Atomistry » Iron » PDB 3v3y-3vks » 3vkr
Atomistry »
  Iron »
    PDB 3v3y-3vks »
      3vkr »

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

Go back to Iron Binding Sites List in 3vkr
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

Go back to Iron Binding Sites List in 3vkr
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

Go back to Iron Binding Sites List in 3vkr
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy