Chlorine in PDB 8vzh: Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp

Protein crystallography data

The structure of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp, PDB code: 8vzh was solved by Y.Kim, M.Maltseva, M.Endres, S.Lee, Y.Yoshikuni, R.Gonzalez, K.Michalska, A.Joachimiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.39 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 120.591, 134.013, 173.399, 90, 90, 90
R / Rfree (%) 16 / 19.5

Other elements in 8vzh:

The structure of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp (pdb code 8vzh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp, PDB code: 8vzh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8vzh

Go back to Chlorine Binding Sites List in 8vzh
Chlorine binding site 1 out of 5 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl610

b:64.4
occ:1.00
 OD2 A:ASP432 3.2 57.1 1.0
OD1 A:ASP432 3.2 40.8 1.0
ND1 A:HIS430 3.4 32.4 1.0
NE A:ARG433 3.5 44.1 1.0
CG A:ASP432 3.6 55.5 1.0
NH2 A:ARG433 4.0 52.2 1.0
CE1 A:HIS430 4.2 40.9 1.0
CZ A:ARG433 4.2 49.5 1.0
CG A:ARG433 4.3 39.0 1.0
CG A:HIS430 4.3 29.3 1.0
CD A:ARG433 4.4 36.8 1.0
CB A:HIS430 4.5 25.7 1.0
O2 A:PO4608 4.8 54.2 1.0
CA A:HIS430 5.0 23.6 1.0

Chlorine binding site 2 out of 5 in 8vzh

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Chlorine binding site 2 out of 5 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl608

b:46.5
occ:1.00
 O B:HOH902 2.6 37.6 1.0
O B:TRP89 3.1 20.6 1.0
NH1 B:ARG272 3.4 21.5 1.0
O B:HOH855 3.6 23.2 1.0
ND2 B:ASN92 3.7 19.9 1.0
OD1 B:ASN92 3.8 29.4 1.0
O B:SER90 3.9 23.8 1.0
O B:HOH725 4.1 27.9 1.0
CG B:ASN92 4.1 20.9 1.0
C B:TRP89 4.2 22.6 1.0
CA B:SER90 4.3 20.3 1.0
C B:SER90 4.3 23.5 1.0
CE2 B:TRP89 4.6 24.1 1.0
CZ B:ARG272 4.6 21.9 1.0
NE1 B:TRP89 4.6 21.6 1.0
N B:SER90 4.7 20.5 1.0
CD2 B:TRP89 4.8 23.8 1.0
CZ2 B:TRP89 4.8 21.9 1.0
NH1 B:ARG152 4.8 35.9 1.0
CD1 B:TRP89 4.9 18.2 1.0
CZ B:ARG152 4.9 31.5 1.0
NH2 B:ARG272 5.0 21.5 1.0

Chlorine binding site 3 out of 5 in 8vzh

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Chlorine binding site 3 out of 5 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl608

b:46.5
occ:1.00
 O C:HOH736 3.0 33.8 1.0
NH2 C:ARG396 3.1 27.9 1.0
NE C:ARG256 3.1 32.4 1.0
NH2 C:ARG256 3.4 26.2 1.0
CE C:MET277 3.6 33.2 1.0
CZ C:ARG256 3.7 35.7 1.0
CD C:PRO238 3.7 26.5 1.0
CA C:SER237 3.8 22.1 1.0
CZ C:ARG396 4.1 30.7 1.0
CD2 C:LEU235 4.1 29.0 1.0
NH1 C:ARG396 4.1 36.1 1.0
SD C:MET277 4.2 37.9 1.0
CD C:ARG256 4.2 28.2 1.0
CB C:SER237 4.3 20.9 1.0
CE C:MET276 4.4 40.6 1.0
O C:ALA236 4.5 27.2 1.0
N C:PRO238 4.5 27.7 1.0
C C:SER237 4.6 26.3 1.0
N C:SER237 4.6 24.8 1.0
CG C:PRO238 4.7 31.2 1.0
CG C:LEU235 4.7 32.2 1.0
O C:MET276 4.9 30.2 1.0
C C:ALA236 4.9 27.0 1.0
NH1 C:ARG256 5.0 32.3 1.0
CD1 C:LEU235 5.0 27.3 1.0

Chlorine binding site 4 out of 5 in 8vzh

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Chlorine binding site 4 out of 5 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl609

b:50.8
occ:1.00
 O C:TRP89 3.1 19.9 1.0
NH1 C:ARG272 3.4 20.7 1.0
O C:HOH859 3.5 25.0 1.0
ND2 C:ASN92 3.8 15.9 1.0
OD1 C:ASN92 3.9 24.8 1.0
O C:SER90 3.9 21.3 1.0
O C:HOH786 4.0 23.8 1.0
C C:TRP89 4.1 23.0 1.0
CG C:ASN92 4.2 21.7 1.0
CA C:SER90 4.2 21.4 1.0
C C:SER90 4.3 23.7 1.0
CE2 C:TRP89 4.4 22.1 1.0
NE1 C:TRP89 4.5 22.1 1.0
NH1 C:ARG152 4.6 21.8 1.0
N C:SER90 4.6 23.3 1.0
CZ C:ARG272 4.6 22.1 1.0
CD2 C:TRP89 4.7 23.6 1.0
CZ2 C:TRP89 4.7 24.6 1.0
CD1 C:TRP89 4.8 19.0 1.0
CG C:TRP89 4.9 21.5 1.0
CZ C:ARG152 5.0 27.4 1.0

Chlorine binding site 5 out of 5 in 8vzh

Go back to Chlorine Binding Sites List in 8vzh
Chlorine binding site 5 out of 5 in the Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of 2-Hydroxyacyl-Coa Lyase/Synthase Tbhacs From Thermoflexaceae Bacterium in the Complex with Thdp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl607

b:50.2
occ:1.00
 O D:TRP89 3.0 26.4 1.0
NH1 D:ARG272 3.3 25.9 1.0
ND2 D:ASN92 3.5 27.7 1.0
O D:SER90 3.6 25.6 1.0
OD1 D:ASN92 3.7 31.1 1.0
CG D:ASN92 3.9 29.8 1.0
O D:HOH730 4.1 35.1 1.0
C D:SER90 4.1 30.1 1.0
C D:TRP89 4.1 26.1 1.0
CA D:SER90 4.2 24.6 1.0
CZ D:ARG272 4.4 28.6 1.0
N D:SER90 4.7 23.8 1.0
NH1 D:ARG152 4.7 30.5 1.0
CE2 D:TRP89 4.7 27.7 1.0
NE1 D:TRP89 4.7 33.6 1.0
NH2 D:ARG272 4.8 26.6 1.0
CZ D:ARG152 4.9 35.6 1.0
CD2 D:TRP89 4.9 23.3 1.0
N D:ASN92 4.9 27.3 1.0
CD1 D:TRP89 5.0 23.7 1.0
N D:ASN91 5.0 23.7 1.0
CZ2 D:TRP89 5.0 24.8 1.0

Reference:

Y.Kim, S.H.Lee, P.Gade, M.Nattermann, N.Maltseva, M.Endres, J.Chen, P.Wichmann, Y.Hu, D.G.Marchal, Y.Yoshikuni, T.J.Erb, R.Gonzalez, K.Michalska, A.Joachimiak. Revealing Reaction Intermediates in One-Carbon Elongation By Thiamine Diphosphate/Coa-Dependent Enzyme Family. Commun Chem V. 7 160 2024.
ISSN: ESSN 2399-3669
PubMed: 39034323
DOI: 10.1038/S42004-024-01242-Y
Page generated: Thu Oct 31 18:06:30 2024

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