Sodium in PDB 4uxx: Structure of DELTA4-Dgka with Amppcp in 9.9 Mag

All present enzymatic activity of Structure of DELTA4-Dgka with Amppcp in 9.9 Mag:
2.7.1.107;

The structure of Structure of DELTA4-Dgka with Amppcp in 9.9 Mag, PDB code: 4uxx was solved by D.Li, L.Vogeley, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.08 / 2.70
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.940, 72.940, 195.760, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 25.8

The structure of Structure of DELTA4-Dgka with Amppcp in 9.9 Mag also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Structure of DELTA4-Dgka with Amppcp in 9.9 Mag (pdb code 4uxx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of DELTA4-Dgka with Amppcp in 9.9 Mag, PDB code: 4uxx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of DELTA4-Dgka with Amppcp in 9.9 Mag


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of DELTA4-Dgka with Amppcp in 9.9 Mag within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1122 b:0.9 occ:1.00 OE2 A:GLU28 2.0 0.9 1.0 CD A:GLU28 2.2 0.7 1.0 OXT A:ACT1123 2.5 1.0 1.0 OE1 A:GLU28 2.5 0.6 1.0 OE1 A:GLU76 2.5 0.3 1.0 C A:ACT1123 2.8 0.4 1.0 O A:ACT1123 2.8 0.7 1.0 CG A:GLU28 3.2 0.8 1.0 CD A:GLU76 3.6 0.6 1.0 CH3 A:ACT1123 3.9 0.8 1.0 OE2 A:GLU76 4.1 0.5 1.0 CB A:GLU28 4.5 0.5 1.0 OG A:SER73 4.7 88.5 1.0 CG A:GLU76 4.9 98.3 1.0 CB A:GLU76 5.0 63.9 1.0

Sodium binding site 2 out of 3 in the Structure of DELTA4-Dgka with Amppcp in 9.9 Mag


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of DELTA4-Dgka with Amppcp in 9.9 Mag within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1126 b:0.1 occ:1.00 OE1 B:GLU76 2.3 0.7 1.0 O B:ACT1125 2.3 0.1 1.0 OE1 B:GLU28 2.5 1.0 1.0 OE2 B:GLU76 2.5 0.1 1.0 CD B:GLU76 2.7 0.4 1.0 OXT B:ACT1125 2.7 0.6 1.0 C B:ACT1125 2.9 0.7 1.0 CD B:GLU28 3.2 0.0 1.0 OE2 B:GLU28 3.3 0.6 1.0 CG B:GLU76 4.1 86.6 1.0 CH3 B:ACT1125 4.4 0.7 1.0 CG B:GLU28 4.7 91.8 1.0 NH2 A:ARG9 4.7 0.8 1.0 CB B:GLU76 4.8 67.1 1.0

Sodium binding site 3 out of 3 in the Structure of DELTA4-Dgka with Amppcp in 9.9 Mag


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of DELTA4-Dgka with Amppcp in 9.9 Mag within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1126 b:89.0 occ:0.50 OE1 C:GLU88 2.4 0.8 1.0 CD C:GLU88 3.3 0.7 1.0 OE2 C:GLU88 3.6 0.3 1.0 NH2 C:ARG92 3.9 77.6 1.0 CD2 C:LEU89 4.3 72.5 1.0 CG C:LEU89 4.5 85.3 1.0 CG C:GLU88 4.6 0.2 1.0 CZ C:ARG92 4.6 80.9 1.0 NH1 C:ARG92 4.8 76.1 1.0 CB C:GLU88 4.9 1.0 1.0 CD1 C:LEU89 5.0 79.7 1.0

D.Li, P.J.Stansfeld, M.S.P.Sansom, A.Keogh, L.Vogeley, N.Howe, J.A.Lyons, D.Aragao, P.Fromme, R.Fromme, S.Basu, I.Grotjohann, C.Kupitz, K.Rendek, U.Weierstall, N.A.Zatsepin, V.Cherezov, W.Liu, S.Bandaru, N.J.English, C.Gati, A.Barty, O.Yefanov, H.N.Chapman, K.Diederichs, M.Messerschmidt, S.Boutet, G.J.Williams, M.Marvin Seibert, M.Caffrey. Ternary Structure Reveals Mechanism of A Membrane Diacylglycerol Kinase. Nat.Commun. V. 6 10140 2015.
ISSN: ESSN 2041-1723
PubMed: 26673816
DOI: 10.1038/NCOMMS10140