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Chlorine in PDB 4d06: Bacterial Chalcone Isomerase Complexed with Naringenin

Enzymatic activity of Bacterial Chalcone Isomerase Complexed with Naringenin

All present enzymatic activity of Bacterial Chalcone Isomerase Complexed with Naringenin:
5.5.1.6;

Protein crystallography data

The structure of Bacterial Chalcone Isomerase Complexed with Naringenin, PDB code: 4d06 was solved by M.Thomsen, G.J.Palm, W.Hinrichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.18 / 2.00
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.165, 187.991, 196.221, 90.00, 90.00, 90.00
R / Rfree (%) 14.023 / 16.277

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Chlorine atom in the Bacterial Chalcone Isomerase Complexed with Naringenin (pdb code 4d06). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 17 binding sites of Chlorine where determined in the Bacterial Chalcone Isomerase Complexed with Naringenin, PDB code: 4d06:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 17 in 4d06

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Chlorine binding site 1 out of 17 in the Bacterial Chalcone Isomerase Complexed with Naringenin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Bacterial Chalcone Isomerase Complexed with Naringenin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:60.0
occ:1.00
 N A:ASP247 3.4 30.4 1.0
O A:HOH2132 3.6 27.7 1.0
OD2 A:ASP247 3.8 30.6 0.5
CG A:ASP247 3.9 30.8 0.5
CB A:GLN246 3.9 28.5 1.0
CB A:ASP247 4.0 30.7 0.5
CA A:GLN246 4.0 28.8 1.0
CB A:ASP247 4.1 34.2 0.5
C A:GLN246 4.2 29.4 1.0
CA A:ASP247 4.3 30.6 0.5
CA A:ASP247 4.3 32.0 0.5
OD1 A:ASP247 4.4 30.8 0.5
O A:HOH2321 4.5 43.5 1.0
O A:HOH2153 4.7 37.9 1.0

Chlorine binding site 2 out of 17 in 4d06

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Chlorine binding site 2 out of 17 in the Bacterial Chalcone Isomerase Complexed with Naringenin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Bacterial Chalcone Isomerase Complexed with Naringenin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:53.7
occ:1.00
 O B:HOH2060 3.2 19.2 0.5
O B:HOH2061 3.2 27.6 0.5
N A:ALA159 3.3 20.5 1.0
CA A:GLY158 3.7 21.4 1.0
O B:HOH2057 3.9 20.1 1.0
CG B:LYS24 3.9 25.9 1.0
C A:GLY158 4.0 21.0 1.0
CB A:ALA159 4.0 20.3 1.0
CD B:ARG27 4.1 19.5 1.0
NE B:ARG27 4.2 19.6 1.0
CA A:ALA159 4.3 20.4 1.0
CE B:LYS24 4.3 30.9 1.0
CD B:LYS24 4.7 28.5 1.0
CZ B:ARG27 4.7 19.7 1.0
CB B:LYS24 4.8 23.7 1.0
O A:HOH2240 4.8 32.6 1.0
CA B:LYS24 4.9 22.2 1.0
O A:HOH2249 5.0 30.2 1.0

Chlorine binding site 3 out of 17 in 4d06

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Chlorine binding site 3 out of 17 in the Bacterial Chalcone Isomerase Complexed with Naringenin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Bacterial Chalcone Isomerase Complexed with Naringenin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:53.1
occ:1.00
 OD2 B:ASP247 3.5 27.8 0.5
N B:ASP247 3.5 25.6 1.0
O B:HOH2151 3.5 48.0 1.0
O B:HOH2302 3.6 25.1 1.0
CB B:ASP247 3.6 28.0 0.5
CG B:ASP247 3.7 27.0 0.5
CB B:GLN246 3.9 23.9 1.0
CB B:ASP247 4.0 26.4 0.5
CA B:GLN246 4.1 24.0 1.0
CA B:ASP247 4.2 26.5 0.5
C B:GLN246 4.3 24.7 1.0
CA B:ASP247 4.3 25.8 0.5
OD1 B:ASP247 4.4 27.0 0.5
OD2 B:ASP247 4.6 31.7 0.5
O B:HOH2303 4.6 44.2 1.0
CG B:ASP247 4.6 29.8 0.5
O B:HOH2150 4.8 33.4 1.0

