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Chlorine in PDB 4i52: Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa

Enzymatic activity of Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa

All present enzymatic activity of Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa:
4.1.3.36;

Protein crystallography data

The structure of Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa, PDB code: 4i52 was solved by H.G.Song, Y.R.Sun, J.Li, Y.Li, M.Jiang, J.H.Zhou, Z.H.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.60 / 2.35
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 138.843, 138.843, 221.217, 90.00, 90.00, 120.00
R / Rfree (%) 22.9 / 25.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa (pdb code 4i52). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa, PDB code: 4i52:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 4i52

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Chlorine binding site 1 out of 9 in the Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:54.3
occ:1.00
 N A:GLY146 2.9 39.6 1.0
O A:HOH420 3.0 53.2 1.0
NE2 A:GLN144 3.0 37.3 1.0
N A:THR145 3.2 39.5 1.0
CA A:GLY146 3.4 38.3 1.0
CA A:GLY122 3.5 40.3 1.0
CZ3 A:TRP174 3.5 28.8 1.0
CH2 A:TRP174 3.6 29.4 1.0
CB A:GLN144 3.8 37.1 1.0
C A:THR145 3.8 39.9 1.0
OG1 A:THR145 3.8 42.6 1.0
CBA A:1HA301 3.9 58.6 1.0
CA A:GLN144 4.0 37.6 1.0
CA A:THR145 4.0 39.7 1.0
C A:GLN144 4.1 38.8 1.0
C A:GLY122 4.1 39.8 1.0
CD A:GLN144 4.2 38.9 1.0
SBO A:1HA301 4.3 59.7 1.0
CE3 A:TRP174 4.5 29.3 1.0
OAJ A:1HA301 4.5 49.8 1.0
N A:GLY122 4.5 42.5 1.0
CG A:GLN144 4.5 36.7 1.0
O A:GLY122 4.6 38.8 1.0
N A:GLY123 4.6 39.3 1.0
CB A:THR145 4.6 41.9 1.0
CZ2 A:TRP174 4.6 29.8 1.0
CBR A:1HA301 4.8 55.7 1.0
C A:GLY146 4.9 36.6 1.0
O A:THR145 4.9 39.2 1.0

Chlorine binding site 2 out of 9 in 4i52

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Chlorine binding site 2 out of 9 in the Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:50.9
occ:1.00
 N B:GLY146 2.9 44.9 1.0
NE2 B:GLN144 3.0 42.2 1.0
N B:THR145 3.2 45.2 1.0
CA B:GLY122 3.5 43.1 1.0
CA B:GLY146 3.5 44.0 1.0
CZ3 B:TRP174 3.5 34.5 1.0
CH2 B:TRP174 3.6 34.1 1.0
CB B:GLN144 3.8 42.1 1.0
C B:THR145 3.9 45.6 1.0
OG1 B:THR145 3.9 43.5 1.0
CBA B:1HA301 3.9 68.6 1.0
CA B:GLN144 3.9 40.8 1.0
CA B:THR145 4.0 44.4 1.0
C B:GLY122 4.0 42.9 1.0
C B:GLN144 4.1 43.0 1.0
SBO B:1HA301 4.1 69.5 1.0
CD B:GLN144 4.1 42.4 1.0
OAJ B:1HA301 4.2 69.6 1.0
CE3 B:TRP174 4.5 33.7 1.0
N B:GLY122 4.5 42.8 1.0
CG B:GLN144 4.5 41.2 1.0
O B:GLY122 4.5 45.9 1.0
N B:GLY123 4.6 44.2 1.0
CB B:THR145 4.6 44.5 1.0
CZ2 B:TRP174 4.6 33.9 1.0
C B:GLY146 5.0 42.5 1.0
CBR B:1HA301 5.0 66.3 1.0
O B:THR145 5.0 43.7 1.0

