Chlorine in PDB 5d4j: Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals

All present enzymatic activity of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals:
1.7.2.1;

The structure of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals, PDB code: 5d4j was solved by Y.Fukuda, K.M.Tse, T.Nakane, T.Nakatsu, M.Suzuki, M.Sugahara, S.Inoue, F.Yumoto, N.Matsugaki, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, M.Yabashi, O.Nureki, M.E.P.Murphy, T.Inoue, S.Iwata, E.Mizohata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.79 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.395, 102.207, 144.506, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23.2

The structure of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals also contains other interesting chemical elements:

Copper

(Cu)

6 atoms

The binding sites of Chlorine atom in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals (pdb code 5d4j). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals, PDB code: 5d4j:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:63.3 occ:1.00 CU B:CU502 2.3 30.2 1.0 OD2 B:ASP98 3.0 41.4 1.0 CD1 A:ILE257 3.3 30.1 1.0 CG1 A:ILE257 3.3 32.6 1.0 NE2 B:HIS135 3.3 30.1 1.0 NE2 A:HIS306 3.4 30.9 1.0 CG2 A:ILE257 3.7 27.0 1.0 CE1 B:HIS135 3.7 28.9 1.0 NE2 B:HIS100 3.8 22.3 1.0 CD2 A:HIS306 3.9 30.8 1.0 CD2 A:HIS255 4.0 30.0 1.0 NE2 A:HIS255 4.0 29.9 1.0 CB A:ILE257 4.1 33.1 1.0 CG B:ASP98 4.2 35.2 1.0 CE1 A:HIS306 4.3 30.6 1.0 CD2 A:LEU308 4.5 24.9 1.0 O A:HOH664 4.5 29.6 1.0 CD2 B:HIS100 4.5 24.7 1.0 CD2 B:HIS135 4.6 27.2 1.0 OD1 B:ASP98 4.7 33.9 1.0 CA A:ILE257 4.7 32.0 1.0 CE1 B:HIS100 4.8 23.0 1.0 CG2 A:VAL304 4.9 27.9 1.0 CG A:HIS255 4.9 31.6 1.0 CE1 A:HIS255 4.9 30.9 1.0

Chlorine binding site 2 out of 3 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:49.2 occ:1.00 CU C:CU603 2.2 27.8 1.0 OD2 C:ASP98 3.0 32.1 1.0 NE2 B:HIS306 3.3 24.5 1.0 NE2 C:HIS135 3.3 24.4 1.0 CG1 B:ILE257 3.4 25.4 1.0 CD1 B:ILE257 3.4 25.8 1.0 CE1 C:HIS135 3.6 27.1 1.0 CG2 B:ILE257 3.7 25.5 1.0 CD2 B:HIS306 3.7 28.0 1.0 NE2 C:HIS100 3.8 28.5 1.0 CD2 B:HIS255 4.1 28.7 1.0 NE2 B:HIS255 4.1 28.4 1.0 CG C:ASP98 4.1 30.1 1.0 CB B:ILE257 4.2 24.8 1.0 CE1 B:HIS306 4.3 24.6 1.0 CD2 B:LEU308 4.5 22.5 1.0 CD2 C:HIS100 4.5 27.3 1.0 O C:HOH808 4.6 27.9 1.0 CD2 C:HIS135 4.6 24.7 1.0 CE1 C:HIS100 4.7 25.7 1.0 OD1 C:ASP98 4.7 29.2 1.0 CA B:ILE257 4.8 25.6 1.0 CG B:HIS255 4.9 29.6 1.0 O C:HOH847 4.9 35.9 1.0 CE1 B:HIS255 4.9 27.4 1.0 CG B:HIS306 4.9 23.4 1.0 ND1 C:HIS135 4.9 26.8 1.0

Chlorine binding site 3 out of 3 in the Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Chloride-Bound Form of A Copper Nitrite Reductase From Alcaligenes Faecals within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl601 b:53.2 occ:1.00 CU A:CU502 2.3 31.0 1.0 CG1 C:ILE257 3.0 28.0 1.0 OD2 A:ASP98 3.0 44.2 1.0 CD1 C:ILE257 3.3 30.0 1.0 NE2 C:HIS306 3.4 26.4 1.0 CD2 C:HIS255 3.5 35.8 1.0 NE2 A:HIS135 3.5 26.0 1.0 NE2 C:HIS255 3.5 31.7 1.0 NE2 A:HIS100 3.6 23.5 1.0 CG2 C:ILE257 3.7 28.1 1.0 CB C:ILE257 3.8 29.8 1.0 CD2 C:HIS306 3.8 25.7 1.0 CG A:ASP98 4.0 35.3 1.0 CE1 A:HIS135 4.0 26.5 1.0 O C:HOH792 4.2 27.2 1.0 CA C:ILE257 4.3 27.5 1.0 CD2 A:HIS100 4.3 25.8 1.0 CE1 C:HIS255 4.4 34.5 1.0 CG C:HIS255 4.4 34.3 1.0 OD1 A:ASP98 4.4 29.6 1.0 CE1 C:HIS306 4.5 26.7 1.0 CE1 A:HIS100 4.6 24.6 1.0 CD2 A:HIS135 4.7 27.0 1.0 ND1 C:HIS255 4.8 31.4 1.0 CD2 C:LEU308 5.0 23.5 1.0

Y.Fukuda, K.M.Tse, T.Nakane, T.Nakatsu, M.Suzuki, M.Sugahara, S.Inoue, T.Masuda, F.Yumoto, N.Matsugaki, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, T.Hatsui, M.Yabashi, O.Nureki, M.E.Murphy, T.Inoue, S.Iwata, E.Mizohata. Redox-Coupled Proton Transfer Mechanism in Nitrite Reductase Revealed By Femtosecond Crystallography Proc.Natl.Acad.Sci.Usa V. 113 2928 2016.
ISSN: ESSN 1091-6490
PubMed: 26929369
DOI: 10.1073/PNAS.1517770113