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Iron in PDB 3b0h: Assimilatory Nitrite Reductase (NII4) From Tobbaco Root

Enzymatic activity of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root

All present enzymatic activity of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root:
1.7.7.1;

Protein crystallography data

The structure of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root, PDB code: 3b0h was solved by S.Nakano, M.Takahashi, A.Sakamoto, H.Morikawa, K.Katayanagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.25 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.343, 112.085, 92.503, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 24.1

Other elements in 3b0h:

The structure of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root also contains other interesting chemical elements:

Potassium (K) 2 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Assimilatory Nitrite Reductase (NII4) From Tobbaco Root (pdb code 3b0h). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Assimilatory Nitrite Reductase (NII4) From Tobbaco Root, PDB code: 3b0h:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 3b0h

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Iron binding site 1 out of 10 in the Assimilatory Nitrite Reductase (NII4) From Tobbaco Root


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:19.5
occ:1.00
 FE A:SRM601 0.0 19.5 1.0
NB A:SRM601 2.0 18.6 1.0
NA A:SRM601 2.1 24.0 1.0
ND A:SRM601 2.1 22.0 1.0
NC A:SRM601 2.2 21.1 1.0
SG A:CYS486 2.4 19.4 1.0
O A:HOH1001 2.5 13.3 1.0
C1B A:SRM601 3.0 20.2 1.0
C4A A:SRM601 3.0 24.1 1.0
C4B A:SRM601 3.0 17.6 1.0
C1C A:SRM601 3.1 18.7 1.0
C1D A:SRM601 3.1 21.4 1.0
C4D A:SRM601 3.1 22.2 1.0
C1A A:SRM601 3.1 23.0 1.0
C4C A:SRM601 3.1 18.8 1.0
CHB A:SRM601 3.2 23.0 1.0
CHC A:SRM601 3.3 18.0 1.0
CHD A:SRM601 3.3 20.4 1.0
CHA A:SRM601 3.4 21.5 1.0
CB A:CYS486 3.5 17.9 1.0
FE2 A:SF4602 4.1 22.9 1.0
C3B A:SRM601 4.2 15.5 1.0
O A:HOH1069 4.3 26.3 1.0
C2B A:SRM601 4.3 17.4 1.0
C3A A:SRM601 4.3 23.7 1.0
CA A:CYS486 4.3 18.4 1.0
C2D A:SRM601 4.4 20.7 1.0
C2C A:SRM601 4.4 17.1 1.0
C2A A:SRM601 4.4 24.9 1.0
C3D A:SRM601 4.4 22.0 1.0
NZ A:LYS224 4.4 15.1 1.0
C3C A:SRM601 4.4 17.2 1.0
NH2 A:ARG109 4.8 11.1 1.0
CDB A:SRM601 4.9 17.8 1.0
CAB A:SRM601 4.9 14.9 1.0
CMA A:SRM601 5.0 22.6 1.0

Iron binding site 2 out of 10 in 3b0h

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Iron binding site 2 out of 10 in the Assimilatory Nitrite Reductase (NII4) From Tobbaco Root


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:20.6
occ:1.00
 FE1 A:SF4602 0.0 20.6 1.0
S3 A:SF4602 2.3 19.8 1.0
S2 A:SF4602 2.3 21.4 1.0
S4 A:SF4602 2.3 23.4 1.0
SG A:CYS482 2.5 22.3 1.0
FE3 A:SF4602 2.7 21.5 1.0
FE2 A:SF4602 2.8 22.9 1.0
FE4 A:SF4602 2.8 19.1 1.0
CB A:CYS482 3.5 23.0 1.0
N A:CYS482 3.6 22.5 1.0
CA A:CYS482 3.9 22.7 1.0
S1 A:SF4602 4.0 19.7 1.0
CB A:ASN484 4.1 17.5 1.0
ND2 A:ASN484 4.1 14.4 1.0
O A:CYS482 4.2 22.8 1.0
C A:GLY481 4.2 22.7 1.0
C A:CYS482 4.3 22.8 1.0
CG A:ASN484 4.5 16.7 1.0
CA A:GLY481 4.5 22.5 1.0
SG A:CYS447 4.5 25.3 1.0
N A:GLY481 4.6 22.3 1.0
N A:ALA450 4.6 24.4 1.0
C A:LYS449 4.7 24.8 1.0
SG A:CYS486 4.7 19.4 1.0
CA A:ALA450 4.7 24.7 1.0
O A:LYS449 4.8 24.8 1.0
N A:ASN484 4.8 19.9 1.0
CB A:LYS449 4.8 25.6 1.0
SG A:CYS441 4.8 18.7 1.0
O A:GLY481 4.9 22.2 1.0
CA A:ASN484 5.0 18.2 1.0

