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Iron in PDB 3vlx: Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form From Tobacco Leaf

Enzymatic activity of Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form From Tobacco Leaf

All present enzymatic activity of Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form From Tobacco Leaf:
1.7.7.1;

Protein crystallography data

The structure of Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form From Tobacco Leaf, PDB code: 3vlx 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) 47.19 / 1.35
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.498, 133.498, 77.770, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 17.5

Other elements in 3vlx:

The structure of Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form From Tobacco Leaf also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form From Tobacco Leaf (pdb code 3vlx). 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 - Ligand Free Form From Tobacco Leaf, PDB code: 3vlx:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3vlx

Go back to Iron Binding Sites List in 3vlx
Iron binding site 1 out of 5 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form 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 - Ligand Free Form From Tobacco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:6.3
occ:1.00
 FE A:SRM601 0.0 6.3 1.0
ND A:SRM601 2.0 6.3 1.0
NB A:SRM601 2.0 5.4 1.0
NA A:SRM601 2.0 6.9 1.0
NC A:SRM601 2.1 6.0 1.0
CL A:CL606 2.4 12.0 1.0
SG A:CYS485 2.4 5.9 1.0
C4A A:SRM601 3.0 6.6 1.0
C1B A:SRM601 3.0 5.7 1.0
C4D A:SRM601 3.0 6.9 1.0
C1D A:SRM601 3.0 6.2 1.0
C1C A:SRM601 3.0 5.5 1.0
C4C A:SRM601 3.0 7.2 1.0
C4B A:SRM601 3.0 5.7 1.0
C1A A:SRM601 3.0 7.3 1.0
CHB A:SRM601 3.3 6.0 1.0
CHD A:SRM601 3.4 6.7 1.0
CHA A:SRM601 3.4 7.9 1.0
CHC A:SRM601 3.4 5.4 1.0
CB A:CYS485 3.4 6.6 1.0
FE2 A:SF4602 4.2 6.6 1.0
CA A:CYS485 4.2 6.2 1.0
O A:HOH1054 4.3 15.7 1.0
C3B A:SRM601 4.3 6.3 1.0
C2D A:SRM601 4.3 7.7 1.0
C3A A:SRM601 4.3 7.1 1.0
C3C A:SRM601 4.3 6.9 1.0
C3D A:SRM601 4.3 8.2 1.0
C2C A:SRM601 4.3 6.4 1.0
C2B A:SRM601 4.3 5.7 1.0
C2A A:SRM601 4.3 7.3 1.0
NZ A:LYS224 4.5 9.6 1.0
NH2 A:ARG109 4.7 6.9 1.0
O A:HOH1031 4.9 14.8 1.0
CMA A:SRM601 4.9 8.3 1.0
CDB A:SRM601 4.9 6.7 1.0
O A:HOH1002 4.9 19.8 1.0
CAB A:SRM601 5.0 5.4 1.0
N A:CYS485 5.0 6.2 1.0

Iron binding site 2 out of 5 in 3vlx

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Iron binding site 2 out of 5 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form 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 - Ligand Free Form From Tobacco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:6.8
occ:1.00
 FE1 A:SF4602 0.0 6.8 1.0
S4 A:SF4602 2.3 6.2 1.0
SG A:CYS481 2.3 7.3 1.0
S2 A:SF4602 2.3 6.9 1.0
S3 A:SF4602 2.3 6.6 1.0
FE4 A:SF4602 2.7 7.0 1.0
FE2 A:SF4602 2.7 6.6 1.0
FE3 A:SF4602 2.8 6.3 1.0
CB A:CYS481 3.4 7.5 1.0
N A:CYS481 3.6 7.0 1.0
CA A:CYS481 3.9 7.3 1.0
S1 A:SF4602 3.9 6.6 1.0
CB A:ASN483 4.1 7.2 1.0
O A:CYS481 4.2 7.5 1.0
C A:GLY480 4.2 7.0 1.0
C A:CYS481 4.3 7.6 1.0
ND2 A:ASN483 4.3 8.4 1.0
CB A:GLN448 4.4 10.8 1.0
SG A:CYS446 4.6 7.8 1.0
N A:GLY480 4.6 6.2 1.0
CA A:GLY480 4.6 6.7 1.0
N A:ASN483 4.7 7.4 1.0
SG A:CYS485 4.7 5.9 1.0
CG A:ASN483 4.7 8.0 1.0
N A:ALA449 4.7 8.7 1.0
CA A:ALA449 4.8 8.3 1.0
C A:GLN448 4.8 9.8 1.0
CA A:ASN483 4.9 6.8 1.0
SG A:CYS440 4.9 6.0 1.0
O A:GLY480 5.0 7.4 1.0
N A:THR484 5.0 6.5 1.0

