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Magnesium in PDB 2jcm: Crystal Structure of Human Cytosolic 5'-Nucleotidase II in Complex with Beryllium Trifluoride

Enzymatic activity of Crystal Structure of Human Cytosolic 5'-Nucleotidase II in Complex with Beryllium Trifluoride

All present enzymatic activity of Crystal Structure of Human Cytosolic 5'-Nucleotidase II in Complex with Beryllium Trifluoride:
3.1.3.5;

Protein crystallography data

The structure of Crystal Structure of Human Cytosolic 5'-Nucleotidase II in Complex with Beryllium Trifluoride, PDB code: 2jcm was solved by K.Wallden, P.Stenmark, C.Arrowsmith, H.Berglund, R.Busam, R.Collins, A.Edwards, M.Ehn, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, B.M.Hallberg, L.Holmberg Schiavone, M.Hogbom, T.Karlberg, T.Kotenyova, A.Magnusdottir, P.Nilsson-Ehle, T.Nyman, D.Ogg, C.Persson, J.Sagemark, M.Sundstrom, J.Uppenberg, A.G.Thorsell, S.Van Den Berg, P.Loppnau, J.Weigelt, M.Welin, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.67 / 2.15
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 91.480, 128.260, 131.010, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26.6

Other elements in 2jcm:

The structure of Crystal Structure of Human Cytosolic 5'-Nucleotidase II in Complex with Beryllium Trifluoride also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Cytosolic 5'-Nucleotidase II in Complex with Beryllium Trifluoride (pdb code 2jcm). 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 Crystal Structure of Human Cytosolic 5'-Nucleotidase II in Complex with Beryllium Trifluoride, PDB code: 2jcm:

Magnesium binding site 1 out of 1 in 2jcm

Go back to Magnesium Binding Sites List in 2jcm
Magnesium binding site 1 out of 1 in the Crystal Structure of Human Cytosolic 5'-Nucleotidase II in Complex with Beryllium Trifluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Cytosolic 5'-Nucleotidase II in Complex with Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1490

b:10.4
occ:1.00
 F2 A:BFD52 1.9 3.6 1.0
O A:HOH2216 2.0 4.2 1.0
O A:HOH2220 2.1 12.1 1.0
O A:ASP54 2.1 5.3 1.0
OD1 A:ASP351 2.1 7.5 1.0
OD2 A:BFD52 2.2 5.7 1.0
CG A:BFD52 3.1 5.1 1.0
BE A:BFD52 3.1 6.1 1.0
C A:ASP54 3.3 5.2 1.0
CG A:ASP351 3.3 5.1 1.0
OD1 A:BFD52 3.4 2.0 1.0
OD2 A:ASP351 3.6 8.9 1.0
CA A:ASP54 3.9 4.7 1.0
CB A:ASP54 3.9 4.7 1.0
F1 A:BFD52 3.9 2.0 1.0
N A:ASP54 3.9 3.9 1.0
O A:HOH2150 4.0 10.0 1.0
O A:HOH2053 4.1 7.8 1.0
F3 A:BFD52 4.1 2.0 1.0
OG1 A:THR56 4.3 2.0 1.0
OD2 A:ASP356 4.3 2.0 1.0
N A:TYR55 4.4 4.3 1.0
CB A:BFD52 4.5 5.1 1.0
CB A:TYR55 4.5 3.2 1.0
CB A:ASP351 4.7 2.8 1.0
C A:MET53 4.7 3.9 1.0
N A:ASP351 4.7 2.7 1.0
CA A:TYR55 4.8 2.7 1.0
C A:TYR55 4.8 3.2 1.0
N A:THR56 4.9 2.0 1.0

Reference:

K.Wallden, P.Stenmark, T.Nyman, S.Flodin, S.Graslund, P.Loppnau, V.Bianchi, P.Nordlund. Crystal Structure of Human Cytosolic 5'- Nucleotidase II: Insights Into Allosteric Regulation and Substrate Recognition J.Biol.Chem. V. 282 17828 2007.
ISSN: ISSN 0021-9258
PubMed: 17405878
DOI: 10.1074/JBC.M700917200
Page generated: Sun Aug 10 11:57:28 2025

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