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Magnesium in PDB 3ipx: X-Ray Structure of Human Deoxycytidine Kinase in Complex with Adp and An Inhibitor

Enzymatic activity of X-Ray Structure of Human Deoxycytidine Kinase in Complex with Adp and An Inhibitor

All present enzymatic activity of X-Ray Structure of Human Deoxycytidine Kinase in Complex with Adp and An Inhibitor:
2.7.1.74;

Protein crystallography data

The structure of X-Ray Structure of Human Deoxycytidine Kinase in Complex with Adp and An Inhibitor, PDB code: 3ipx was solved by L.W.Tari, R.V.Swanson, M.Hunter, I.Hoffman, T.R.Stouch, K.G.Carson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.97 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.238, 80.238, 93.950, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 27.8

Other elements in 3ipx:

The structure of X-Ray Structure of Human Deoxycytidine Kinase in Complex with Adp and An Inhibitor also contains other interesting chemical elements:

Fluorine (F) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Human Deoxycytidine Kinase in Complex with Adp and An Inhibitor (pdb code 3ipx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the X-Ray Structure of Human Deoxycytidine Kinase in Complex with Adp and An Inhibitor, PDB code: 3ipx:

Magnesium binding site 1 out of 1 in 3ipx

Go back to Magnesium Binding Sites List in 3ipx
Magnesium binding site 1 out of 1 in the X-Ray Structure of Human Deoxycytidine Kinase in Complex with Adp and An Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Human Deoxycytidine Kinase in Complex with Adp and An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg263

b:48.8
occ:1.00
O A:HOH265 2.2 51.7 1.0
O A:HOH264 2.4 51.8 1.0
O2B A:ADP261 2.5 32.7 1.0
OE1 A:GLU127 2.5 36.1 1.0
OG A:SER35 2.7 38.8 1.0
PB A:ADP261 3.5 34.2 1.0
CD A:GLU127 3.6 37.1 1.0
CB A:SER35 3.6 37.3 1.0
O A:HOH417 3.7 52.2 1.0
O3B A:ADP261 3.7 35.1 1.0
O A:HOH433 3.8 51.4 1.0
N A:SER35 3.8 36.8 1.0
OE2 A:GLU127 4.0 37.8 1.0
O A:HOH291 4.1 47.1 1.0
CA A:SER35 4.2 37.3 1.0
O1B A:ADP261 4.4 30.2 1.0
O1A A:ADP261 4.5 35.1 1.0
CB A:LYS34 4.6 38.1 1.0
O3A A:ADP261 4.6 34.6 1.0
O A:HOH285 4.7 37.7 1.0
C A:LYS34 4.7 37.7 1.0
NZ A:LYS34 4.8 34.8 1.0
CG A:GLU127 4.9 37.2 1.0
PA A:ADP261 4.9 34.2 1.0
O2A A:ADP261 4.9 34.3 1.0
OE2 A:GLU53 4.9 35.3 1.0
O A:HOH267 5.0 31.4 1.0

Reference:

T.C.Jessop, J.E.Tarver, M.Carlsen, A.Xu, J.P.Healy, A.Heim-Riether, Q.Fu, J.A.Taylor, D.J.Augeri, M.Shen, T.R.Stouch, R.V.Swanson, L.W.Tari, M.Hunter, I.Hoffman, P.E.Keyes, X.C.Yu, M.Miranda, Q.Liu, J.C.Swaffield, S.David Kimball, A.Nouraldeen, A.G.Wilson, A.M.Foushee, K.Jhaver, R.Finch, S.Anderson, T.Oravecz, K.G.Carson. Lead Optimization and Structure-Based Design of Potent and Bioavailable Deoxycytidine Kinase Inhibitors. Bioorg.Med.Chem.Lett. V. 19 6784 2009.
ISSN: ISSN 0960-894X
PubMed: 19836232
DOI: 10.1016/J.BMCL.2009.09.081
Page generated: Mon Dec 14 08:17:22 2020

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