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

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

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

Protein crystallography data

The structure of Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with Low X-Ray Dose, PDB code: 3vkp 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) 29.25 / 1.40
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.107, 133.107, 77.796, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 18.9

Other elements in 3vkp:

The structure of Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with Low 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 Low X-Ray Dose (pdb code 3vkp). 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 Low X-Ray Dose, PDB code: 3vkp:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3vkp

Go back to Iron Binding Sites List in 3vkp
Iron binding site 1 out of 5 in the Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with Low 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 Low X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:8.7
occ:1.00
FE A:SRM601 0.0 8.7 1.0
N A:NO2606 1.9 14.5 1.0
NB A:SRM601 2.0 7.9 1.0
ND A:SRM601 2.0 9.3 1.0
NA A:SRM601 2.0 8.6 1.0
NC A:SRM601 2.0 8.5 1.0
SG A:CYS485 2.4 8.8 1.0
O2 A:NO2606 2.8 16.0 1.0
C4A A:SRM601 3.0 8.8 1.0
C1B A:SRM601 3.0 8.1 1.0
C4D A:SRM601 3.0 9.8 1.0
C1C A:SRM601 3.0 8.4 1.0
C1D A:SRM601 3.0 9.8 1.0
C4B A:SRM601 3.0 7.4 1.0
C4C A:SRM601 3.0 9.5 1.0
C1A A:SRM601 3.0 8.9 1.0
O1 A:NO2606 3.1 16.6 1.0
CHB A:SRM601 3.3 7.9 1.0
CHC A:SRM601 3.4 7.7 1.0
CHD A:SRM601 3.4 9.7 1.0
CHA A:SRM601 3.4 9.6 1.0
CB A:CYS485 3.4 8.5 1.0
FE4 A:SF4602 4.1 8.4 1.0
CA A:CYS485 4.2 8.2 1.0
C3B A:SRM601 4.3 9.0 1.0
C3D A:SRM601 4.3 9.1 1.0
C2A A:SRM601 4.3 8.8 1.0
C3A A:SRM601 4.3 8.7 1.0
C2C A:SRM601 4.3 8.6 1.0
C2D A:SRM601 4.3 9.3 1.0
C2B A:SRM601 4.3 8.0 1.0
C3C A:SRM601 4.3 8.8 1.0
O A:HOH1054 4.3 19.6 1.0
NZ A:LYS224 4.4 10.3 1.0
CMA A:SRM601 4.8 10.3 1.0
NH2 A:ARG109 4.8 8.5 1.0
CDB A:SRM601 4.9 8.5 1.0
CAB A:SRM601 5.0 8.2 1.0
N A:CYS485 5.0 8.4 1.0

Iron binding site 2 out of 5 in 3vkp

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Iron binding site 2 out of 5 in the Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with Low 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 Low X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:9.1
occ:1.00
FE1 A:SF4602 0.0 9.1 1.0
S3 A:SF4602 2.3 8.5 1.0
SG A:CYS481 2.3 9.4 1.0
S4 A:SF4602 2.3 9.0 1.0
S2 A:SF4602 2.3 9.1 1.0
FE3 A:SF4602 2.7 9.0 1.0
FE4 A:SF4602 2.7 8.4 1.0
FE2 A:SF4602 2.8 8.3 1.0
CB A:CYS481 3.3 9.7 1.0
N A:CYS481 3.6 9.3 1.0
CA A:CYS481 3.9 9.4 1.0
S1 A:SF4602 3.9 8.4 1.0
CB A:ASN483 4.1 9.1 1.0
O A:CYS481 4.2 8.8 1.0
C A:GLY480 4.2 9.6 1.0
C A:CYS481 4.2 9.7 1.0
ND2 A:ASN483 4.3 10.1 1.0
SG A:CYS446 4.5 9.7 1.0
N A:GLY480 4.6 9.4 1.0
CA A:GLY480 4.6 9.9 1.0
N A:ASN483 4.6 9.7 1.0
CG A:ASN483 4.6 9.7 1.0
SG A:CYS485 4.7 8.8 1.0
CB A:GLN448 4.7 11.9 1.0
N A:ALA449 4.7 10.5 1.0
CA A:ALA449 4.7 10.5 1.0
C A:GLN448 4.8 11.0 1.0
CA A:ASN483 4.9 9.2 1.0
SG A:CYS440 4.9 8.8 1.0
O A:GLY480 4.9 10.3 1.0
O A:GLN448 4.9 11.5 1.0
N A:THR484 5.0 9.1 1.0

Iron binding site 3 out of 5 in 3vkp

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Iron binding site 3 out of 5 in the Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with Low 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 Low X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:8.3
occ:1.00
FE2 A:SF4602 0.0 8.3 1.0
S4 A:SF4602 2.3 9.0 1.0
SG A:CYS440 2.3 8.8 1.0
S1 A:SF4602 2.3 8.4 1.0
S3 A:SF4602 2.3 8.5 1.0
FE4 A:SF4602 2.6 8.4 1.0
FE3 A:SF4602 2.7 9.0 1.0
FE1 A:SF4602 2.8 9.1 1.0
CB A:CYS440 3.3 8.5 1.0
N A:GLY480 3.6 9.4 1.0
S2 A:SF4602 3.9 9.1 1.0
N A:GLY442 4.1 8.9 1.0
CA A:GLY480 4.1 9.9 1.0
OG1 A:THR479 4.3 9.1 1.0
CB A:CYS485 4.5 8.5 1.0
N A:CYS481 4.5 9.3 1.0
N A:THR441 4.5 8.6 1.0
SG A:CYS485 4.5 8.8 1.0
CA A:CYS440 4.6 8.7 1.0
CA A:GLY442 4.6 8.8 1.0
C A:GLY480 4.7 9.6 1.0
C A:CYS440 4.7 8.5 1.0
C A:THR479 4.8 9.5 1.0
SG A:CYS446 4.8 9.7 1.0
SG A:CYS481 4.9 9.4 1.0
CA A:THR479 5.0 9.5 1.0

Iron binding site 4 out of 5 in 3vkp

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Iron binding site 4 out of 5 in the Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with Low 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 Low X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:9.0
occ:1.00
FE3 A:SF4602 0.0 9.0 1.0
SG A:CYS446 2.3 9.7 1.0
S1 A:SF4602 2.3 8.4 1.0
S2 A:SF4602 2.3 9.1 1.0
S4 A:SF4602 2.3 9.0 1.0
FE2 A:SF4602 2.7 8.3 1.0
FE1 A:SF4602 2.7 9.1 1.0
FE4 A:SF4602 2.7 8.4 1.0
CB A:CYS446 3.2 10.2 1.0
S3 A:SF4602 3.9 8.5 1.0
C3A A:SRM601 4.3 8.7 1.0
CBA A:SRM601 4.4 9.3 1.0
N A:ALA449 4.5 10.5 1.0
C4A A:SRM601 4.6 8.8 1.0
CA A:CYS446 4.6 9.9 1.0
SG A:CYS481 4.6 9.4 1.0
CB A:ALA449 4.6 10.6 1.0
SG A:CYS440 4.7 8.8 1.0
N A:GLY442 4.8 8.9 1.0
CA A:ALA449 4.8 10.5 1.0
CB A:GLN448 4.8 11.9 1.0
SG A:CYS485 4.9 8.8 1.0

Iron binding site 5 out of 5 in 3vkp

Go back to Iron Binding Sites List in 3vkp
Iron binding site 5 out of 5 in the Assimilatory Nitrite Reductase (NII3) - NO2 Complex From Tobbaco Leaf Analysed with Low 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 Low X-Ray Dose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:8.4
occ:1.00
FE4 A:SF4602 0.0 8.4 1.0
S2 A:SF4602 2.3 9.1 1.0
SG A:CYS485 2.3 8.8 1.0
S1 A:SF4602 2.3 8.4 1.0
S3 A:SF4602 2.3 8.5 1.0
FE2 A:SF4602 2.6 8.3 1.0
FE3 A:SF4602 2.7 9.0 1.0
FE1 A:SF4602 2.7 9.1 1.0
CB A:CYS485 3.2 8.5 1.0
NA A:SRM601 3.7 8.6 1.0
C4A A:SRM601 3.7 8.8 1.0
S4 A:SF4602 3.9 9.0 1.0
CHB A:SRM601 4.1 7.9 1.0
FE A:SRM601 4.1 8.7 1.0
N A:CYS485 4.2 8.4 1.0
CB A:ASN483 4.3 9.1 1.0
CA A:CYS485 4.3 8.2 1.0
C1A A:SRM601 4.3 8.9 1.0
C3A A:SRM601 4.3 8.7 1.0
ND A:SRM601 4.5 9.3 1.0
C1B A:SRM601 4.5 8.1 1.0
SG A:CYS440 4.6 8.8 1.0
NB A:SRM601 4.6 7.9 1.0
SG A:CYS481 4.7 9.4 1.0
CB A:CYS440 4.7 8.5 1.0
SG A:CYS446 4.7 9.7 1.0
C4D A:SRM601 4.8 9.8 1.0
CHA A:SRM601 4.8 9.6 1.0
ND2 A:ASN483 4.9 10.1 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 Dec 13 15:24:37 2020

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