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Sodium in PDB 6c4p: Crystal Structures of Cystathionine Beta-Synthase From Saccharomyces Cerevisiae: the Structure of the Pmp Complex

Enzymatic activity of Crystal Structures of Cystathionine Beta-Synthase From Saccharomyces Cerevisiae: the Structure of the Pmp Complex

All present enzymatic activity of Crystal Structures of Cystathionine Beta-Synthase From Saccharomyces Cerevisiae: the Structure of the Pmp Complex:
4.2.1.22;

Protein crystallography data

The structure of Crystal Structures of Cystathionine Beta-Synthase From Saccharomyces Cerevisiae: the Structure of the Pmp Complex, PDB code: 6c4p was solved by C.A.Kreinbring, Y.Tu, D.Liu, D.B.Berkowitz, G.A.Petsko, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 80.733, 80.733, 207.923, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 21.1

Other elements in 6c4p:

The structure of Crystal Structures of Cystathionine Beta-Synthase From Saccharomyces Cerevisiae: the Structure of the Pmp Complex also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structures of Cystathionine Beta-Synthase From Saccharomyces Cerevisiae: the Structure of the Pmp Complex (pdb code 6c4p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structures of Cystathionine Beta-Synthase From Saccharomyces Cerevisiae: the Structure of the Pmp Complex, PDB code: 6c4p:

Sodium binding site 1 out of 1 in 6c4p

Go back to Sodium Binding Sites List in 6c4p
Sodium binding site 1 out of 1 in the Crystal Structures of Cystathionine Beta-Synthase From Saccharomyces Cerevisiae: the Structure of the Pmp Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structures of Cystathionine Beta-Synthase From Saccharomyces Cerevisiae: the Structure of the Pmp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:50.5
occ:1.00
 O A:HOH634 2.2 50.6 1.0
O A:HOH637 2.2 66.1 1.0
O A:HOH679 2.4 50.3 1.0
O A:GLY120 2.5 35.5 1.0
O A:HOH651 2.8 39.2 1.0
C A:GLY120 3.6 34.1 1.0
CA A:GLY120 4.3 34.8 1.0
N A:THR100 4.4 37.0 0.5
N A:THR100 4.4 37.7 0.5
CA A:ARG99 4.4 38.6 1.0
OE2 A:GLU122 4.4 49.4 1.0
N A:ALA121 4.6 33.8 1.0
CG A:ARG99 4.6 39.7 1.0
O A:THR100 4.6 38.5 0.5
O A:THR100 4.7 37.4 0.5
O A:HOH622 4.7 38.2 1.0
CA A:ALA121 4.7 35.1 1.0
OG1 A:THR100 4.7 37.6 0.5
O A:TYR98 4.8 38.2 1.0
CB A:ARG99 4.9 39.2 1.0
C A:ARG99 5.0 38.1 1.0

Reference:

Y.Tu, C.A.Kreinbring, M.Hill, C.Liu, G.A.Petsko, C.D.Mccune, D.B.Berkowitz, D.Liu, D.Ringe. Crystal Structures of Cystathionine Beta-Synthase From Saccharomyces Cerevisiae: One Enzymatic Step at A Time. Biochemistry V. 57 3134 2018.
ISSN: ISSN 1520-4995
PubMed: 29630349
DOI: 10.1021/ACS.BIOCHEM.8B00092
Page generated: Mon Aug 18 03:58:28 2025

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