Atomistry » Iron » PDB 4r33-4rxn » 4rvy
Atomistry »
  Iron »
    PDB 4r33-4rxn »
      4rvy »

Iron in PDB 4rvy: Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)

Enzymatic activity of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)

All present enzymatic activity of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3):
1.10.3.9;

Protein crystallography data

The structure of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3), PDB code: 4rvy was solved by C.Kupitz, S.Basu, I.Grotjohann, R.Fromme, N.Zatsepin, K.N.Rendek, M.Hunter, R.L.Shoeman, T.A.White, D.Wang, D.James, J.-H.Yang, D.E.Cobb, B.Reeder, R.G.Sierra, H.Liu, A.Barty, A.Aquila, D.Deponte, R.Kirian, S.Bari, J.J.Bergkamp, K.Beyerlein, M.J.Bogan, C.Caleman, T.-C.Chao, C.E.Conrad, K.M.Davis, H.Fleckenstein, L.Galli, S.P.Hau-Riege, S.Kassemeyer, H.Laksmono, M.Liang, L.Lomb, S.Marchesini, A.V.Martin, M.Messerschmidt, D.Milathianaki, K.Nass, A.Ros, S.Roy-Chowdhury, K.Schmidt, M.Seibert, J.Steinbrener, F.Stellato, L.Yan, C.Yoon, T.A.Moore, A.L.Moore, Y.Pushkar, G.J.Williams, S.Boutet, R.B.Doak, U.Weierstall, M.Frank, H.N.Chapman, J.C.H.Spence, P.Fromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 102.30 / 5.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 136.610, 228.090, 308.680, 90.00, 90.00, 90.00
R / Rfree (%) 28.1 / 29.1

Other elements in 4rvy:

The structure of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Manganese (Mn) 8 atoms
Calcium (Ca) 8 atoms
Chlorine (Cl) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) (pdb code 4rvy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3), PDB code: 4rvy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4rvy

Go back to Iron Binding Sites List in 4rvy
Iron binding site 1 out of 6 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:26.6
occ:1.00
NE2 D:HIS214 2.1 22.5 1.0
NE2 A:HIS215 2.2 24.5 1.0
NE2 A:HIS272 2.2 26.4 1.0
O2 A:BCT612 2.3 39.9 1.0
O1 A:BCT612 2.3 39.1 1.0
NE2 D:HIS268 2.3 25.1 1.0
C A:BCT612 2.6 40.5 1.0
CE1 A:HIS215 3.1 25.0 1.0
CD2 D:HIS214 3.1 22.7 1.0
CE1 D:HIS214 3.1 23.1 1.0
CE1 A:HIS272 3.1 26.7 1.0
CD2 A:HIS215 3.2 22.6 1.0
CE1 D:HIS268 3.2 25.7 1.0
CD2 A:HIS272 3.3 27.2 1.0
CD2 D:HIS268 3.4 24.6 1.0
O3 A:BCT612 3.9 42.0 1.0
ND1 A:HIS215 4.2 25.0 1.0
ND1 D:HIS214 4.2 22.4 1.0
CG D:HIS214 4.2 22.9 1.0
ND1 A:HIS272 4.3 26.8 1.0
CG A:HIS215 4.3 25.1 1.0
ND1 D:HIS268 4.4 25.1 1.0
CG A:HIS272 4.4 27.3 1.0
CG D:HIS268 4.5 23.8 1.0
CG2 A:VAL219 4.6 27.0 1.0
CG2 D:VAL218 4.7 24.1 1.0

Iron binding site 2 out of 6 in 4rvy

Go back to Iron Binding Sites List in 4rvy
Iron binding site 2 out of 6 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe602

b:26.6
occ:1.00
NE2 d:HIS214 2.1 22.5 1.0
NE2 a:HIS215 2.2 24.5 1.0
NE2 a:HIS272 2.2 26.4 1.0
O1 a:BCT612 2.3 39.9 1.0
O2 a:BCT612 2.3 39.1 1.0
NE2 d:HIS268 2.3 25.1 1.0
C a:BCT612 2.6 40.5 1.0
CE1 a:HIS215 3.1 25.0 1.0
CD2 d:HIS214 3.1 22.7 1.0
CE1 d:HIS214 3.1 23.1 1.0
CE1 a:HIS272 3.1 26.7 1.0
CD2 a:HIS215 3.2 22.6 1.0
CE1 d:HIS268 3.2 25.7 1.0
CD2 a:HIS272 3.3 27.2 1.0
CD2 d:HIS268 3.4 24.6 1.0
O3 a:BCT612 3.9 42.0 1.0
ND1 a:HIS215 4.2 25.0 1.0
ND1 d:HIS214 4.2 22.4 1.0
CG d:HIS214 4.2 22.9 1.0
ND1 a:HIS272 4.3 26.8 1.0
CG a:HIS215 4.3 25.1 1.0
ND1 d:HIS268 4.4 25.1 1.0
CG a:HIS272 4.4 27.3 1.0
CG d:HIS268 4.5 23.8 1.0
CG2 a:VAL219 4.6 27.0 1.0
CG2 d:VAL218 4.7 24.1 1.0

