Sodium in PDB 5mms: Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant

All present enzymatic activity of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant:
4.2.1.22;

The structure of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant, PDB code: 5mms was solved by J.B.Vicente, H.G.Colaco, F.Malagrino, P.E.Santo, A.Gutierres, T.M.Bandeiras, P.Leandro, J.A.Brito, A.Giuffre, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.35 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	86.174, 86.783, 97.786, 102.67, 103.07, 111.19
R / Rfree (%)	18.2 / 22.1

The structure of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Sodium atom in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant (pdb code 5mms). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant, PDB code: 5mms:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range: probe atom residue distance (Å) B Occ E:Na501 b:40.1 occ:1.00 O E:GLU342 2.9 35.6 1.0 N D:ILE80 3.1 30.6 1.0 OE1 E:GLU342 3.6 56.0 1.0 CA D:ASP79 3.7 29.4 1.0 CB D:ASP79 3.7 32.7 1.0 CB D:ILE80 3.8 31.0 1.0 CG2 D:ILE80 3.8 32.2 1.0 C E:GLU342 3.8 36.5 1.0 C D:ASP79 3.8 31.1 1.0 CA D:ILE80 4.0 29.0 1.0 CA E:GLU342 4.0 34.5 1.0 ND2 E:ASN93 4.1 29.8 1.0 CB E:GLU342 4.1 36.0 1.0 O E:ARG91 4.2 40.9 1.0 CG1 E:VAL90 4.2 32.8 1.0 CG2 D:VAL160 4.3 33.4 1.0 CG1 D:VAL160 4.4 35.1 1.0 CD E:GLU342 4.6 57.5 1.0 CG E:GLU342 4.9 46.6 1.0 CB D:VAL160 5.0 34.7 1.0

Sodium binding site 2 out of 3 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range: probe atom residue distance (Å) B Occ E:Na504 b:33.0 occ:1.00 O E:HOH1101 2.6 24.8 1.0 O E:ILE92 3.0 35.7 1.0 CA E:GLY96 3.2 38.7 1.0 N E:GLY96 3.7 39.5 1.0 N E:LYS97 3.7 40.9 1.0 C E:GLY96 3.7 43.4 1.0 CB E:LEU105 3.8 31.4 1.0 C E:ILE92 4.1 35.5 1.0 O E:CYS103 4.2 44.3 1.0 CE E:LYS97 4.2 54.5 1.0 N E:LEU105 4.2 34.7 1.0 CG E:LYS97 4.2 41.4 1.0 CD E:LYS97 4.3 46.0 1.0 CD2 E:LEU105 4.5 41.2 1.0 CA E:LEU105 4.6 31.7 1.0 O E:GLY96 4.7 44.1 1.0 CB E:ILE92 4.8 33.2 1.0 CA E:LYS97 4.8 41.1 1.0 CG E:LEU105 4.8 36.1 1.0 CB E:LEU101 4.8 37.1 1.0 CG2 E:ILE92 4.8 34.0 1.0 CD2 E:LEU101 4.8 42.3 1.0 O E:ASN93 4.9 39.4 1.0 C E:ASN93 4.9 38.0 1.0 N E:ASN93 4.9 31.5 1.0 CA E:ASN93 4.9 31.8 1.0 C E:ILE95 4.9 43.0 1.0 NZ E:LYS97 5.0 68.0 1.0

Sodium binding site 3 out of 3 in the Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Cystathionine Beta-Synthase (Cbs) P.P49L DELTA409-551 Variant within 5.0Å range: probe atom residue distance (Å) B Occ F:Na501 b:30.2 occ:1.00 O F:GLU342 2.6 31.9 1.0 O F:HOH1125 2.8 25.9 1.0 N B:ILE80 3.1 32.6 1.0 C F:GLU342 3.5 33.4 1.0 CG2 B:ILE80 3.6 37.3 1.0 CB B:ASP79 3.7 35.3 1.0 CB B:ILE80 3.7 36.1 1.0 OE1 F:GLU342 3.8 66.3 1.0 CA B:ASP79 3.8 32.9 1.0 CA F:GLU342 3.8 29.8 1.0 C B:ASP79 3.9 34.0 1.0 CG2 B:VAL160 3.9 37.2 1.0 CA B:ILE80 4.0 32.8 1.0 CG1 B:VAL160 4.1 40.1 1.0 CB F:GLU342 4.1 30.4 1.0 ND2 F:ASN93 4.3 42.2 1.0 CB B:VAL160 4.6 38.6 1.0 O F:ARG91 4.6 37.2 1.0 CD F:GLU342 4.7 54.4 1.0 CG1 F:VAL90 4.7 35.4 1.0 N F:GLY343 4.7 30.5 1.0 CG F:GLU342 5.0 42.5 1.0 CG B:ASP79 5.0 57.5 1.0

J.B.Vicente, H.G.Colaco, F.Malagrino, P.E.Santo, A.Gutierres, T.M.Bandeiras, P.Leandro, J.A.Brito, A.Giuffre. A Clinically Relevant Variant of the Human Hydrogen Sulfide-Synthesizing Enzyme Cystathionine Beta-Synthase: Increased Co Reactivity As A Novel Molecular Mechanism of Pathogenicity? Oxid Med Cell Longev V.2017 40321 2017.
ISSN: ISSN 1942-0994
PubMed: 28421128
DOI: 10.1155/2017/8940321