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Iron in PDB 4tnh: Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution

Enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution

All present enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution, PDB code: 4tnh was solved by J.Kern, R.Tran, R.Alonso-Mori, S.Koroidov, N.Echols, J.Hattne, M.Ibrahim, S.Gul, H.Laksmono, R.G.Sierra, R.J.Gildea, G.Han, J.Hellmich, B.Lassalle-Kaiser, R.Chatterjee, A.Brewster, C.A.Stan, C.Gloeckner, A.Lampe, D.Difiore, D.Milathianaki, A.R.Fry, M.M.Seibert, J.E.Koglin, E.Gallo, J.Uhlig, D.Sokaras, T.-C.Weng, P.H.Zwart, D.E.Skinner, M.J.Bogan, M.Messerschmidt, P.Glatzel, G.J.Williams, S.Boutet, P.D.Adams, A.Zouni, J.Messinger, N.K.Sauter, U.Bergmann, J.Yano, V.K.Yachandra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.93 / 4.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 132.885, 229.033, 307.715, 90.00, 90.00, 90.00
R / Rfree (%) 28.1 / 29.2

Other elements in 4tnh:

The structure of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Manganese (Mn) 8 atoms
Chlorine (Cl) 2 atoms
Calcium (Ca) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution (pdb code 4tnh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution, PDB code: 4tnh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4tnh

Go back to Iron Binding Sites List in 4tnh
Iron binding site 1 out of 6 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:0.5
occ:1.00
NE2 D:HIS214 2.5 0.9 1.0
NE2 A:HIS215 2.5 0.0 1.0
NE2 A:HIS272 2.5 0.2 1.0
NE2 D:HIS268 2.7 0.7 1.0
O3 D:BCT403 2.7 0.9 1.0
O2 D:BCT403 2.7 0.7 1.0
C D:BCT403 3.1 0.9 1.0
CD2 D:HIS214 3.2 0.5 1.0
CD2 A:HIS272 3.3 0.4 1.0
CD2 A:HIS215 3.4 0.4 1.0
CE1 A:HIS215 3.4 0.5 1.0
CE1 D:HIS268 3.5 0.2 1.0
CE1 A:HIS272 3.5 0.8 1.0
CE1 D:HIS214 3.6 0.5 1.0
CD2 D:HIS268 3.6 0.6 1.0
O1 D:BCT403 4.2 0.8 1.0
CG D:HIS214 4.4 0.7 1.0
ND1 A:HIS215 4.5 0.7 1.0
CG A:HIS272 4.5 0.8 1.0
CG A:HIS215 4.5 0.7 1.0
ND1 A:HIS272 4.6 0.5 1.0
ND1 D:HIS214 4.6 0.8 1.0
ND1 D:HIS268 4.7 0.9 1.0
OH D:TYR244 4.7 0.1 1.0
CG D:HIS268 4.7 0.0 1.0
CG2 D:VAL218 4.8 0.0 1.0

Iron binding site 2 out of 6 in 4tnh

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Iron binding site 2 out of 6 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:1.0
occ:1.00
FE F:HEM101 0.0 1.0 1.0
NC F:HEM101 2.1 0.5 1.0
NA F:HEM101 2.1 0.6 1.0
NB F:HEM101 2.1 0.7 1.0
ND F:HEM101 2.1 0.1 1.0
NE2 E:HIS23 2.6 0.5 1.0
NE2 F:HIS24 2.6 0.3 1.0
CE1 F:HIS24 3.0 0.6 1.0
C4C F:HEM101 3.1 1.0 1.0
C1D F:HEM101 3.1 0.7 1.0
C4D F:HEM101 3.1 0.9 1.0
C1A F:HEM101 3.1 1.0 1.0
C4A F:HEM101 3.1 0.5 1.0
C1C F:HEM101 3.1 0.6 1.0
C1B F:HEM101 3.1 0.4 1.0
C4B F:HEM101 3.1 0.2 1.0
CD2 E:HIS23 3.3 0.4 1.0
CHD F:HEM101 3.4 0.0 1.0
CHA F:HEM101 3.4 0.4 1.0
CHB F:HEM101 3.5 0.9 1.0
CHC F:HEM101 3.5 0.0 1.0
CE1 E:HIS23 3.6 0.6 1.0
CD2 F:HIS24 3.7 0.7 1.0
ND1 F:HIS24 4.1 0.7 1.0
C2D F:HEM101 4.2 0.1 1.0
C3D F:HEM101 4.2 0.4 1.0
C2A F:HEM101 4.3 0.8 1.0
C3C F:HEM101 4.3 0.5 1.0
C3A F:HEM101 4.3 0.2 1.0
C2C F:HEM101 4.3 0.6 1.0
C2B F:HEM101 4.3 0.4 1.0
C3B F:HEM101 4.3 0.6 1.0
CG F:HIS24 4.5 0.2 1.0
CG E:HIS23 4.5 0.1 1.0
ND1 E:HIS23 4.6 1.0 1.0
NE1 F:TRP20 4.8 0.6 1.0

