.0
FE3 B:SF4601 2.7 30.9 1.0
FE1 B:SF4601 2.7 28.5 1.0
CB B:CYS446 3.1 36.2 1.0
N B:CYS446 3.7 36.1 1.0
S2 B:SF4601 3.9 30.1 1.0
N B:LEU488 3.9 37.3 1.0
CA B:CYS446 4.0 37.2 1.0
CB B:LEU488 4.3 41.7 1.0
CB B:CYS449 4.3 31.5 1.0
CB B:LYS445 4.4 40.1 1.0
N B:CYS489 4.5 34.6 1.0
C B:LYS445 4.5 36.2 1.0
CA B:LEU488 4.5 37.7 1.0
N B:LYS445 4.7 33.1 1.0
SG B:CYS449 4.7 32.0 1.0
O B:HOH735 4.7 43.2 1.0
CA B:LYS445 4.8 36.5 1.0
SG B:CYS443 4.8 29.7 1.0
C B:SER487 4.9 37.3 1.0
C B:LEU488 4.9 38.9 1.0
CA B:SER487 4.9 34.8 1.0
SG B:CYS489 5.0 32.4 1.0
O B:CYS446 5.0 38.8 1.0
CG B:LEU488 5.0 48.4 1.0
C B:CYS446 5.0 37.8 1.0

Iron binding site 5 out of 12 in 6vw7

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Iron binding site 5 out of 12 in the Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:30.9
occ:1.00
 FE3 B:SF4601 0.0 30.9 1.0
S1 B:SF4601 2.2 34.1 1.0
S2 B:SF4601 2.3 30.1 1.0
S4 B:SF4601 2.3 34.4 1.0
SG B:CYS443 2.4 29.7 1.0
FE2 B:SF4601 2.7 33.3 1.0
FE4 B:SF4601 2.7 29.6 1.0
FE1 B:SF4601 2.7 28.5 1.0
CB B:CYS443 3.4 31.4 1.0
N B:CYS443 3.7 32.4 1.0
CA B:CYS443 3.9 33.1 1.0
S3 B:SF4601 3.9 31.8 1.0
N B:GLY444 4.0 31.1 1.0
N B:LYS445 4.0 33.1 1.0
CB B:LYS445 4.1 40.1 1.0
C B:CYS443 4.2 33.2 1.0
CG2 B:VAL289 4.3 27.1 1.0
CA B:LYS445 4.7 36.5 1.0
OG B:SER442 4.7 31.3 1.0
SG B:CYS489 4.8 32.4 1.0
N B:CYS446 4.8 36.1 1.0
CB B:VAL289 4.8 30.9 1.0
C B:SER442 4.8 32.6 1.0
SG B:CYS446 4.9 36.4 1.0
CG1 B:VAL271 4.9 31.2 1.0
C B:GLY444 4.9 34.2 1.0
SG B:CYS449 4.9 32.0 1.0
CA B:GLY444 5.0 32.3 1.0

Iron binding site 6 out of 12 in 6vw7

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Iron binding site 6 out of 12 in the Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:29.6
occ:1.00
 FE4 B:SF4601 0.0 29.6 1.0
S2 B:SF4601 2.3 30.1 1.0
S1 B:SF4601 2.3 34.1 1.0
S3 B:SF4601 2.3 31.8 1.0
SG B:CYS449 2.5 32.0 1.0
FE1 B:SF4601 2.7 28.5 1.0
FE2 B:SF4601 2.7 33.3 1.0
FE3 B:SF4601 2.7 30.9 1.0
CB B:CYS449 3.1 31.5 1.0
S4 B:SF4601 3.8 34.4 1.0
OG B:SER442 3.9 31.3 1.0
N B:GLY492 4.0 31.1 1.0
CG B:MET491 4.2 33.0 1.0
CB B:MET491 4.2 30.5 1.0
N B:CYS443 4.5 32.4 1.0
CA B:GLY492 4.5 29.8 1.0
CB B:SER442 4.5 31.3 1.0
CA B:SER442 4.5 32.1 1.0
CA B:CYS449 4.5 36.8 1.0
SG B:CYS489 4.7 32.4 1.0
CB B:CYS446 4.7 36.2 1.0
C B:MET491 4.9 30.7 1.0
SG B:CYS446 4.9 36.4 1.0

Iron binding site 7 out of 12 in 6vw7

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Iron binding site 7 out of 12 in the Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:21.0
occ:1.00
 FE1 C:FES301 0.0 21.0 1.0
S2 C:FES301 2.2 23.8 1.0
S1 C:FES301 2.2 23.0 1.0
SG C:CYS86 2.4 21.7 1.0
SG C:CYS91 2.4 21.7 1.0
FE2 C:FES301 2.8 18.9 1.0
CB C:CYS86 3.3 22.0 1.0
CB C:CYS91 3.4 22.5 1.0
N C:CYS91 3.9 21.7 1.0
CA C:CYS127 4.0 20.7 1.0
CA C:CYS91 4.2 23.9 1.0
N C:LEU128 4.4 20.2 1.0
N C:CYS127 4.5 19.7 1.0
CB C:ALA136 4.6 20.8 1.0
CB C:CYS127 4.6 19.2 1.0
SG C:CYS127 4.7 20.5 1.0
CA C:CYS86 4.7 22.9 1.0
C C:CYS127 4.7 22.1 1.0
CB C:ALA88 4.8 19.9 1.0
CA C:CYS131 4.8 21.2 1.0
O C:HOH405 4.9 25.8 1.0
O C:ALA88 4.9 22.5 1.0
N C:ALA88 4.9 21.5 1.0
CB C:ALA90 5.0 21.0 1.0
SG C:CYS131 5.0 18.9 1.0
C C:ALA90 5.0 22.9 1.0

Iron binding site 8 out of 12 in 6vw7

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Iron binding site 8 out of 12 in the Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:18.9
occ:1.00
 FE2 C:FES301 0.0 18.9 1.0
S2 C:FES301 2.2 23.8 1.0
S1 C:FES301 2.2 23.0 1.0
SG C:CYS131 2.4 18.9 1.0
SG C:CYS127 2.5 20.5 1.0
FE1 C:FES301 2.8 21.0 1.0
CB C:CYS131 3.3 16.6 1.0
CB C:CYS127 3.4 19.2 1.0
CA C:CYS131 3.6 21.2 1.0
CA C:CYS127 3.6 20.7 1.0
N C:CYS131 3.8 18.3 1.0
N C:LEU128 4.0 20.2 1.0
N C:GLY129 4.1 20.2 1.0
N D:GLY189 4.1 20.5 1.0
C C:CYS127 4.2 22.1 1.0
N C:GLN130 4.3 19.4 1.0
CA D:SER188 4.4 20.5 1.0
CB C:ALA90 4.5 21.0 1.0
SG C:CYS86 4.5 21.7 1.0
C C:GLN130 4.5 19.8 1.0
CA C:GLY129 4.6 18.7 1.0
SG C:CYS91 4.7 21.7 1.0
N C:CYS127 4.8 19.7 1.0
CB D:SER188 4.8 20.3 1.0
C D:SER188 4.8 22.1 1.0
C C:GLY129 4.8 18.8 1.0
C C:LEU128 5.0 20.2 1.0

Iron binding site 9 out of 12 in 6vw7

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Iron binding site 9 out of 12 in the Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe601

b:32.6
occ:1.00
 FE1 D:SF4601 0.0 32.6 1.0
S4 D:SF4601 2.3 36.6 1.0
S3 D:SF4601 2.3 35.2 1.0
S2 D:SF4601 2.3 35.0 1.0
SG D:CYS489 2.4 31.6 1.0
FE4 D:SF4601 2.7 25.8 1.0
FE2 D:SF4601 2.7 33.5 1.0
FE3 D:SF4601 2.8 31.0 1.0
CB D:CYS489 3.4 27.2 1.0
N D:CYS489 3.6 32.0 1.0
CA D:CYS489 3.9 31.7 1.0
S1 D:SF4601 3.9 37.0 1.0
CB D:MET491 4.0 30.5 1.0
CG2 D:VAL289 4.0 28.3 1.0
O D:CYS489 4.1 31.6 1.0
C D:CYS489 4.2 32.2 1.0
N D:GLY492 4.4 25.3 1.0
C D:LEU488 4.5 36.9 1.0
N D:MET491 4.6 29.5 1.0
CB D:VAL289 4.7 32.3 1.0
N D:LEU488 4.8 36.3 1.0
CA D:MET491 4.8 28.3 1.0
CG D:MET491 4.9 31.2 1.0
SG D:CYS443 4.9 32.9 1.0
CG2 D:VAL271 4.9 26.0 0.7
SG D:CYS449 5.0 27.9 1.0
SG D:CYS446 5.0 37.0 1.0
N D:ALA490 5.0 33.4 1.0

Iron binding site 10 out of 12 in 6vw7

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Iron binding site 10 out of 12 in the Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Formate Dehydrogenase Fdsabg Subcomplex Fdsbg From C. Necator - Nadh Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe601

b:33.5
occ:1.00
 FE2 D:SF4601 0.0 33.5 1.0
S1 D:SF4601 2.3 37.0 1.0
S4 D:SF4601 2.3 36.6 1.0
S3 D:SF4601 2.3 35.2 1.0
SG D:CYS446 2.4 37.0 1.0
FE3 D:SF4601 2.7 31.0 1.0
FE4 D:SF4601 2.7 25.8 1.0
FE1 D:SF4601 2.7 32.6 1.0
CB D:CYS446 3.1 31.4 1.0
N D:CYS446 3.8 30.3 1.0
S2 D:SF4601 3.9 35.0 1.0
N D:LEU488 3.9 36.3 1.0
CA D:CYS446 4.0 33.0 1.0
CB D:LEU488 4.2 45.4 1.0
CB D:CYS449 4.3 26.4 1.0
CB D:LYS445 4.3 34.8 1.0
C D:LYS445 4.5 33.8 1.0
N D:CYS489 4.5 32.0 1.0
CA D:LEU488 4.5 40.0 1.0
SG D:CYS449 4.7 27.9 1.0
N D:LYS445 4.7 28.6 1.0
CA D:LYS445 4.7 31.0 1.0
SG D:CYS443 4.8 32.9 1.0
C D:SER487 4.9 34.8 1.0
C D:LEU488 4.9 36.9 1.0
CA D:SER487 4.9 32.4 1.0

Reference:

T.Young, D.Niks, S.Hakopian, T.K.Tam, R.Hille, G.Blaha. Crystallographic and Kinetic Analyses of the Fdsbg Subcomplex of the Cytosolic Formate Dehydrogenase Fdsabg From Cupriavidus Necator Journal of Biological 2020CHEMISTRY.
Page generated: Wed Aug 7 13:35:36 2024

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