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Manganese 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:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III, PDB code: 8hbb:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 8hbb

Go back to Manganese Binding Sites List in 8hbb
Manganese binding site 1 out of 5 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn301

b:39.0
occ:1.00
 OD2 A:ASP186 1.9 41.6 1.0
NE2 A:HIS239 1.9 41.5 1.0
NE2 A:HIS184 1.9 41.8 1.0
CE1 A:HIS239 2.7 41.5 1.0
CE1 A:HIS184 2.7 41.8 1.0
CL A:CL302 2.9 37.6 1.0
CG A:ASP186 2.9 41.6 1.0
CD2 A:HIS239 3.0 41.5 1.0
CD2 A:HIS184 3.1 41.8 1.0
OD1 A:ASP186 3.5 41.6 1.0
ND1 A:HIS239 3.8 41.5 1.0
ND1 A:HIS184 3.9 41.8 1.0
NH2 A:ARG256 4.0 39.4 1.0
CG A:HIS239 4.0 41.5 1.0
CG A:HIS184 4.1 41.8 1.0
CB A:ASP186 4.1 41.6 1.0
N A:ASP186 4.8 41.6 1.0
CA A:ASP186 4.8 41.6 1.0
CZ A:ARG256 4.9 39.4 1.0
CD1 A:LEU195 5.0 38.6 1.0

Manganese binding site 2 out of 5 in 8hbb

Go back to Manganese Binding Sites List in 8hbb
Manganese binding site 2 out of 5 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
B:Mn301

b:52.0
occ:1.00
 NE2 B:HIS184 2.0 47.8 1.0
OD2 B:ASP186 2.0 48.8 1.0
NE2 B:HIS239 2.0 47.6 1.0
OD1 B:ASP186 2.2 48.8 1.0
CG B:ASP186 2.3 48.8 1.0
CE1 B:HIS239 2.3 47.6 1.0
CD2 B:HIS184 2.8 47.8 1.0
CE1 B:HIS184 2.9 47.8 1.0
CD2 B:HIS239 3.3 47.6 1.0
ND1 B:HIS239 3.6 47.6 1.0
CB B:ASP186 3.7 48.8 1.0
ND1 B:HIS184 3.8 47.8 1.0
CG B:HIS184 3.9 47.8 1.0
CG B:HIS239 4.1 47.6 1.0
N B:ASP186 4.3 48.8 1.0
CA B:ASP186 4.4 48.8 1.0
NH2 B:ARG256 4.4 44.9 1.0
CD1 B:LEU195 4.8 44.4 1.0
O B:HIS184 4.9 47.8 1.0

Manganese binding site 3 out of 5 in 8hbb

Go back to Manganese Binding Sites List in 8hbb
Manganese binding site 3 out of 5 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn303

b:49.4
occ:1.00
 OD1 B:ASN202 2.7 41.0 1.0
O B:ILE201 3.5 40.0 1.0
ND2 A:ASN103 3.9 38.2 1.0
CG B:ASN202 3.9 41.0 1.0
CG2 A:THR107 4.0 38.8 1.0
CD2 B:HIS223 4.3 41.9 1.0
CG B:HIS223 4.5 41.9 1.0
CA B:ASN202 4.5 41.0 1.0
C B:ILE201 4.6 40.0 1.0
CB B:ASN202 4.7 41.0 1.0
NE2 B:HIS223 4.7 41.9 1.0
CB B:HIS223 4.8 41.9 1.0
ND2 B:ASN202 4.8 41.0 1.0

Manganese binding site 4 out of 5 in 8hbb

Go back to Manganese Binding Sites List in 8hbb
Manganese binding site 4 out of 5 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn301

b:56.2
occ:1.00
 NE2 C:HIS239 1.8 54.7 1.0
OD2 C:ASP186 2.0 57.6 1.0
NE2 C:HIS184 2.0 55.1 1.0
CE1 C:HIS184 2.7 55.1 1.0
CE1 C:HIS239 2.8 54.7 1.0
CD2 C:HIS239 2.8 54.7 1.0
CG C:ASP186 3.1 57.6 1.0
CD2 C:HIS184 3.2 55.1 1.0
OD1 C:ASP186 3.7 57.6 1.0
ND1 C:HIS239 3.8 54.7 1.0
CG C:HIS239 3.9 54.7 1.0
ND1 C:HIS184 3.9 55.1 1.0
NH2 C:ARG256 3.9 58.8 1.0
CG C:HIS184 4.1 55.1 1.0
CB C:ASP186 4.2 57.6 1.0
CD2 C:LEU195 4.3 55.2 1.0
CD1 C:LEU195 4.7 55.2 1.0
CZ C:ARG256 4.7 58.8 1.0
N C:ASP186 4.9 57.6 1.0

Manganese binding site 5 out of 5 in 8hbb

Go back to Manganese Binding Sites List in 8hbb
Manganese binding site 5 out of 5 in the Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Caenorhabditis Elegans Nmad-1 in Complex with Ligand III within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:57.7
occ:1.00
 NE2 D:HIS239 1.8 54.3 1.0
OD1 D:ASP186 1.9 59.1 1.0
NE2 D:HIS184 2.0 55.0 1.0
CD2 D:HIS239 2.7 54.3 1.0
CE1 D:HIS184 2.8 55.0 1.0
CE1 D:HIS239 2.9 54.3 1.0
CG D:ASP186 3.0 59.1 1.0
CD2 D:HIS184 3.0 55.0 1.0
OD2 D:ASP186 3.6 59.1 1.0
CG D:HIS239 3.8 54.3 1.0
ND1 D:HIS239 3.9 54.3 1.0
ND1 D:HIS184 3.9 55.0 1.0
CG D:HIS184 4.1 55.0 1.0
CB D:ASP186 4.2 59.1 1.0
N D:ASP186 4.6 59.1 1.0
CD1 D:LEU195 4.7 55.5 1.0
CA D:ASP186 4.8 59.1 1.0
CD1 D:ILE181 4.9 55.6 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: Sun Oct 6 12:27:13 2024

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