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Iron in PDB 4ixq: Rt Fs X-Ray Diffraction of Photosystem II, Dark State

Enzymatic activity of Rt Fs X-Ray Diffraction of Photosystem II, Dark State

All present enzymatic activity of Rt Fs X-Ray Diffraction of Photosystem II, Dark State:
1.10.3.9;

Protein crystallography data

The structure of Rt Fs X-Ray Diffraction of Photosystem II, Dark State, PDB code: 4ixq was solved by J.Kern, R.Alonso-Mori, R.Tran, J.Hattne, R.J.Gildea, N.Echols, C.Gloeckner, J.Hellmich, H.Laksmono, R.G.Sierra, B.Lassalle-Kaiser, S.Koroidov, A.Lampe, G.Han, S.Gul, D.Difiore, D.Milathianaki, A.R.Fry, A.Miahnahri, D.W.Schafer, M.Messerschmidt, M.M.Seibert, J.E.Koglin, D.Sokaras, T.-C.Weng, J.Sellberg, M.J.Latimer, R.W.Grosse-Kunstleve, P.H.Zwart, W.E.White, P.Glatzel, P.D.Adams, M.J.Bogan, G.J.Williams, S.Boutet, J.Messinger, A.Zouni, N.K.Sauter, V.K.Yachandra, U.Bergmann, J.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.94 / 5.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 131.864, 227.511, 307.219, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 31.4

Other elements in 4ixq:

The structure of Rt Fs X-Ray Diffraction of Photosystem II, Dark State 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 Fs X-Ray Diffraction of Photosystem II, Dark State (pdb code 4ixq). 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 Fs X-Ray Diffraction of Photosystem II, Dark State, PDB code: 4ixq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4ixq

Go back to Iron Binding Sites List in 4ixq
Iron binding site 1 out of 6 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:60.8
occ:1.00
NE2 A:HIS215 2.3 74.9 1.0
NE2 D:HIS214 2.4 75.3 1.0
NE2 A:HIS272 2.5 73.4 1.0
O2 A:BCT402 2.6 84.7 1.0
NE2 D:HIS268 2.7 74.9 1.0
O3 A:BCT402 2.8 88.0 1.0
CE1 A:HIS215 3.1 81.5 1.0
CD2 D:HIS214 3.1 72.1 1.0
C A:BCT402 3.1 89.4 1.0
CD2 A:HIS215 3.2 73.2 1.0
CD2 A:HIS272 3.3 73.5 1.0
CE1 A:HIS272 3.4 74.7 1.0
CE1 D:HIS214 3.6 79.4 1.0
CE1 D:HIS268 3.6 79.2 1.0
CD2 D:HIS268 3.6 70.2 1.0
ND1 A:HIS215 4.1 84.7 1.0
CG A:HIS215 4.1 78.4 1.0
O1 A:BCT402 4.3 93.5 1.0
CG D:HIS214 4.4 76.7 1.0
CG A:HIS272 4.4 76.1 1.0
ND1 A:HIS272 4.4 75.7 1.0
ND1 D:HIS214 4.6 79.8 1.0
ND1 D:HIS268 4.7 75.4 1.0
CG D:HIS268 4.8 71.3 1.0
CG2 D:VAL218 4.9 77.2 1.0
CG2 A:VAL219 4.9 79.2 1.0

Iron binding site 2 out of 6 in 4ixq

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Iron binding site 2 out of 6 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:95.3
occ:1.00
FE F:HEM101 0.0 95.3 1.0
NC F:HEM101 2.0 97.8 1.0
NB F:HEM101 2.0 0.5 1.0
NA F:HEM101 2.1 0.8 1.0
ND F:HEM101 2.1 0.4 1.0
NE2 F:HIS24 2.6 92.9 1.0
NE2 E:HIS23 2.7 0.5 1.0
CE1 F:HIS24 2.9 94.9 1.0
C4C F:HEM101 3.0 100.0 1.0
C1B F:HEM101 3.1 0.3 1.0
C1C F:HEM101 3.1 99.5 1.0
C1D F:HEM101 3.1 0.7 1.0
C4A F:HEM101 3.1 0.0 1.0
C1A F:HEM101 3.1 0.5 1.0
C4B F:HEM101 3.1 0.9 1.0
C4D F:HEM101 3.1 0.3 1.0
CD2 E:HIS23 3.3 98.7 1.0
CHD F:HEM101 3.4 97.6 1.0
CHB F:HEM101 3.4 0.1 1.0
CHC F:HEM101 3.5 0.2 1.0
CHA F:HEM101 3.5 0.2 1.0
CD2 F:HIS24 3.7 90.2 1.0
CE1 E:HIS23 3.8 98.0 1.0
ND1 F:HIS24 4.0 92.1 1.0
C3C F:HEM101 4.3 0.1 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 0.3 1.0
C2A F:HEM101 4.3 0.4 1.0
C3A F:HEM101 4.3 0.0 1.0
C2D F:HEM101 4.3 0.1 1.0
C3D F:HEM101 4.3 0.4 1.0
CG F:HIS24 4.4 91.5 1.0
CG E:HIS23 4.5 94.3 1.0
ND1 E:HIS23 4.7 92.5 1.0
NE1 F:TRP20 4.8 0.7 1.0

