Sodium in PDB 4ib0: X-Ray Structure of Camp Dependent Protein Kinase A in Complex with High Na+ Concentration, Adp and Phosphorylated Peptide PSP20

All present enzymatic activity of X-Ray Structure of Camp Dependent Protein Kinase A in Complex with High Na+ Concentration, Adp and Phosphorylated Peptide PSP20:
2.7.11.11;

The structure of X-Ray Structure of Camp Dependent Protein Kinase A in Complex with High Na+ Concentration, Adp and Phosphorylated Peptide PSP20, PDB code: 4ib0 was solved by O.Gerlits, A.Kovalevsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.270, 79.202, 98.041, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 28.7

The binding sites of Sodium atom in the X-Ray Structure of Camp Dependent Protein Kinase A in Complex with High Na+ Concentration, Adp and Phosphorylated Peptide PSP20 (pdb code 4ib0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of Camp Dependent Protein Kinase A in Complex with High Na+ Concentration, Adp and Phosphorylated Peptide PSP20, PDB code: 4ib0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of Camp Dependent Protein Kinase A in Complex with High Na+ Concentration, Adp and Phosphorylated Peptide PSP20


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Camp Dependent Protein Kinase A in Complex with High Na+ Concentration, Adp and Phosphorylated Peptide PSP20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:19.3 occ:1.00 O1B A:ADP403 2.2 28.9 1.0 O S:HOH727 2.3 50.0 1.0 O1P S:SEP621 2.3 27.6 1.0 OD2 A:ASP184 2.5 22.1 1.0 OD1 A:ASP184 2.6 31.9 1.0 O A:HOH1188 2.6 34.9 1.0 O A:HOH1001 2.6 12.1 0.5 CG A:ASP184 2.9 28.2 1.0 PB A:ADP403 3.5 34.4 1.0 P S:SEP621 3.6 37.0 1.0 O3B A:ADP403 3.7 30.4 1.0 O3P S:SEP621 3.8 40.2 1.0 O S:HOH701 3.8 28.4 1.0 NA A:NA402 4.2 15.8 1.0 NZ A:LYS72 4.2 27.9 1.0 CA A:GLY186 4.2 21.5 1.0 OD2 A:ASP166 4.4 28.9 1.0 CB A:ASP184 4.4 23.6 1.0 O2B A:ADP403 4.4 27.8 1.0 O A:HOH1057 4.5 28.8 0.5 OG S:SEP621 4.6 35.8 1.0 N A:GLY186 4.6 17.3 1.0 O3A A:ADP403 4.6 29.7 1.0 O2P S:SEP621 4.7 42.1 1.0 O2A A:ADP403 4.8 30.2 1.0 O A:HOH1005 4.8 12.3 0.5 CB S:SEP621 5.0 31.0 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of Camp Dependent Protein Kinase A in Complex with High Na+ Concentration, Adp and Phosphorylated Peptide PSP20


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Camp Dependent Protein Kinase A in Complex with High Na+ Concentration, Adp and Phosphorylated Peptide PSP20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:15.8 occ:1.00 O3B A:ADP403 2.0 30.4 1.0 O2A A:ADP403 2.1 30.2 1.0 O A:HOH1002 2.4 30.3 1.0 OD2 A:ASP184 2.5 22.1 1.0 OD1 A:ASN171 2.6 33.5 1.0 O S:HOH701 2.7 28.4 1.0 O S:HOH728 2.8 41.4 1.0 PB A:ADP403 3.3 34.4 1.0 CG A:ASP184 3.4 28.2 1.0 PA A:ADP403 3.5 30.8 1.0 CG A:ASN171 3.5 23.5 1.0 O1P S:SEP621 3.7 27.6 1.0 ND2 A:ASN171 3.7 24.0 1.0 O1B A:ADP403 3.8 28.9 1.0 CB A:ASP184 3.9 23.6 1.0 O3A A:ADP403 3.9 29.7 1.0 NA A:NA401 4.2 19.3 1.0 CE A:LYS168 4.3 16.6 1.0 C5' A:ADP403 4.4 30.1 1.0 O1A A:ADP403 4.4 27.0 1.0 OD1 A:ASP184 4.5 31.9 1.0 NZ A:LYS168 4.5 18.0 1.0 O5' A:ADP403 4.5 34.1 1.0 O S:HOH710 4.5 37.0 1.0 OD2 A:ASP166 4.5 28.9 1.0 O2B A:ADP403 4.6 27.8 1.0 O3' A:ADP403 4.7 29.9 1.0 O2P S:SEP621 4.7 42.1 1.0 CB A:ASN171 4.9 26.7 1.0 P S:SEP621 4.9 37.0 1.0 CA A:GLY52 5.0 53.3 1.0

O.Gerlits, A.Das, M.M.Keshwani, S.Taylor, M.J.Waltman, P.Langan, W.T.Heller, A.Kovalevsky. Metal-Free Camp-Dependent Protein Kinase Can Catalyze Phosphoryl Transfer. Biochemistry V. 53 3179 2014.
ISSN: ISSN 0006-2960
PubMed: 24786636
DOI: 10.1021/BI5000965