Sodium in PDB 1v1r: Crosstalk Between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine

All present enzymatic activity of Crosstalk Between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine:
1.2.4.4;

The structure of Crosstalk Between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine, PDB code: 1v1r was solved by J.Li, R.M.Wynn, M.Machius, J.L.Chuang, S.Karthikeyan, D.R.Tomchick, D.T.Chuang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.77 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.135, 145.135, 69.226, 90.00, 90.00, 120.00
R / Rfree (%)	15.7 / 18.3

The structure of Crosstalk Between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Crosstalk Between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine (pdb code 1v1r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crosstalk Between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine, PDB code: 1v1r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crosstalk Between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crosstalk Between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1402 b:39.0 occ:1.00 O3 A:SO41405 2.2 15.4 0.5 O A:HOH2156 2.2 40.7 1.0 OE1 A:GLU193 2.6 19.8 1.0 O3 A:SO41405 2.6 32.5 0.5 OE2 A:GLU193 2.7 31.3 1.0 O4 A:SO41405 2.8 36.6 0.5 OD1 A:ASN222 2.9 39.9 1.0 CD A:GLU193 2.9 23.0 1.0 O4 A:SO41405 3.2 26.5 0.5 S A:SO41405 3.2 19.4 0.5 S A:SO41405 3.3 33.1 0.5 CG A:ASN222 3.6 37.3 1.0 ND2 A:ASN222 3.7 42.5 1.0 O1 A:SO41405 4.0 21.9 0.5 O2 A:SO41405 4.0 35.3 0.5 N A:GLU193 4.2 11.1 1.0 O2 A:SO41405 4.3 5.4 0.5 CG A:GLU193 4.4 16.6 1.0 O1 A:SO41405 4.5 34.9 0.5 O A:ARG220 4.5 15.2 0.5 N A:GLY194 4.5 10.6 1.0 CA A:GLY192 4.6 8.5 1.0 NH1 A:ARG220 4.7 20.1 0.5 NH2 A:ARG220 4.7 21.7 0.5 O A:ARG220 4.8 14.3 0.5 N A:ASN222 4.8 24.1 1.0 C A:GLY192 4.8 8.5 1.0 O A:HOH2155 4.8 35.5 1.0 CB A:ASN222 4.8 31.6 1.0

Sodium binding site 2 out of 2 in the Crosstalk Between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crosstalk Between Cofactor Binding and the Phosphorylation Loop Conformation in the Bckd Machine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1403 b:15.7 occ:1.00 O2 A:SO41405 3.0 5.4 0.5 N A:GLY192 3.1 7.3 1.0 O A:HOH2084 3.2 15.5 1.0 O A:HOH2166 3.3 24.6 1.0 CB A:ALA195 3.5 11.0 1.0 CG A:GLN112 3.6 11.8 1.0 O4 A:SO41405 3.7 26.5 0.5 CB A:GLN112 3.7 10.9 1.0 NH2 A:ARG220 3.8 21.7 0.5 NH2 A:ARG220 3.9 31.4 0.5 CA A:GLY192 3.9 8.5 1.0 S A:SO41405 3.9 19.4 0.5 CA A:PHE191 3.9 6.8 1.0 C A:PHE191 3.9 6.6 1.0 CD2 A:LEU164 4.1 17.9 1.0 NH1 A:ARG220 4.1 29.6 0.5 O A:HOH2277 4.1 42.4 1.0 O4 A:SO41405 4.2 36.6 0.5 CZ A:ARG220 4.3 30.1 0.5 CB A:PHE191 4.3 7.7 1.0 CD A:GLN112 4.7 13.4 1.0 C A:GLY192 4.7 8.5 1.0 O A:GLY192 4.7 8.1 1.0 N A:ALA195 4.7 9.4 1.0 O1 A:SO41405 4.7 21.9 0.5 CA A:ALA195 4.8 8.6 1.0 OE1 A:GLN112 4.8 11.8 1.0 CZ A:ARG220 5.0 20.8 0.5

J.Li, R.M.Wynn, M.Machius, J.L.Chuang, S.Karthikeyan, D.R.Tomchick, D.T.Chuang. Cross-Talk Between Thiamin Diphosphate Binding and Phosphorylation Loop Conformation in Human Branched-Chain {Alpha}-Keto Acid Decarboxylase/Dehydrogenase J.Biol.Chem. V. 279 32968 2004.
ISSN: ISSN 0021-9258
PubMed: 15166214
DOI: 10.1074/JBC.M403611200