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Iron in PDB 11yo: Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution

Enzymatic activity of Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution

All present enzymatic activity of Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution:
1.10.3.9;

Protein crystallography data

The structure of Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution, PDB code: 11yo was solved by J.Wang, W.H.Armstrong, V.S.Batista, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.65 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.958, 221.646, 307.786, 90, 90, 90
R / Rfree (%) 18.4 / 24.3

Other elements in 11yo:

The structure of Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Calcium (Ca) 2 atoms
Manganese (Mn) 8 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution (pdb code 11yo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution, PDB code: 11yo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 11yo

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Iron binding site 1 out of 6 in the Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:28.8
occ:1.00
 NE2 D:HIS214 2.2 32.0 1.0
NE2 A:HIS215 2.2 28.1 1.0
O1 D:BCT401 2.2 26.0 1.0
NE2 D:HIS268 2.2 34.1 1.0
NE2 A:HIS272 2.3 35.3 1.0
O2 D:BCT401 2.5 31.3 1.0
C D:BCT401 2.5 35.0 1.0
CE1 A:HIS215 2.8 34.1 1.0
CE1 D:HIS214 2.9 22.9 1.0
CE1 D:HIS268 3.1 29.6 1.0
CE1 A:HIS272 3.2 31.5 1.0
CD2 D:HIS268 3.3 30.5 1.0
CD2 A:HIS272 3.3 29.9 1.0
CD2 D:HIS214 3.4 27.6 1.0
CD2 A:HIS215 3.4 38.3 1.0
O3 D:BCT401 3.9 38.0 1.0
ND1 A:HIS215 4.1 27.3 1.0
ND1 D:HIS214 4.1 23.9 1.0
ND1 D:HIS268 4.3 26.9 1.0
ND1 A:HIS272 4.3 37.4 1.0
CG D:HIS214 4.4 23.1 1.0
CG A:HIS215 4.4 35.2 1.0
CG D:HIS268 4.4 31.3 1.0
CG A:HIS272 4.4 29.1 1.0
CG2 A:VAL219 4.6 34.1 1.0
OH D:TYR244 4.8 34.9 1.0
CG2 D:VAL218 5.0 27.4 1.0

Iron binding site 2 out of 6 in 11yo

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Iron binding site 2 out of 6 in the Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:48.4
occ:1.00
 FE F:HEC101 0.0 48.4 1.0
ND F:HEC101 1.9 39.9 1.0
NC F:HEC101 2.0 41.3 1.0
NA F:HEC101 2.0 50.5 1.0
NB F:HEC101 2.1 36.8 1.0
NE2 E:HIS23 2.1 56.5 1.0
NE2 F:HIS24 2.2 47.7 1.0
C4D F:HEC101 2.9 50.5 1.0
CD2 F:HIS24 2.9 39.3 1.0
C1D F:HEC101 2.9 44.7 1.0
C1A F:HEC101 2.9 47.4 1.0
C4C F:HEC101 3.0 39.2 1.0
CD2 E:HIS23 3.1 50.0 1.0
C4B F:HEC101 3.1 44.8 1.0
C1C F:HEC101 3.1 41.4 1.0
C4A F:HEC101 3.1 46.3 1.0
C1B F:HEC101 3.1 47.8 1.0
CE1 E:HIS23 3.2 56.7 1.0
CHA F:HEC101 3.3 45.4 1.0
CE1 F:HIS24 3.3 49.0 1.0
CHD F:HEC101 3.3 31.9 1.0
CHC F:HEC101 3.5 42.2 1.0
CHB F:HEC101 3.5 45.5 1.0
C3D F:HEC101 4.1 44.7 1.0
C2D F:HEC101 4.1 40.6 1.0
CG F:HIS24 4.1 49.3 1.0
C2A F:HEC101 4.2 51.5 1.0
CG E:HIS23 4.2 48.5 1.0
ND1 E:HIS23 4.2 58.0 1.0
C3A F:HEC101 4.3 54.4 1.0
ND1 F:HIS24 4.3 52.9 1.0
C3C F:HEC101 4.3 39.8 1.0
C2C F:HEC101 4.3 43.3 1.0
C3B F:HEC101 4.3 46.2 1.0
C2B F:HEC101 4.3 48.4 1.0
CD1 E:ILE22 4.5 53.6 0.1
CZ2 F:TRP20 4.9 38.2 1.0
CE1 E:TYR19 4.9 58.2 1.0
NE1 F:TRP20 4.9 47.3 1.0