Iron binding site 3 out of 10 in 3b0h

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Iron binding site 3 out of 10 in the Assimilatory Nitrite Reductase (NII4) From Tobbaco Root


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:22.9
occ:1.00
 FE2 A:SF4602 0.0 22.9 1.0
SG A:CYS486 2.3 19.4 1.0
S1 A:SF4602 2.3 19.7 1.0
S3 A:SF4602 2.3 19.8 1.0
S4 A:SF4602 2.3 23.4 1.0
FE4 A:SF4602 2.6 19.1 1.0
FE3 A:SF4602 2.7 21.5 1.0
FE1 A:SF4602 2.8 20.6 1.0
CB A:CYS486 3.1 17.9 1.0
S2 A:SF4602 3.8 21.4 1.0
NA A:SRM601 3.9 24.0 1.0
CHB A:SRM601 4.0 23.0 1.0
C4A A:SRM601 4.0 24.1 1.0
FE A:SRM601 4.1 19.5 1.0
N A:CYS486 4.2 18.4 1.0
CB A:ASN484 4.2 17.5 1.0
CA A:CYS486 4.3 18.4 1.0
C1A A:SRM601 4.3 23.0 1.0
C3A A:SRM601 4.5 23.7 1.0
ND A:SRM601 4.6 22.0 1.0
C4D A:SRM601 4.6 22.2 1.0
SG A:CYS441 4.6 18.7 1.0
C1B A:SRM601 4.6 20.2 1.0
ND2 A:ASN484 4.7 14.4 1.0
CB A:CYS441 4.7 18.2 1.0
NB A:SRM601 4.8 18.6 1.0
CHA A:SRM601 4.8 21.5 1.0
SG A:CYS447 4.8 25.3 1.0
SG A:CYS482 4.9 22.3 1.0

Iron binding site 4 out of 10 in 3b0h

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Iron binding site 4 out of 10 in the Assimilatory Nitrite Reductase (NII4) From Tobbaco Root


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:21.5
occ:1.00
 FE3 A:SF4602 0.0 21.5 1.0
SG A:CYS447 2.2 25.3 1.0
S2 A:SF4602 2.3 21.4 1.0
S1 A:SF4602 2.3 19.7 1.0
S4 A:SF4602 2.3 23.4 1.0
FE4 A:SF4602 2.7 19.1 1.0
FE2 A:SF4602 2.7 22.9 1.0
FE1 A:SF4602 2.7 20.6 1.0
CB A:CYS447 3.1 22.8 1.0
S3 A:SF4602 3.9 19.8 1.0
C3A A:SRM601 4.3 23.7 1.0
CBA A:SRM601 4.4 24.2 1.0
N A:ALA450 4.4 24.4 1.0
CA A:CYS447 4.5 22.9 1.0
C4A A:SRM601 4.6 24.1 1.0
CDA A:SRM601 4.7 25.4 1.0
SG A:CYS441 4.7 18.7 1.0
CB A:LYS449 4.8 25.6 1.0
CB A:ALA450 4.8 24.0 1.0
CHB A:SRM601 4.8 23.0 1.0
CA A:ALA450 4.9 24.7 1.0
N A:GLY443 4.9 20.0 1.0
C A:LYS449 4.9 24.8 1.0
SG A:CYS482 4.9 22.3 1.0
SG A:CYS486 4.9 19.4 1.0
C2A A:SRM601 5.0 24.9 1.0
CB A:THR442 5.0 17.6 1.0

Iron binding site 5 out of 10 in 3b0h

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Iron binding site 5 out of 10 in the Assimilatory Nitrite Reductase (NII4) From Tobbaco Root


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:19.1
occ:1.00
 FE4 A:SF4602 0.0 19.1 1.0
SG A:CYS441 2.3 18.7 1.0
S2 A:SF4602 2.3 21.4 1.0
S1 A:SF4602 2.3 19.7 1.0
S3 A:SF4602 2.3 19.8 1.0
FE2 A:SF4602 2.6 22.9 1.0
FE3 A:SF4602 2.7 21.5 1.0
FE1 A:SF4602 2.8 20.6 1.0
CB A:CYS441 3.2 18.2 1.0
N A:GLY481 3.7 22.3 1.0
S4 A:SF4602 3.9 23.4 1.0
CA A:GLY481 4.1 22.5 1.0
N A:GLY443 4.2 20.0 1.0
CB A:CYS486 4.4 17.9 1.0
OG1 A:THR480 4.4 22.5 1.0
N A:THR442 4.5 19.0 1.0
CA A:CYS441 4.5 19.2 1.0
SG A:CYS486 4.6 19.4 1.0
C A:CYS441 4.6 19.1 1.0
N A:CYS482 4.6 22.5 1.0
C A:GLY481 4.7 22.7 1.0
C A:THR480 4.8 22.5 1.0
CA A:GLY443 4.8 20.8 1.0
SG A:CYS447 4.8 25.3 1.0
CA A:THR480 5.0 22.5 1.0

Iron binding site 6 out of 10 in 3b0h

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Iron binding site 6 out of 10 in the Assimilatory Nitrite Reductase (NII4) From Tobbaco Root


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:21.4
occ:1.00
 FE B:SRM601 0.0 21.4 1.0
NC B:SRM601 2.1 17.3 1.0
ND B:SRM601 2.1 20.3 1.0
NA B:SRM601 2.1 22.5 1.0
NB B:SRM601 2.1 17.2 1.0
O B:HOH705 2.3 11.1 1.0
SG B:CYS486 2.4 18.4 1.0
C1D B:SRM601 2.9 19.9 1.0
C4C B:SRM601 3.0 17.4 1.0
C4D B:SRM601 3.0 20.9 1.0
C1B B:SRM601 3.0 17.0 1.0
C4A B:SRM601 3.1 22.2 1.0
C1A B:SRM601 3.1 22.8 1.0
C1C B:SRM601 3.1 15.8 1.0
C4B B:SRM601 3.1 14.5 1.0
CHD B:SRM601 3.3 17.3 1.0
CHB B:SRM601 3.4 18.2 1.0
CHC B:SRM601 3.4 15.6 1.0
CHA B:SRM601 3.4 20.2 1.0
CB B:CYS486 3.5 18.4 1.0
FE2 B:SF4602 4.2 20.6 1.0
C2D B:SRM601 4.2 18.7 1.0
C3B B:SRM601 4.3 14.4 1.0
C3D B:SRM601 4.3 21.0 1.0
NZ B:LYS224 4.3 11.4 1.0
C3C B:SRM601 4.3 17.6 1.0
CA B:CYS486 4.3 18.3 1.0
C2C B:SRM601 4.3 16.0 1.0
C2B B:SRM601 4.3 15.0 1.0
C3A B:SRM601 4.3 20.8 1.0
C2A B:SRM601 4.3 22.0 1.0
NH2 B:ARG109 4.9 6.4 1.0
CMA B:SRM601 4.9 19.7 1.0
CDB B:SRM601 4.9 14.8 1.0

Iron binding site 7 out of 10 in 3b0h

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Iron binding site 7 out of 10 in the Assimilatory Nitrite Reductase (NII4) From Tobbaco Root


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:21.3
occ:1.00
 FE1 B:SF4602 0.0 21.3 1.0
S2 B:SF4602 2.3 21.9 1.0
S3 B:SF4602 2.3 21.8 1.0
S4 B:SF4602 2.3 19.4 1.0
SG B:CYS482 2.4 22.7 1.0
FE3 B:SF4602 2.7 23.2 1.0
FE4 B:SF4602 2.7 21.9 1.0
FE2 B:SF4602 2.8 20.6 1.0
CB B:CYS482 3.4 22.3 1.0
N B:CYS482 3.7 22.2 1.0
S1 B:SF4602 3.9 20.6 1.0
CA B:CYS482 4.0 22.6 1.0
CB B:ASN484 4.1 22.3 1.0
ND2 B:ASN484 4.2 21.1 1.0
C B:GLY481 4.2 22.2 1.0
CB B:LYS449 4.4 28.2 1.0
C B:CYS482 4.4 22.9 1.0
O B:CYS482 4.4 22.8 1.0
CA B:GLY481 4.5 21.6 1.0
N B:GLY481 4.5 21.1 1.0
SG B:CYS447 4.5 25.1 1.0
CG B:ASN484 4.6 21.8 1.0
C B:LYS449 4.6 27.1 1.0
O B:LYS449 4.7 26.5 1.0
SG B:CYS486 4.7 18.4 1.0
N B:ALA450 4.8 26.9 1.0
CA B:ALA450 4.8 26.5 1.0
N B:ASN484 4.9 22.9 1.0
SG B:CYS441 4.9 18.6 1.0
O B:GLY481 4.9 22.8 1.0

Iron binding site 8 out of 10 in 3b0h

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Iron binding site 8 out of 10 in the Assimilatory Nitrite Reductase (NII4) From Tobbaco Root


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:20.6
occ:1.00
 FE2 B:SF4602 0.0 20.6 1.0
SG B:CYS486 2.2 18.4 1.0
S4 B:SF4602 2.3 19.4 1.0
S3 B:SF4602 2.3 21.8 1.0
S1 B:SF4602 2.3 20.6 1.0
FE4 B:SF4602 2.7 21.9 1.0
FE3 B:SF4602 2.8 23.2 1.0
FE1 B:SF4602 2.8 21.3 1.0
CB B:CYS486 3.0 18.4 1.0
C4A B:SRM601 3.7 22.2 1.0
NA B:SRM601 3.8 22.5 1.0
S2 B:SF4602 3.9 21.9 1.0
N B:CYS486 4.1 20.1 1.0
FE B:SRM601 4.2 21.4 1.0
CA B:CYS486 4.2 18.3 1.0
CB B:ASN484 4.2 22.3 1.0
ND B:SRM601 4.3 20.3 1.0
CHB B:SRM601 4.3 18.2 1.0
C1A B:SRM601 4.3 22.8 1.0
C3A B:SRM601 4.4 20.8 1.0
CHA B:SRM601 4.5 20.2 1.0
C1B B:SRM601 4.5 17.0 1.0
SG B:CYS441 4.6 18.6 1.0
CB B:CYS441 4.7 20.2 1.0
ND2 B:ASN484 4.7 21.1 1.0
C4D B:SRM601 4.7 20.9 1.0
NB B:SRM601 4.7 17.2 1.0
SG B:CYS482 4.7 22.7 1.0
SG B:CYS447 4.8 25.1 1.0
C2A B:SRM601 5.0 22.0 1.0

Iron binding site 9 out of 10 in 3b0h

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Iron binding site 9 out of 10 in the Assimilatory Nitrite Reductase (NII4) From Tobbaco Root


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:23.2
occ:1.00
 FE3 B:SF4602 0.0 23.2 1.0
SG B:CYS447 2.3 25.1 1.0
S4 B:SF4602 2.3 19.4 1.0
S2 B:SF4602 2.3 21.9 1.0
S1 B:SF4602 2.3 20.6 1.0
FE1 B:SF4602 2.7 21.3 1.0
FE4 B:SF4602 2.7 21.9 1.0
FE2 B:SF4602 2.8 20.6 1.0
CB B:CYS447 3.2 24.7 1.0
S3 B:SF4602 3.9 21.8 1.0
C3A B:SRM601 4.3 20.8 1.0
CB B:LYS449 4.4 28.2 1.0
CBA B:SRM601 4.4 20.1 1.0
C4A B:SRM601 4.4 22.2 1.0
N B:ALA450 4.5 26.9 1.0
CA B:CYS447 4.6 25.0 1.0
SG B:CYS441 4.7 18.6 1.0
N B:GLY443 4.7 20.5 1.0
CDA B:SRM601 4.7 24.3 1.0
SG B:CYS482 4.8 22.7 1.0
CB B:ALA450 4.8 26.5 1.0
SG B:CYS486 4.9 18.4 1.0
C B:LYS449 4.9 27.1 1.0
CA B:ALA450 4.9 26.5 1.0
CG B:LYS449 5.0 28.8 1.0
N B:LYS449 5.0 26.9 1.0
CA B:LYS449 5.0 27.6 1.0

Iron binding site 10 out of 10 in 3b0h

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Iron binding site 10 out of 10 in the Assimilatory Nitrite Reductase (NII4) From Tobbaco Root


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Assimilatory Nitrite Reductase (NII4) From Tobbaco Root within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe602

b:21.9
occ:1.00
 FE4 B:SF4602 0.0 21.9 1.0
S2 B:SF4602 2.3 21.9 1.0
SG B:CYS441 2.3 18.6 1.0
S1 B:SF4602 2.3 20.6 1.0
S3 B:SF4602 2.3 21.8 1.0
FE2 B:SF4602 2.7 20.6 1.0
FE3 B:SF4602 2.7 23.2 1.0
FE1 B:SF4602 2.7 21.3 1.0
CB B:CYS441 3.2 20.2 1.0
N B:GLY481 3.5 21.1 1.0
S4 B:SF4602 3.9 19.4 1.0
CA B:GLY481 4.0 21.6 1.0
N B:GLY443 4.0 20.5 1.0
OG1 B:THR480 4.3 20.4 1.0
CB B:CYS486 4.4 18.4 1.0
N B:THR442 4.4 20.7 1.0
CA B:CYS441 4.5 20.5 1.0
SG B:CYS486 4.6 18.4 1.0
N B:CYS482 4.6 22.2 1.0
CA B:GLY443 4.6 21.0 1.0
C B:THR480 4.6 21.3 1.0
C B:CYS441 4.6 20.6 1.0
C B:GLY481 4.7 22.2 1.0
CA B:THR480 4.8 20.8 1.0
SG B:CYS447 4.9 25.1 1.0
SG B:CYS482 5.0 22.7 1.0

Reference:

S.Nakano, M.Takahashi, A.Sakamoto, H.Morikawa, K.Katayanagi. Structure-Function Relationship of Assimilatory Nitrite Reductases From the Leaf and Root of Tobacco Based on High Resolution Structures Protein Sci. V. 21 383 2012.
ISSN: ISSN 0961-8368
PubMed: 22238192
DOI: 10.1002/PRO.2025
Page generated: Sun Aug 4 07:28:01 2024

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