Atomistry » Iron » PDB 8iap-8ird » 8ir5
Atomistry »
  Iron »
    PDB 8iap-8ird »
      8ir5 »

Iron in PDB 8ir5: Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions

Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions

All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions:
1.10.3.9;

Protein crystallography data

The structure of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions, PDB code: 8ir5 was solved by H.Li, M.Suga, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.75, 231.6, 288.28, 90, 90, 90
R / Rfree (%) 14.5 / 17.5

Other elements in 8ir5:

The structure of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Manganese (Mn) 8 atoms
Magnesium (Mg) 72 atoms
Calcium (Ca) 9 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions (pdb code 8ir5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions, PDB code: 8ir5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8ir5

Go back to Iron Binding Sites List in 8ir5
Iron binding site 1 out of 6 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:52.3
occ:1.00
NE2 A:HIS215 2.1 54.5 1.0
O2 D:BCT401 2.1 57.8 1.0
NE2 D:HIS214 2.1 52.3 1.0
O1 D:BCT401 2.2 55.2 1.0
NE2 D:HIS268 2.2 45.8 1.0
NE2 A:HIS272 2.3 53.1 1.0
C D:BCT401 2.4 60.7 1.0
CE1 A:HIS215 2.9 52.6 1.0
CE1 D:HIS214 3.0 48.2 1.0
CE1 A:HIS272 3.2 52.4 1.0
CE1 D:HIS268 3.2 45.3 1.0
CD2 D:HIS214 3.2 42.9 1.0
CD2 A:HIS215 3.2 51.3 1.0
CD2 D:HIS268 3.3 45.9 1.0
CD2 A:HIS272 3.4 48.2 1.0
O3 D:BCT401 3.7 66.5 1.0
ND1 A:HIS215 4.1 50.0 1.0
ND1 D:HIS214 4.2 45.4 1.0
CG A:HIS215 4.3 54.1 1.0
CG D:HIS214 4.3 49.2 1.0
ND1 D:HIS268 4.3 48.7 1.0
ND1 A:HIS272 4.3 50.6 1.0
CG D:HIS268 4.4 46.4 1.0
CG A:HIS272 4.5 52.0 1.0
CG2 A:VAL219 4.6 50.9 1.0
CG2 D:VAL218 4.9 47.2 1.0
OH D:TYR244 5.0 57.7 1.0

Iron binding site 2 out of 6 in 8ir5

Go back to Iron Binding Sites List in 8ir5
Iron binding site 2 out of 6 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe102

b:63.2
occ:1.00
FE F:HEM102 0.0 63.2 1.0
ND F:HEM102 2.0 63.3 1.0
NA F:HEM102 2.0 72.5 1.0
NE2 E:HIS23 2.1 64.0 1.0
NE2 F:HIS24 2.1 64.0 1.0
NC F:HEM102 2.1 68.5 1.0
NB F:HEM102 2.1 63.2 1.0
C4D F:HEM102 2.9 72.7 1.0
C1D F:HEM102 3.0 66.8 1.0
C1A F:HEM102 3.0 69.6 1.0
CD2 F:HIS24 3.0 64.5 1.0
CE1 E:HIS23 3.0 70.0 1.0
C4A F:HEM102 3.0 71.4 1.0
C4C F:HEM102 3.1 61.0 1.0
C1B F:HEM102 3.1 71.0 1.0
C4B F:HEM102 3.1 64.7 1.0
CD2 E:HIS23 3.1 71.0 1.0
CE1 F:HIS24 3.1 65.3 1.0
C1C F:HEM102 3.1 61.9 1.0
CHA F:HEM102 3.4 68.6 1.0
CHD F:HEM102 3.4 60.2 1.0
CHB F:HEM102 3.5 67.2 1.0
CHC F:HEM102 3.5 62.8 1.0
ND1 E:HIS23 4.2 62.7 1.0
C3D F:HEM102 4.2 64.4 1.0
C2A F:HEM102 4.2 75.0 1.0
C2D F:HEM102 4.2 63.9 1.0
CG F:HIS24 4.2 67.6 1.0
ND1 F:HIS24 4.2 63.0 1.0
C3A F:HEM102 4.2 74.3 1.0
CG E:HIS23 4.2 66.5 1.0
C3C F:HEM102 4.3 67.5 1.0
C2C F:HEM102 4.3 64.3 1.0
C2B F:HEM102 4.3 71.1 1.0
C3B F:HEM102 4.3 69.6 1.0
CE1 E:TYR19 4.9 71.2 1.0
NE1 F:TRP20 5.0 69.3 1.0

Iron binding site 3 out of 6 in 8ir5

Go back to Iron Binding Sites List in 8ir5
Iron binding site 3 out of 6 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:50.6
occ:1.00
FE V:HEC201 0.0 50.6 1.0
NA V:HEC201 2.0 51.3 1.0
NC V:HEC201 2.0 48.8 1.0
NB V:HEC201 2.0 53.2 1.0
NE2 V:HIS41 2.1 51.8 1.0
NE2 V:HIS92 2.1 50.4 1.0
ND V:HEC201 2.1 50.8 1.0
CD2 V:HIS92 3.0 49.8 1.0
C4A V:HEC201 3.0 54.3 1.0
C1B V:HEC201 3.0 49.0 1.0
C1A V:HEC201 3.0 57.8 1.0
CD2 V:HIS41 3.0 51.9 1.0
C1C V:HEC201 3.1 53.9 1.0
C4C V:HEC201 3.1 51.6 1.0
CE1 V:HIS41 3.1 53.0 1.0
C4B V:HEC201 3.1 52.8 1.0
C1D V:HEC201 3.1 49.7 1.0
C4D V:HEC201 3.1 52.3 1.0
CE1 V:HIS92 3.1 47.9 1.0
CHB V:HEC201 3.4 54.4 1.0
CHD V:HEC201 3.4 50.8 1.0
CHC V:HEC201 3.4 52.1 1.0
CHA V:HEC201 3.5 51.9 1.0
CG V:HIS92 4.2 53.5 1.0
ND1 V:HIS92 4.2 51.2 1.0
ND1 V:HIS41 4.2 48.3 1.0
CG V:HIS41 4.2 47.6 1.0
C3A V:HEC201 4.2 56.7 1.0
C2A V:HEC201 4.2 52.1 1.0
C2B V:HEC201 4.3 53.4 1.0
C3B V:HEC201 4.3 48.1 1.0
C2C V:HEC201 4.3 51.5 1.0
C3D V:HEC201 4.3 52.2 1.0
C3C V:HEC201 4.3 51.3 1.0
C2D V:HEC201 4.3 49.1 1.0
CE2 V:TYR75 4.9 52.7 1.0

Iron binding site 4 out of 6 in 8ir5

Go back to Iron Binding Sites List in 8ir5
Iron binding site 4 out of 6 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe401

b:55.1
occ:1.00
NE2 a:HIS215 2.1 58.3 1.0
O2 d:BCT401 2.1 60.2 1.0
NE2 d:HIS214 2.2 56.8 1.0
NE2 d:HIS268 2.3 54.4 1.0
NE2 a:HIS272 2.3 54.5 1.0
O1 d:BCT401 2.4 58.4 1.0
C d:BCT401 2.6 68.4 1.0
CE1 a:HIS215 3.0 57.6 1.0
CE1 d:HIS214 3.2 52.0 1.0
CD2 d:HIS214 3.2 48.8 1.0
CD2 a:HIS215 3.2 53.4 1.0
CE1 a:HIS272 3.2 50.9 1.0
CE1 d:HIS268 3.2 52.0 1.0
CD2 d:HIS268 3.3 50.2 1.0
CD2 a:HIS272 3.3 53.7 1.0
O3 d:BCT401 3.9 77.5 1.0
ND1 a:HIS215 4.1 53.5 1.0
CG a:HIS215 4.3 58.1 1.0
ND1 d:HIS214 4.3 52.1 1.0
CG d:HIS214 4.4 57.3 1.0
ND1 a:HIS272 4.4 54.5 1.0
ND1 d:HIS268 4.4 52.5 1.0
CG d:HIS268 4.4 53.5 1.0
CG a:HIS272 4.4 52.5 1.0
CG2 a:VAL219 4.6 54.0 1.0
CG2 d:VAL218 4.9 48.0 1.0
OH d:TYR244 5.0 58.9 1.0

Iron binding site 5 out of 6 in 8ir5

Go back to Iron Binding Sites List in 8ir5
Iron binding site 5 out of 6 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Fe101

