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Xenon in PDB 2a7a: On the Routine Use of Soft X-Rays in Macromolecular Crystallography, Part III- the Optimal Data Collection Wavelength

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: 2a7a 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 / 1.75
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 61.968, 85.059, 88.367, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.6

Other elements in 2a7a:

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:

Manganese (Mn) 1 atom
Calcium (Ca) 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 2a7a). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 5 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: 2a7a:
Jump to Xenon binding site number: 1; 2; 3; 4; 5;

Xenon binding site 1 out of 5 in 2a7a

Go back to Xenon Binding Sites List in 2a7a
Xenon binding site 1 out of 5 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:Xe303

b:2.5
occ:0.40
CD2 A:PHE212 3.6 10.8 1.0
CE2 A:PHE212 3.7 10.6 1.0
CG1 A:VAL5 3.7 11.7 1.0
CD1 A:ILE214 3.8 10.8 1.0
O A:VAL5 3.8 6.9 1.0
CG1 A:ILE214 3.9 8.8 1.0
CD2 A:LEU61 4.0 8.7 1.0
CA A:ALA6 4.0 6.1 1.0
O A:PHE212 4.0 7.7 1.0
N A:VAL7 4.1 6.0 1.0
C A:VAL5 4.1 6.5 1.0
C A:ALA6 4.1 6.1 1.0
CG2 A:VAL7 4.2 10.1 1.0
N A:ALA6 4.2 5.9 1.0
CD1 A:LEU61 4.2 5.5 1.0
CZ A:PHE191 4.3 7.9 0.8
CG2 A:ILE52 4.4 6.9 1.0
CA A:PHE213 4.6 6.0 1.0
N A:ILE214 4.7 4.8 1.0
CB A:VAL5 4.7 7.8 1.0
CG A:LEU61 4.7 6.8 1.0
C A:PHE212 4.7 6.6 1.0
O A:ALA6 4.7 6.2 1.0
C A:PHE213 4.8 4.7 1.0
CB A:ILE214 4.8 5.8 1.0
CG A:PHE212 4.9 6.0 1.0
CB A:VAL7 4.9 6.8 1.0
CZ A:PHE212 4.9 8.4 1.0
N A:PHE213 5.0 5.6 1.0

Xenon binding site 2 out of 5 in 2a7a

Go back to Xenon Binding Sites List in 2a7a
Xenon binding site 2 out of 5 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:Xe304

b:8.8
occ:0.15
CG1 A:ILE53 3.3 8.8 1.0
CG2 A:VAL64 3.4 10.5 1.0
CD1 A:ILE53 3.6 9.4 1.0
O A:HIS51 3.7 7.6 1.0
N A:VAL64 3.8 5.2 1.0
C A:ALA63 3.9 5.9 1.0
CA A:ALA63 4.0 5.0 1.0
O A:SER62 4.0 5.9 1.0
CB A:VAL64 4.1 6.2 1.0
C A:HIS51 4.1 6.8 1.0
CB A:HIS51 4.2 7.3 1.0
C A:SER62 4.2 6.9 1.0
N A:ALA63 4.2 6.6 1.0
CG2 A:ILE53 4.2 8.0 1.0
CB A:ILE53 4.4 5.0 1.0
N A:ILE53 4.4 4.2 1.0
O A:ALA63 4.5 5.9 1.0
CA A:VAL64 4.6 5.7 1.0
N A:ILE52 4.6 5.1 1.0
CB A:SER62 4.6 6.5 1.0
CA A:ILE52 4.7 6.2 1.0
C A:ILE52 4.7 6.1 1.0
CA A:HIS51 4.9 6.6 1.0

Xenon binding site 3 out of 5 in 2a7a

Go back to Xenon Binding Sites List in 2a7a
Xenon binding site 3 out of 5 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 3 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:Xe305

b:8.8
occ:0.30
XE A:XE307 3.2 2.5 0.1
O A:ILE181 3.8 13.2 1.0
CB A:ILE181 3.8 12.9 1.0
CG2 A:ILE181 4.0 15.6 1.0
C A:SER190 4.0 8.5 1.0
CD2 A:PHE191 4.0 13.8 0.8
N A:SER190 4.1 6.2 1.0
CB A:ALA189 4.1 4.5 1.0
O A:SER190 4.1 7.8 1.0
C A:ALA189 4.2 6.2 1.0
CA A:SER190 4.2 7.3 1.0
CA A:ILE181 4.2 11.4 1.0
CD2 A:TYR54 4.2 4.6 1.0
O A:ALA189 4.3 6.1 1.0
N A:PHE191 4.3 7.2 1.0
CB A:PHE191 4.4 7.1 1.0
C A:ILE181 4.5 12.1 1.0
CE2 A:TYR54 4.5 4.0 1.0
XE A:XE306 4.6 2.0 0.2
CA A:ALA189 4.7 4.4 1.0
CG A:PHE191 4.7 8.0 0.8
CA A:PHE191 5.0 7.3 1.0

Xenon binding site 4 out of 5 in 2a7a

Go back to Xenon Binding Sites List in 2a7a
Xenon binding site 4 out of 5 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 4 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:Xe306

b:2.0
occ:0.20
CG2 A:ILE181 3.1 15.6 1.0
XE A:XE307 3.1 2.5 0.1
CD1 A:ILE214 3.5 10.8 1.0
CD2 A:PHE191 3.6 13.8 0.8
CZ A:PHE111 3.7 7.9 1.0
CG A:PHE191 3.9 8.0 0.8
CE1 A:PHE111 4.0 9.1 1.0
CG1 A:VAL91 4.0 9.2 1.0
CE2 A:PHE191 4.1 10.7 0.8
CG2 A:ILE214 4.1 4.4 1.0
CG1 A:ILE214 4.2 8.8 1.0
CB A:PHE191 4.2 7.1 1.0
CG2 A:VAL89 4.3 3.9 1.0
CB A:ILE181 4.3 12.9 1.0
CG1 A:VAL179 4.5 10.7 1.0
XE A:XE305 4.6 8.8 0.3
CD1 A:PHE191 4.7 14.1 0.8
CD1 A:ILE181 4.8 18.0 1.0
CB A:ILE214 4.8 5.8 1.0
CZ A:PHE191 4.9 7.9 0.8
CE2 A:PHE111 4.9 9.6 1.0
CG1 A:ILE181 5.0 13.1 1.0

Xenon binding site 5 out of 5 in 2a7a

Go back to Xenon Binding Sites List in 2a7a
Xenon binding site 5 out of 5 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 5 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:Xe307

b:2.5
occ:0.10
XE A:XE306 3.1 2.0 0.2
CD2 A:PHE191 3.2 13.8 0.8
XE A:XE305 3.2 8.8 0.3
CE2 A:PHE191 3.4 10.7 0.8
CD1 A:LEU81 3.8 10.5 1.0
CD1 A:ILE214 3.9 10.8 1.0
CG2 A:ILE181 3.9 15.6 1.0
CD1 A:ILE181 3.9 18.0 1.0
CB A:ILE181 4.1 12.9 1.0
CD2 A:TYR54 4.2 4.6 1.0
CB A:LEU81 4.3 6.8 1.0
CG A:PHE191 4.4 8.0 0.8
CD1 A:LEU85 4.4 9.0 1.0
CE2 A:TYR54 4.6 4.0 1.0
CG A:LEU81 4.6 9.4 1.0
CG1 A:ILE181 4.6 13.1 1.0
CZ A:PHE191 4.7 7.9 0.8
CG A:TYR54 4.9 6.9 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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