Atomistry » Iron » PDB 3vkt-3vti » 3vlz
Atomistry »
  Iron »
    PDB 3vkt-3vti »
      3vlz »

Iron in PDB 3vlz: Assimilatory Nitrite Reductase (NII3) - N226K Mutant - SO3 Full Complex From Tobacco Leaf

Enzymatic activity of Assimilatory Nitrite Reductase (NII3) - N226K Mutant - SO3 Full Complex From Tobacco Leaf

All present enzymatic activity of Assimilatory Nitrite Reductase (NII3) - N226K Mutant - SO3 Full Complex From Tobacco Leaf:
1.7.7.1;

Protein crystallography data

The structure of Assimilatory Nitrite Reductase (NII3) - N226K Mutant - SO3 Full Complex From Tobacco Leaf, PDB code: 3vlz 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) 29.20 / 2.07
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 132.889, 132.889, 77.646, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 28.2

Other elements in 3vlz:

The structure of Assimilatory Nitrite Reductase (NII3) - N226K Mutant - SO3 Full Complex From Tobacco Leaf 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) - N226K Mutant - SO3 Full Complex From Tobacco Leaf (pdb code 3vlz). 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) - N226K Mutant - SO3 Full Complex From Tobacco Leaf, PDB code: 3vlz:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3vlz

Go back to Iron Binding Sites List in 3vlz
Iron binding site 1 out of 5 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - SO3 Full Complex From Tobacco Leaf


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) - N226K Mutant - SO3 Full Complex From Tobacco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:21.1
occ:1.00
 FE A:SRM601 0.0 21.1 1.0
ND A:SRM601 2.1 16.2 1.0
NA A:SRM601 2.1 18.0 1.0
NB A:SRM601 2.1 14.2 1.0
NC A:SRM601 2.1 15.5 1.0
S A:SO3606 2.4 24.7 1.0
SG A:CYS485 2.4 14.2 1.0
C1D A:SRM601 3.0 17.8 1.0
C4C A:SRM601 3.0 15.4 1.0
C4A A:SRM601 3.0 19.9 1.0
C1B A:SRM601 3.0 13.8 1.0
O1 A:SO3606 3.1 24.8 1.0
C4B A:SRM601 3.1 14.4 1.0
C4D A:SRM601 3.1 18.8 1.0
C1C A:SRM601 3.1 14.6 1.0
C1A A:SRM601 3.1 19.5 1.0
CHD A:SRM601 3.2 18.0 1.0
O2 A:SO3606 3.2 27.4 1.0
O3 A:SO3606 3.3 25.8 1.0
CHB A:SRM601 3.3 15.3 1.0
CB A:CYS485 3.4 15.1 1.0
CHC A:SRM601 3.4 14.9 1.0
CHA A:SRM601 3.4 17.3 1.0
FE2 A:SF4602 4.2 17.2 1.0
CA A:CYS485 4.3 15.3 1.0
C3C A:SRM601 4.3 16.2 1.0
C2D A:SRM601 4.3 19.3 1.0
C2B A:SRM601 4.3 14.5 1.0
C3A A:SRM601 4.3 19.2 1.0
C3B A:SRM601 4.3 12.4 1.0
C3D A:SRM601 4.3 19.6 1.0
C2C A:SRM601 4.3 14.9 1.0
C2A A:SRM601 4.4 20.1 1.0
NZ A:LYS224 4.5 29.0 1.0
NH2 A:ARG109 4.8 19.9 1.0
CMA A:SRM601 4.8 24.1 1.0
CDB A:SRM601 4.9 13.5 1.0
CAB A:SRM601 5.0 11.4 1.0

Iron binding site 2 out of 5 in 3vlz

Go back to Iron Binding Sites List in 3vlz
Iron binding site 2 out of 5 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - SO3 Full Complex From Tobacco Leaf


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) - N226K Mutant - SO3 Full Complex From Tobacco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:16.7
occ:1.00
 FE1 A:SF4602 0.0 16.7 1.0
S4 A:SF4602 2.3 18.4 1.0
S2 A:SF4602 2.3 18.0 1.0
S3 A:SF4602 2.3 16.6 1.0
SG A:CYS481 2.4 16.2 1.0
FE4 A:SF4602 2.7 18.9 1.0
FE3 A:SF4602 2.7 14.9 1.0
FE2 A:SF4602 2.8 17.2 1.0
CB A:CYS481 3.4 14.5 1.0
N A:CYS481 3.6 14.8 1.0
S1 A:SF4602 3.9 16.8 1.0
CA A:CYS481 4.0 14.6 1.0
CB A:ASN483 4.0 15.9 1.0
C A:GLY480 4.2 14.2 1.0
O A:CYS481 4.2 15.4 1.0
ND2 A:ASN483 4.3 14.5 1.0
C A:CYS481 4.3 15.0 1.0
SG A:CYS446 4.5 20.2 1.0
N A:GLY480 4.6 12.6 1.0
CA A:GLY480 4.6 13.0 1.0
CG A:ASN483 4.6 17.8 1.0
SG A:CYS485 4.6 14.2 1.0
CB A:GLN448 4.6 20.0 1.0
O A:GLN448 4.7 21.0 1.0
C A:GLN448 4.7 20.7 1.0
CA A:ALA449 4.8 18.9 1.0
N A:ASN483 4.8 16.0 1.0
N A:ALA449 4.8 20.0 1.0
SG A:CYS440 4.8 15.3 1.0
O A:GLY480 4.9 15.1 1.0
CA A:ASN483 4.9 16.2 1.0

