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Chlorine in PDB 3vkt: Assimilatory Nitrite Reductase (NII3) - NH2OH Complex From Tobbaco Leaf

Enzymatic activity of Assimilatory Nitrite Reductase (NII3) - NH2OH Complex From Tobbaco Leaf

All present enzymatic activity of Assimilatory Nitrite Reductase (NII3) - NH2OH Complex From Tobbaco Leaf:
1.7.7.1;

Protein crystallography data

The structure of Assimilatory Nitrite Reductase (NII3) - NH2OH Complex From Tobbaco Leaf, PDB code: 3vkt 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) 37.29 / 1.30
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.514, 133.514, 77.660, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 16.4

Other elements in 3vkt:

The structure of Assimilatory Nitrite Reductase (NII3) - NH2OH Complex From Tobbaco 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) - NH2OH Complex From Tobbaco Leaf (pdb code 3vkt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Assimilatory Nitrite Reductase (NII3) - NH2OH Complex From Tobbaco Leaf, PDB code: 3vkt:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3vkt

Go back to Chlorine Binding Sites List in 3vkt
Chlorine binding site 1 out of 2 in the Assimilatory Nitrite Reductase (NII3) - NH2OH Complex From Tobbaco 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) - NH2OH Complex From Tobbaco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:10.0
occ:1.00
O A:HOH1285 3.0 15.4 1.0
N A:MET175 3.1 5.8 1.0
O A:HOH1065 3.1 8.2 1.0
NH1 A:ARG179 3.7 5.8 1.0
CA A:MET175 3.7 6.0 1.0
CE2 A:PHE96 3.9 6.3 1.0
CG A:MET175 4.0 6.8 1.0
CMA A:SRM601 4.0 6.9 1.0
CD A:LYS91 4.1 9.1 1.0
C A:GLY174 4.1 5.6 1.0
SD A:MET175 4.1 9.2 1.0
CA A:GLY174 4.2 5.7 1.0
O A:HOH1054 4.2 7.5 1.0
CB A:MET175 4.5 6.2 1.0
CD2 A:PHE96 4.6 6.3 1.0
CZ A:ARG179 4.6 5.0 1.0
O3D A:SRM601 4.7 7.9 1.0
CE A:LYS91 4.8 9.7 1.0
CZ A:PHE96 4.8 6.1 1.0
O A:HOH1221 4.8 15.9 1.0
O A:HOA606 4.8 12.8 1.0
CHA A:SRM601 4.9 5.8 1.0
NZ A:LYS91 4.9 11.1 1.0
NH2 A:ARG179 4.9 5.5 1.0
CG A:LYS91 4.9 8.0 1.0
C A:MET175 4.9 5.7 1.0
CB A:LYS91 5.0 6.6 1.0

Chlorine binding site 2 out of 2 in 3vkt

Go back to Chlorine Binding Sites List in 3vkt
Chlorine binding site 2 out of 2 in the Assimilatory Nitrite Reductase (NII3) - NH2OH Complex From Tobbaco 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) - NH2OH Complex From Tobbaco Leaf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:12.7
occ:1.00
O A:HOH1018 3.1 8.7 1.0
O A:HOH1133 3.1 19.7 1.0
N A:LYS100 3.3 9.5 1.0
N A:ARG99 3.5 8.1 1.0
CA A:GLY447 3.8 8.3 1.0
CB A:LYS100 3.9 10.9 1.0
CB A:ARG99 4.1 8.8 1.0
CA A:ARG99 4.1 8.7 1.0
C A:ARG98 4.1 7.5 1.0
N A:GLY447 4.2 7.5 1.0
CA A:LYS100 4.2 10.4 1.0
C A:ARG99 4.2 9.2 1.0
O A:HIS97 4.2 6.6 1.0
CA A:ARG98 4.5 7.1 1.0
NE2 A:GLN448 4.6 11.6 0.5
O A:HOH1433 4.6 25.9 1.0
C A:GLY447 4.9 8.7 1.0
O A:HOH2037 4.9 42.4 1.0
O A:ARG98 4.9 7.7 1.0
N A:ASN101 4.9 10.1 1.0
NH1 A:ARG98 5.0 7.2 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: Sat Dec 12 10:17:43 2020

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