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Iron 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:

Xenon (Xe) 2 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the M.Acetivorans Protoglobin in Complex with Azide and Xenon, PDB code: 3zjs:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 3zjs

Go back to Iron Binding Sites List in 3zjs
Iron 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 Iron with other atoms in the Fe 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:Fe200

b:11.1
occ:1.00
FE A:HEM200 0.0 11.1 1.0
NA A:HEM200 2.0 12.2 1.0
NC A:HEM200 2.0 8.7 1.0
NB A:HEM200 2.0 8.9 1.0
NE2 A:HIS120 2.1 9.7 1.0
ND A:HEM200 2.1 11.9 1.0
N1 A:AZI201 2.8 10.1 1.0
N2 A:AZI201 2.9 17.3 1.0
CE1 A:HIS120 2.9 8.4 1.0
C4A A:HEM200 3.0 13.3 1.0
C1B A:HEM200 3.0 3.1 1.0
C4C A:HEM200 3.0 15.9 1.0
C1C A:HEM200 3.0 12.7 1.0
C1A A:HEM200 3.1 12.6 1.0
C4B A:HEM200 3.1 10.8 1.0
C4D A:HEM200 3.1 15.1 1.0
C1D A:HEM200 3.1 13.7 1.0
CD2 A:HIS120 3.2 8.4 1.0
CHB A:HEM200 3.3 8.3 1.0
CHD A:HEM200 3.4 12.1 1.0
CHC A:HEM200 3.4 10.3 1.0
CHA A:HEM200 3.4 10.7 1.0
N3 A:AZI201 3.4 13.6 1.0
ND1 A:HIS120 4.1 7.6 1.0
C3A A:HEM200 4.2 13.6 1.0
C3C A:HEM200 4.2 8.9 1.0
CG A:HIS120 4.2 9.8 1.0
C2B A:HEM200 4.2 8.1 1.0
C2C A:HEM200 4.3 14.4 1.0
C2A A:HEM200 4.3 15.6 1.0
C3B A:HEM200 4.3 10.1 1.0
C3D A:HEM200 4.3 16.7 1.0
C2D A:HEM200 4.3 18.2 1.0
CE2 A:PHE93 5.0 22.1 1.0

Iron binding site 2 out of 2 in 3zjs

Go back to Iron Binding Sites List in 3zjs
Iron 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 Iron with other atoms in the Fe 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:Fe200

b:11.1
occ:1.00
FE B:HEM200 0.0 11.1 1.0
NA B:HEM200 2.0 13.2 1.0
NC B:HEM200 2.0 8.5 1.0
NB B:HEM200 2.0 9.5 1.0
NE2 B:HIS120 2.1 9.9 1.0
ND B:HEM200 2.1 12.8 1.0
N1 B:AZI201 2.8 8.9 1.0
CE1 B:HIS120 2.9 8.3 1.0
N2 B:AZI201 2.9 17.8 1.0
C4A B:HEM200 3.0 14.4 1.0
C1B B:HEM200 3.0 3.3 1.0
C4C B:HEM200 3.0 15.4 1.0
C1C B:HEM200 3.1 12.2 1.0
C1A B:HEM200 3.1 12.9 1.0
C4B B:HEM200 3.1 12.2 1.0
C1D B:HEM200 3.1 14.2 1.0
C4D B:HEM200 3.1 15.8 1.0
CD2 B:HIS120 3.2 7.9 1.0
CHB B:HEM200 3.3 10.0 1.0
CHD B:HEM200 3.4 12.6 1.0
CHC B:HEM200 3.4 12.0 1.0
CHA B:HEM200 3.4 11.2 1.0
N3 B:AZI201 3.5 13.2 1.0
ND1 B:HIS120 4.1 8.8 1.0
C3A B:HEM200 4.2 15.1 1.0
C2B B:HEM200 4.2 8.6 1.0
CG B:HIS120 4.2 10.2 1.0
C3C B:HEM200 4.2 8.5 1.0
C2C B:HEM200 4.3 13.1 1.0
C2A B:HEM200 4.3 15.6 1.0
C3B B:HEM200 4.3 10.8 1.0
C3D B:HEM200 4.3 16.8 1.0
C2D B:HEM200 4.3 18.5 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: Sun Dec 13 15:27:15 2020

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