Iron binding site 3 out of 6 in 11yo

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Iron binding site 3 out of 6 in the Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:29.9
occ:1.00
 FE V:HEC201 0.0 29.9 1.0
NA V:HEC201 1.9 23.9 1.0
NB V:HEC201 2.0 30.8 1.0
NC V:HEC201 2.0 32.2 1.0
ND V:HEC201 2.1 24.8 1.0
NE2 V:HIS92 2.1 39.9 1.0
NE2 V:HIS41 2.1 31.8 1.0
C4A V:HEC201 2.9 30.4 1.0
C1B V:HEC201 3.0 28.7 1.0
C1A V:HEC201 3.0 32.9 1.0
CD2 V:HIS41 3.0 26.3 1.0
CD2 V:HIS92 3.0 36.0 1.0
C1C V:HEC201 3.0 34.6 1.0
C4C V:HEC201 3.0 29.7 1.0
C4B V:HEC201 3.1 30.6 1.0
CE1 V:HIS92 3.1 25.7 1.0
C1D V:HEC201 3.1 28.3 1.0
C4D V:HEC201 3.1 27.8 1.0
CE1 V:HIS41 3.2 29.0 1.0
CHB V:HEC201 3.3 27.8 1.0
CHD V:HEC201 3.4 32.5 1.0
CHC V:HEC201 3.4 37.6 1.0
CHA V:HEC201 3.5 29.0 1.0
C3A V:HEC201 4.1 31.2 1.0
ND1 V:HIS92 4.2 34.2 1.0
CG V:HIS92 4.2 39.1 1.0
C2A V:HEC201 4.2 26.2 1.0
C2B V:HEC201 4.2 32.1 1.0
C2C V:HEC201 4.2 29.9 1.0
CG V:HIS41 4.2 33.7 1.0
C3C V:HEC201 4.2 27.8 1.0
C3B V:HEC201 4.2 28.3 1.0
ND1 V:HIS41 4.3 31.3 1.0
C3D V:HEC201 4.3 17.7 1.0
C2D V:HEC201 4.4 28.9 1.0
CE1 V:TYR75 4.9 32.7 1.0
OH V:TYR75 4.9 36.5 1.0

Iron binding site 4 out of 6 in 11yo

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Iron binding site 4 out of 6 in the Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe401

b:44.5
occ:1.00
 NE2 a:HIS215 2.2 28.0 1.0
NE2 d:HIS214 2.3 28.4 1.0
NE2 d:HIS268 2.3 40.0 1.0
NE2 a:HIS272 2.4 37.2 1.0
O1 a:BCT409 2.4 31.4 1.0
O2 a:BCT409 2.5 32.8 1.0
C a:BCT409 2.7 40.9 1.0
CE1 a:HIS215 3.1 38.4 1.0
CE1 d:HIS214 3.1 34.0 1.0
CE1 a:HIS272 3.2 32.7 1.0
CD2 a:HIS215 3.3 37.8 1.0
CE1 d:HIS268 3.3 35.8 1.0
CD2 d:HIS268 3.3 34.0 1.0
CD2 d:HIS214 3.4 32.4 1.0
CD2 a:HIS272 3.4 36.6 1.0
O3 a:BCT409 4.1 49.8 1.0
ND1 a:HIS215 4.2 28.7 1.0
ND1 d:HIS214 4.3 36.9 1.0
CG a:HIS215 4.3 22.7 1.0
ND1 a:HIS272 4.4 36.9 1.0
ND1 d:HIS268 4.4 37.7 1.0
CG d:HIS214 4.4 35.1 1.0
CG d:HIS268 4.5 38.7 1.0
CG a:HIS272 4.5 36.8 1.0
CG2 a:VAL219 4.7 42.1 1.0
OH d:TYR244 4.9 42.1 1.0
CG2 d:VAL218 5.0 35.5 1.0

