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Chlorine 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
Iron (Fe) 5 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 3 in 3vlx

Go back to Chlorine Binding Sites List in 3vlx
Chlorine binding site 1 out of 3 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form From Tobacco Leaf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl604

b:18.2
occ:1.00
 O A:HOH1285 2.9 19.3 1.0
O A:HOH1002 3.0 19.8 1.0
N A:MET175 3.1 7.6 1.0
O A:HOH1065 3.2 11.6 1.0
CA A:MET175 3.7 7.9 1.0
NH1 A:ARG179 3.8 8.1 1.0
CG A:MET175 3.9 9.1 1.0
CD A:LYS91 3.9 10.9 1.0
CE2 A:PHE96 3.9 7.9 1.0
SD A:MET175 3.9 12.8 1.0
C A:GLY174 4.1 7.3 1.0
CMA A:SRM601 4.1 8.3 1.0
CA A:GLY174 4.2 7.4 1.0
CB A:MET175 4.4 8.4 1.0
O A:HOH1054 4.4 15.7 1.0
CD2 A:PHE96 4.6 8.0 1.0
CE A:LYS91 4.7 12.3 1.0
NZ A:LYS91 4.7 14.2 1.0
O A:HOH1908 4.8 38.8 1.0
CZ A:ARG179 4.8 7.4 1.0
O3D A:SRM601 4.8 14.2 1.0
CG A:LYS91 4.8 9.2 1.0
CZ A:PHE96 4.9 7.9 1.0
O A:HOH1221 4.9 20.8 1.0
CB A:LYS91 4.9 7.7 1.0
C A:MET175 4.9 7.8 1.0
CHA A:SRM601 5.0 7.9 1.0

Chlorine binding site 2 out of 3 in 3vlx

Go back to Chlorine Binding Sites List in 3vlx
Chlorine binding site 2 out of 3 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form From Tobacco Leaf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl605

b:14.9
occ:1.00
 O A:HOH1133 3.0 23.4 1.0
O A:HOH1018 3.2 11.1 1.0
N A:LYS100 3.3 11.1 1.0
O A:HOH1894 3.4 24.3 1.0
N A:ARG99 3.5 9.6 1.0
CB A:LYS100 3.8 12.8 1.0
CA A:GLY447 3.8 9.8 1.0
CB A:ARG99 4.1 10.7 1.0
CA A:ARG99 4.1 10.4 1.0
C A:ARG98 4.1 9.1 1.0
CA A:LYS100 4.2 12.3 1.0
N A:GLY447 4.2 9.1 1.0
C A:ARG99 4.2 10.8 1.0
O A:HIS97 4.3 8.4 1.0
CA A:ARG98 4.5 8.8 1.0
O A:HOH1768 4.5 52.5 1.0
O A:HOH1429 4.6 36.4 1.0
NE2 A:GLN448 4.7 13.5 0.5
C A:GLY447 4.9 10.5 1.0
N A:ASN101 4.9 12.0 1.0
O A:ARG98 4.9 9.2 1.0
NH1 A:ARG98 5.0 7.9 1.0

Chlorine binding site 3 out of 3 in 3vlx

Go back to Chlorine Binding Sites List in 3vlx
Chlorine binding site 3 out of 3 in the Assimilatory Nitrite Reductase (NII3) - N226K Mutant - Ligand Free Form From Tobacco Leaf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl606

b:12.0
occ:1.00
 FE A:SRM601 2.4 6.3 1.0
NB A:SRM601 3.0 5.4 1.0
O A:HOH1002 3.1 19.8 1.0
O A:HOH1054 3.1 15.7 1.0
NA A:SRM601 3.1 6.9 1.0
NC A:SRM601 3.2 6.0 1.0
ND A:SRM601 3.2 6.3 1.0
NH2 A:ARG179 3.3 9.3 1.0
NH2 A:ARG109 3.6 6.9 1.0
NH1 A:ARG109 3.6 7.2 1.0
C4B A:SRM601 3.6 5.7 1.0
NZ A:LYS224 3.7 9.6 1.0
C1A A:SRM601 3.7 7.3 1.0
O A:HOH1022 3.7 12.1 1.0
C1C A:SRM601 3.8 5.5 1.0
O A:HOH1031 3.8 14.8 1.0
C4D A:SRM601 3.8 6.9 1.0
CHC A:SRM601 3.8 5.4 1.0
CHA A:SRM601 3.9 7.9 1.0
C1B A:SRM601 3.9 5.7 1.0
CZ A:ARG109 3.9 6.2 1.0
C4A A:SRM601 4.0 6.6 1.0
C4C A:SRM601 4.1 7.2 1.0
C1D A:SRM601 4.1 6.2 1.0
CHB A:SRM601 4.3 6.0 1.0
CAB A:SRM601 4.4 5.4 1.0
CZ A:ARG179 4.5 7.4 1.0
CMA A:SRM601 4.5 8.3 1.0
C3B A:SRM601 4.5 6.3 1.0
CHD A:SRM601 4.5 6.7 1.0
CE A:LYS224 4.6 9.2 1.0
C2A A:SRM601 4.7 7.3 1.0
CBB A:SRM601 4.7 6.2 1.0
NH1 A:ARG179 4.7 8.1 1.0
SG A:CYS485 4.7 5.9 1.0
C2C A:SRM601 5.0 6.4 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: Sat Dec 12 10:17:48 2020

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