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Sodium in PDB 1o1z: Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) (TM1621) From Thermotoga Maritima at 1.60 A Resolution

Enzymatic activity of Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) (TM1621) From Thermotoga Maritima at 1.60 A Resolution

All present enzymatic activity of Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) (TM1621) From Thermotoga Maritima at 1.60 A Resolution:
3.1.4.46;

Protein crystallography data

The structure of Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) (TM1621) From Thermotoga Maritima at 1.60 A Resolution, PDB code: 1o1z was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.18 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 132.410, 41.790, 51.720, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 18

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) (TM1621) From Thermotoga Maritima at 1.60 A Resolution (pdb code 1o1z). 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 Glycerophosphodiester Phosphodiesterase (Gdpd) (TM1621) From Thermotoga Maritima at 1.60 A Resolution, PDB code: 1o1z:

Sodium binding site 1 out of 1 in 1o1z

Go back to Sodium Binding Sites List in 1o1z
Sodium binding site 1 out of 1 in the Crystal Structure of Glycerophosphodiester Phosphodiesterase (Gdpd) (TM1621) From Thermotoga Maritima at 1.60 A Resolution


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 Glycerophosphodiester Phosphodiesterase (Gdpd) (TM1621) From Thermotoga Maritima at 1.60 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:15.2
occ:1.00
 O A:ARG114 2.2 16.4 1.0
O A:SER111 2.4 10.3 1.0
O A:HOH656 2.4 21.7 1.0
C A:ARG114 3.3 14.3 1.0
C A:SER111 3.5 11.8 1.0
O A:LYS112 3.6 25.7 1.0
N A:ARG114 3.8 18.4 1.0
C A:LYS112 3.9 19.9 1.0
CA A:ARG114 4.1 18.9 1.0
CA A:LYS112 4.1 12.9 1.0
CD1 A:LEU117 4.2 12.3 1.0
N A:LYS112 4.3 11.6 1.0
N A:LYS115 4.3 12.2 1.0
O A:HOH921 4.4 35.4 1.0
O A:HOH653 4.5 19.8 1.0
CA A:SER111 4.5 10.0 1.0
CB A:SER111 4.5 12.4 1.0
CA A:LYS115 4.5 9.0 1.0
CB A:ARG114 4.6 20.7 1.0
N A:LYS113 4.6 16.6 1.0
C A:LYS113 4.7 23.2 1.0
O A:HOH765 4.9 31.4 1.0
CG A:LEU117 4.9 9.9 1.0
O A:HOH738 5.0 29.4 1.0

Reference:

E.Santelli, R.Schwarzenbacher, D.Mcmullan, T.Biorac, L.S.Brinen, J.M.Canaves, J.Cambell, X.Dai, A.M.Deacon, M.A.Elsliger, S.Eshagi, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, S.A.Lesley, T.M.Mcphillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, K.Quijano, F.Rezezadeh, A.Robb, R.C.Stevens, H.Van Den Bedem, J.Velasquez, J.Vincent, F.Von Delft, X.Wang, B.West, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, I.A.Wilson. Crystal Structure of A Glycerophosphodiester Phosphodiesterase (Gdpd) From Thermotoga Maritima (TM1621) at 1.60 A Resolution. Proteins V. 56 167 2004.
ISSN: ISSN 0887-3585
PubMed: 15162496
DOI: 10.1002/PROT.20120
Page generated: Sun Aug 17 06:50:17 2025

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