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Sodium in PDB 2oyc: Crystal Structure of Human Pyridoxal Phosphate Phosphatase

Enzymatic activity of Crystal Structure of Human Pyridoxal Phosphate Phosphatase

All present enzymatic activity of Crystal Structure of Human Pyridoxal Phosphate Phosphatase:
3.1.3.74;

Protein crystallography data

The structure of Crystal Structure of Human Pyridoxal Phosphate Phosphatase, PDB code: 2oyc was solved by U.A.Ramagopal, J.Freeman, M.Izuka, R.Toro, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structural Genomics(Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.90 / 1.72
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 54.329, 54.329, 213.200, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.3

Other elements in 2oyc:

The structure of Crystal Structure of Human Pyridoxal Phosphate Phosphatase also contains other interesting chemical elements:

Tungsten (W) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Pyridoxal Phosphate Phosphatase (pdb code 2oyc). 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 Crystal Structure of Human Pyridoxal Phosphate Phosphatase, PDB code: 2oyc:

Sodium binding site 1 out of 1 in 2oyc

Go back to Sodium Binding Sites List in 2oyc
Sodium binding site 1 out of 1 in the Crystal Structure of Human Pyridoxal Phosphate Phosphatase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Pyridoxal Phosphate Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:30.7
occ:1.00
OD2 A:ASP25 2.2 33.4 1.0
OD1 A:ASP238 2.3 24.9 1.0
O A:HOH519 2.3 36.7 1.0
O A:HOH506 2.3 35.1 1.0
O A:ASP27 2.4 23.2 1.0
CG A:ASP238 3.2 23.9 1.0
CG A:ASP25 3.2 28.7 1.0
OD2 A:ASP238 3.4 22.9 1.0
C A:ASP27 3.6 21.8 1.0
O A:HOH430 4.0 35.5 1.0
OD1 A:ASP25 4.0 31.4 1.0
CB A:ASP25 4.0 25.1 1.0
OD2 A:ASP243 4.1 26.2 1.0
O A:HOH404 4.2 27.5 1.0
CB A:ASP27 4.3 22.2 1.0
CA A:ASP27 4.4 22.4 1.0
N A:GLY28 4.5 22.2 1.0
CA A:GLY28 4.5 20.8 1.0
N A:ASP27 4.5 22.4 1.0
CB A:ASP238 4.6 21.2 1.0
O A:HOH408 4.6 30.4 1.0
CG2 A:VAL29 4.6 21.1 1.0
O A:HOH491 4.6 46.2 1.0
O A:HOH487 4.7 41.8 1.0
N A:ASP238 4.8 21.8 1.0

Reference:

S.C.Almo, J.B.Bonanno, J.M.Sauder, S.Emtage, T.P.Dilorenzo, V.Malashkevich, S.R.Wasserman, S.Swaminathan, S.Eswaramoorthy, R.Agarwal, D.Kumaran, M.Madegowda, S.Ragumani, Y.Patskovsky, J.Alvarado, U.A.Ramagopal, J.Faber-Barata, M.R.Chance, A.Sali, A.Fiser, Z.Y.Zhang, D.S.Lawrence, S.K.Burley. Structural Genomics of Protein Phosphatases. J.Struct.Funct.Genom. V. 8 121 2007.
ISSN: ISSN 1345-711X
PubMed: 18058037
DOI: 10.1007/S10969-007-9036-1
Page generated: Tue Dec 15 05:53:10 2020

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