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Xenon in PDB 3zjs: M.Acetivorans Protoglobin in Complex with Azide and Xenon

Protein crystallography data

The structure of M.Acetivorans Protoglobin in Complex with Azide and Xenon, PDB code: 3zjs was solved by A.Pesce, L.Tilleman, J.Donne, E.Aste, P.Ascenzi, C.Ciaccio, M.Coletta, L.Moens, C.Viappiani, S.Dewilde, M.Bolognesi, M.Nardini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.27 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.980, 48.120, 80.490, 90.00, 94.61, 90.00
R / Rfree (%) 22.007 / 27.414

Other elements in 3zjs:

The structure of M.Acetivorans Protoglobin in Complex with Azide and Xenon also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the M.Acetivorans Protoglobin in Complex with Azide and Xenon (pdb code 3zjs). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 2 binding sites of Xenon where determined in the M.Acetivorans Protoglobin in Complex with Azide and Xenon, PDB code: 3zjs:
Jump to Xenon binding site number: 1; 2;

Xenon binding site 1 out of 2 in 3zjs

Go back to Xenon Binding Sites List in 3zjs
Xenon binding site 1 out of 2 in the M.Acetivorans Protoglobin in Complex with Azide and Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of M.Acetivorans Protoglobin in Complex with Azide and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1196

b:46.5
occ:0.60
CE A:MET153 3.3 31.1 1.0
CD1 A:ILE149 3.7 19.6 1.0
CG2 A:THR152 3.8 32.3 1.0
CG2 A:ILE56 3.9 26.8 1.0
O A:ILE149 4.0 19.5 1.0
CE1 A:PHE93 4.1 25.4 1.0
CB A:THR152 4.2 31.9 1.0
SD A:MET153 4.2 40.0 1.0
CZ A:PHE93 4.3 22.1 1.0
CB A:TRP60 4.3 28.2 1.0
CG A:TRP60 4.4 34.0 1.0
CD2 A:TRP60 4.6 35.0 1.0
CA A:ILE149 4.6 16.3 1.0
CG2 A:ILE149 4.6 10.1 1.0
CE3 A:TRP60 4.8 31.0 1.0
C A:ILE149 4.8 19.6 1.0
CG1 A:ILE149 4.9 19.1 1.0
OG1 A:THR152 4.9 32.8 1.0
CB A:ILE149 5.0 17.7 1.0
CD1 A:TRP60 5.0 39.4 1.0

Xenon binding site 2 out of 2 in 3zjs

Go back to Xenon Binding Sites List in 3zjs
Xenon binding site 2 out of 2 in the M.Acetivorans Protoglobin in Complex with Azide and Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of M.Acetivorans Protoglobin in Complex with Azide and Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe1196

b:46.5
occ:0.60
CE B:MET153 3.3 30.6 1.0
CD1 B:ILE149 3.6 19.2 1.0
CG2 B:THR152 3.7 32.0 1.0
CG2 B:ILE56 3.9 26.6 1.0
CE1 B:PHE93 4.0 25.4 1.0
O B:ILE149 4.0 19.4 1.0
CB B:THR152 4.2 31.6 1.0
CZ B:PHE93 4.2 22.3 1.0
SD B:MET153 4.2 38.9 1.0
CB B:TRP60 4.3 28.0 1.0
CG B:TRP60 4.4 34.2 1.0
CD2 B:TRP60 4.6 35.5 1.0
CA B:ILE149 4.6 15.6 1.0
CG2 B:ILE149 4.7 8.5 1.0
C B:ILE149 4.8 19.5 1.0
CE3 B:TRP60 4.8 31.5 1.0
CG1 B:ILE149 4.9 19.2 1.0
OG1 B:THR152 4.9 32.5 1.0
CD1 B:TRP60 4.9 39.2 1.0
CB B:ILE149 5.0 17.0 1.0

Reference:

A.Pesce, L.Tilleman, J.Donne, E.Aste, P.Ascenzi, C.Ciaccio, M.Coletta, L.Moens, C.Viappiani, S.Dewilde, M.Bolognesi, M.Nardini. Structure and Haem-Distal Site Plasticity in Methanosarcina Acetivorans Protoglobin. Plos One V. 8 66144 2013.
ISSN: ISSN 1932-6203
PubMed: 23776624
DOI: 10.1371/JOURNAL.PONE.0066144
Page generated: Wed Dec 16 02:40:03 2020

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