Iron binding site 3 out of 6 in 4ixq

Go back to Iron Binding Sites List in 4ixq
Iron binding site 3 out of 6 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:46.7
occ:1.00
FE V:HEM201 0.0 46.7 1.0
NC V:HEM201 2.0 59.2 1.0
NB V:HEM201 2.0 52.3 1.0
NA V:HEM201 2.1 61.7 1.0
ND V:HEM201 2.1 65.2 1.0
NE2 V:HIS67 2.4 51.8 1.0
NE2 V:HIS118 2.5 65.3 1.0
C1C V:HEM201 3.0 64.1 1.0
C4B V:HEM201 3.0 54.7 1.0
C4C V:HEM201 3.0 64.3 1.0
C1B V:HEM201 3.1 60.6 1.0
C1A V:HEM201 3.1 65.8 1.0
C1D V:HEM201 3.1 68.7 1.0
C4A V:HEM201 3.1 63.9 1.0
C4D V:HEM201 3.1 72.9 1.0
CD2 V:HIS67 3.2 58.7 1.0
CD2 V:HIS118 3.3 69.0 1.0
CHC V:HEM201 3.4 60.2 1.0
CE1 V:HIS118 3.4 67.7 1.0
CHD V:HEM201 3.4 63.9 1.0
CE1 V:HIS67 3.4 58.6 1.0
CHB V:HEM201 3.5 65.3 1.0
CHA V:HEM201 3.5 71.4 1.0
C2C V:HEM201 4.2 72.3 1.0
C3B V:HEM201 4.3 59.5 1.0
C3C V:HEM201 4.3 69.9 1.0
C2B V:HEM201 4.3 64.0 1.0
C3A V:HEM201 4.3 64.3 1.0
C2A V:HEM201 4.3 65.0 1.0
C2D V:HEM201 4.3 75.7 1.0
C3D V:HEM201 4.4 76.4 1.0
CG V:HIS118 4.4 68.6 1.0
ND1 V:HIS118 4.4 69.8 1.0
CG V:HIS67 4.4 64.0 1.0
ND1 V:HIS67 4.5 61.5 1.0
CE1 V:TYR101 4.9 69.5 1.0

Iron binding site 4 out of 6 in 4ixq

Go back to Iron Binding Sites List in 4ixq
Iron binding site 4 out of 6 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe403

b:70.9
occ:1.00
NE2 a:HIS215 2.5 67.5 1.0
O2 d:BCT401 2.5 77.5 1.0
NE2 a:HIS272 2.5 83.8 1.0
NE2 d:HIS214 2.6 71.7 1.0
NE2 d:HIS268 2.6 81.5 1.0
O3 d:BCT401 2.7 80.1 1.0
C d:BCT401 3.0 82.8 1.0
CD2 d:HIS214 3.3 69.6 1.0
CD2 a:HIS215 3.3 69.3 1.0
CE1 a:HIS215 3.3 72.1 1.0
CE1 a:HIS272 3.4 87.1 1.0
CD2 a:HIS272 3.5 78.5 1.0
CE1 d:HIS268 3.5 82.6 1.0
CD2 d:HIS268 3.6 79.9 1.0
CE1 d:HIS214 3.7 72.1 1.0
O1 d:BCT401 4.1 85.3 1.0
ND1 a:HIS215 4.4 72.0 1.0
CG a:HIS215 4.4 69.5 1.0
ND1 a:HIS272 4.5 84.8 1.0
CG d:HIS214 4.5 70.2 1.0
CG a:HIS272 4.6 78.0 1.0
ND1 d:HIS268 4.6 81.0 1.0
ND1 d:HIS214 4.7 71.0 1.0
CG d:HIS268 4.7 79.0 1.0
OH d:TYR244 4.8 77.8 1.0
CG2 a:VAL219 4.9 83.6 1.0
CG2 d:VAL218 5.0 78.4 1.0