Chlorine binding site 4 out of 17 in 4d06

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Chlorine binding site 4 out of 17 in the Bacterial Chalcone Isomerase Complexed with Naringenin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Bacterial Chalcone Isomerase Complexed with Naringenin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:54.3
occ:1.00
 O A:HOH2034 3.2 27.7 0.5
N B:ALA159 3.5 19.8 1.0
O B:HOH2101 3.6 61.6 1.0
CA B:GLY158 3.8 21.0 1.0
O A:HOH2061 3.9 22.1 1.0
CG A:LYS24 4.0 22.0 1.0
O A:HOH2082 4.1 43.2 1.0
CB B:ALA159 4.1 19.5 1.0
CD A:ARG27 4.1 18.7 1.0
C B:GLY158 4.2 20.4 1.0
NE A:ARG27 4.3 18.6 1.0
CA B:ALA159 4.4 19.4 1.0
CE A:LYS24 4.5 24.0 1.0
CD A:LYS24 4.7 22.9 1.0
CB A:LYS24 4.7 21.4 1.0
O B:HOH2213 4.8 27.0 1.0
CZ A:ARG27 4.9 18.7 1.0
CA A:LYS24 4.9 20.7 1.0
NZ A:LYS24 5.0 24.8 1.0

Chlorine binding site 5 out of 17 in 4d06

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Chlorine binding site 5 out of 17 in the Bacterial Chalcone Isomerase Complexed with Naringenin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Bacterial Chalcone Isomerase Complexed with Naringenin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:52.6
occ:1.00
 N C:ASP247 3.4 29.3 1.0
O C:HOH2308 3.6 23.7 1.0
CG C:ASP247 3.8 40.8 1.0
CB C:GLN246 3.9 26.1 1.0
CB C:ASP247 4.0 34.9 1.0
CA C:GLN246 4.0 26.7 1.0
OD2 C:ASP247 4.0 48.9 1.0
OD1 C:ASP247 4.1 50.1 1.0
C C:GLN246 4.2 27.7 1.0
CA C:ASP247 4.3 30.8 1.0
O C:HOH2307 4.8 40.0 1.0
O C:HOH2149 4.9 39.4 1.0

Chlorine binding site 6 out of 17 in 4d06

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Chlorine binding site 6 out of 17 in the Bacterial Chalcone Isomerase Complexed with Naringenin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Bacterial Chalcone Isomerase Complexed with Naringenin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:60.6
occ:1.00
 O C:HOH2242 2.9 47.8 1.0
N C:LYS175 3.5 31.0 1.0
CG C:LYS175 3.8 29.7 1.0
CB C:LYS175 3.9 30.0 1.0
OD1 C:ASP174 4.0 51.0 1.0
CA C:ASP174 4.3 34.8 1.0
CA C:LYS175 4.3 30.3 1.0
C C:ASP174 4.3 32.9 1.0
O C:HOH2124 4.4 51.0 1.0
CG C:ASP174 4.6 43.3 1.0
CD C:LYS175 4.9 29.1 1.0
O C:VAL173 4.9 32.1 1.0
CB C:ASP174 5.0 39.2 1.0

Chlorine binding site 7 out of 17 in 4d06

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Chlorine binding site 7 out of 17 in the Bacterial Chalcone Isomerase Complexed with Naringenin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Bacterial Chalcone Isomerase Complexed with Naringenin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:54.6
occ:1.00
 N C:ALA159 3.4 19.5 1.0
O D:HOH2049 3.8 19.4 1.0
CG D:LYS24 3.8 21.5 1.0
CA C:GLY158 3.9 20.4 1.0
CB C:ALA159 4.1 19.4 1.0
CD D:ARG27 4.1 18.9 1.0
O D:HOH2063 4.1 39.9 1.0
C C:GLY158 4.2 20.0 1.0
NE D:ARG27 4.3 18.9 1.0
CE D:LYS24 4.3 23.9 1.0
CA C:ALA159 4.4 19.4 1.0
CD D:LYS24 4.5 22.7 1.0
CB D:LYS24 4.6 20.4 1.0
CA D:LYS24 4.8 19.7 1.0
CZ D:ARG27 4.9 19.0 1.0
NZ D:LYS24 5.0 24.7 1.0