Iron binding site 3 out of 5 in 3vlx

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Iron binding site 3 out of 5 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form 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 - Ligand Free Form From Tobacco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:6.6
occ:1.00
 FE2 A:SF4602 0.0 6.6 1.0
S3 A:SF4602 2.3 6.6 1.0
SG A:CYS485 2.3 5.9 1.0
S1 A:SF4602 2.3 6.6 1.0
S4 A:SF4602 2.4 6.2 1.0
FE3 A:SF4602 2.6 6.3 1.0
FE4 A:SF4602 2.7 7.0 1.0
FE1 A:SF4602 2.7 6.8 1.0
CB A:CYS485 3.2 6.6 1.0
NA A:SRM601 3.8 6.9 1.0
C4A A:SRM601 3.8 6.6 1.0
S2 A:SF4602 3.9 6.9 1.0
CHB A:SRM601 4.1 6.0 1.0
FE A:SRM601 4.2 6.3 1.0
N A:CYS485 4.2 6.2 1.0
CB A:ASN483 4.3 7.2 1.0
CA A:CYS485 4.3 6.2 1.0
C1A A:SRM601 4.3 7.3 1.0
C3A A:SRM601 4.3 7.1 1.0
ND A:SRM601 4.6 6.3 1.0
C1B A:SRM601 4.6 5.7 1.0
SG A:CYS440 4.6 6.0 1.0
NB A:SRM601 4.7 5.4 1.0
SG A:CYS481 4.7 7.3 1.0
CB A:CYS440 4.8 5.8 1.0
SG A:CYS446 4.8 7.8 1.0
C4D A:SRM601 4.9 6.9 1.0
CHA A:SRM601 4.9 7.9 1.0
ND2 A:ASN483 4.9 8.4 1.0
C2A A:SRM601 5.0 7.3 1.0

Iron binding site 4 out of 5 in 3vlx

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Iron binding site 4 out of 5 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form 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 - Ligand Free Form From Tobacco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:6.3
occ:1.00
 FE3 A:SF4602 0.0 6.3 1.0
S2 A:SF4602 2.3 6.9 1.0
S1 A:SF4602 2.3 6.6 1.0
SG A:CYS440 2.3 6.0 1.0
S4 A:SF4602 2.3 6.2 1.0
FE2 A:SF4602 2.6 6.6 1.0
FE4 A:SF4602 2.7 7.0 1.0
FE1 A:SF4602 2.8 6.8 1.0
CB A:CYS440 3.3 5.8 1.0
N A:GLY480 3.7 6.2 1.0
S3 A:SF4602 3.9 6.6 1.0
N A:GLY442 4.1 6.7 1.0
CA A:GLY480 4.1 6.7 1.0
OG1 A:THR479 4.3 6.5 1.0
CB A:CYS485 4.5 6.6 1.0
N A:CYS481 4.5 7.0 1.0
SG A:CYS485 4.5 5.9 1.0
N A:THR441 4.6 6.3 1.0
CA A:GLY442 4.6 7.3 1.0
CA A:CYS440 4.6 5.9 1.0
C A:GLY480 4.7 7.0 1.0
C A:CYS440 4.7 6.0 1.0
C A:THR479 4.8 6.5 1.0
SG A:CYS446 4.9 7.8 1.0
CA A:THR479 4.9 6.5 1.0
SG A:CYS481 5.0 7.3 1.0

Iron binding site 5 out of 5 in 3vlx

Go back to Iron Binding Sites List in 3vlx
Iron binding site 5 out of 5 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form 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 - Ligand Free Form From Tobacco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:7.0
occ:1.00
 FE4 A:SF4602 0.0 7.0 1.0
S1 A:SF4602 2.3 6.6 1.0
SG A:CYS446 2.3 7.8 1.0
S2 A:SF4602 2.3 6.9 1.0
S3 A:SF4602 2.3 6.6 1.0
FE1 A:SF4602 2.7 6.8 1.0
FE3 A:SF4602 2.7 6.3 1.0
FE2 A:SF4602 2.7 6.6 1.0
CB A:CYS446 3.2 8.3 1.0
S4 A:SF4602 3.9 6.2 1.0
C3A A:SRM601 4.3 7.1 1.0
CBA A:SRM601 4.4 6.5 1.0
N A:ALA449 4.4 8.7 1.0
CB A:GLN448 4.5 10.8 1.0
SG A:CYS481 4.7 7.3 1.0
CA A:CYS446 4.7 8.5 1.0
C4A A:SRM601 4.7 6.6 1.0
CB A:ALA449 4.7 8.5 1.0
SG A:CYS440 4.8 6.0 1.0
CA A:ALA449 4.8 8.3 1.0
N A:GLY442 4.8 6.7 1.0
CG A:GLN448 4.9 13.6 1.0
SG A:CYS485 4.9 5.9 1.0
C A:GLN448 5.0 9.8 1.0
CDA A:SRM601 5.0 9.9 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

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