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Iron in PDB 6i2z: Isolated Globin Domain of the Bordetella Pertussis Globin-Coupled Sensor

Protein crystallography data

The structure of Isolated Globin Domain of the Bordetella Pertussis Globin-Coupled Sensor, PDB code: 6i2z was solved by F.Germani, A.De Schutter, B.Cuypers, H.Berghmans, M.-L.Van Hauwaert, S.Bruno, A.Mozzarelli, L.Moens, S.Van Doorslaer, M.Bolognesi, A.Pesce, S.Dewilde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.81 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.960, 86.720, 41.820, 90.00, 93.34, 90.00
R / Rfree (%) 20.9 / 24

Iron Binding Sites:

The binding sites of Iron atom in the Isolated Globin Domain of the Bordetella Pertussis Globin-Coupled Sensor (pdb code 6i2z). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Isolated Globin Domain of the Bordetella Pertussis Globin-Coupled Sensor, PDB code: 6i2z:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6i2z

Go back to Iron Binding Sites List in 6i2z
Iron binding site 1 out of 2 in the Isolated Globin Domain of the Bordetella Pertussis Globin-Coupled Sensor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Isolated Globin Domain of the Bordetella Pertussis Globin-Coupled Sensor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:39.0
occ:1.00
FE A:HEM200 0.0 39.0 1.0
ND A:HEM200 1.9 42.1 1.0
NA A:HEM200 2.0 41.8 1.0
NE2 A:HIS99 2.1 26.4 1.0
NB A:HEM200 2.1 40.5 1.0
NC A:HEM200 2.1 41.4 1.0
CE1 A:HIS99 2.8 27.9 1.0
C1D A:HEM200 2.9 42.2 1.0
C4D A:HEM200 2.9 44.0 1.0
C1A A:HEM200 3.0 43.1 1.0
C4A A:HEM200 3.0 41.7 1.0
O A:HOH308 3.1 10.5 1.0
C1B A:HEM200 3.1 40.8 1.0
C4B A:HEM200 3.1 39.2 1.0
C4C A:HEM200 3.1 40.0 1.0
C1C A:HEM200 3.1 38.9 1.0
CD2 A:HIS99 3.3 28.4 1.0
CHA A:HEM200 3.3 43.8 1.0
CHD A:HEM200 3.4 41.1 1.0
CHB A:HEM200 3.4 41.6 1.0
CHC A:HEM200 3.5 39.3 1.0
ND1 A:HIS99 4.0 28.9 1.0
C2D A:HEM200 4.2 42.7 1.0
C3D A:HEM200 4.2 44.8 1.0
CD1 A:LEU65 4.2 62.0 1.0
C2A A:HEM200 4.2 42.7 1.0
C3A A:HEM200 4.2 41.7 1.0
CG A:HIS99 4.3 28.9 1.0
C2B A:HEM200 4.3 39.0 1.0
C2C A:HEM200 4.3 37.4 1.0
C3C A:HEM200 4.3 37.9 1.0
C3B A:HEM200 4.4 37.9 1.0

Iron binding site 2 out of 2 in 6i2z

Go back to Iron Binding Sites List in 6i2z
Iron binding site 2 out of 2 in the Isolated Globin Domain of the Bordetella Pertussis Globin-Coupled Sensor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Isolated Globin Domain of the Bordetella Pertussis Globin-Coupled Sensor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe200

b:63.6
occ:1.00
FE B:HEM200 0.0 63.6 1.0
ND B:HEM200 1.9 70.4 1.0
NA B:HEM200 2.0 64.5 1.0
NC B:HEM200 2.1 66.3 1.0
NB B:HEM200 2.1 62.4 1.0
NE2 B:HIS99 2.3 46.3 1.0
O B:HOH302 2.9 1.0 1.0
C1D B:HEM200 2.9 73.5 1.0
C4D B:HEM200 2.9 71.8 1.0
C1A B:HEM200 3.0 65.9 1.0
C4A B:HEM200 3.0 65.9 1.0
CE1 B:HIS99 3.0 49.2 1.0
C1B B:HEM200 3.1 62.3 1.0
C4B B:HEM200 3.1 60.9 1.0
C4C B:HEM200 3.1 69.2 1.0
C1C B:HEM200 3.1 64.9 1.0
CD2 B:HIS99 3.3 48.2 1.0
CHA B:HEM200 3.4 69.9 1.0
CHD B:HEM200 3.4 72.9 1.0
CHB B:HEM200 3.4 65.3 1.0
CHC B:HEM200 3.5 64.2 1.0
ND1 B:HIS99 4.1 49.2 1.0
C2D B:HEM200 4.2 74.4 1.0
C2A B:HEM200 4.2 66.5 1.0
C3D B:HEM200 4.2 73.8 1.0
C3A B:HEM200 4.2 67.0 1.0
CG B:HIS99 4.3 48.2 1.0
C3C B:HEM200 4.3 66.7 1.0
C2C B:HEM200 4.3 64.4 1.0
C2B B:HEM200 4.3 58.2 1.0
C3B B:HEM200 4.4 56.8 1.0

Reference:

F.Germani, M.Nardini, A.De Schutter, B.Cuypers, H.Berghmans, M.L.Van Hauwaert, B.Stefano, A.Mozzarelli, L.Moens, S.Van Doorslaer, M.Bolognesi, A.Pesce, S.Dewilde. Structural and Functional Characterization of the Globin-Coupled Sensors of Azotobacter Vinelandii and Bordetella Pertussis. Antioxid.Redox Signal. 2019.
ISSN: ESSN 1557-7716
PubMed: 31559835
DOI: 10.1089/ARS.2018.7690
Page generated: Tue Aug 6 22:03:50 2024

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