Iron binding site 3 out of 6 in 4rvy

Go back to Iron Binding Sites List in 4rvy
Iron binding site 3 out of 6 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:40.0
occ:1.00
FE F:HEM101 0.0 40.0 1.0
NB F:HEM101 2.0 40.8 1.0
NE2 E:HIS23 2.1 45.2 1.0
NA F:HEM101 2.1 41.9 1.0
ND F:HEM101 2.1 40.7 1.0
NE2 F:HIS24 2.1 37.9 1.0
NC F:HEM101 2.1 40.2 1.0
CE1 E:HIS23 3.0 45.2 1.0
C4D F:HEM101 3.0 42.0 1.0
C1A F:HEM101 3.0 42.4 1.0
C4B F:HEM101 3.1 41.4 1.0
CE1 F:HIS24 3.1 38.7 1.0
C1B F:HEM101 3.1 42.4 1.0
C4A F:HEM101 3.1 42.3 1.0
CD2 F:HIS24 3.1 37.4 1.0
C1C F:HEM101 3.1 39.8 1.0
C1D F:HEM101 3.1 40.8 1.0
CD2 E:HIS23 3.1 44.9 1.0
C4C F:HEM101 3.1 40.0 1.0
CHA F:HEM101 3.4 41.8 1.0
CHC F:HEM101 3.4 40.0 1.0
CHB F:HEM101 3.5 42.4 1.0
CHD F:HEM101 3.5 40.0 1.0
ND1 E:HIS23 4.1 44.6 1.0
ND1 F:HIS24 4.2 37.6 1.0
CG E:HIS23 4.2 45.8 1.0
CG F:HIS24 4.2 37.6 1.0
C2A F:HEM101 4.2 43.3 1.0
C3D F:HEM101 4.2 41.8 1.0
C3A F:HEM101 4.3 43.4 1.0
C2D F:HEM101 4.3 41.0 1.0
C3B F:HEM101 4.3 41.9 1.0
C2B F:HEM101 4.3 42.5 1.0
C2C F:HEM101 4.3 39.6 1.0
C3C F:HEM101 4.3 40.2 1.0
CE2 E:TYR19 4.7 48.8 1.0
NE1 F:TRP20 4.9 40.1 1.0

Iron binding site 4 out of 6 in 4rvy

Go back to Iron Binding Sites List in 4rvy
Iron binding site 4 out of 6 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Fe101

b:40.0
occ:1.00
FE f:HEM101 0.0 40.0 1.0
NB f:HEM101 2.0 40.8 1.0
NE2 e:HIS23 2.1 45.2 1.0
NA f:HEM101 2.1 41.9 1.0
ND f:HEM101 2.1 40.7 1.0
NE2 f:HIS24 2.1 37.9 1.0
NC f:HEM101 2.1 40.2 1.0
CE1 e:HIS23 3.0 45.2 1.0
C4D f:HEM101 3.0 42.0 1.0
C1A f:HEM101 3.0 42.4 1.0
C4B f:HEM101 3.1 41.4 1.0
CE1 f:HIS24 3.1 38.7 1.0
C1B f:HEM101 3.1 42.4 1.0
C4A f:HEM101 3.1 42.3 1.0
CD2 f:HIS24 3.1 37.4 1.0
C1C f:HEM101 3.1 39.8 1.0
C1D f:HEM101 3.1 40.8 1.0
CD2 e:HIS23 3.1 44.9 1.0
C4C f:HEM101 3.1 40.0 1.0
CHA f:HEM101 3.4 41.8 1.0
CHC f:HEM101 3.4 40.0 1.0
CHB f:HEM101 3.5 42.4 1.0
CHD f:HEM101 3.5 40.0 1.0
ND1 e:HIS23 4.1 44.6 1.0
ND1 f:HIS24 4.2 37.6 1.0
CG e:HIS23 4.2 45.8 1.0
CG f:HIS24 4.2 37.6 1.0
C2A f:HEM101 4.2 43.3 1.0
C3D f:HEM101 4.2 41.8 1.0
C3A f:HEM101 4.3 43.4 1.0
C2D f:HEM101 4.3 41.0 1.0
C3B f:HEM101 4.3 41.9 1.0
C2B f:HEM101 4.3 42.5 1.0
C2C f:HEM101 4.3 39.6 1.0
C3C f:HEM101 4.3 40.2 1.0
CE2 e:TYR19 4.7 48.8 1.0
NE1 f:TRP20 4.9 40.1 1.0

