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Sodium in PDB 2x98: H.Salinarum Alkaline Phosphatase

Enzymatic activity of H.Salinarum Alkaline Phosphatase

All present enzymatic activity of H.Salinarum Alkaline Phosphatase:
3.1.3.1;

Protein crystallography data

The structure of H.Salinarum Alkaline Phosphatase, PDB code: 2x98 was solved by A.Wende, P.Johansson, M.Grininger, D.Oesterhelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 72.143, 152.524, 86.799, 90.00, 110.00, 90.00
R / Rfree (%) 16.042 / 19.771

Other elements in 2x98:

The structure of H.Salinarum Alkaline Phosphatase also contains other interesting chemical elements:

Magnesium (Mg) 11 atoms
Zinc (Zn) 4 atoms
Chlorine (Cl) 13 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the H.Salinarum Alkaline Phosphatase (pdb code 2x98). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the H.Salinarum Alkaline Phosphatase, PDB code: 2x98:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2x98

Go back to Sodium Binding Sites List in 2x98
Sodium binding site 1 out of 2 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of H.Salinarum Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1482

b:8.0
occ:0.50
O A:ARG98 2.2 4.2 1.0
OD1 A:ASP453 2.2 7.8 1.0
CG A:ASP453 3.1 9.5 1.0
C A:ARG98 3.3 4.3 1.0
CA A:ASP453 3.5 6.8 1.0
CB A:ASP453 3.6 7.5 1.0
N A:ARG98 3.7 4.7 1.0
CG A:ARG98 3.9 7.1 1.0
CA A:ARG98 4.0 4.4 1.0
CD A:ARG98 4.1 8.5 1.0
OD2 A:ASP453 4.1 6.9 1.0
C A:ASP453 4.3 7.2 1.0
N A:GLY99 4.4 3.0 1.0
CB A:ARG98 4.6 3.3 1.0
CA A:GLY99 4.7 4.2 1.0
N A:ASP453 4.7 8.1 1.0
O A:PHE452 4.7 8.2 1.0
O A:ASP453 4.9 7.7 1.0
C A:SER97 4.9 6.2 1.0
N A:ALA454 4.9 6.9 1.0

Sodium binding site 2 out of 2 in 2x98

Go back to Sodium Binding Sites List in 2x98
Sodium binding site 2 out of 2 in the H.Salinarum Alkaline Phosphatase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of H.Salinarum Alkaline Phosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1483

b:9.7
occ:0.50
O B:ARG98 2.1 5.8 1.0
OD1 B:ASP453 2.2 7.8 1.0
CG B:ASP453 3.1 8.6 1.0
C B:ARG98 3.3 6.3 1.0
CA B:ASP453 3.5 6.8 1.0
CB B:ASP453 3.6 6.8 1.0
N B:ARG98 3.6 5.9 1.0
CG B:ARG98 3.8 10.7 1.0
CA B:ARG98 4.0 6.0 1.0
CD B:ARG98 4.1 10.0 1.0
OD2 B:ASP453 4.1 6.8 1.0
C B:ASP453 4.3 7.5 1.0
N B:GLY99 4.4 5.8 1.0
CB B:ARG98 4.5 4.9 1.0
CA B:GLY99 4.6 7.0 1.0
N B:ASP453 4.6 6.6 1.0
O B:PHE452 4.7 7.8 1.0
O B:ASP453 4.8 8.3 1.0
C B:SER97 4.8 7.4 1.0
N B:ALA454 4.8 8.8 1.0

Reference:

A.Wende, P.Johansson, R.Vollrath, M.Dyall-Smith, D.Oesterhelt, M.Grininger. Structural and Biochemical Characterization of A Halophilic Archaeal Alkaline Phosphatase. J.Mol.Biol. V. 400 52 2010.
ISSN: ISSN 0022-2836
PubMed: 20438737
DOI: 10.1016/J.JMB.2010.04.057
Page generated: Tue Dec 15 05:59:04 2020

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