Chlorine in PDB 9jff: Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate

Enzymatic activity of Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate

All present enzymatic activity of Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate:
4.1.1.81;

Protein crystallography data

The structure of Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate, PDB code: 9jff was solved by M.Jiang, S.Guo, X.Chen, Q.Wei, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.31 / 2.15
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 160.074, 160.074, 160.074, 90, 90, 90
R / Rfree (%) 15.6 / 19.2

Other elements in 9jff:

The structure of Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate (pdb code 9jff). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate, PDB code: 9jff:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 9jff

Go back to Chlorine Binding Sites List in 9jff
Chlorine binding site 1 out of 3 in the Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate


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 L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl413

b:49.7
occ:1.00
 O A:HOH844 2.9 52.4 1.0
N A:ASN70 3.2 30.2 1.0
OD1 A:ASN70 3.5 31.6 0.5
C A:ARG68 3.6 30.0 1.0
CA A:ARG68 3.6 27.2 1.0
CA A:ASN70 3.6 30.1 0.5
CA A:ASN70 3.6 30.1 0.5
O A:HOH614 3.7 31.2 1.0
N A:THR69 3.8 27.6 1.0
O A:ARG68 3.9 21.5 1.0
CB A:ARG68 4.0 29.6 1.0
CG A:ASN70 4.2 32.3 0.5
O A:HOH627 4.2 50.2 1.0
O A:HOH630 4.2 37.2 1.0
C A:THR69 4.4 30.3 1.0
CG A:ARG68 4.4 38.5 1.0
CB A:ASN70 4.5 30.4 0.5
CB A:ASN70 4.6 30.4 0.5
CA A:THR69 4.7 26.0 1.0
C A:ASN70 4.7 30.9 1.0
N A:GLY71 4.8 26.0 1.0
N A:ARG68 4.9 23.8 1.0
O A:ALA64 4.9 23.3 1.0

Chlorine binding site 2 out of 3 in 9jff

Go back to Chlorine Binding Sites List in 9jff
Chlorine binding site 2 out of 3 in the Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate


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 L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl414

b:23.4
occ:1.00
 N A:GLY31 3.1 16.8 1.0
NZ A:LYS199 3.3 40.6 1.0
C8 A:33P404 3.5 22.5 1.0
C9 A:33P404 3.6 23.0 1.0
CA A:GLY31 3.7 16.8 1.0
CE A:LYS199 3.8 29.5 1.0
CB A:THR30 3.8 17.7 1.0
C10 A:33P404 3.8 18.1 1.0
CG A:LYS199 3.9 28.1 1.0
CG1 A:ILE32 3.9 23.0 1.0
CZ A:PHE172 3.9 22.0 1.0
C A:GLY31 3.9 18.3 1.0
N A:ILE32 4.0 19.3 1.0
N7 A:33P404 4.1 26.4 1.0
C A:THR30 4.1 24.8 1.0
CA A:THR30 4.2 19.2 1.0
CD A:LYS199 4.5 30.8 1.0
OG1 A:THR30 4.5 21.4 1.0
CE1 A:PHE172 4.5 22.9 1.0
O A:GLY31 4.6 23.3 1.0
CD1 A:ILE32 4.6 21.1 1.0
C4A A:33P404 4.7 26.8 1.0
CG2 A:THR30 4.7 15.3 1.0
CA A:ILE32 4.8 20.4 1.0
CE2 A:PHE172 5.0 24.1 1.0
CB A:ILE32 5.0 21.4 1.0

Chlorine binding site 3 out of 3 in 9jff

Go back to Chlorine Binding Sites List in 9jff
Chlorine binding site 3 out of 3 in the Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate


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 L-Threonine-O-3-Phosphate Decarboxylase Cobc in Complex with Reaction Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl415

b:82.3
occ:1.00
 O A:HOH842 3.1 56.2 1.0
N A:GLY20 3.3 30.7 1.0
CA A:GLY19 3.8 29.4 1.0
C A:GLY19 4.1 34.4 1.0
CA A:GLY20 4.2 33.4 1.0
O A:HOH754 4.5 51.2 1.0
O A:HOH506 4.7 40.8 1.0
C A:GLY20 4.9 37.2 1.0

Reference:

M.Jiang, S.Guo, X.Chen, Q.Wei, M.Wang. Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase Cobc From Sinorhizobium Meliloti Involved in Vitamin B 12 Biosynthesis. Biochem.Biophys.Res.Commun. V. 734 50767 2024.
ISSN: ESSN 1090-2104
PubMed: 39366178
DOI: 10.1016/J.BBRC.2024.150767
Page generated: Thu Oct 31 18:17:35 2024

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