Chlorine binding site 8 out of 17 in 4d06

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Chlorine binding site 8 out of 17 in the Bacterial Chalcone Isomerase Complexed with Naringenin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Bacterial Chalcone Isomerase Complexed with Naringenin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:48.7
occ:1.00
 N D:ASP247 3.2 22.0 1.0
O D:HOH2277 3.4 26.7 1.0
OD2 D:ASP247 3.7 29.8 1.0
CB D:ASP247 3.8 24.4 1.0
CG D:ASP247 3.8 26.5 1.0
CB D:GLN246 3.8 20.6 1.0
CA D:GLN246 3.8 20.8 1.0
C D:GLN246 4.0 21.2 1.0
CA D:ASP247 4.1 22.8 1.0
OD1 D:ASP247 4.3 28.4 1.0
O D:HOH2131 4.8 31.3 1.0
O D:HOH2276 4.8 37.7 1.0
O D:HOH2269 4.8 31.3 1.0

Chlorine binding site 9 out of 17 in 4d06

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Chlorine binding site 9 out of 17 in the Bacterial Chalcone Isomerase Complexed with Naringenin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Bacterial Chalcone Isomerase Complexed with Naringenin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:56.5
occ:1.00
 O D:HOH2031 2.6 55.7 1.0
O D:HOH2117 3.1 43.8 1.0
O C:HOH2282 3.2 47.1 1.0
N D:GLU19 3.3 21.2 1.0
OG D:SER18 3.9 22.9 1.0
CA D:SER18 3.9 21.2 1.0
CB D:GLU19 4.0 21.7 1.0
C D:SER18 4.1 21.1 1.0
CG D:GLU19 4.2 22.0 1.0
CA D:GLU19 4.2 21.4 1.0
CB D:SER18 4.4 21.9 1.0
O D:HOH2027 4.7 25.3 1.0
N D:ASP20 5.0 21.1 1.0

Chlorine binding site 10 out of 17 in 4d06

Go back to Chlorine Binding Sites List in 4d06
Chlorine binding site 10 out of 17 in the Bacterial Chalcone Isomerase Complexed with Naringenin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Bacterial Chalcone Isomerase Complexed with Naringenin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:49.1
occ:1.00
 O C:HOH2054 3.1 48.1 1.0
O D:HOH2087 3.2 46.6 1.0
N D:ALA159 3.3 18.9 1.0
CA D:GLY158 3.7 19.1 1.0
O C:HOH2053 3.9 19.6 1.0
CG C:LYS24 3.9 19.7 1.0
O C:HOH2075 4.0 48.8 1.0
CB D:ALA159 4.0 18.8 1.0
C D:GLY158 4.0 18.9 1.0
CD C:ARG27 4.2 17.9 1.0
CA D:ALA159 4.2 18.8 1.0
CE C:LYS24 4.3 20.7 1.0
NE C:ARG27 4.4 17.9 1.0
O D:HOH2181 4.6 24.0 1.0
CD C:LYS24 4.6 20.2 1.0
CB C:LYS24 4.8 19.3 1.0
NZ C:LYS24 4.8 21.0 1.0
O C:HOH2055 4.9 18.7 1.0
CA C:LYS24 4.9 18.9 1.0
CZ C:ARG27 4.9 18.0 1.0

Reference:

M.Thomsen, A.Tuukkanen, J.Dickerhoff, G.J.Palm, H.Kratzat, D.I.Svergun, K.Weisz, U.T.Bornscheuer, W.Hinrichs. Structure and Catalytic Mechanism of the Evolutionarily Unique Bacterial Chalcone Isomerase Acta Crystallogr.,Sect.D V. 71 907 2015.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004715001935
Page generated: Sun Jul 21 11:38:36 2024

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