Iron in PDB 8gbk: DRI1 Hemoprotein Variant H79A-R90A with A Zinc-Mirror Heme Site

Protein crystallography data

The structure of DRI1 Hemoprotein Variant H79A-R90A with A Zinc-Mirror Heme Site, PDB code: 8gbk was solved by E.F.Yee, C.Blaby-Haas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 2.90
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 91.815, 91.815, 144.306, 90, 90, 90
R / Rfree (%) 31.1 / 32.6

Iron Binding Sites:

The binding sites of Iron atom in the DRI1 Hemoprotein Variant H79A-R90A with A Zinc-Mirror Heme Site (pdb code 8gbk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the DRI1 Hemoprotein Variant H79A-R90A with A Zinc-Mirror Heme Site, PDB code: 8gbk:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8gbk

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Iron binding site 1 out of 4 in the DRI1 Hemoprotein Variant H79A-R90A with A Zinc-Mirror Heme Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of DRI1 Hemoprotein Variant H79A-R90A with A Zinc-Mirror Heme Site within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:49.4
occ:1.00
 FE H:HEB201 0.0 49.4 1.0
NB H:HEB201 2.0 50.4 1.0
NA H:HEB201 2.0 53.7 1.0
NC H:HEB201 2.1 49.8 1.0
ND H:HEB201 2.1 49.5 1.0
C4B H:HEB201 2.9 51.3 1.0
C1C H:HEB201 3.0 56.7 1.0
C1B H:HEB201 3.0 53.7 1.0
C1A H:HEB201 3.0 58.6 1.0
C4D H:HEB201 3.0 60.0 1.0
C4A H:HEB201 3.0 61.1 1.0
C4C H:HEB201 3.1 49.8 1.0
C1D H:HEB201 3.1 51.5 1.0
CHC H:HEB201 3.3 61.2 1.0
CHA H:HEB201 3.4 64.5 1.0
CHB H:HEB201 3.4 61.1 1.0
CHD H:HEB201 3.5 55.1 1.0
NE2 H:HIS16 3.5 65.5 1.0
CE1 G:HIS21 3.8 56.6 1.0
NE2 H:HIS21 3.8 60.2 1.0
CE1 G:HIS16 4.0 61.4 1.0
C3B H:HEB201 4.2 56.0 1.0
HHC H:HEB201 4.2 73.5 1.0
C2B H:HEB201 4.2 51.0 1.0
C2A H:HEB201 4.2 55.9 1.0
C2C H:HEB201 4.3 63.7 1.0
C3A H:HEB201 4.3 65.0 1.0
C3D H:HEB201 4.3 65.2 1.0
C3C H:HEB201 4.3 56.2 1.0
HHA H:HEB201 4.3 77.5 1.0
C2D H:HEB201 4.3 54.4 1.0
NE2 G:HIS21 4.3 52.4 1.0
HHB H:HEB201 4.3 73.4 1.0
CE1 H:HIS16 4.4 76.5 1.0
CD2 H:HIS16 4.4 63.5 1.0
CE1 H:HIS21 4.5 54.1 1.0
HHD H:HEB201 4.6 66.2 1.0
CD2 H:HIS21 4.8 55.7 1.0
NE2 G:HIS16 4.8 66.9 1.0
ND1 G:HIS21 4.8 55.3 1.0
ND1 G:HIS16 4.9 72.7 1.0

Iron binding site 2 out of 4 in 8gbk

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Iron binding site 2 out of 4 in the DRI1 Hemoprotein Variant H79A-R90A with A Zinc-Mirror Heme Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of DRI1 Hemoprotein Variant H79A-R90A with A Zinc-Mirror Heme Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:58.4
occ:1.00
 FE E:HEB201 0.0 58.4 1.0
NB E:HEB201 2.0 58.5 1.0
NA E:HEB201 2.0 71.3 1.0
NC E:HEB201 2.1 65.5 1.0
ND E:HEB201 2.1 59.8 1.0
C4B E:HEB201 3.0 61.2 1.0
C1C E:HEB201 3.0 71.7 1.0
C1B E:HEB201 3.0 62.8 1.0
C1A E:HEB201 3.0 73.2 1.0
C4D E:HEB201 3.0 67.6 1.0
C4A E:HEB201 3.0 75.8 1.0
C4C E:HEB201 3.1 69.7 1.0
C1D E:HEB201 3.1 77.0 1.0
CHC E:HEB201 3.4 69.6 1.0
CHA E:HEB201 3.4 72.8 1.0
CHB E:HEB201 3.4 71.5 1.0
CE1 B:HIS21 3.5 65.4 1.0
CHD E:HEB201 3.5 76.6 1.0
CE1 E:HIS21 3.8 72.1 1.0
NE2 B:HIS21 4.0 68.1 1.0
NE2 E:HIS16 4.1 69.0 1.0
C3B E:HEB201 4.2 64.9 1.0
C2B E:HEB201 4.2 63.7 1.0
HHC E:HEB201 4.2 83.5 1.0
C2A E:HEB201 4.2 76.2 1.0
C2C E:HEB201 4.3 74.2 1.0
C3A E:HEB201 4.3 82.1 1.0
C3C E:HEB201 4.3 70.2 1.0
C3D E:HEB201 4.3 75.7 1.0
C2D E:HEB201 4.3 81.2 1.0
NE2 E:HIS21 4.3 65.5 1.0
HHA E:HEB201 4.3 87.3 1.0
NE2 B:HIS16 4.4 79.7 1.0
HHB E:HEB201 4.4 85.8 1.0
ND1 B:HIS21 4.5 67.5 1.0
HHD E:HEB201 4.5 91.9 1.0
CD1 B:ILE83 4.8 64.4 1.0
ND1 E:HIS21 4.9 76.5 1.0

Iron binding site 3 out of 4 in 8gbk

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Iron binding site 3 out of 4 in the DRI1 Hemoprotein Variant H79A-R90A with A Zinc-Mirror Heme Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of DRI1 Hemoprotein Variant H79A-R90A with A Zinc-Mirror Heme Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:66.9
occ:1.00
 FE A:HEB201 0.0 66.9 1.0
NB A:HEB201 2.0 69.5 1.0
NA A:HEB201 2.1 76.2 1.0
NC A:HEB201 2.1 78.0 1.0
ND A:HEB201 2.1 74.7 1.0
C4B A:HEB201 3.0 78.3 1.0
C1B A:HEB201 3.0 77.1 1.0
C1C A:HEB201 3.0 81.3 1.0
C1A A:HEB201 3.0 77.5 1.0
C4A A:HEB201 3.0 85.3 1.0
C4D A:HEB201 3.1 73.3 1.0
C4C A:HEB201 3.1 81.5 1.0
C1D A:HEB201 3.1 80.2 1.0
CHC A:HEB201 3.4 84.0 1.0
CHA A:HEB201 3.4 77.9 1.0
CHB A:HEB201 3.4 87.8 1.0
CHD A:HEB201 3.5 78.8 1.0
NE2 C:HIS16 3.7 72.4 1.0
CE1 C:HIS21 3.8 80.0 1.0
CE1 A:HIS21 3.8 76.8 1.0
NE2 C:HIS21 4.1 83.7 1.0
NE2 A:HIS16 4.2 76.3 1.0
C3B A:HEB201 4.2 84.9 1.0
C2B A:HEB201 4.2 75.3 1.0
C2A A:HEB201 4.3 77.2 1.0
C3A A:HEB201 4.3 80.4 1.0
C2C A:HEB201 4.3 85.1 1.0
C3C A:HEB201 4.3 80.1 1.0
C3D A:HEB201 4.3 77.0 1.0
HHC A:HEB201 4.3 100.8 1.0
C2D A:HEB201 4.3 81.2 1.0
NE2 A:HIS21 4.4 70.6 1.0
HHA A:HEB201 4.4 93.4 1.0
HHB A:HEB201 4.4 105.3 1.0
CD2 C:HIS16 4.5 75.0 1.0
HHD A:HEB201 4.5 94.6 1.0
CE1 C:HIS16 4.6 83.6 1.0
ND1 C:HIS21 4.7 79.8 1.0
CD1 C:ILE83 4.8 65.9 1.0
ND1 A:HIS21 4.9 80.0 1.0

Iron binding site 4 out of 4 in 8gbk

Go back to Iron Binding Sites List in 8gbk
Iron binding site 4 out of 4 in the DRI1 Hemoprotein Variant H79A-R90A with A Zinc-Mirror Heme Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of DRI1 Hemoprotein Variant H79A-R90A with A Zinc-Mirror Heme Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:60.5
occ:1.00
 FE D:HEB201 0.0 60.5 1.0
NB D:HEB201 2.0 90.3 1.0
NA D:HEB201 2.1 86.0 1.0
NC D:HEB201 2.1 72.0 1.0
ND D:HEB201 2.1 69.1 1.0
C4B D:HEB201 3.0 86.5 1.0
C1B D:HEB201 3.0 86.6 1.0
C1C D:HEB201 3.0 84.1 1.0
C1A D:HEB201 3.0 89.9 1.0
C4D D:HEB201 3.0 81.8 1.0
C4A D:HEB201 3.1 95.7 1.0
C4C D:HEB201 3.1 77.5 1.0
C1D D:HEB201 3.1 80.8 1.0
CHC D:HEB201 3.4 83.4 1.0
CHA D:HEB201 3.4 84.5 1.0
CHB D:HEB201 3.4 87.6 1.0
CHD D:HEB201 3.5 80.9 1.0
CE1 F:HIS21 3.8 80.1 1.0
CE1 D:HIS21 3.9 84.7 1.0
C3B D:HEB201 4.2 91.7 1.0
NE2 F:HIS21 4.2 77.1 1.0
C2B D:HEB201 4.2 83.6 1.0
NE2 F:HIS16 4.3 93.8 1.0
C3C D:HEB201 4.3 83.0 1.0
C2C D:HEB201 4.3 94.7 1.0
C2A D:HEB201 4.3 101.8 1.0
C3D D:HEB201 4.3 82.8 1.0
C3A D:HEB201 4.3 92.7 1.0
C2D D:HEB201 4.3 84.3 1.0
HHC D:HEB201 4.4 100.1 1.0
HHB D:HEB201 4.4 105.2 1.0
NE2 D:HIS21 4.4 82.4 1.0
HHA D:HEB201 4.4 101.4 1.0
NE2 D:HIS16 4.5 84.7 1.0
HHD D:HEB201 4.5 97.1 1.0
ND1 D:HIS21 4.9 81.1 1.0
ND1 F:HIS21 4.9 76.1 1.0

Reference:

N.Grosjean, E.F.Yee, D.Kumaran, K.Chopra, M.Abernathy, S.Biswas, J.Byrnes, D.F.Kreitler, J.F.Cheng, A.Ghosh, S.C.Almo, M.Iwai, K.K.Niyogi, H.B.Pakrasi, R.Sarangi, H.Van Dam, L.Yang, I.K.Blaby, C.E.Blaby-Haas. A Hemoprotein with A Zinc-Mirror Heme Site Ties Heme Availability to Carbon Metabolism in Cyanobacteria. Nat Commun V. 15 3167 2024.
ISSN: ESSN 2041-1723
PubMed: 38609367
DOI: 10.1038/S41467-024-47486-Z
Page generated: Sat Aug 10 04:42:51 2024

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