Chlorine binding site 3 out of 9 in 4i52

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Chlorine binding site 3 out of 9 in the Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:89.9
occ:1.00
 N C:GLY146 3.0 55.6 1.0
NE2 C:GLN144 3.3 50.4 1.0
CA C:GLY122 3.4 48.2 1.0
CA C:GLY146 3.4 54.2 1.0
CBA C:1HA301 3.4 71.9 1.0
SBO C:1HA301 3.4 70.2 1.0
N C:THR145 3.5 52.6 1.0
O C:HOH431 3.5 53.4 1.0
CZ3 C:TRP174 3.7 31.7 1.0
CH2 C:TRP174 3.8 32.6 1.0
OG1 C:THR145 3.8 54.4 1.0
C C:THR145 3.9 56.6 1.0
C C:GLY122 4.0 48.7 1.0
OAJ C:1HA301 4.0 61.0 1.0
CA C:THR145 4.2 55.4 1.0
CB C:GLN144 4.2 47.9 1.0
CA C:GLN144 4.3 48.9 1.0
C C:GLN144 4.4 50.6 1.0
N C:GLY123 4.4 49.6 1.0
CD C:GLN144 4.5 50.3 1.0
CBR C:1HA301 4.5 69.5 1.0
N C:GLY122 4.5 46.0 1.0
O C:GLY122 4.6 52.5 1.0
CB C:THR145 4.7 56.4 1.0
CE3 C:TRP174 4.8 31.9 1.0
CZ2 C:TRP174 4.9 33.5 1.0
CAY C:1HA301 4.9 72.3 1.0
CG C:GLN144 4.9 48.5 1.0
C C:GLY146 5.0 53.5 1.0
O C:THR145 5.0 53.6 1.0

Chlorine binding site 4 out of 9 in 4i52

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Chlorine binding site 4 out of 9 in the Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:39.0
occ:1.00
 NE2 D:GLN144 2.9 28.5 1.0
N D:GLY146 3.0 31.2 1.0
O D:HOH429 3.0 28.0 1.0
N D:THR145 3.2 28.8 1.0
CA D:GLY122 3.3 31.1 1.0
O D:HOH432 3.5 50.5 1.0
CZ3 D:TRP174 3.6 24.2 1.0
CH2 D:TRP174 3.6 24.1 1.0
CA D:GLY146 3.6 33.2 1.0
CB D:GLN144 3.8 27.3 1.0
CBA D:1HA301 3.8 35.2 1.0
OG1 D:THR145 3.8 32.4 1.0
C D:GLY122 3.9 30.6 1.0
CA D:GLN144 3.9 26.8 1.0
C D:THR145 4.0 31.5 1.0
SBO D:1HA301 4.0 37.2 1.0
C D:GLN144 4.0 28.3 1.0
CD D:GLN144 4.0 28.5 1.0
CA D:THR145 4.1 30.9 1.0
N D:GLY122 4.3 30.6 1.0
O D:GLY122 4.4 35.0 1.0
N D:GLY123 4.4 29.6 1.0
CG D:GLN144 4.5 27.1 1.0
OAJ D:1HA301 4.5 29.6 1.0
CE3 D:TRP174 4.6 24.1 1.0
CB D:THR145 4.6 31.3 1.0
CZ2 D:TRP174 4.6 24.0 1.0
CBR D:1HA301 4.9 32.9 1.0

Chlorine binding site 5 out of 9 in 4i52

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Chlorine binding site 5 out of 9 in the Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl302

