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Calcium in PDB 3n9v: Crystal Structure of INPP5B

Enzymatic activity of Crystal Structure of INPP5B

All present enzymatic activity of Crystal Structure of INPP5B:
3.1.3.36;

Protein crystallography data

The structure of Crystal Structure of INPP5B, PDB code: 3n9v was solved by L.Tresaugues, M.Welin, C.H.Arrowsmith, H.Berglund, C.Bountra, R.Collins, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, I.Johansson, T.Karlberg, S.Kol, T.Kotenyova, M.Moche, T.Nyman, C.Persson, H.Schuler, P.Schutz, M.I.Siponen, A.G.Thorsell, S.Van Der Berg, E.Wahlberg, J.Weigelt, M.Wisniewska, P.Nordlund, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.66 / 2.65
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.160, 110.660, 159.380, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.1

Other elements in 3n9v:

The structure of Crystal Structure of INPP5B also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of INPP5B (pdb code 3n9v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of INPP5B, PDB code: 3n9v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3n9v

Go back to Calcium Binding Sites List in 3n9v
Calcium binding site 1 out of 2 in the Crystal Structure of INPP5B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of INPP5B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca64

b:76.7
occ:1.00
O A:THR371 2.1 63.9 1.0
O A:HOH24 2.3 49.1 1.0
OD1 A:ASP414 2.4 65.6 1.0
O A:HOH39 2.5 56.9 1.0
CG A:ASP414 3.2 60.8 1.0
C A:THR371 3.3 57.0 1.0
OD2 A:ASP414 3.3 60.5 1.0
O A:GLY372 3.8 56.0 1.0
CA A:GLY372 3.9 54.5 1.0
N A:GLY372 4.0 53.0 1.0
OG1 A:THR371 4.3 46.5 1.0
CB A:THR371 4.3 51.5 1.0
C A:GLY372 4.3 57.9 1.0
CA A:THR371 4.4 55.0 1.0
O A:HOH23 4.5 62.1 1.0
O A:ARG410 4.5 62.5 1.0
CB A:ASP414 4.7 54.9 1.0
CA A:GLY375 4.9 64.9 1.0
CB A:ALA402 4.9 42.1 1.0

Calcium binding site 2 out of 2 in 3n9v

Go back to Calcium Binding Sites List in 3n9v
Calcium binding site 2 out of 2 in the Crystal Structure of INPP5B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of INPP5B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca63

b:93.1
occ:1.00
O B:THR371 2.1 77.0 1.0
OD1 B:ASP414 2.5 84.7 1.0
O B:HOH4 2.8 66.8 1.0
C B:THR371 3.3 70.9 1.0
CG B:ASP414 3.4 84.5 1.0
OD2 B:ASP414 3.5 85.0 1.0
O B:GLY372 3.6 72.7 1.0
CA B:GLY372 3.9 67.2 1.0
N B:GLY372 4.1 67.2 1.0
C B:GLY372 4.2 70.3 1.0
CB B:THR371 4.3 71.2 1.0
CA B:THR371 4.4 68.8 1.0
OG1 B:THR371 4.4 73.6 1.0
CA B:GLY375 4.6 76.8 1.0
O B:ARG410 4.7 85.1 1.0
CB B:ASP414 4.8 82.9 1.0
CB B:ALA402 4.9 72.9 1.0

Reference:

L.Tresaugues, C.Silvander, S.Flodin, M.Welin, T.Nyman, S.Graslund, M.Hammarstrom, H.Berglund, P.Nordlund. Structural Basis For Phosphoinositide Substrate Recognition, Catalysis, and Membrane Interactions in Human Inositol Polyphosphate 5-Phosphatases Structure V. 22 744 2014.
ISSN: ISSN 0969-2126
PubMed: 24704254
DOI: 10.1016/J.STR.2014.01.013
Page generated: Sat Dec 12 04:21:53 2020

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