b:76.9
occ:1.00
FE f:HEM101 0.0 76.9 1.0
ND f:HEM101 2.0 76.0 1.0
NA f:HEM101 2.0 90.8 1.0
NE2 e:HIS23 2.1 87.3 1.0
NC f:HEM101 2.1 78.9 1.0
NE2 f:HIS24 2.1 80.8 1.0
NB f:HEM101 2.1 72.0 1.0
C4D f:HEM101 2.9 81.0 1.0
C1D f:HEM101 3.0 73.6 1.0
CD2 f:HIS24 3.0 76.6 1.0
C1A f:HEM101 3.0 85.5 1.0
CD2 e:HIS23 3.0 80.9 1.0
C4C f:HEM101 3.1 71.6 1.0
C4A f:HEM101 3.1 87.6 1.0
C4B f:HEM101 3.1 79.3 1.0
C1B f:HEM101 3.1 81.1 1.0
CE1 e:HIS23 3.1 83.6 1.0
C1C f:HEM101 3.1 69.3 1.0
CE1 f:HIS24 3.1 79.2 1.0
CHA f:HEM101 3.4 80.3 1.0
CHD f:HEM101 3.4 72.6 1.0
CHB f:HEM101 3.5 83.1 1.0
CHC f:HEM101 3.5 73.9 1.0
CG f:HIS24 4.1 75.3 1.0
C3D f:HEM101 4.2 82.4 1.0
ND1 e:HIS23 4.2 83.7 1.0
C2D f:HEM101 4.2 82.5 1.0
CG e:HIS23 4.2 82.8 1.0
ND1 f:HIS24 4.2 77.6 1.0
C2A f:HEM101 4.2 90.9 1.0
C3A f:HEM101 4.2 94.3 1.0
C3C f:HEM101 4.3 70.1 1.0
C2C f:HEM101 4.3 74.3 1.0
C2B f:HEM101 4.3 83.6 1.0
C3B f:HEM101 4.3 78.5 1.0
CE1 e:TYR19 4.9 81.1 1.0
NE1 f:TRP20 5.0 84.7 1.0

Iron binding site 6 out of 6 in 8ir5

Go back to Iron Binding Sites List in 8ir5
Iron binding site 6 out of 6 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:60.3
occ:1.00
FE v:HEC201 0.0 60.3 1.0
NA v:HEC201 2.0 61.6 1.0
NC v:HEC201 2.0 62.3 1.0
ND v:HEC201 2.1 62.5 1.0
NB v:HEC201 2.1 62.7 1.0
NE2 v:HIS92 2.1 63.3 1.0
NE2 v:HIS41 2.1 63.2 1.0
C1A v:HEC201 3.0 57.8 1.0
C4D v:HEC201 3.0 61.6 1.0
CD2 v:HIS92 3.0 59.3 1.0
CD2 v:HIS41 3.0 62.8 1.0
C4A v:HEC201 3.1 64.6 1.0
C1C v:HEC201 3.1 62.9 1.0
CE1 v:HIS92 3.1 58.6 1.0
CE1 v:HIS41 3.1 63.8 1.0
C4B v:HEC201 3.1 60.8 1.0
C4C v:HEC201 3.1 63.5 1.0
C1D v:HEC201 3.1 57.9 1.0
C1B v:HEC201 3.1 60.4 1.0
CHA v:HEC201 3.4 58.1 1.0
CHC v:HEC201 3.4 62.7 1.0
CHD v:HEC201 3.4 56.2 1.0
CHB v:HEC201 3.5 63.6 1.0
ND1 v:HIS92 4.2 64.1 1.0
ND1 v:HIS41 4.2 62.9 1.0
CG v:HIS92 4.2 59.8 1.0
CG v:HIS41 4.2 64.7 1.0
C2A v:HEC201 4.2 64.5 1.0
C3A v:HEC201 4.3 66.8 1.0
C3D v:HEC201 4.3 63.5 1.0
C2C v:HEC201 4.3 60.4 1.0
C2D v:HEC201 4.3 60.5 1.0
C3B v:HEC201 4.3 60.8 1.0
C2B v:HEC201 4.3 57.0 1.0
C3C v:HEC201 4.3 58.0 1.0
CE1 v:TYR75 4.9 62.0 1.0

Reference:

H.Li, Y.Nakajima, E.Nango, S.Owada, D.Yamada, K.Hashimoto, F.Luo, R.Tanaka, F.Akita, K.Kato, J.M.Kang, Y.Saitoh, S.Kishi, H.Yu, N.Matsubara, H.Fujii, M.Sugahara, M.Suzuki, T.Masuda, T.Kimura, T.N.Thao, S.Yonekura, L.J.Yu, T.Tosha, K.Tono, Y.Joti, T.Hatsui, M.Yabashi, M.Kubo, S.Iwata, H.Isobe, K.Yamaguchi, M.Suga, J.R.Shen. Oxygen-Evolving Photosystem II Structures During S1-S2-S3 Transitions. Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06987-5
Page generated: Sat Aug 10 06:00:42 2024

Last articles

Ca in 2OW9
Ca in 2OXE
Ca in 2OXS
Ca in 2OX8
Ca in 2OW2
Ca in 2OWL
Ca in 2OVZ
Ca in 2OVX
Ca in 2OW4
Ca in 2OW0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy