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Sodium in PDB 5dwk: Diacylglycerol Kinase Solved By Multi Crystal Multi Orientation Native Sad

Enzymatic activity of Diacylglycerol Kinase Solved By Multi Crystal Multi Orientation Native Sad

All present enzymatic activity of Diacylglycerol Kinase Solved By Multi Crystal Multi Orientation Native Sad:
2.7.1.107;

Protein crystallography data

The structure of Diacylglycerol Kinase Solved By Multi Crystal Multi Orientation Native Sad, PDB code: 5dwk was solved by T.Weinert, V.Olieric, A.D.Finke, D.Li, M.Caffrey, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.79 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.290, 91.570, 143.720, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.5

Other elements in 5dwk:

The structure of Diacylglycerol Kinase Solved By Multi Crystal Multi Orientation Native Sad also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Diacylglycerol Kinase Solved By Multi Crystal Multi Orientation Native Sad (pdb code 5dwk). 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 Diacylglycerol Kinase Solved By Multi Crystal Multi Orientation Native Sad, PDB code: 5dwk:

Sodium binding site 1 out of 1 in 5dwk

Go back to Sodium Binding Sites List in 5dwk
Sodium binding site 1 out of 1 in the Diacylglycerol Kinase Solved By Multi Crystal Multi Orientation Native Sad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Diacylglycerol Kinase Solved By Multi Crystal Multi Orientation Native Sad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:72.5
occ:1.00
 O B:SER60 2.6 41.4 0.6
O B:SER60 2.7 39.9 0.4
OD2 A:ASP107 2.8 83.7 1.0
C B:SER60 3.4 38.3 0.6
CD2 A:LEU64 3.5 29.4 1.0
C B:SER60 3.5 37.6 0.4
CB B:SER60 3.5 28.6 0.6
CB B:LEU64 3.5 27.9 1.0
CB B:SER60 3.6 32.2 0.4
N B:LEU64 3.6 34.3 1.0
CA B:SER60 3.7 37.6 0.6
CA B:SER60 3.7 36.0 0.4
CG A:ASP107 3.7 60.9 1.0
CA B:LEU64 3.8 41.6 1.0
CD1 B:LEU64 4.3 33.6 1.0
OD1 A:ASP107 4.3 59.9 1.0
CG B:LEU64 4.4 37.1 1.0
OG B:SER60 4.4 38.5 0.4
C B:MET63 4.4 41.6 1.0
OG B:SER60 4.5 40.1 0.6
CD1 B:ILE67 4.5 37.2 1.0
CB B:MET63 4.6 41.3 1.0
N B:SER61 4.6 38.6 1.0
CB A:ASP107 4.7 37.8 1.0
CD2 B:LEU64 5.0 28.3 1.0
CG A:LEU64 5.0 49.3 1.0

Reference:

V.Olieric, T.Weinert, A.D.Finke, C.Anders, D.Li, N.Olieric, C.N.Borca, M.O.Steinmetz, M.Caffrey, M.Jinek, M.Wang. Data-Collection Strategy For Challenging Native Sad Phasing. Acta Crystallogr D Struct V. 72 421 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26960129
DOI: 10.1107/S2059798315024110
Page generated: Tue Dec 15 10:52:08 2020

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