Sodium in PDB 4coo: Crystal Structure of Human Cystathionine Beta-Synthase (DELTA516-525) at 2.0 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Human Cystathionine Beta-Synthase (DELTA516-525) at 2.0 Angstrom Resolution:
4.2.1.22;

The structure of Crystal Structure of Human Cystathionine Beta-Synthase (DELTA516-525) at 2.0 Angstrom Resolution, PDB code: 4coo was solved by T.J.Mccorvie, J.Kopec, M.Vollamar, C.Strain-Damerell, S.Bushell, A.Bradley, C.Tallant, W.Kiyani, D.S.Froese, E.S.Carpenter, N.Burgess-Brown, F.Von Delft, C.Arrowsmith, A.Edwards, C.Bountra, W.W.Yue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	95.56 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.264, 116.193, 167.990, 90.00, 90.00, 90.00
R / Rfree (%)	17.381 / 20.068

The structure of Crystal Structure of Human Cystathionine Beta-Synthase (DELTA516-525) at 2.0 Angstrom Resolution also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Cystathionine Beta-Synthase (DELTA516-525) at 2.0 Angstrom Resolution (pdb code 4coo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Cystathionine Beta-Synthase (DELTA516-525) at 2.0 Angstrom Resolution, PDB code: 4coo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Cystathionine Beta-Synthase (DELTA516-525) at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Cystathionine Beta-Synthase (DELTA516-525) at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1558 b:28.7 occ:1.00 O A:HOH2125 3.0 34.9 1.0 N A:GLY305 3.2 25.0 1.0 NZ A:LYS172 3.3 31.1 1.0 CE A:MET173 3.5 27.1 1.0 O A:ILE306 3.6 24.4 1.0 CE A:LYS172 3.7 32.6 1.0 O A:VAL303 3.8 27.0 1.0 CA A:GLU304 3.9 25.4 1.0 N A:ILE306 3.9 25.1 1.0 CA A:GLY305 4.0 25.7 1.0 C A:GLU304 4.0 25.4 1.0 CE1 A:TYR301 4.2 28.1 1.0 OH A:TYR301 4.3 28.3 1.0 C A:GLY305 4.3 24.3 1.0 SD A:MET173 4.5 24.9 1.0 C A:ILE306 4.5 26.1 1.0 CB A:SER147 4.6 25.8 1.0 CZ A:TYR301 4.6 28.8 1.0 CD A:LYS172 4.7 32.8 1.0 C A:VAL303 4.7 27.6 1.0 N A:GLU304 4.8 24.1 1.0 O A:GLY307 4.8 26.8 1.0 CB A:GLU304 4.9 25.0 1.0 CA A:ILE306 4.9 25.2 1.0 O A:HOH2048 5.0 37.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Cystathionine Beta-Synthase (DELTA516-525) at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Cystathionine Beta-Synthase (DELTA516-525) at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1545 b:34.3 occ:1.00 O B:HOH2058 2.8 40.8 1.0 N B:GLY305 3.2 31.2 1.0 NZ B:LYS172 3.4 37.8 1.0 O B:HOH2103 3.5 49.6 1.0 CE B:MET173 3.6 35.0 1.0 CE B:LYS172 3.6 38.5 1.0 O B:ILE306 3.6 31.5 1.0 CA B:GLU304 3.9 29.9 1.0 O B:VAL303 3.9 32.6 1.0 N B:ILE306 3.9 32.2 1.0 C B:GLU304 4.0 31.2 1.0 CA B:GLY305 4.1 32.0 1.0 CE1 B:TYR301 4.2 32.4 1.0 C B:GLY305 4.3 32.8 1.0 OH B:TYR301 4.3 33.1 1.0 SD B:MET173 4.4 32.9 1.0 C B:ILE306 4.5 32.5 1.0 CD B:LYS172 4.6 37.3 1.0 CB B:SER147 4.6 31.1 1.0 CZ B:TYR301 4.7 33.9 1.0 C B:VAL303 4.7 31.2 1.0 O B:GLY307 4.8 32.4 1.0 N B:GLU304 4.8 29.3 1.0 CB B:GLU304 4.8 28.7 1.0 CA B:ILE306 4.8 32.6 1.0 O B:HOH2030 4.9 46.5 1.0

T.J.Mccorvie, J.Kopec, S.Hyung, F.Fitzpatrick, X.Feng, D.Termine, C.Strain-Damerell, M.Vollmar, J.Fleming, J.M.Janz, C.Bulawa, W.W.Yue. Inter-Domain Communication of Human Cystathionine Beta Synthase: Structural Basis of S-Adenosyl-L-Methionine Activation. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25336647
DOI: 10.1074/JBC.M114.610782