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

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

Go back to Iron Binding Sites List in 3vkp
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

Go back to Iron Binding Sites List in 3vkp
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

Go back to Iron Binding Sites List in 3vkp
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 Aug 4 21:55:17 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy