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Sodium in PDB 2a7d: On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength

Enzymatic activity of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength

All present enzymatic activity of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength:
3.2.1.17;

Protein crystallography data

The structure of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength, PDB code: 2a7d was solved by C.Mueller-Dieckmann, S.Panjikar, P.A.Tucker, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.66
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.050, 77.050, 37.210, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.2

Other elements in 2a7d:

The structure of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength also contains other interesting chemical elements:

Xenon (Xe) 2 atoms
Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength (pdb code 2a7d). 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 On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength, PDB code: 2a7d:

Sodium binding site 1 out of 1 in 2a7d

Go back to Sodium Binding Sites List in 2a7d
Sodium binding site 1 out of 1 in the On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:18.8
occ:1.00
 O A:SER60 2.2 16.4 1.0
O A:CYS64 2.3 15.6 1.0
O A:HOH326 2.4 20.6 1.0
O A:ARG73 2.4 20.9 1.0
O A:HOH304 2.5 17.1 1.0
CB A:SER72 2.9 27.2 1.0
OG A:SER72 3.1 40.3 1.0
C A:SER60 3.4 16.9 1.0
C A:CYS64 3.4 15.2 1.0
C A:ARG73 3.5 22.3 1.0
CA A:ASN65 3.9 16.2 1.0
N A:ARG73 4.0 24.8 1.0
CA A:SER60 4.0 15.0 1.0
N A:ASN65 4.1 15.7 1.0
CA A:SER72 4.1 28.4 1.0
C A:SER72 4.1 27.0 1.0
CB A:SER60 4.2 15.3 1.0
N A:CYS64 4.3 15.6 1.0
CA A:ARG73 4.3 24.1 1.0
N A:ASN74 4.4 20.7 1.0
C A:ARG61 4.5 21.5 1.0
O A:ARG61 4.5 21.7 1.0
N A:ARG61 4.5 18.9 1.0
CA A:CYS64 4.5 15.3 1.0
CA A:ASN74 4.5 19.4 1.0
N A:ASP66 4.6 15.7 1.0
CB A:THR69 4.6 21.9 1.0
OD1 A:ASN65 4.6 19.7 1.0
CL A:CL202 4.7 16.3 0.5
O A:SER72 4.7 27.1 1.0
CB A:ASN74 4.7 18.5 1.0
CA A:ARG61 4.7 21.1 1.0
CB A:ASN65 4.7 16.3 1.0
N A:TRP62 4.8 20.3 1.0
C A:ASN65 4.8 14.9 1.0
N A:TRP63 4.9 16.6 1.0
C A:TRP62 5.0 17.5 1.0
O A:THR69 5.0 20.7 1.0
O A:HOH389 5.0 32.3 1.0

Reference:

C.Mueller-Dieckmann, S.Panjikar, P.A.Tucker, M.S.Weiss. On the Routine Use of Soft X-Rays in Macromolecular Crystallography. Part III. the Optimal Data-Collection Wavelength. Acta Crystallogr.,Sect.D V. 61 1263 2005.
ISSN: ISSN 0907-4449
PubMed: 16131760
DOI: 10.1107/S0907444905021475
Page generated: Mon Oct 7 01:48:48 2024

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