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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

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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

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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

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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

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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

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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

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