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Iron in PDB 5h92: Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal

Enzymatic activity of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal

All present enzymatic activity of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal:
1.8.7.1;

Protein crystallography data

The structure of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal, PDB code: 5h92 was solved by G.Kurisu, M.Nakayama, T.Hase, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.27 / 2.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 103.414, 103.406, 122.434, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 23.2

Other elements in 5h92:

The structure of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal (pdb code 5h92). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal, PDB code: 5h92:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 5h92

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Iron binding site 1 out of 12 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:27.5
occ:1.00
 FE1 A:SF4701 0.0 27.5 1.0
S4 A:SF4701 2.3 26.9 1.0
S2 A:SF4701 2.3 24.4 1.0
SG A:CYS540 2.3 27.2 1.0
S3 A:SF4701 2.3 26.7 1.0
FE4 A:SF4701 2.7 25.6 1.0
FE3 A:SF4701 2.7 25.6 1.0
FE2 A:SF4701 2.7 27.0 1.0
CB A:CYS540 3.4 26.8 1.0
N A:CYS540 3.8 26.3 1.0
S1 A:SF4701 3.9 26.0 1.0
CA A:CYS540 4.0 25.7 1.0
CB A:ASN542 4.1 24.2 1.0
ND2 A:ASN542 4.1 28.2 1.0
C A:CYS540 4.2 24.7 1.0
O A:CYS540 4.2 23.4 1.0
C A:GLY539 4.5 26.6 1.0
N A:ASN542 4.6 25.2 1.0
SG A:CYS500 4.6 27.9 1.0
CG A:ASN542 4.6 28.8 1.0
N A:GLY539 4.7 26.5 1.0
SG A:CYS544 4.7 27.6 1.0
CB A:LEU502 4.7 29.5 1.0
SG A:CYS494 4.8 25.1 1.0
CA A:ASN542 4.9 25.3 1.0
N A:ALA503 4.9 31.4 1.0
C A:LEU502 4.9 31.0 1.0
O A:LEU502 4.9 32.0 1.0
CA A:ALA503 4.9 31.7 1.0
CA A:GLY539 5.0 25.3 1.0
N A:PRO541 5.0 23.3 1.0

Iron binding site 2 out of 12 in 5h92

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Iron binding site 2 out of 12 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:27.0
occ:1.00
 FE2 A:SF4701 0.0 27.0 1.0
SG A:CYS544 2.2 27.6 1.0
S3 A:SF4701 2.3 26.7 1.0
S1 A:SF4701 2.3 26.0 1.0
S4 A:SF4701 2.3 26.9 1.0
FE3 A:SF4701 2.6 25.6 1.0
FE1 A:SF4701 2.7 27.5 1.0
FE4 A:SF4701 2.8 25.6 1.0
CB A:CYS544 3.2 26.7 1.0
NA A:SRM702 3.8 25.8 1.0
S2 A:SF4701 3.9 24.4 1.0
C4A A:SRM702 4.0 29.6 1.0
FE A:SRM702 4.2 27.2 1.0
C1A A:SRM702 4.3 27.6 1.0
N A:CYS544 4.4 25.7 1.0
CHB A:SRM702 4.4 26.1 1.0
CB A:ASN542 4.4 24.2 1.0
CA A:CYS544 4.4 27.4 1.0
ND A:SRM702 4.4 28.0 1.0
SG A:CYS494 4.5 25.1 1.0
CB A:CYS494 4.5 23.3 1.0
C3A A:SRM702 4.5 26.6 1.0
C4D A:SRM702 4.6 27.7 1.0
SG A:CYS500 4.7 27.9 1.0
CHA A:SRM702 4.7 25.6 1.0
SG A:CYS540 4.8 27.2 1.0
C2A A:SRM702 4.9 30.2 1.0
NB A:SRM702 4.9 26.0 1.0
C1B A:SRM702 4.9 25.0 1.0

Iron binding site 3 out of 12 in 5h92

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Iron binding site 3 out of 12 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:25.6
occ:1.00
 FE3 A:SF4701 0.0 25.6 1.0
SG A:CYS494 2.2 25.1 1.0
S2 A:SF4701 2.2 24.4 1.0
S4 A:SF4701 2.3 26.9 1.0
S1 A:SF4701 2.3 26.0 1.0
FE2 A:SF4701 2.6 27.0 1.0
FE4 A:SF4701 2.7 25.6 1.0
FE1 A:SF4701 2.7 27.5 1.0
CB A:CYS494 3.2 23.3 1.0
N A:GLY539 3.8 26.5 1.0
S3 A:SF4701 3.8 26.7 1.0
N A:ALA496 4.2 25.0 1.0
CA A:ALA496 4.3 26.8 1.0
CB A:THR538 4.4 25.3 1.0
CB A:ALA496 4.5 26.2 1.0
SG A:CYS544 4.5 27.6 1.0
CB A:CYS544 4.5 26.7 1.0
CA A:GLY539 4.5 25.3 1.0
CA A:CYS494 4.5 24.6 1.0
N A:CYS540 4.6 26.3 1.0
CA A:THR538 4.6 24.9 1.0
C A:THR538 4.7 25.8 1.0
C A:CYS494 4.8 23.6 1.0
CG2 A:THR538 4.8 22.1 1.0
SG A:CYS500 4.8 27.9 1.0
N A:PRO495 4.9 23.4 1.0
SG A:CYS540 4.9 27.2 1.0
C A:GLY539 4.9 26.6 1.0

Iron binding site 4 out of 12 in 5h92

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Iron binding site 4 out of 12 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:25.6
occ:1.00
 FE4 A:SF4701 0.0 25.6 1.0
SG A:CYS500 2.2 27.9 1.0
S1 A:SF4701 2.3 26.0 1.0
S3 A:SF4701 2.3 26.7 1.0
S2 A:SF4701 2.3 24.4 1.0
FE3 A:SF4701 2.7 25.6 1.0
FE1 A:SF4701 2.7 27.5 1.0
FE2 A:SF4701 2.8 27.0 1.0
CB A:CYS500 3.3 27.6 1.0
S4 A:SF4701 4.0 26.9 1.0
N A:ALA503 4.3 31.4 1.0
CA A:ALA496 4.3 26.8 1.0
CBA A:SRM702 4.4 25.6 1.0
N A:ALA496 4.5 25.0 1.0
CDA A:SRM702 4.5 28.4 1.0
C3A A:SRM702 4.6 26.6 1.0
CB A:LEU502 4.6 29.5 1.0
SG A:CYS494 4.7 25.1 1.0
SG A:CYS540 4.7 27.2 1.0
CA A:CYS500 4.7 28.4 1.0
CA A:ALA503 4.7 31.7 1.0
CB A:ALA503 4.8 31.3 1.0
C A:LEU502 4.8 31.0 1.0
C4A A:SRM702 4.9 29.6 1.0
SG A:CYS544 4.9 27.6 1.0
C2A A:SRM702 4.9 30.2 1.0
CAA A:SRM702 4.9 30.0 1.0

Iron binding site 5 out of 12 in 5h92

Go back to Iron Binding Sites List in 5h92
Iron binding site 5 out of 12 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:27.2
occ:1.00
 FE A:SRM702 0.0 27.2 1.0
O1 A:PO4703 2.0 38.4 1.0
NB A:SRM702 2.0 26.0 1.0
NC A:SRM702 2.1 24.9 1.0
NA A:SRM702 2.1 25.8 1.0
ND A:SRM702 2.1 28.0 1.0
SG A:CYS544 2.4 27.6 1.0
C1B A:SRM702 3.0 25.0 1.0
C1C A:SRM702 3.1 26.7 1.0
C4B A:SRM702 3.1 22.3 1.0
C4A A:SRM702 3.1 29.6 1.0
C4C A:SRM702 3.1 25.6 1.0
C1A A:SRM702 3.1 27.6 1.0
C1D A:SRM702 3.1 25.9 1.0
C4D A:SRM702 3.1 27.7 1.0
P A:PO4703 3.2 45.2 1.0
O4 A:PO4703 3.3 44.9 1.0
CHC A:SRM702 3.4 23.2 1.0
CHD A:SRM702 3.4 26.3 1.0
CHA A:SRM702 3.4 25.6 1.0
CHB A:SRM702 3.4 26.1 1.0
CB A:CYS544 3.5 26.7 1.0
O2 A:PO4703 4.2 48.8 1.0
O3 A:PO4703 4.2 44.6 1.0
FE2 A:SF4701 4.2 27.0 1.0
CA A:CYS544 4.2 27.4 1.0
C2D A:SRM702 4.3 27.1 1.0
C2C A:SRM702 4.3 25.3 1.0
C3D A:SRM702 4.3 25.7 1.0
C3C A:SRM702 4.3 20.4 1.0
C3A A:SRM702 4.3 26.6 1.0
C2B A:SRM702 4.4 23.9 1.0
C3B A:SRM702 4.4 25.9 1.0
C2A A:SRM702 4.4 30.2 1.0
CAB A:SRM702 4.6 25.6 1.0
NH2 A:ARG124 4.7 25.5 1.0
NZ A:LYS276 4.7 29.9 1.0
CDB A:SRM702 4.9 23.2 1.0
NZ A:LYS278 4.9 25.9 1.0
CMA A:SRM702 5.0 27.0 1.0

