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Xenon 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:

Chlorine (Cl) 8 atoms
Sodium (Na) 1 atom

Xenon Binding Sites:

The binding sites of Xenon 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 Xenon atom.
In total 2 binding sites of Xenon where determined in the On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength, PDB code: 2a7d:
Jump to Xenon binding site number: 1; 2;

Xenon binding site 1 out of 2 in 2a7d

Go back to Xenon Binding Sites List in 2a7d
Xenon binding site 1 out of 2 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 Xenon with other atoms in the Xe 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:Xe300

b:21.8
occ:0.18
OG1 A:THR43 3.1 19.9 1.0
O A:HOH376 3.7 32.7 1.0
CB A:THR43 3.8 16.5 1.0
C A:THR43 4.0 16.5 1.0
N A:ARG45 4.0 17.0 1.0
O A:THR43 4.0 18.6 1.0
N A:ASN44 4.1 16.3 1.0
CA A:ASN44 4.2 17.6 1.0
C A:ASN44 4.3 16.6 1.0
CB A:ARG45 4.5 18.5 1.0
CA A:THR43 4.6 16.1 1.0
CG2 A:THR51 4.7 16.8 1.0
CA A:ARG45 4.7 17.8 1.0
O A:HOH368 4.8 39.6 1.0
NH2 A:ARG68 4.8 23.4 1.0

Xenon binding site 2 out of 2 in 2a7d

Go back to Xenon Binding Sites List in 2a7d
Xenon binding site 2 out of 2 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 Xenon with other atoms in the Xe binding site number 2 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:Xe301

b:36.1
occ:0.25
CG2 A:ILE55 3.3 20.1 1.0
CD1 A:LEU56 3.5 22.9 1.0
CG2 A:VAL92 3.6 19.9 1.0
CE A:MET12 3.7 17.0 1.0
CB A:SER91 3.9 16.1 1.0
CG A:LEU56 3.9 16.8 1.0
CD1 A:ILE88 4.0 20.5 1.0
CB A:ILE88 4.1 18.6 1.0
N A:VAL92 4.1 14.8 1.0
C A:SER91 4.4 15.0 1.0
CA A:VAL92 4.4 16.8 1.0
CG A:MET12 4.5 17.2 1.0
O A:ILE88 4.5 18.1 1.0
CG1 A:ILE88 4.5 20.0 1.0
CG2 A:ILE88 4.6 20.6 1.0
CD1 A:LEU17 4.6 22.3 1.0
CB A:VAL92 4.6 17.4 1.0
CB A:ILE55 4.7 17.1 1.0
CA A:SER91 4.8 15.9 1.0
CB A:LEU56 4.8 17.0 1.0
O A:SER91 4.8 16.2 1.0
OG A:SER91 5.0 15.8 1.0
SD A:MET12 5.0 19.9 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: Wed Dec 16 02:39:36 2020

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