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Iron in PDB 4fby: Fs X-Ray Diffraction of Photosystem II

Enzymatic activity of Fs X-Ray Diffraction of Photosystem II

All present enzymatic activity of Fs X-Ray Diffraction of Photosystem II:
1.10.3.9;

Protein crystallography data

The structure of Fs X-Ray Diffraction of Photosystem II, PDB code: 4fby was solved by J.Kern, R.Alonso-Mori, J.Hellmich, R.Tran, J.Hattne, H.Laksmono, C.Gloeckner, N.Echols, R.G.Sierra, J.Sellberg, B.Lassalle-Kaiser, R.J.Gildea, P.Glatzel, R.W.Grosse-Kunstleve, M.J.Latimer, T.A.Mcqueen, D.Difiore, A.R.Fry, M.M.Messerschmidt, A.Miahnahri, D.W.Schafer, M.M.Seibert, D.Sokaras, T.-C.Weng, P.H.Zwart, W.E.White, P.D.Adams, M.J.Bogan, S.Boutet, G.J.Williams, J.Messinger, N.K.Sauter, A.Zouni, 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) 85.89 / 6.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 130.783, 227.764, 308.630, 90.00, 90.00, 90.00
R / Rfree (%) 36.6 / 38.5

Other elements in 4fby:

The structure of Fs X-Ray Diffraction of Photosystem II also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Fs X-Ray Diffraction of Photosystem II (pdb code 4fby). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Fs X-Ray Diffraction of Photosystem II, PDB code: 4fby:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4fby

Go back to Iron Binding Sites List in 4fby
Iron binding site 1 out of 6 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe413

b:0.3
occ:1.00
NE2 A:HIS215 2.4 0.6 1.0
NE2 D:HIS214 2.5 0.6 1.0
NE2 A:HIS272 2.5 0.4 1.0
O3 D:BCT410 2.5 0.8 1.0
O2 D:BCT410 2.6 0.6 1.0
NE2 D:HIS268 2.6 0.3 1.0
C D:BCT410 2.9 0.9 1.0
CD2 D:HIS214 3.2 0.5 1.0
CE1 A:HIS215 3.2 0.9 1.0
CD2 A:HIS215 3.4 1.0 1.0
CE1 A:HIS272 3.4 1.0 1.0
CD2 A:HIS272 3.4 0.5 1.0
CE1 D:HIS268 3.5 0.3 1.0
CD2 D:HIS268 3.6 0.5 1.0
CE1 D:HIS214 3.6 0.4 1.0
O1 D:BCT410 4.1 0.3 1.0
ND1 A:HIS215 4.2 0.2 1.0
CG A:HIS215 4.3 0.2 1.0
CG D:HIS214 4.4 0.9 1.0
ND1 A:HIS272 4.5 0.5 1.0
CG A:HIS272 4.5 0.5 1.0
ND1 D:HIS214 4.6 0.6 1.0
ND1 D:HIS268 4.6 0.2 1.0
CG D:HIS268 4.7 0.6 1.0
OH D:TYR244 4.8 0.5 1.0
CG2 D:VAL218 4.9 0.1 1.0
CG2 A:VAL219 5.0 0.1 1.0

Iron binding site 2 out of 6 in 4fby

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


Mono view


Stereo pair view

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

b:0.1
occ:1.00
FE E:HEM101 0.0 0.1 1.0
NC E:HEM101 2.0 0.6 1.0
NB E:HEM101 2.1 1.0 1.0
NA E:HEM101 2.1 0.4 1.0
ND E:HEM101 2.1 0.6 1.0
NE2 E:HIS23 2.5 0.0 1.0
NE2 F:HIS24 2.5 0.9 1.0
C4C E:HEM101 3.0 0.7 1.0
C1C E:HEM101 3.1 0.9 1.0
C1B E:HEM101 3.1 0.5 1.0
CD2 E:HIS23 3.1 0.6 1.0
C1A E:HEM101 3.1 0.5 1.0
CE1 F:HIS24 3.1 0.5 1.0
C1D E:HEM101 3.1 0.6 1.0
C4B E:HEM101 3.1 0.4 1.0
C4D E:HEM101 3.1 0.4 1.0
C4A E:HEM101 3.1 0.6 1.0
CHD E:HEM101 3.4 0.4 1.0
CHC E:HEM101 3.4 0.9 1.0
CHB E:HEM101 3.5 0.5 1.0
CHA E:HEM101 3.5 0.6 1.0
CD2 F:HIS24 3.6 0.7 1.0
CE1 E:HIS23 3.6 0.7 1.0
ND1 F:HIS24 4.2 0.7 1.0
C3C E:HEM101 4.2 0.8 1.0
C2C E:HEM101 4.3 0.2 1.0
C2B E:HEM101 4.3 1.0 1.0
C3B E:HEM101 4.3 0.5 1.0
C2A E:HEM101 4.3 0.5 1.0
C3A E:HEM101 4.3 0.8 1.0
C3D E:HEM101 4.3 0.7 1.0
C2D E:HEM101 4.3 0.3 1.0
CG E:HIS23 4.3 0.1 1.0
CG F:HIS24 4.4 0.6 1.0
ND1 E:HIS23 4.6 0.6 1.0
NE1 F:TRP20 4.9 0.9 1.0