b:54.3
occ:1.00
 N E:GLY146 2.9 37.2 1.0
NE2 E:GLN144 3.0 37.1 1.0
O E:HOH444 3.1 41.4 1.0
N E:THR145 3.2 36.0 1.0
CA E:GLY122 3.4 35.7 1.0
CA E:GLY146 3.5 37.8 1.0
CZ3 E:TRP174 3.6 27.5 1.0
CH2 E:TRP174 3.6 26.9 1.0
CBA E:1HA301 3.8 44.5 1.0
OG1 E:THR145 3.8 38.0 1.0
CB E:GLN144 3.8 36.4 1.0
C E:THR145 3.9 38.5 1.0
CA E:GLN144 3.9 35.5 1.0
C E:GLY122 4.0 34.4 1.0
CA E:THR145 4.0 37.4 1.0
C E:GLN144 4.0 35.5 1.0
CD E:GLN144 4.1 37.3 1.0
SBO E:1HA301 4.1 47.3 1.0
N E:GLY122 4.4 36.3 1.0
O E:GLY122 4.5 36.7 1.0
N E:GLY123 4.5 32.4 1.0
OAJ E:1HA301 4.5 37.8 1.0
CG E:GLN144 4.5 37.6 1.0
CE3 E:TRP174 4.5 28.4 1.0
CB E:THR145 4.6 37.1 1.0
CZ2 E:TRP174 4.7 26.7 1.0
O E:THR145 5.0 38.1 1.0
CBR E:1HA301 5.0 41.8 1.0

Chlorine binding site 6 out of 9 in 4i52

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Chlorine binding site 6 out of 9 in the Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl302

b:45.8
occ:1.00
 O F:HOH442 2.9 43.1 1.0
NE2 F:GLN144 3.0 31.3 1.0
O F:HOH434 3.0 39.5 1.0
N F:GLY146 3.2 33.5 1.0
CA F:GLY122 3.3 34.2 1.0
N F:THR145 3.5 30.0 1.0
CH2 F:TRP174 3.7 27.7 1.0
CZ3 F:TRP174 3.7 28.4 1.0
SBO F:1HA301 3.7 45.3 1.0
CA F:GLY146 3.7 32.4 1.0
CBA F:1HA301 3.8 47.5 1.0
C F:GLY122 3.8 32.8 1.0
OG1 F:THR145 3.9 32.4 1.0
OAJ F:1HA301 4.0 42.5 1.0
CB F:GLN144 4.1 31.1 1.0
C F:THR145 4.1 33.0 1.0
CA F:GLN144 4.2 30.9 1.0
CD F:GLN144 4.2 31.4 1.0
N F:GLY123 4.2 32.5 1.0
O F:GLY122 4.3 33.8 1.0
CA F:THR145 4.3 32.1 1.0
C F:GLN144 4.4 30.8 1.0
N F:GLY122 4.4 36.1 1.0
CBR F:1HA301 4.5 44.0 1.0
CZ2 F:TRP174 4.7 27.3 1.0
CG F:GLN144 4.7 31.6 1.0
CE3 F:TRP174 4.7 28.0 1.0
CB F:THR145 4.8 32.3 1.0
OAF F:1HA301 4.9 41.0 1.0

Chlorine binding site 7 out of 9 in 4i52

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Chlorine binding site 7 out of 9 in the Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl302

b:57.5
occ:1.00
 NE2 G:GLN144 2.9 50.3 1.0
N G:GLY146 3.0 46.5 1.0
N G:THR145 3.3 48.5 1.0
CZ3 G:TRP174 3.4 32.8 1.0
CA G:GLY122 3.4 46.2 1.0
CH2 G:TRP174 3.5 34.6 1.0
CA G:GLY146 3.5 44.0 1.0
CB G:GLN144 3.8 46.9 1.0
OG1 G:THR145 3.9 48.3 1.0
C G:THR145 3.9 47.8 1.0
CA G:GLN144 3.9 46.9 1.0
SBO G:1HA301 4.0 57.4 1.0
C G:GLY122 4.0 46.4 1.0
CD G:GLN144 4.1 50.1 1.0
C G:GLN144 4.1 48.1 1.0
CA G:THR145 4.1 47.9 1.0
CBA G:1HA301 4.3 58.4 1.0
OAJ G:1HA301 4.3 60.5 1.0
CE3 G:TRP174 4.4 32.9 1.0
O G:GLY122 4.5 46.9 1.0
CG G:GLN144 4.5 48.6 1.0
N G:GLY122 4.5 43.9 1.0
N G:GLY123 4.5 44.1 1.0
CZ2 G:TRP174 4.5 34.1 1.0
CB G:THR145 4.7 48.2 1.0
CBR G:1HA301 4.8 58.7 1.0