Iron binding site 3 out of 6 in 4tnh

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Iron binding site 3 out of 6 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:0.2
occ:1.00
FE V:HEM201 0.0 0.2 1.0
NC V:HEM201 2.1 0.8 1.0
NA V:HEM201 2.1 0.8 1.0
NB V:HEM201 2.1 0.5 1.0
ND V:HEM201 2.1 1.0 1.0
NE2 V:HIS67 2.5 0.1 1.0
NE2 V:HIS118 2.6 0.7 1.0
C4B V:HEM201 3.0 0.5 1.0
C1B V:HEM201 3.0 0.2 1.0
C1C V:HEM201 3.1 0.6 1.0
C4A V:HEM201 3.1 0.3 1.0
C4C V:HEM201 3.1 0.5 1.0
C1D V:HEM201 3.1 0.9 1.0
C1A V:HEM201 3.1 0.1 1.0
C4D V:HEM201 3.1 0.9 1.0
CD2 V:HIS67 3.2 0.6 1.0
CD2 V:HIS118 3.4 0.1 1.0
CHB V:HEM201 3.4 0.9 1.0
CHC V:HEM201 3.4 0.7 1.0
CHD V:HEM201 3.4 0.2 1.0
CE1 V:HIS118 3.4 0.9 1.0
CHA V:HEM201 3.5 0.3 1.0
CE1 V:HIS67 3.5 0.3 1.0
C2B V:HEM201 4.2 0.8 1.0
C3B V:HEM201 4.2 0.2 1.0
C2C V:HEM201 4.3 0.5 1.0
C3A V:HEM201 4.3 0.2 1.0
C3C V:HEM201 4.3 0.6 1.0
C2A V:HEM201 4.3 0.1 1.0
C2D V:HEM201 4.3 0.3 1.0
C3D V:HEM201 4.3 0.1 1.0
CG V:HIS67 4.4 0.3 1.0
ND1 V:HIS118 4.4 1.0 1.0
CG V:HIS118 4.4 1.0 1.0
ND1 V:HIS67 4.5 0.1 1.0
CE1 V:TYR101 4.9 0.4 1.0

Iron binding site 4 out of 6 in 4tnh

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Iron binding site 4 out of 6 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe403

b:0.5
occ:1.00
NE2 d:HIS214 2.6 0.8 1.0
NE2 a:HIS272 2.6 0.0 1.0
NE2 a:HIS215 2.6 0.8 1.0
O2 d:BCT403 2.6 0.6 1.0
O3 d:BCT403 2.7 0.3 1.0
NE2 d:HIS268 2.7 0.6 1.0
C d:BCT403 3.1 0.8 1.0
CD2 d:HIS214 3.3 0.4 1.0
CD2 a:HIS272 3.4 0.3 1.0
CE1 a:HIS215 3.5 0.9 1.0
CD2 a:HIS215 3.5 0.3 1.0
CE1 d:HIS268 3.5 0.1 1.0
CE1 a:HIS272 3.6 0.9 1.0
CE1 d:HIS214 3.6 0.9 1.0
CD2 d:HIS268 3.7 0.8 1.0
O1 d:BCT403 4.2 0.5 1.0
CG a:HIS272 4.5 0.1 1.0
ND1 a:HIS215 4.5 0.8 1.0
CG d:HIS214 4.5 0.6 1.0
CG a:HIS215 4.6 0.4 1.0
ND1 a:HIS272 4.6 0.6 1.0
OH d:TYR244 4.6 1.0 1.0
ND1 d:HIS214 4.6 0.4 1.0
ND1 d:HIS268 4.7 0.2 1.0
CG d:HIS268 4.8 0.6 1.0
CG2 d:VAL218 4.8 0.8 1.0

Iron binding site 5 out of 6 in 4tnh

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Iron binding site 5 out of 6 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Fe101

b:0.3
occ:1.00
FE f:HEM101 0.0 0.3 1.0
NC f:HEM101 2.0 0.6 1.0
NA f:HEM101 2.1 0.2 1.0
NB f:HEM101 2.1 0.7 1.0
ND f:HEM101 2.1 0.7 1.0
NE2 e:HIS23 2.6 0.1 1.0
NE2 f:HIS24 2.6 0.9 1.0
CE1 f:HIS24 3.0 0.9 1.0
C4C f:HEM101 3.1 0.6 1.0
C1D f:HEM101 3.1 0.6 1.0
C4D f:HEM101 3.1 0.7 1.0
C1A f:HEM101 3.1 0.7 1.0
C1C f:HEM101 3.1 1.0 1.0
C4A f:HEM101 3.1 0.9 1.0
C1B f:HEM101 3.1 0.4 1.0
C4B f:HEM101 3.1 0.0 1.0
CD2 e:HIS23 3.3 0.8 1.0
CHD f:HEM101 3.4 0.5 1.0
CHA f:HEM101 3.4 0.6 1.0
CHC f:HEM101 3.5 0.6 1.0
CHB f:HEM101 3.5 0.2 1.0
CE1 e:HIS23 3.7 0.9 1.0
CD2 f:HIS24 3.7 0.7 1.0
ND1 f:HIS24 4.1 0.4 1.0
C2D f:HEM101 4.3 0.5 1.0
C3D f:HEM101 4.3 0.4 1.0
C2A f:HEM101 4.3 0.8 1.0
C3C f:HEM101 4.3 0.9 1.0
C3A f:HEM101 4.3 0.4 1.0
C2C f:HEM101 4.3 0.4 1.0
C2B f:HEM101 4.3 0.2 1.0
C3B f:HEM101 4.3 0.6 1.0
CG f:HIS24 4.5 0.9 1.0
CG e:HIS23 4.5 0.5 1.0
ND1 e:HIS23 4.6 0.5 1.0
NE1 f:TRP20 4.8 0.2 1.0

Iron binding site 6 out of 6 in 4tnh

Go back to Iron Binding Sites List in 4tnh
Iron binding site 6 out of 6 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:0.7
occ:1.00
FE v:HEM201 0.0 0.7 1.0
NC v:HEM201 2.1 0.2 1.0
NA v:HEM201 2.1 0.6 1.0
NB v:HEM201 2.1 0.2 1.0
ND v:HEM201 2.1 0.9 1.0
NE2 v:HIS67 2.5 0.4 1.0
NE2 v:HIS118 2.6 0.7 1.0
C4B v:HEM201 3.0 0.0 1.0
C1B v:HEM201 3.1 0.6 1.0
C1C v:HEM201 3.1 0.7 1.0
C1A v:HEM201 3.1 1.0 1.0
C4C v:HEM201 3.1 0.6 1.0
C4A v:HEM201 3.1 0.4 1.0
C4D v:HEM201 3.1 0.3 1.0
C1D v:HEM201 3.1 0.7 1.0
CD2 v:HIS67 3.3 0.8 1.0
CD2 v:HIS118 3.4 0.7 1.0
CHC v:HEM201 3.4 0.7 1.0
CHD v:HEM201 3.4 0.7 1.0
CHA v:HEM201 3.4 1.0 1.0
CHB v:HEM201 3.4 0.3 1.0
CE1 v:HIS118 3.5 0.4 1.0
CE1 v:HIS67 3.6 0.4 1.0
C3B v:HEM201 4.2 0.2 1.0
C2B v:HEM201 4.2 0.6 1.0
C2C v:HEM201 4.3 0.6 1.0
C2A v:HEM201 4.3 0.6 1.0
C3C v:HEM201 4.3 0.8 1.0
C3A v:HEM201 4.3 0.2 1.0
C2D v:HEM201 4.3 0.1 1.0
C3D v:HEM201 4.3 0.7 1.0
CG v:HIS67 4.4 0.7 1.0
CG v:HIS118 4.4 0.6 1.0
ND1 v:HIS118 4.5 0.3 1.0
ND1 v:HIS67 4.6 0.0 1.0
CE1 v:TYR101 4.9 0.3 1.0

Reference:

J.Kern, R.Tran, R.Alonso-Mori, S.Koroidov, N.Echols, J.Hattne, M.Ibrahim, S.Gul, H.Laksmono, R.G.Sierra, R.J.Gildea, G.Han, J.Hellmich, B.Lassalle-Kaiser, R.Chatterjee, A.S.Brewster, C.A.Stan, C.Glockner, A.Lampe, D.Difiore, D.Milathianaki, A.R.Fry, M.M.Seibert, J.E.Koglin, E.Gallo, J.Uhlig, D.Sokaras, T.C.Weng, P.H.Zwart, D.E.Skinner, M.J.Bogan, M.Messerschmidt, P.Glatzel, G.J.Williams, S.Boutet, P.D.Adams, A.Zouni, J.Messinger, N.K.Sauter, U.Bergmann, J.Yano, V.K.Yachandra. Taking Snapshots of Photosynthetic Water Oxidation Using Femtosecond X-Ray Diffraction and Spectroscopy. Nat Commun V. 5 4371 2014.
ISSN: ESSN 2041-1723
PubMed: 25006873
DOI: 10.1038/NCOMMS5371
Page generated: Mon Aug 5 10:21:03 2024

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