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Sodium in PDB 3d6a: Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.

Protein crystallography data

The structure of Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate., PDB code: 3d6a was solved by Y.Chen, N.Carpino, N.Nassar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.95 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.205, 116.665, 121.471, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.7

Other elements in 3d6a:

The structure of Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. also contains other interesting chemical elements:

Tungsten (W) 4 atoms
Magnesium (Mg) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. (pdb code 3d6a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate., PDB code: 3d6a:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3d6a

Go back to Sodium Binding Sites List in 3d6a
Sodium binding site 1 out of 4 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


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 the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na623

b:36.1
occ:1.00
O A:HOH627 1.8 25.4 1.0
NH2 A:ARG365 2.8 26.7 1.0
NH1 A:ARG369 3.7 32.1 1.0
W A:W624 3.8 28.6 1.0
CG A:GLN372 3.9 33.4 1.0
CD A:GLN372 3.9 36.6 1.0
OE1 A:GLN372 4.1 30.8 1.0
CZ A:ARG365 4.2 26.6 1.0
CD A:ARG369 4.2 29.1 1.0
CZ A:ARG369 4.4 33.1 1.0
NE2 A:GLN372 4.4 37.7 1.0
O D:HOH624 4.4 28.8 1.0
NE A:ARG369 4.5 30.3 1.0
O D:HOH657 4.6 40.1 1.0
CE1 A:HIS366 4.7 21.4 1.0
CG A:ARG369 4.7 27.9 1.0
O D:HOH637 4.9 32.4 1.0
NE A:ARG365 4.9 26.1 1.0
NE2 A:HIS366 4.9 19.1 1.0
O A:HOH626 5.0 25.2 1.0

Sodium binding site 2 out of 4 in 3d6a

Go back to Sodium Binding Sites List in 3d6a
Sodium binding site 2 out of 4 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1

b:48.5
occ:1.00
O B:HOH623 2.1 35.6 1.0
NH2 B:ARG365 3.3 30.0 1.0
NH1 B:ARG369 3.9 35.0 1.0
W B:W7 4.0 34.0 1.0
CD B:ARG369 4.1 31.9 1.0
CG B:GLN372 4.1 39.7 1.0
CD B:GLN372 4.3 42.7 1.0
OE1 B:GLN372 4.3 41.5 1.0
CZ B:ARG369 4.3 33.6 1.0
NE B:ARG369 4.4 31.5 1.0
O B:HOH624 4.5 34.4 1.0
CZ B:ARG365 4.6 30.3 1.0
CG B:ARG369 4.8 31.4 1.0
CE1 B:HIS366 4.9 24.4 1.0

Sodium binding site 3 out of 4 in 3d6a

Go back to Sodium Binding Sites List in 3d6a
Sodium binding site 3 out of 4 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3

b:38.9
occ:1.00
O C:HOH15 2.1 26.8 1.0
NH2 C:ARG365 2.8 27.4 1.0
W C:W12 3.8 32.5 1.0
NH1 C:ARG369 3.8 24.2 1.0
OE1 C:GLN372 4.0 38.0 1.0
CD C:ARG369 4.0 24.4 1.0
CG C:GLN372 4.0 36.5 1.0
CD C:GLN372 4.1 39.7 1.0
O C:HOH14 4.1 29.6 1.0
CZ C:ARG365 4.2 28.2 1.0
CZ C:ARG369 4.4 26.9 1.0
NE C:ARG369 4.5 25.5 1.0
CE1 C:HIS366 4.6 26.3 1.0
NE2 C:HIS366 4.8 27.3 1.0
NE2 C:GLN372 4.8 38.9 1.0
NE C:ARG365 4.9 28.9 1.0

Sodium binding site 4 out of 4 in 3d6a

Go back to Sodium Binding Sites List in 3d6a
Sodium binding site 4 out of 4 in the Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the 2H-Phosphatase Domain of Sts-2 in Complex with Tungstate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na623

b:38.3
occ:1.00
O D:HOH625 1.8 26.8 1.0
NH2 D:ARG365 2.8 30.5 1.0
W D:W17 3.5 30.6 1.0
NH1 D:ARG369 3.8 37.0 1.0
O A:HOH628 3.8 26.3 1.0
OE1 D:GLN372 3.9 36.9 1.0
O D:HOH642 3.9 35.9 1.0
CD D:ARG369 4.0 31.6 1.0
CD D:GLN372 4.2 39.0 1.0
CZ D:ARG365 4.2 31.7 1.0
CG D:GLN372 4.2 35.8 1.0
O A:HOH659 4.3 34.1 1.0
CZ D:ARG369 4.5 37.1 1.0
CE1 D:HIS366 4.5 25.7 1.0
NE D:ARG369 4.6 33.5 1.0
CG D:ARG369 4.7 31.4 1.0
O A:HOH661 4.7 35.7 1.0
O D:HOH626 4.8 25.1 1.0
O D:HOH627 4.9 24.0 1.0
NE D:ARG365 4.9 31.2 1.0
NE2 D:HIS366 4.9 29.6 1.0

Reference:

Y.Chen, J.Jakoncic, N.Carpino, N.Nassar. Structural and Functional Characterization of the 2H-Phosphatase Domain of Sts-2 Reveals An Acid-Dependent Phosphatase Activity. Biochemistry V. 48 1681 2009.
ISSN: ISSN 0006-2960
PubMed: 19196006
DOI: 10.1021/BI802219N
Page generated: Tue Dec 15 06:08:29 2020

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