Chlorine binding site 8 out of 9 in 4i52

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Chlorine binding site 8 out of 9 in the Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl302

b:47.5
occ:1.00
 NE2 H:GLN144 2.8 38.5 1.0
N H:GLY146 3.1 35.3 1.0
CA H:GLY122 3.3 35.9 1.0
O H:HOH404 3.3 40.8 1.0
N H:THR145 3.4 35.1 1.0
CH2 H:TRP174 3.5 32.4 1.0
CZ3 H:TRP174 3.5 30.6 1.0
CA H:GLY146 3.7 35.5 1.0
C H:GLY122 3.8 36.3 1.0
CB H:GLN144 3.9 36.0 1.0
CBA H:1HA301 4.0 42.6 1.0
OG1 H:THR145 4.0 36.3 1.0
CA H:GLN144 4.0 35.9 1.0
SBO H:1HA301 4.0 41.5 1.0
CD H:GLN144 4.0 38.3 1.0
C H:THR145 4.1 35.0 1.0
C H:GLN144 4.2 35.2 1.0
CA H:THR145 4.2 34.7 1.0
O H:GLY122 4.3 38.1 1.0
OAJ H:1HA301 4.3 42.3 1.0
N H:GLY123 4.3 35.3 1.0
N H:GLY122 4.4 35.9 1.0
CG H:GLN144 4.5 36.9 1.0
CZ2 H:TRP174 4.5 32.4 1.0
CE3 H:TRP174 4.6 31.9 1.0
CB H:THR145 4.8 35.5 1.0
CBR H:1HA301 5.0 42.1 1.0

Chlorine binding site 9 out of 9 in 4i52

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Chlorine binding site 9 out of 9 in the Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Scmenb Im Complex with 1-Hydroxy-2-Naphthoyl-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl302

b:48.1
occ:1.00
 NE2 I:GLN144 2.9 35.0 1.0
N I:GLY146 3.1 34.7 1.0
N I:THR145 3.2 34.0 1.0
CA I:GLY122 3.3 32.2 1.0
O I:HOH420 3.5 35.6 1.0
CZ3 I:TRP174 3.6 25.8 1.0
CH2 I:TRP174 3.6 25.5 1.0
CA I:GLY146 3.6 33.3 1.0
CBA I:1HA301 3.7 42.8 1.0
CB I:GLN144 3.8 32.9 1.0
C I:GLY122 3.8 32.4 1.0
OG1 I:THR145 3.9 34.7 1.0
SBO I:1HA301 3.9 42.8 1.0
CA I:GLN144 3.9 32.2 1.0
C I:THR145 4.0 34.2 1.0
CD I:GLN144 4.1 33.6 1.0
C I:GLN144 4.1 33.6 1.0
CA I:THR145 4.1 35.1 1.0
OAJ I:1HA301 4.3 40.9 1.0
O I:GLY122 4.3 31.6 1.0
N I:GLY122 4.3 32.7 1.0
N I:GLY123 4.4 31.5 1.0
CG I:GLN144 4.5 32.7 1.0
CE3 I:TRP174 4.6 26.8 1.0
CZ2 I:TRP174 4.6 26.4 1.0
CB I:THR145 4.7 35.4 1.0
CBR I:1HA301 4.8 44.1 1.0

Reference:

Y.Sun, H.Song, J.Li, Y.Li, M.Jiang, J.Zhou, Z.Guo. Structural Basis of the Induced-Fit Mechanism of 1,4-Dihydroxy-2-Naphthoyl Coenzyme A Synthase From the Crotonase Fold Superfamily Plos One V. 8 63095 2013.
ISSN: ESSN 1932-6203
PubMed: 23658663
DOI: 10.1371/JOURNAL.PONE.0063095
Page generated: Sun Jul 21 16:23:22 2024

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