Zinc in PDB 5d56: In Meso in Situ Serial X-Ray Crystallography Structure of Diacylglycerol Kinase, Dgka, at 100 K

Enzymatic activity of In Meso in Situ Serial X-Ray Crystallography Structure of Diacylglycerol Kinase, Dgka, at 100 K

All present enzymatic activity of In Meso in Situ Serial X-Ray Crystallography Structure of Diacylglycerol Kinase, Dgka, at 100 K:
2.7.1.107;

Protein crystallography data

The structure of In Meso in Situ Serial X-Ray Crystallography Structure of Diacylglycerol Kinase, Dgka, at 100 K, PDB code: 5d56 was solved by C.-Y.Huang, N.Howe, V.Olieric, R.Warshamanage, K.Diederichs, M.Wang, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.52 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.800, 93.040, 143.050, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 28.3

Zinc Binding Sites:

The binding sites of Zinc atom in the In Meso in Situ Serial X-Ray Crystallography Structure of Diacylglycerol Kinase, Dgka, at 100 K (pdb code 5d56). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the In Meso in Situ Serial X-Ray Crystallography Structure of Diacylglycerol Kinase, Dgka, at 100 K, PDB code: 5d56:

Zinc binding site 1 out of 1 in 5d56

Go back to Zinc Binding Sites List in 5d56
Zinc binding site 1 out of 1 in the In Meso in Situ Serial X-Ray Crystallography Structure of Diacylglycerol Kinase, Dgka, at 100 K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of In Meso in Situ Serial X-Ray Crystallography Structure of Diacylglycerol Kinase, Dgka, at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:0.9
occ:0.64
OE2 D:GLU28 2.1 0.9 1.0
OE1 D:GLU76 2.2 0.8 1.0
OE1 D:GLU28 2.5 0.8 1.0
CD D:GLU28 2.6 0.1 1.0
OE2 D:GLU76 2.6 0.2 1.0
O D:ACT203 2.7 0.3 1.0
CD D:GLU76 2.7 0.7 1.0
OA2 D:FLC202 3.6 0.3 1.0
C D:ACT203 3.6 0.9 1.0
OXT D:ACT203 3.7 0.3 1.0
OA1 D:FLC202 3.8 0.2 1.0
CG D:GLU28 4.0 82.3 1.0
CAC D:FLC202 4.2 0.4 1.0
CG D:GLU76 4.2 0.7 1.0
CB D:GLU76 4.9 93.3 1.0

Reference:

C.Y.Huang, V.Olieric, P.Ma, N.Howe, L.Vogeley, X.Liu, R.Warshamanage, T.Weinert, E.Panepucci, B.Kobilka, K.Diederichs, M.Wang, M.Caffrey. In Meso in Situ Serial X-Ray Crystallography of Soluble and Membrane Proteins at Cryogenic Temperatures. Acta Crystallogr D Struct V. 72 93 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26894538
DOI: 10.1107/S2059798315021683
Page generated: Wed Dec 16 06:08:06 2020

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