Iron binding site 3 out of 5 in 3vlz

Go back to Iron Binding Sites List in 3vlz
Iron binding site 3 out of 5 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - SO3 Full Complex From Tobacco Leaf


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) - N226K Mutant - SO3 Full Complex From Tobacco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:17.2
occ:1.00
 FE2 A:SF4602 0.0 17.2 1.0
SG A:CYS485 2.2 14.2 1.0
S3 A:SF4602 2.3 16.6 1.0
S4 A:SF4602 2.3 18.4 1.0
S1 A:SF4602 2.3 16.8 1.0
FE3 A:SF4602 2.6 14.9 1.0
FE4 A:SF4602 2.7 18.9 1.0
FE1 A:SF4602 2.8 16.7 1.0
CB A:CYS485 3.1 15.1 1.0
C4A A:SRM601 3.7 19.9 1.0
NA A:SRM601 3.9 18.0 1.0
S2 A:SF4602 3.9 18.0 1.0
N A:CYS485 4.1 14.9 1.0
FE A:SRM601 4.2 21.1 1.0
CA A:CYS485 4.2 15.3 1.0
CB A:ASN483 4.3 15.9 1.0
C1A A:SRM601 4.3 19.5 1.0
C3A A:SRM601 4.3 19.2 1.0
CHB A:SRM601 4.4 15.3 1.0
C1B A:SRM601 4.4 13.8 1.0
SG A:CYS440 4.5 15.3 1.0
ND A:SRM601 4.6 16.2 1.0
NB A:SRM601 4.7 14.2 1.0
CB A:CYS440 4.7 12.7 1.0
SG A:CYS446 4.8 20.2 1.0
SG A:CYS481 4.8 16.2 1.0
ND2 A:ASN483 4.9 14.5 1.0
C4D A:SRM601 5.0 18.8 1.0
C2A A:SRM601 5.0 20.1 1.0

Iron binding site 4 out of 5 in 3vlz

Go back to Iron Binding Sites List in 3vlz
Iron binding site 4 out of 5 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - SO3 Full Complex From Tobacco Leaf


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) - N226K Mutant - SO3 Full Complex From Tobacco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:14.9
occ:1.00
 FE3 A:SF4602 0.0 14.9 1.0
S2 A:SF4602 2.3 18.0 1.0
SG A:CYS440 2.3 15.3 1.0
S1 A:SF4602 2.3 16.8 1.0
S4 A:SF4602 2.4 18.4 1.0
FE2 A:SF4602 2.6 17.2 1.0
FE4 A:SF4602 2.7 18.9 1.0
FE1 A:SF4602 2.7 16.7 1.0
CB A:CYS440 3.3 12.7 1.0
N A:GLY480 3.6 12.6 1.0
S3 A:SF4602 3.9 16.6 1.0
CA A:GLY480 4.1 13.0 1.0
N A:GLY442 4.1 15.4 1.0
OG1 A:THR479 4.3 14.7 1.0
N A:CYS481 4.5 14.8 1.0
SG A:CYS485 4.5 14.2 1.0
CB A:CYS485 4.5 15.1 1.0
CA A:CYS440 4.6 13.2 1.0
N A:THR441 4.6 13.9 1.0
C A:GLY480 4.6 14.2 1.0
CA A:GLY442 4.6 14.9 1.0
C A:CYS440 4.7 13.0 1.0
C A:THR479 4.7 12.6 1.0
SG A:CYS446 4.8 20.2 1.0
CA A:THR479 5.0 12.0 1.0

Iron binding site 5 out of 5 in 3vlz

Go back to Iron Binding Sites List in 3vlz
Iron binding site 5 out of 5 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - SO3 Full Complex From Tobacco Leaf


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) - N226K Mutant - SO3 Full Complex From Tobacco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:18.9
occ:1.00
 FE4 A:SF4602 0.0 18.9 1.0
SG A:CYS446 2.3 20.2 1.0
S1 A:SF4602 2.3 16.8 1.0
S2 A:SF4602 2.3 18.0 1.0
S3 A:SF4602 2.3 16.6 1.0
FE3 A:SF4602 2.7 14.9 1.0
FE1 A:SF4602 2.7 16.7 1.0
FE2 A:SF4602 2.7 17.2 1.0
CB A:CYS446 3.2 19.1 1.0
S4 A:SF4602 3.9 18.4 1.0
CBA A:SRM601 4.3 21.5 1.0
C3A A:SRM601 4.4 19.2 1.0
N A:ALA449 4.6 20.0 1.0
CB A:GLN448 4.6 20.0 1.0
C4A A:SRM601 4.6 19.9 1.0
CA A:CYS446 4.6 19.2 1.0
CB A:ALA449 4.7 19.2 1.0
SG A:CYS440 4.7 15.3 1.0
SG A:CYS481 4.7 16.2 1.0
SG A:CYS485 4.8 14.2 1.0
CA A:ALA449 4.8 18.9 1.0
N A:GLY442 4.9 15.4 1.0
C A:GLN448 4.9 20.7 1.0
CAA A:SRM601 5.0 22.0 1.0

Reference:

S.Nakano, M.Takahashi, A.Sakamoto, H.Morikawa, K.Katayanagi. X-Ray Crystal Structure of A Mutant Assimilatory Nitrite Reductase That Shows Sulfite Reductase-Like Activity Chem.Biodivers. V. 9 1989 2012.
ISSN: ISSN 1612-1872
PubMed: 22976986
DOI: 10.1002/CBDV.201100442
Page generated: Sun Aug 4 22:00:27 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