Iron binding site 6 out of 12 in 5h92

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Iron binding site 6 out of 12 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:34.3
occ:1.00
 FE1 B:SF4701 0.0 34.3 1.0
S4 B:SF4701 2.3 32.6 1.0
S2 B:SF4701 2.3 34.3 1.0
S3 B:SF4701 2.3 34.8 1.0
SG B:CYS540 2.4 36.0 1.0
FE4 B:SF4701 2.7 35.2 1.0
FE3 B:SF4701 2.7 34.3 1.0
FE2 B:SF4701 2.7 32.0 1.0
CB B:CYS540 3.5 35.6 1.0
N B:CYS540 3.8 33.6 1.0
S1 B:SF4701 3.9 31.5 1.0
CA B:CYS540 4.0 35.4 1.0
CB B:ASN542 4.1 31.6 1.0
ND2 B:ASN542 4.1 33.2 1.0
O B:CYS540 4.2 34.6 1.0
C B:CYS540 4.3 34.6 1.0
C B:GLY539 4.5 34.2 1.0
CG B:ASN542 4.6 35.1 1.0
N B:ASN542 4.6 34.3 1.0
SG B:CYS500 4.6 38.2 1.0
SG B:CYS544 4.6 31.5 1.0
N B:GLY539 4.6 33.8 1.0
SG B:CYS494 4.8 31.5 1.0
CB B:LEU502 4.8 36.6 1.0
CA B:GLY539 4.8 34.4 1.0
CA B:ASN542 4.8 33.8 1.0
C B:LEU502 4.9 39.2 1.0
N B:ALA503 4.9 39.7 1.0
CA B:ALA503 4.9 39.7 1.0
O B:LEU502 5.0 40.8 1.0

Iron binding site 7 out of 12 in 5h92

Go back to Iron Binding Sites List in 5h92
Iron binding site 7 out of 12 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:32.0
occ:1.00
 FE2 B:SF4701 0.0 32.0 1.0
SG B:CYS544 2.2 31.5 1.0
S3 B:SF4701 2.3 34.8 1.0
S4 B:SF4701 2.3 32.6 1.0
S1 B:SF4701 2.3 31.5 1.0
FE3 B:SF4701 2.6 34.3 1.0
FE1 B:SF4701 2.7 34.3 1.0
FE4 B:SF4701 2.7 35.2 1.0
CB B:CYS544 3.1 28.9 1.0
NA B:SRM702 3.9 35.9 1.0
S2 B:SF4701 3.9 34.3 1.0
C4A B:SRM702 4.1 36.1 1.0
FE B:SRM702 4.3 33.9 1.0
C1A B:SRM702 4.3 35.4 1.0
N B:CYS544 4.3 30.5 1.0
CA B:CYS544 4.3 29.8 1.0
ND B:SRM702 4.4 32.4 1.0
CHB B:SRM702 4.4 33.1 1.0
CB B:ASN542 4.4 31.6 1.0
CB B:CYS494 4.4 31.7 1.0
SG B:CYS494 4.5 31.5 1.0
C3A B:SRM702 4.6 35.1 1.0
C4D B:SRM702 4.7 35.4 1.0
SG B:CYS500 4.8 38.2 1.0
CHA B:SRM702 4.8 33.5 1.0
NB B:SRM702 4.9 31.3 1.0
SG B:CYS540 4.9 36.0 1.0
C2A B:SRM702 4.9 37.4 1.0
C1B B:SRM702 4.9 33.5 1.0

Iron binding site 8 out of 12 in 5h92

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Iron binding site 8 out of 12 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:34.3
occ:1.00
 FE3 B:SF4701 0.0 34.3 1.0
SG B:CYS494 2.3 31.5 1.0
S2 B:SF4701 2.3 34.3 1.0
S4 B:SF4701 2.3 32.6 1.0
S1 B:SF4701 2.3 31.5 1.0
FE2 B:SF4701 2.6 32.0 1.0
FE1 B:SF4701 2.7 34.3 1.0
FE4 B:SF4701 2.7 35.2 1.0
CB B:CYS494 3.1 31.7 1.0
N B:GLY539 3.8 33.8 1.0
S3 B:SF4701 3.8 34.8 1.0
N B:ALA496 4.2 34.8 1.0
CA B:ALA496 4.3 35.2 1.0
CB B:ALA496 4.3 34.4 1.0
CB B:THR538 4.4 32.5 1.0
CB B:CYS544 4.4 28.9 1.0
SG B:CYS544 4.4 31.5 1.0
CA B:GLY539 4.4 34.4 1.0
CA B:CYS494 4.5 31.6 1.0
N B:CYS540 4.6 33.6 1.0
CA B:THR538 4.6 32.7 1.0
C B:CYS494 4.7 33.4 1.0
C B:THR538 4.7 33.9 1.0
CG2 B:THR538 4.7 32.1 1.0
N B:PRO495 4.8 32.9 1.0
C B:GLY539 4.9 34.2 1.0
SG B:CYS500 4.9 38.2 1.0
CD B:PRO495 5.0 32.8 1.0
SG B:CYS540 5.0 36.0 1.0

Iron binding site 9 out of 12 in 5h92

Go back to Iron Binding Sites List in 5h92
Iron binding site 9 out of 12 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:35.2
occ:1.00
 FE4 B:SF4701 0.0 35.2 1.0
S1 B:SF4701 2.2 31.5 1.0
SG B:CYS500 2.3 38.2 1.0
S3 B:SF4701 2.3 34.8 1.0
S2 B:SF4701 2.3 34.3 1.0
FE1 B:SF4701 2.7 34.3 1.0
FE3 B:SF4701 2.7 34.3 1.0
FE2 B:SF4701 2.7 32.0 1.0
CB B:CYS500 3.2 37.7 1.0
S4 B:SF4701 3.9 32.6 1.0
CA B:ALA496 4.3 35.2 1.0
N B:ALA503 4.4 39.7 1.0
CBA B:SRM702 4.4 32.1 1.0
N B:ALA496 4.4 34.8 1.0
CDA B:SRM702 4.5 37.1 1.0
C3A B:SRM702 4.6 35.1 1.0
CB B:ALA503 4.7 38.1 1.0
CA B:CYS500 4.7 38.8 1.0
CA B:ALA503 4.7 39.7 1.0
SG B:CYS494 4.7 31.5 1.0
CB B:LEU502 4.7 36.6 1.0
SG B:CYS540 4.7 36.0 1.0
C B:LEU502 4.8 39.2 1.0
SG B:CYS544 4.9 31.5 1.0
C4A B:SRM702 4.9 36.1 1.0
C2A B:SRM702 4.9 37.4 1.0

Iron binding site 10 out of 12 in 5h92

Go back to Iron Binding Sites List in 5h92
Iron binding site 10 out of 12 in the Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the Complex Between Maize Sulfite Reductase and Ferredoxin in the Form-3 Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe702

b:33.9
occ:1.00
 FE B:SRM702 0.0 33.9 1.0
O1 B:PO4703 1.8 44.0 1.0
NC B:SRM702 2.1 31.0 1.0
NB B:SRM702 2.1 31.3 1.0
ND B:SRM702 2.1 32.4 1.0
NA B:SRM702 2.1 35.9 1.0
SG B:CYS544 2.5 31.5 1.0
P B:PO4703 3.0 42.6 1.0
C4B B:SRM702 3.0 28.4 1.0
C4C B:SRM702 3.1 31.1 1.0
C4D B:SRM702 3.1 35.4 1.0
C1C B:SRM702 3.1 32.7 1.0
C1A B:SRM702 3.1 35.4 1.0
C1D B:SRM702 3.1 33.0 1.0
C1B B:SRM702 3.1 33.5 1.0
C4A B:SRM702 3.1 36.1 1.0
O4 B:PO4703 3.2 46.5 1.0
CHC B:SRM702 3.3 31.4 1.0
CHA B:SRM702 3.4 33.5 1.0
CHD B:SRM702 3.4 31.6 1.0
CHB B:SRM702 3.5 33.1 1.0
CB B:CYS544 3.5 28.9 1.0
O3 B:PO4703 3.8 49.6 1.0
O2 B:PO4703 4.1 51.2 1.0
CA B:CYS544 4.2 29.8 1.0
FE2 B:SF4701 4.3 32.0 1.0
C3D B:SRM702 4.3 33.8 1.0
C3C B:SRM702 4.3 28.5 1.0
C2D B:SRM702 4.3 33.0 1.0
C2C B:SRM702 4.3 29.8 1.0
C3A B:SRM702 4.4 35.1 1.0
C2B B:SRM702 4.4 32.2 1.0
C3B B:SRM702 4.4 31.8 1.0
C2A B:SRM702 4.4 37.4 1.0
NH2 B:ARG124 4.6 33.0 1.0
NZ B:LYS276 4.7 37.8 1.0
CAB B:SRM702 4.7 32.0 1.0
NZ B:LYS278 4.8 27.8 1.0
CDB B:SRM702 5.0 32.1 1.0

Reference:

J.Y.Kim, M.Nakayama, H.Toyota, G.Kurisu, T.Hase. Structural and Mutational Studies of An Electron Transfer Complex of Maize Sulfite Reductase and Ferredoxin. J.Biochem. V. 160 101 2016.
ISSN: ISSN 0021-924X
PubMed: 26920048
DOI: 10.1093/JB/MVW016
Page generated: Tue Aug 6 01:52:33 2024

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