Iron binding site 3 out of 6 in 4fby

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Iron binding site 3 out of 6 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

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

b:1.0
occ:1.00
FE V:HEM201 0.0 1.0 1.0
NB V:HEM201 2.0 0.0 1.0
NC V:HEM201 2.0 0.5 1.0
ND V:HEM201 2.1 0.8 1.0
NA V:HEM201 2.1 0.6 1.0
NE2 V:HIS67 2.5 0.4 1.0
NE2 V:HIS118 2.5 0.6 1.0
C4B V:HEM201 3.0 0.3 1.0
C1C V:HEM201 3.0 0.7 1.0
C4D V:HEM201 3.1 0.3 1.0
C1D V:HEM201 3.1 0.8 1.0
C4C V:HEM201 3.1 0.6 1.0
C1A V:HEM201 3.1 0.4 1.0
C1B V:HEM201 3.1 0.4 1.0
C4A V:HEM201 3.1 0.5 1.0
CE1 V:HIS118 3.2 0.7 1.0
CD2 V:HIS67 3.2 0.4 1.0
CD2 V:HIS118 3.3 0.8 1.0
CHC V:HEM201 3.4 0.4 1.0
CHA V:HEM201 3.4 1.0 1.0
CHD V:HEM201 3.4 0.6 1.0
CHB V:HEM201 3.5 0.9 1.0
CE1 V:HIS67 3.5 0.8 1.0
ND1 V:HIS118 4.2 0.9 1.0
C3B V:HEM201 4.2 0.0 1.0
CG V:HIS118 4.2 0.6 1.0
C2C V:HEM201 4.3 0.5 1.0
C2B V:HEM201 4.3 0.6 1.0
C3C V:HEM201 4.3 0.7 1.0
C3D V:HEM201 4.3 0.5 1.0
C2D V:HEM201 4.3 0.3 1.0
C2A V:HEM201 4.3 0.3 1.0
C3A V:HEM201 4.3 0.2 1.0
CG V:HIS67 4.4 0.7 1.0
ND1 V:HIS67 4.6 0.6 1.0
CE1 V:TYR101 4.9 0.5 1.0

Iron binding site 4 out of 6 in 4fby

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Iron binding site 4 out of 6 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fs X-Ray Diffraction of Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe414

b:1.0
occ:1.00
NE2 Q:HIS214 2.4 0.2 1.0
NE2 G:HIS215 2.4 0.9 1.0
NE2 G:HIS272 2.5 0.7 1.0
O3 Q:BCT411 2.5 0.4 1.0
O2 Q:BCT411 2.6 0.1 1.0
NE2 Q:HIS268 2.6 0.7 1.0
C Q:BCT411 2.9 0.2 1.0
CD2 Q:HIS214 3.2 0.5 1.0
CE1 G:HIS215 3.2 0.9 1.0
CD2 G:HIS215 3.3 0.5 1.0
CE1 G:HIS272 3.4 0.9 1.0
CD2 G:HIS272 3.4 0.4 1.0
CE1 Q:HIS214 3.5 0.7 1.0
CE1 Q:HIS268 3.5 0.3 1.0
CD2 Q:HIS268 3.5 0.3 1.0
O1 Q:BCT411 4.1 1.0 1.0
ND1 G:HIS215 4.2 0.1 1.0
CG G:HIS215 4.3 0.2 1.0
CG Q:HIS214 4.4 0.0 1.0
ND1 G:HIS272 4.5 1.0 1.0
CG G:HIS272 4.5 0.0 1.0
ND1 Q:HIS214 4.6 1.0 1.0
ND1 Q:HIS268 4.6 0.5 1.0
CG Q:HIS268 4.7 0.5 1.0
OH Q:TYR244 4.9 0.8 1.0
CG2 G:VAL219 4.9 0.2 1.0
CG2 Q:VAL218 5.0 0.6 1.0