Iron binding site 5 out of 6 in 4ixq

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Iron binding site 5 out of 6 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Fe101

b:77.8
occ:1.00
FE f:HEM101 0.0 77.8 1.0
NC f:HEM101 2.0 99.0 1.0
NA f:HEM101 2.0 0.9 1.0
NB f:HEM101 2.1 99.1 1.0
ND f:HEM101 2.1 0.8 1.0
NE2 e:HIS23 2.6 0.4 1.0
NE2 f:HIS24 2.7 96.2 1.0
CE1 f:HIS24 3.0 92.9 1.0
C1A f:HEM101 3.1 0.5 1.0
C4C f:HEM101 3.1 0.7 1.0
C1C f:HEM101 3.1 0.9 1.0
C1B f:HEM101 3.1 0.1 1.0
C4A f:HEM101 3.1 0.2 1.0
C4B f:HEM101 3.1 0.8 1.0
C1D f:HEM101 3.1 0.5 1.0
C4D f:HEM101 3.1 0.5 1.0
CD2 e:HIS23 3.3 99.2 1.0
CHC f:HEM101 3.4 0.8 1.0
CHD f:HEM101 3.4 0.5 1.0
CHB f:HEM101 3.4 0.0 1.0
CHA f:HEM101 3.4 0.6 1.0
CE1 e:HIS23 3.7 0.4 1.0
CD2 f:HIS24 3.7 97.3 1.0
ND1 f:HIS24 4.1 89.4 1.0
C2A f:HEM101 4.3 0.9 1.0
C2B f:HEM101 4.3 0.9 1.0
C3C f:HEM101 4.3 0.8 1.0
C2C f:HEM101 4.3 0.0 1.0
C3A f:HEM101 4.3 0.1 1.0
C3B f:HEM101 4.3 0.8 1.0
C3D f:HEM101 4.3 0.1 1.0
C2D f:HEM101 4.3 0.6 1.0
CG e:HIS23 4.5 99.7 1.0
CG f:HIS24 4.5 93.7 1.0
ND1 e:HIS23 4.7 0.8 1.0
NE1 f:TRP20 4.8 0.1 1.0

Iron binding site 6 out of 6 in 4ixq

Go back to Iron Binding Sites List in 4ixq
Iron binding site 6 out of 6 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:61.3
occ:1.00
FE v:HEM201 0.0 61.3 1.0
NB v:HEM201 2.1 67.4 1.0
NC v:HEM201 2.1 65.6 1.0
NA v:HEM201 2.1 65.6 1.0
ND v:HEM201 2.1 69.2 1.0
NE2 v:HIS67 2.5 59.3 1.0
NE2 v:HIS118 2.6 64.8 1.0
C4B v:HEM201 3.1 68.4 1.0
C1C v:HEM201 3.1 67.1 1.0
C1A v:HEM201 3.1 66.3 1.0
C4D v:HEM201 3.1 73.7 1.0
C1D v:HEM201 3.1 70.3 1.0
C4C v:HEM201 3.1 68.1 1.0
C1B v:HEM201 3.1 70.8 1.0
C4A v:HEM201 3.1 67.0 1.0
CD2 v:HIS67 3.3 65.4 1.0
CD2 v:HIS118 3.3 67.2 1.0
CHC v:HEM201 3.4 67.8 1.0
CHA v:HEM201 3.4 70.0 1.0
CHD v:HEM201 3.5 69.1 1.0
CE1 v:HIS118 3.5 64.2 1.0
CHB v:HEM201 3.5 70.5 1.0
CE1 v:HIS67 3.6 66.4 1.0
C2C v:HEM201 4.3 69.7 1.0
C3B v:HEM201 4.3 69.6 1.0
C2A v:HEM201 4.3 65.4 1.0
C3C v:HEM201 4.3 69.3 1.0
C2B v:HEM201 4.3 71.8 1.0
C2D v:HEM201 4.3 75.0 1.0
C3D v:HEM201 4.3 78.4 1.0
C3A v:HEM201 4.3 63.8 1.0
CG v:HIS118 4.4 65.2 1.0
ND1 v:HIS118 4.4 61.7 1.0
CG v:HIS67 4.5 64.8 1.0
ND1 v:HIS67 4.6 65.4 1.0
CE1 v:TYR101 4.9 71.1 1.0

Reference:

J.Kern, R.Alonso-Mori, R.Tran, J.Hattne, R.J.Gildea, N.Echols, C.Glockner, J.Hellmich, H.Laksmono, R.G.Sierra, B.Lassalle-Kaiser, S.Koroidov, A.Lampe, G.Han, S.Gul, D.Difiore, D.Milathianaki, A.R.Fry, A.Miahnahri, D.W.Schafer, M.Messerschmidt, M.M.Seibert, J.E.Koglin, D.Sokaras, T.C.Weng, J.Sellberg, M.J.Latimer, R.W.Grosse-Kunstleve, P.H.Zwart, W.E.White, P.Glatzel, P.D.Adams, M.J.Bogan, G.J.Williams, S.Boutet, J.Messinger, A.Zouni, N.K.Sauter, V.K.Yachandra, U.Bergmann, J.Yano. Simultaneous Femtosecond X-Ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. Science V. 340 491 2013.
ISSN: ISSN 0036-8075
PubMed: 23413188
DOI: 10.1126/SCIENCE.1234273
Page generated: Sun Dec 13 15:38:07 2020

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