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Iron in PDB 3vkr: Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose

Enzymatic activity of Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose

All present enzymatic activity of Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose:
1.7.7.1;

Protein crystallography data

The structure of Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose, PDB code: 3vkr 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) 37.22 / 1.60
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 134.165, 134.165, 78.002, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 16.5

Other elements in 3vkr:

The structure of Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose (pdb code 3vkr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose, PDB code: 3vkr:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3vkr

Go back to Iron Binding Sites List in 3vkr
Iron binding site 1 out of 5 in the Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose


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 (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:7.3
occ:1.00
 FE A:SRM601 0.0 7.3 1.0
N A:NO2606 1.9 19.4 1.0
NB A:SRM601 2.0 5.8 1.0
NA A:SRM601 2.0 7.1 1.0
ND A:SRM601 2.0 5.4 1.0
NC A:SRM601 2.1 6.2 1.0
SG A:CYS485 2.4 6.7 1.0
O2 A:NO2606 3.0 22.1 1.0
O1 A:NO2606 3.0 19.5 1.0
C4A A:SRM601 3.0 5.9 1.0
C1B A:SRM601 3.0 5.1 1.0
C4D A:SRM601 3.0 7.2 1.0
C4B A:SRM601 3.0 6.1 1.0
C1D A:SRM601 3.0 6.4 1.0
C1C A:SRM601 3.0 6.0 1.0
C4C A:SRM601 3.0 6.6 1.0
C1A A:SRM601 3.1 7.5 1.0
CHB A:SRM601 3.3 5.9 1.0
CHC A:SRM601 3.4 6.0 1.0
CB A:CYS485 3.4 5.8 1.0
CHA A:SRM601 3.4 6.9 1.0
CHD A:SRM601 3.4 7.4 1.0
FE4 A:SF4602 4.2 6.9 1.0
CA A:CYS485 4.2 6.2 1.0
C3B A:SRM601 4.3 6.1 1.0
C3D A:SRM601 4.3 7.3 1.0
C2B A:SRM601 4.3 6.0 1.0
C2D A:SRM601 4.3 7.8 1.0
C3A A:SRM601 4.3 6.2 1.0
C2C A:SRM601 4.3 6.7 1.0
C2A A:SRM601 4.3 7.7 1.0
C3C A:SRM601 4.3 6.2 1.0
O A:HOH1054 4.4 17.5 1.0
NZ A:LYS224 4.4 7.8 1.0
NH2 A:ARG109 4.8 7.4 1.0
CMA A:SRM601 4.9 8.2 1.0
CDB A:SRM601 4.9 6.2 1.0
CAB A:SRM601 5.0 6.3 1.0
N A:CYS485 5.0 6.3 1.0

Iron binding site 2 out of 5 in 3vkr

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Iron binding site 2 out of 5 in the Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose


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 (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:7.2
occ:1.00
 FE1 A:SF4602 0.0 7.2 1.0
S3 A:SF4602 2.3 7.2 1.0
SG A:CYS481 2.3 7.6 1.0
S4 A:SF4602 2.3 7.9 1.0
S2 A:SF4602 2.3 7.3 1.0
FE3 A:SF4602 2.7 7.1 1.0
FE4 A:SF4602 2.7 6.9 1.0
FE2 A:SF4602 2.8 6.9 1.0
CB A:CYS481 3.4 7.3 1.0
N A:CYS481 3.6 7.3 1.0
CA A:CYS481 3.9 7.3 1.0
S1 A:SF4602 3.9 7.6 1.0
CB A:ASN483 4.1 7.9 1.0
O A:CYS481 4.2 7.1 1.0
C A:GLY480 4.2 7.5 1.0
C A:CYS481 4.3 7.8 1.0
ND2 A:ASN483 4.3 8.6 1.0
SG A:CYS446 4.5 7.9 1.0
N A:GLY480 4.6 7.2 1.0
CA A:GLY480 4.6 7.1 1.0
N A:ASN483 4.6 7.2 1.0
CB A:GLN448 4.7 11.1 1.0
CG A:ASN483 4.7 8.8 1.0
SG A:CYS485 4.7 6.7 1.0
N A:ALA449 4.7 8.5 1.0
CA A:ALA449 4.7 7.5 1.0
C A:GLN448 4.8 9.3 1.0
CA A:ASN483 4.9 7.6 1.0
SG A:CYS440 4.9 7.0 1.0
N A:THR484 4.9 7.4 1.0
O A:GLY480 5.0 7.6 1.0
O A:GLN448 5.0 9.6 1.0

Iron binding site 3 out of 5 in 3vkr

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Iron binding site 3 out of 5 in the Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose


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 (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:6.9
occ:1.00
 FE2 A:SF4602 0.0 6.9 1.0
S4 A:SF4602 2.3 7.9 1.0
S1 A:SF4602 2.3 7.6 1.0
SG A:CYS440 2.3 7.0 1.0
S3 A:SF4602 2.3 7.2 1.0
FE4 A:SF4602 2.6 6.9 1.0
FE3 A:SF4602 2.7 7.1 1.0
FE1 A:SF4602 2.8 7.2 1.0
CB A:CYS440 3.3 7.0 1.0
N A:GLY480 3.7 7.2 1.0
S2 A:SF4602 3.9 7.3 1.0
N A:GLY442 4.1 6.5 1.0
CA A:GLY480 4.1 7.1 1.0
OG1 A:THR479 4.2 7.1 1.0
N A:THR441 4.5 6.3 1.0
CB A:CYS485 4.5 5.8 1.0
N A:CYS481 4.6 7.3 1.0
SG A:CYS485 4.6 6.7 1.0
CA A:CYS440 4.6 6.6 1.0
CA A:GLY442 4.6 6.8 1.0
C A:CYS440 4.7 6.6 1.0
C A:GLY480 4.7 7.5 1.0
C A:THR479 4.7 7.4 1.0
SG A:CYS446 4.9 7.9 1.0
CA A:THR479 4.9 6.9 1.0
SG A:CYS481 5.0 7.6 1.0

Iron binding site 4 out of 5 in 3vkr

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Iron binding site 4 out of 5 in the Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose


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 (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:7.1
occ:1.00
 FE3 A:SF4602 0.0 7.1 1.0
S1 A:SF4602 2.3 7.6 1.0
SG A:CYS446 2.3 7.9 1.0
S2 A:SF4602 2.3 7.3 1.0
S4 A:SF4602 2.3 7.9 1.0
FE1 A:SF4602 2.7 7.2 1.0
FE4 A:SF4602 2.7 6.9 1.0
FE2 A:SF4602 2.7 6.9 1.0
CB A:CYS446 3.2 8.4 1.0
S3 A:SF4602 3.9 7.2 1.0
C3A A:SRM601 4.3 6.2 1.0
CBA A:SRM601 4.4 6.5 1.0
N A:ALA449 4.4 8.5 1.0
CB A:ALA449 4.6 8.3 1.0
CA A:CYS446 4.6 8.5 1.0
SG A:CYS481 4.6 7.6 1.0
C4A A:SRM601 4.7 5.9 1.0
CB A:GLN448 4.7 11.1 1.0
CA A:ALA449 4.8 7.5 1.0
N A:GLY442 4.8 6.5 1.0
SG A:CYS440 4.8 7.0 1.0
CDA A:SRM601 5.0 9.4 1.0
SG A:CYS485 5.0 6.7 1.0
O A:HOH2052 5.0 28.2 1.0
C A:GLN448 5.0 9.3 1.0

Iron binding site 5 out of 5 in 3vkr

Go back to Iron Binding Sites List in 3vkr
Iron binding site 5 out of 5 in the Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose


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 (NII3) - NO2 Complex From Tobbaco Leaf Analysed with High X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:6.9
occ:1.00
 FE4 A:SF4602 0.0 6.9 1.0
S2 A:SF4602 2.3 7.3 1.0
S1 A:SF4602 2.3 7.6 1.0
SG A:CYS485 2.3 6.7 1.0
S3 A:SF4602 2.3 7.2 1.0
FE2 A:SF4602 2.6 6.9 1.0
FE3 A:SF4602 2.7 7.1 1.0
FE1 A:SF4602 2.7 7.2 1.0
CB A:CYS485 3.2 5.8 1.0
NA A:SRM601 3.8 7.1 1.0
C4A A:SRM601 3.8 5.9 1.0
S4 A:SF4602 3.9 7.9 1.0
CHB A:SRM601 4.1 5.9 1.0
FE A:SRM601 4.2 7.3 1.0
N A:CYS485 4.2 6.3 1.0
C1A A:SRM601 4.3 7.5 1.0
CB A:ASN483 4.3 7.9 1.0
CA A:CYS485 4.3 6.2 1.0
C3A A:SRM601 4.3 6.2 1.0
ND A:SRM601 4.6 5.4 1.0
C1B A:SRM601 4.6 5.1 1.0
SG A:CYS440 4.6 7.0 1.0
NB A:SRM601 4.7 5.8 1.0
SG A:CYS481 4.7 7.6 1.0
CB A:CYS440 4.7 7.0 1.0
SG A:CYS446 4.8 7.9 1.0
CHA A:SRM601 4.8 6.9 1.0
ND2 A:ASN483 4.9 8.6 1.0
C4D A:SRM601 4.9 7.2 1.0
C2A A:SRM601 5.0 7.7 1.0

Reference:

S.Nakano, M.Takahashi, A.Sakamoto, H.Morikawa, K.Katayanagi. The Reductive Reaction Mechanism of Tobacco Nitrite Reductase Derived From A Combination of Crystal Structures and Ultraviolet-Visible Microspectroscopy Proteins V. 80 2035 2012.
ISSN: ISSN 0887-3585
PubMed: 22499059
DOI: 10.1002/PROT.24094
Page generated: Sun Aug 4 21:55:26 2024

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