Iron binding site 5 out of 6 in 4fby

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


Mono view


Stereo pair view

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

b:0.2
occ:1.00
FE R:HEM101 0.0 0.2 1.0
NC R:HEM101 2.0 0.9 1.0
NB R:HEM101 2.1 0.1 1.0
NA R:HEM101 2.1 1.0 1.0
ND R:HEM101 2.1 0.3 1.0
NE2 R:HIS23 2.5 0.3 1.0
NE2 S:HIS24 2.5 0.8 1.0
C4C R:HEM101 3.0 0.3 1.0
CE1 S:HIS24 3.0 0.7 1.0
C1C R:HEM101 3.1 0.2 1.0
C1A R:HEM101 3.1 0.1 1.0
C1B R:HEM101 3.1 0.4 1.0
C4B R:HEM101 3.1 0.2 1.0
C4D R:HEM101 3.1 0.3 1.0
C1D R:HEM101 3.1 0.9 1.0
C4A R:HEM101 3.1 0.1 1.0
CD2 R:HIS23 3.1 0.2 1.0
CHD R:HEM101 3.4 0.2 1.0
CHC R:HEM101 3.4 0.5 1.0
CHA R:HEM101 3.4 0.8 1.0
CHB R:HEM101 3.5 0.1 1.0
CD2 S:HIS24 3.6 0.8 1.0
CE1 R:HIS23 3.6 0.3 1.0
ND1 S:HIS24 4.2 0.1 1.0
C3C R:HEM101 4.3 0.4 1.0
C2C R:HEM101 4.3 0.9 1.0
C2B R:HEM101 4.3 0.1 1.0
C2A R:HEM101 4.3 0.8 1.0
C3B R:HEM101 4.3 1.0 1.0
C3A R:HEM101 4.3 1.0 1.0
C3D R:HEM101 4.3 0.1 1.0
C2D R:HEM101 4.3 0.1 1.0
CG R:HIS23 4.4 0.2 1.0
CG S:HIS24 4.4 0.6 1.0
ND1 R:HIS23 4.6 0.3 1.0
NE1 S:TRP20 4.9 0.6 1.0

Iron binding site 6 out of 6 in 4fby

Go back to Iron Binding Sites List in 4fby
Iron binding site 6 out of 6 in the Fs X-Ray Diffraction of Photosystem II


Mono view


Stereo pair view

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

b:0.5
occ:1.00
FE i:HEM201 0.0 0.5 1.0
NB i:HEM201 2.0 0.8 1.0
ND i:HEM201 2.0 0.7 1.0
NC i:HEM201 2.1 0.8 1.0
NA i:HEM201 2.1 0.6 1.0
NE2 i:HIS118 2.5 0.1 1.0
NE2 i:HIS67 2.5 0.1 1.0
C4B i:HEM201 3.0 0.9 1.0
C4D i:HEM201 3.0 0.0 1.0
C1C i:HEM201 3.1 0.9 1.0
C1D i:HEM201 3.1 0.2 1.0
C1A i:HEM201 3.1 0.1 1.0
C4C i:HEM201 3.1 0.4 1.0
C1B i:HEM201 3.1 0.6 1.0
C4A i:HEM201 3.1 0.4 1.0
CE1 i:HIS118 3.2 0.8 1.0
CD2 i:HIS67 3.3 0.8 1.0
CD2 i:HIS118 3.3 0.0 1.0
CHC i:HEM201 3.4 0.9 1.0
CHA i:HEM201 3.4 0.6 1.0
CHD i:HEM201 3.4 0.5 1.0
CHB i:HEM201 3.5 0.9 1.0
CE1 i:HIS67 3.6 0.7 1.0
ND1 i:HIS118 4.2 0.5 1.0
CG i:HIS118 4.2 0.8 1.0
C3B i:HEM201 4.3 0.6 1.0
C3D i:HEM201 4.3 0.6 1.0
C2C i:HEM201 4.3 0.4 1.0
C2D i:HEM201 4.3 0.9 1.0
C2B i:HEM201 4.3 0.3 1.0
C3C i:HEM201 4.3 0.3 1.0
C2A i:HEM201 4.3 0.4 1.0
C3A i:HEM201 4.3 0.2 1.0
CG i:HIS67 4.5 0.9 1.0
ND1 i:HIS67 4.6 0.1 1.0
CE1 i:TYR101 5.0 0.5 1.0

Reference:

J.Kern, R.Alonso-Mori, J.Hellmich, R.Tran, J.Hattne, H.Laksmono, C.Glockner, N.Echols, R.G.Sierra, J.Sellberg, B.Lassalle-Kaiser, R.J.Gildea, P.Glatzel, R.W.Grosse-Kunstleve, M.J.Latimer, T.A.Mcqueen, D.Difiore, A.R.Fry, M.Messerschmidt, A.Miahnahri, D.W.Schafer, M.M.Seibert, D.Sokaras, T.C.Weng, P.H.Zwart, W.E.White, P.D.Adams, M.J.Bogan, S.Boutet, G.J.Williams, J.Messinger, N.K.Sauter, A.Zouni, U.Bergmann, J.Yano, V.K.Yachandra. Room Temperature Femtosecond X-Ray Diffraction of Photosystem II Microcrystals. Proc.Natl.Acad.Sci.Usa V. 109 9721 2012.
ISSN: ISSN 0027-8424
PubMed: 22665786
DOI: 10.1073/PNAS.1204598109
Page generated: Mon Aug 5 02:12:07 2024

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