Chlorine in PDB 8hbb: Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III

Enzymatic activity of Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III

All present enzymatic activity of Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III:
1.14.11.51;

Protein crystallography data

The structure of Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III, PDB code: 8hbb was solved by G.Shang, Z.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.18 / 3.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.176, 75.328, 118.184, 90, 113.19, 90
R / Rfree (%) 26 / 28.2

Other elements in 8hbb:

The structure of Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III also contains other interesting chemical elements:

Manganese (Mn) 5 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III (pdb code 8hbb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III, PDB code: 8hbb:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8hbb

Go back to Chlorine Binding Sites List in 8hbb
Chlorine binding site 1 out of 4 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III


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 Caenorhabditis Elegans Nmad-1 in Complex with Ligand III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:37.6
occ:1.00
 MN A:MN301 2.9 39.0 1.0
CE1 A:HIS184 3.7 41.8 1.0
NE2 A:HIS239 3.7 41.5 1.0
CD1 A:ILE181 3.9 41.0 1.0
NE2 A:HIS184 3.9 41.8 1.0
CD2 A:HIS239 3.9 41.5 1.0
OD2 A:ASP186 4.4 41.6 1.0
NH2 A:ARG256 4.5 39.4 1.0
CG2 A:ILE181 4.6 41.0 1.0
OH A:TYR173 4.6 39.5 1.0
CD1 A:LEU171 4.7 38.4 1.0
CG1 A:ILE181 4.8 41.0 1.0
CG2 A:THR254 4.8 37.5 1.0
ND1 A:HIS184 4.9 41.8 1.0

Chlorine binding site 2 out of 4 in 8hbb

Go back to Chlorine Binding Sites List in 8hbb
Chlorine binding site 2 out of 4 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III


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 Caenorhabditis Elegans Nmad-1 in Complex with Ligand III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:37.4
occ:1.00
 OE1 A:GLU172 2.9 39.5 1.0
OD1 A:ASP106 3.4 38.2 1.0
NH1 B:ARG249 3.6 39.8 1.0
CZ B:ARG249 3.7 39.8 1.0
CD A:GLU172 3.9 39.5 1.0
OD2 A:ASP106 4.0 38.2 1.0
OD2 B:ASP106 4.0 39.9 1.0
NE B:ARG249 4.0 39.8 1.0
CD1 A:ILE251 4.0 37.2 1.0
CG A:ASP106 4.1 38.2 1.0
NH2 B:ARG249 4.1 39.8 1.0
CG A:GLU172 4.3 39.5 1.0
CD B:ARG249 4.3 39.8 1.0
CD1 A:ILE201 4.4 37.1 1.0
CG1 A:ILE251 4.6 37.2 1.0
NE1 A:TRP110 4.7 39.0 1.0
CG B:ASP106 5.0 39.9 1.0
CE2 A:TRP110 5.0 39.0 1.0
OE2 A:GLU172 5.0 39.5 1.0

Chlorine binding site 3 out of 4 in 8hbb

Go back to Chlorine Binding Sites List in 8hbb
Chlorine binding site 3 out of 4 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III


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 Caenorhabditis Elegans Nmad-1 in Complex with Ligand III within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:42.9
occ:1.00
 NH2 B:ARG250 3.0 40.6 1.0
OH B:TYR173 3.2 42.0 1.0
CB B:ALA252 3.7 40.8 1.0
CZ B:TYR173 4.0 42.0 1.0
CZ B:ARG250 4.1 40.6 1.0
OG B:SER197 4.1 42.9 1.0
CE2 B:TYR173 4.1 42.0 1.0
NH1 B:ARG250 4.3 40.6 1.0
CD1 B:LEU171 4.5 41.2 1.0
CG2 B:VAL241 4.7 44.2 1.0
CB B:SER197 4.8 42.9 1.0
CE B:MET206 4.8 45.0 1.0
CG2 B:ILE181 4.9 45.5 1.0
OG1 B:THR254 5.0 42.7 1.0

Chlorine binding site 4 out of 4 in 8hbb

Go back to Chlorine Binding Sites List in 8hbb
Chlorine binding site 4 out of 4 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III


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 Caenorhabditis Elegans Nmad-1 in Complex with Ligand III within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:47.8
occ:1.00
 NH2 C:ARG250 3.2 52.5 1.0
NH1 C:ARG250 3.6 52.5 1.0
CG2 C:VAL241 3.7 53.9 1.0
CZ C:ARG250 3.9 52.5 1.0
OG C:SER197 3.9 52.5 1.0
CB C:ALA252 4.1 53.4 1.0
CB C:SER197 4.3 52.5 1.0
CE C:MET206 4.3 52.1 1.0
SD C:MET206 4.8 52.1 1.0

Reference:

G.Shang, M.Yang, M.Li, L.Ma, Y.Liu, J.Ma, Y.Chen, X.Wang, S.Fan, M.Xie, W.Wu, S.Dai, Z.Chen. Structural Basis of Nucleic Acid Recognition and 6MA Demethylation By Caenorhabditis Elegans Nmad-1A. Int J Mol Sci V. 25 2024.
ISSN: ESSN 1422-0067
PubMed: 38255759
DOI: 10.3390/IJMS25020686
Page generated: Tue Jul 30 10:17:54 2024

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