Iron binding site 5 out of 6 in 11yo

Go back to Iron Binding Sites List in 11yo
Iron binding site 5 out of 6 in the Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Fe101

b:57.7
occ:1.00
 FE f:HEC101 0.0 57.7 1.0
NC f:HEC101 1.9 52.1 1.0
ND f:HEC101 2.0 49.6 1.0
NB f:HEC101 2.0 51.8 1.0
NA f:HEC101 2.1 50.2 1.0
NE2 f:HIS24 2.1 57.4 1.0
NE2 e:HIS23 2.2 60.3 1.0
C4C f:HEC101 2.9 55.0 1.0
C1D f:HEC101 2.9 48.7 1.0
C1B f:HEC101 3.0 53.2 1.0
C1C f:HEC101 3.0 50.3 1.0
CD2 f:HIS24 3.0 50.8 1.0
CD2 e:HIS23 3.0 59.8 1.0
C4A f:HEC101 3.1 51.8 1.0
C4B f:HEC101 3.1 58.9 1.0
C4D f:HEC101 3.1 46.6 1.0
CE1 f:HIS24 3.1 52.6 1.0
C1A f:HEC101 3.2 56.0 1.0
CHD f:HEC101 3.2 46.6 1.0
CE1 e:HIS23 3.3 59.6 1.0
CHB f:HEC101 3.4 56.0 1.0
CHC f:HEC101 3.5 51.4 1.0
CHA f:HEC101 3.5 53.3 1.0
C3C f:HEC101 4.1 51.5 1.0
C2D f:HEC101 4.1 45.7 1.0
C2C f:HEC101 4.2 49.8 1.0
CG f:HIS24 4.2 49.8 1.0
ND1 f:HIS24 4.2 56.2 1.0
C2B f:HEC101 4.2 50.6 1.0
CG e:HIS23 4.2 56.5 1.0
C3D f:HEC101 4.2 40.7 1.0
C3B f:HEC101 4.3 48.0 1.0
C3A f:HEC101 4.3 59.5 1.0
ND1 e:HIS23 4.3 61.9 1.0
C2A f:HEC101 4.4 53.6 1.0
CE1 e:TYR19 4.9 61.7 1.0
NE1 f:TRP20 5.0 62.1 1.0
CZ2 f:TRP20 5.0 48.9 1.0

Iron binding site 6 out of 6 in 11yo

Go back to Iron Binding Sites List in 11yo
Iron binding site 6 out of 6 in the Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Single-Conformation Model Re-Refinement of 2F/S3-Rich Psii Intermediate Structure at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:33.8
occ:1.00
 FE v:HEC201 0.0 33.8 1.0
NB v:HEC201 1.9 34.5 1.0
ND v:HEC201 2.0 29.2 1.0
NC v:HEC201 2.0 34.4 1.0
NE2 v:HIS41 2.1 30.0 1.0
NA v:HEC201 2.2 33.2 1.0
NE2 v:HIS92 2.2 36.7 1.0
C1B v:HEC201 2.9 30.6 1.0
C1D v:HEC201 3.0 27.2 1.0
C4B v:HEC201 3.0 32.7 1.0
C4C v:HEC201 3.0 31.6 1.0
CE1 v:HIS41 3.0 29.2 1.0
C1C v:HEC201 3.1 32.7 1.0
C4D v:HEC201 3.1 34.5 1.0
CD2 v:HIS92 3.1 36.2 1.0
C4A v:HEC201 3.1 34.6 1.0
CD2 v:HIS41 3.1 36.8 1.0
C1A v:HEC201 3.2 38.0 1.0
CE1 v:HIS92 3.2 37.1 1.0
CHD v:HEC201 3.3 26.5 1.0
CHB v:HEC201 3.4 32.6 1.0
CHC v:HEC201 3.4 31.6 1.0
CHA v:HEC201 3.5 33.8 1.0
C2B v:HEC201 4.2 38.3 1.0
C3B v:HEC201 4.2 31.9 1.0
ND1 v:HIS41 4.2 41.6 1.0
C2D v:HEC201 4.2 28.0 1.0
C3C v:HEC201 4.2 36.4 1.0
CG v:HIS41 4.3 35.9 1.0
C2C v:HEC201 4.3 33.0 1.0
C3D v:HEC201 4.3 32.0 1.0
CG v:HIS92 4.3 33.8 1.0
ND1 v:HIS92 4.3 45.2 1.0
C3A v:HEC201 4.4 39.2 1.0
C2A v:HEC201 4.4 38.3 1.0
CE1 v:TYR75 5.0 37.8 1.0

Reference:

J.Wang, W.H.Armstrong, V.S.Batista. Do Crystallographic Xfel Data Support Binding of A Water Molecule to the Oxygen-Evolving Complex of Photosystem II Exposed to Two Flashes of Light? Proc. Natl. Acad. Sci. V. 118 82118 2021U.S.A..
ISSN: ISSN 0027-8424
PubMed: 34117119
DOI: 10.1073/PNAS.202398211
Page generated: Sun Oct 4 08:33:49 2026

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