Sodium in PDB 3ze3: Crystal Structure of the Integral Membrane Diacylglycerol Kinase - DELTA7

All present enzymatic activity of Crystal Structure of the Integral Membrane Diacylglycerol Kinase - DELTA7:
2.7.1.107;

The structure of Crystal Structure of the Integral Membrane Diacylglycerol Kinase - DELTA7, PDB code: 3ze3 was solved by D.Li, V.E.Pye, J.A.Lyons, L.Vogeley, D.Aragao, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.89 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.060, 91.540, 143.650, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 21.7

The structure of Crystal Structure of the Integral Membrane Diacylglycerol Kinase - DELTA7 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Integral Membrane Diacylglycerol Kinase - DELTA7 (pdb code 3ze3). 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 the Integral Membrane Diacylglycerol Kinase - DELTA7, PDB code: 3ze3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Integral Membrane Diacylglycerol Kinase - DELTA7


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 the Integral Membrane Diacylglycerol Kinase - DELTA7 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na1122 b:56.8 occ:1.00 OG1 E:THR111 2.4 38.2 1.0 OG D:SER60 2.6 29.3 0.4 O E:HOH2020 2.6 38.3 1.0 O E:HOH2021 3.4 64.4 1.0 CB E:THR111 3.4 42.2 1.0 CB D:SER60 3.4 27.6 0.6 CB D:SER60 3.5 28.6 0.4 CB E:SER61 3.6 37.6 1.0 CG2 E:THR111 3.6 43.3 1.0 OD2 E:ASP107 3.9 62.6 1.0 OG D:SER60 4.0 33.1 0.6 OD1 E:ASP107 4.0 72.6 1.0 O D:HOH2024 4.0 50.4 1.0 CG1 D:VAL56 4.1 41.4 1.0 CG E:ASP107 4.2 61.9 1.0 O E:ASP107 4.2 38.4 1.0 CA E:SER61 4.3 40.9 1.0 OG E:SER61 4.7 45.1 1.0 O E:LEU57 4.7 37.7 1.0 CA D:SER60 4.8 29.4 0.4 CA D:SER60 4.8 30.3 0.6 CA E:THR111 4.8 45.9 1.0 O E:HOH2006 4.8 31.6 1.0 C E:ASP107 4.9 38.3 1.0 N E:SER61 4.9 38.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Integral Membrane Diacylglycerol Kinase - DELTA7


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 the Integral Membrane Diacylglycerol Kinase - DELTA7 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na1122 b:53.9 occ:1.00 O F:HOH2024 2.5 57.0 1.0 O F:SER60 2.7 29.6 1.0 O D:HOH2044 3.0 48.2 1.0 OD2 D:ASP107 3.1 66.1 1.0 C F:SER60 3.5 39.4 1.0 CD2 D:LEU64 3.5 26.7 1.0 CB F:SER60 3.6 34.3 0.4 CB F:SER60 3.7 34.2 0.6 CB F:LEU64 3.7 33.7 1.0 N F:LEU64 3.7 35.6 1.0 CA F:SER60 3.8 37.0 0.4 CA F:SER60 3.8 37.0 0.6 O F:HOH2005 3.9 48.3 1.0 CA F:LEU64 3.9 37.1 1.0 CG D:ASP107 4.0 55.2 1.0 O D:HOH2019 4.1 61.5 1.0 CB F:MET63 4.4 34.3 0.5 CD1 F:LEU64 4.4 30.6 1.0 C F:MET63 4.4 37.0 1.0 OG F:SER60 4.4 38.0 0.4 CB F:MET63 4.5 36.2 0.5 CG F:LEU64 4.6 37.3 1.0 OG F:SER60 4.6 36.5 0.6 OD1 D:ASP107 4.6 54.0 1.0 N F:SER61 4.6 40.2 1.0 CD1 F:ILE67 4.8 30.5 1.0 O D:HOH2027 4.9 51.2 1.0 O E:HOH2001 4.9 67.8 1.0 CA F:MET63 4.9 37.7 0.5 CA F:MET63 4.9 38.1 0.5

D.Li, J.A.Lyons, V.E.Pye, L.Vogeley, D.Aragao, C.P.Kenyon, S.T.A.Shah, C.Doherty, M.Aherne, M.Caffrey. Crystal Structure of the Integral Membrane Diacylglycerol Kinase. Nature V. 497 521 2013.
ISSN: ISSN 0028-0836
PubMed: 23676677
DOI: 10.1038/NATURE12179