Iron binding site 5 out of 6 in 4rvy

Go back to Iron Binding Sites List in 4rvy
Iron binding site 5 out of 6 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:24.9
occ:1.00
FE V:HEM201 0.0 24.9 1.0
NC V:HEM201 2.0 23.8 1.0
NA V:HEM201 2.0 24.1 1.0
NE2 V:HIS41 2.0 23.6 1.0
NB V:HEM201 2.1 24.1 1.0
ND V:HEM201 2.1 24.7 1.0
NE2 V:HIS92 2.1 27.9 1.0
CD2 V:HIS41 3.0 22.9 1.0
C4C V:HEM201 3.0 24.8 1.0
C1B V:HEM201 3.1 24.5 1.0
CE1 V:HIS41 3.1 22.1 1.0
C4A V:HEM201 3.1 24.7 1.0
C1D V:HEM201 3.1 24.8 1.0
C1C V:HEM201 3.1 25.4 1.0
CD2 V:HIS92 3.1 27.3 1.0
C1A V:HEM201 3.1 24.2 1.0
C4D V:HEM201 3.1 23.9 1.0
C4B V:HEM201 3.1 23.9 1.0
CE1 V:HIS92 3.1 27.6 1.0
CHD V:HEM201 3.4 24.3 1.0
CHB V:HEM201 3.4 24.5 1.0
CHA V:HEM201 3.5 23.2 1.0
CHC V:HEM201 3.5 24.9 1.0
ND1 V:HIS41 4.2 22.5 1.0
CG V:HIS41 4.2 22.6 1.0
ND1 V:HIS92 4.2 28.1 1.0
CG V:HIS92 4.2 27.8 1.0
C3C V:HEM201 4.3 24.6 1.0
C2C V:HEM201 4.3 24.2 1.0
C2B V:HEM201 4.3 24.9 1.0
C3A V:HEM201 4.3 24.6 1.0
C3B V:HEM201 4.3 25.5 1.0
C2A V:HEM201 4.3 24.6 1.0
C3D V:HEM201 4.3 24.5 1.0
C2D V:HEM201 4.3 24.0 1.0
CE1 V:TYR75 4.7 27.7 1.0

Iron binding site 6 out of 6 in 4rvy

Go back to Iron Binding Sites List in 4rvy
Iron binding site 6 out of 6 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:24.9
occ:1.00
FE v:HEM201 0.0 24.9 1.0
NC v:HEM201 2.0 23.8 1.0
NA v:HEM201 2.0 24.1 1.0
NE2 v:HIS41 2.0 23.6 1.0
NB v:HEM201 2.1 24.1 1.0
ND v:HEM201 2.1 24.7 1.0
NE2 v:HIS92 2.1 27.9 1.0
CD2 v:HIS41 3.0 22.9 1.0
C4C v:HEM201 3.0 24.8 1.0
C1B v:HEM201 3.1 24.5 1.0
CE1 v:HIS41 3.1 22.1 1.0
C4A v:HEM201 3.1 24.7 1.0
C1D v:HEM201 3.1 24.8 1.0
C1C v:HEM201 3.1 25.4 1.0
CD2 v:HIS92 3.1 27.3 1.0
C1A v:HEM201 3.1 24.2 1.0
C4D v:HEM201 3.1 23.9 1.0
C4B v:HEM201 3.1 23.9 1.0
CE1 v:HIS92 3.1 27.6 1.0
CHB v:HEM201 3.4 24.5 1.0
CHD v:HEM201 3.4 24.3 1.0
CHA v:HEM201 3.5 23.2 1.0
CHC v:HEM201 3.5 24.9 1.0
ND1 v:HIS41 4.2 22.5 1.0
CG v:HIS41 4.2 22.6 1.0
ND1 v:HIS92 4.2 28.1 1.0
CG v:HIS92 4.2 27.8 1.0
C3C v:HEM201 4.3 24.6 1.0
C2C v:HEM201 4.3 24.2 1.0
C2B v:HEM201 4.3 24.9 1.0
C3A v:HEM201 4.3 24.6 1.0
C3B v:HEM201 4.3 25.5 1.0
C2A v:HEM201 4.3 24.6 1.0
C3D v:HEM201 4.3 24.5 1.0
C2D v:HEM201 4.3 24.0 1.0
CE1 v:TYR75 4.7 27.7 1.0

Reference:

C.Kupitz, S.Basu, I.Grotjohann, R.Fromme, N.A.Zatsepin, K.N.Rendek, M.S.Hunter, R.L.Shoeman, T.A.White, D.Wang, D.James, J.H.Yang, D.E.Cobb, B.Reeder, R.G.Sierra, H.Liu, A.Barty, A.L.Aquila, D.Deponte, R.A.Kirian, S.Bari, J.J.Bergkamp, K.R.Beyerlein, M.J.Bogan, C.Caleman, T.C.Chao, C.E.Conrad, K.M.Davis, H.Fleckenstein, L.Galli, S.P.Hau-Riege, S.Kassemeyer, H.Laksmono, M.Liang, L.Lomb, S.Marchesini, A.V.Martin, M.Messerschmidt, D.Milathianaki, K.Nass, A.Ros, S.Roy-Chowdhury, K.Schmidt, M.Seibert, J.Steinbrener, F.Stellato, L.Yan, C.Yoon, T.A.Moore, A.L.Moore, Y.Pushkar, G.J.Williams, S.Boutet, R.B.Doak, U.Weierstall, M.Frank, H.N.Chapman, J.C.Spence, P.Fromme. Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. Nature V. 513 261 2014.
ISSN: ISSN 0028-0836
PubMed: 25043005
DOI: 10.1038/NATURE13453
Page generated: Mon Aug 5 09:30:33 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy