Atomistry » Manganese » PDB 8f4d-8hl8 » 8hbb
Atomistry »
  Manganese »
    PDB 8f4d-8hl8 »
      8hbb »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy