Atomistry » Calcium » PDB 4p4i-4pjs » 4pbu
Atomistry »
  Calcium »
    PDB 4p4i-4pjs »
      4pbu »

Calcium in PDB 4pbu: Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State

Enzymatic activity of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State

All present enzymatic activity of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State:
1.10.3.9;

Protein crystallography data

The structure of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State, PDB code: 4pbu 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.A.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) 100.64 / 5.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 133.250, 226.260, 307.090, 90.00, 90.00, 90.00
R / Rfree (%) 26.1 / 26.2

Other elements in 4pbu:

The structure of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State also contains other interesting chemical elements:

Magnesium (Mg) 71 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State (pdb code 4pbu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State, PDB code: 4pbu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4pbu

Go back to Calcium Binding Sites List in 4pbu
Calcium binding site 1 out of 9 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:24.6
occ:1.00
CA1 A:OEX601 0.0 24.6 1.0
O1 A:OEX601 2.3 22.5 1.0
OD2 A:ASP170 2.4 23.9 1.0
O2 A:OEX601 2.5 25.2 1.0
O5 A:OEX601 2.5 24.1 1.0
O A:ALA344 2.5 25.6 1.0
CG A:ASP170 3.2 22.6 1.0
OD1 A:ASP170 3.4 23.1 1.0
MN2 A:OEX601 3.4 22.9 1.0
OE1 A:GLU189 3.4 26.4 1.0
MN3 A:OEX601 3.4 23.5 1.0
C A:ALA344 3.5 25.1 1.0
MN1 A:OEX601 3.5 22.6 1.0
OXT A:ALA344 3.7 25.0 1.0
MN4 A:OEX601 3.8 26.3 1.0
O3 A:OEX601 3.9 23.3 1.0
O4 A:OEX601 4.0 26.6 1.0
NH1 C:ARG357 4.0 26.4 1.0
OE2 A:GLU189 4.1 25.1 1.0
CD A:GLU189 4.1 24.6 1.0
NH2 C:ARG357 4.2 23.9 1.0
CB A:ASP170 4.4 21.7 1.0
CZ C:ARG357 4.6 27.5 1.0
OH A:TYR161 4.8 22.4 1.0
OE1 A:GLN165 4.8 23.9 1.0
CA A:ALA344 4.8 24.7 1.0
OE1 C:GLU354 4.8 22.6 1.0
OE2 C:GLU354 5.0 23.1 1.0

Calcium binding site 2 out of 9 in 4pbu

Go back to Calcium Binding Sites List in 4pbu
Calcium binding site 2 out of 9 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:76.3
occ:1.00
OD1 B:ASN438 2.7 29.1 1.0
CG B:ASN438 3.9 27.1 1.0
O B:SER439 4.5 22.6 1.0
OE1 O:GLU181 4.6 47.5 1.0
CA B:ASN438 4.6 24.5 1.0
OE2 B:GLU435 4.6 33.7 1.0
ND2 B:ASN438 4.7 29.5 1.0
OE2 O:GLU181 4.8 46.2 1.0
C B:ASN438 4.8 23.9 1.0
CB B:ASN438 4.8 25.2 1.0
O B:ASN438 5.0 23.6 1.0

Calcium binding site 3 out of 9 in 4pbu

Go back to Calcium Binding Sites List in 4pbu
Calcium binding site 3 out of 9 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:56.6
occ:1.00
OXT F:ARG45 2.6 30.8 1.0
O F:ARG45 3.0 30.5 1.0
C F:ARG45 3.2 31.1 1.0
OE1 V:GLU23 4.2 45.7 1.0
OE2 V:GLU23 4.4 46.5 1.0
CD V:GLU23 4.5 44.0 1.0
O A:ALA309 4.7 28.4 1.0
CA F:ARG45 4.7 31.3 1.0

Calcium binding site 4 out of 9 in 4pbu

Go back to Calcium Binding Sites List in 4pbu
Calcium binding site 4 out of 9 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:49.3
occ:1.00
O O:THR138 2.5 43.6 1.0
O O:VAL201 2.5 39.5 1.0
OD1 O:ASN200 2.5 41.9 1.0
CG O:ASN200 3.6 40.6 1.0
C O:THR138 3.6 43.6 1.0
C O:VAL201 3.7 39.0 1.0
ND2 O:ASN200 4.0 42.7 1.0
N O:VAL201 4.3 38.3 1.0
CA O:SER139 4.4 43.6 1.0
N O:SER139 4.4 43.6 1.0
CA O:THR138 4.5 43.7 1.0
CA O:VAL201 4.6 38.6 1.0
N O:ALA202 4.6 39.6 1.0
CA O:ALA202 4.6 40.1 1.0
C O:ASN200 4.6 38.1 1.0
O O:THR140 4.7 42.2 1.0
CB O:THR138 4.8 43.6 1.0
C O:SER139 4.8 43.3 1.0
CB O:ASN200 4.9 38.6 1.0

Calcium binding site 5 out of 9 in 4pbu

Go back to Calcium Binding Sites List in 4pbu
Calcium binding site 5 out of 9 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca401

b:27.5
occ:1.00
CA1 a:OEX401 0.0 27.5 1.0
OD2 a:ASP170 2.4 26.2 1.0
O1 a:OEX401 2.4 25.1 1.0
O a:ALA344 2.5 29.4 1.0
O2 a:OEX401 2.5 27.3 1.0
O5 a:OEX401 2.8 28.1 1.0
CG a:ASP170 3.2 25.1 1.0
OE1 a:GLU189 3.2 28.6 1.0
MN2 a:OEX401 3.3 26.7 1.0
MN3 a:OEX401 3.4 25.5 1.0
C a:ALA344 3.4 29.3 1.0
MN1 a:OEX401 3.5 26.0 1.0
OD1 a:ASP170 3.5 25.9 1.0
OXT a:ALA344 3.7 29.4 1.0
MN4 a:OEX401 3.8 28.7 1.0
O3 a:OEX401 3.9 27.1 1.0
O4 a:OEX401 4.0 27.7 1.0
CD a:GLU189 4.0 27.2 1.0
NH1 c:ARG357 4.0 31.8 1.0
OE2 a:GLU189 4.1 26.6 1.0
NH2 c:ARG357 4.2 30.8 1.0
CB a:ASP170 4.5 23.9 1.0
CZ c:ARG357 4.6 30.5 1.0
OE1 a:GLN165 4.6 25.1 1.0
OH a:TYR161 4.7 23.5 1.0
OE1 c:GLU354 4.8 26.2 1.0
CA a:ALA344 4.8 28.9 1.0
OE2 c:GLU354 4.9 25.8 1.0
OD1 a:ASP342 5.0 24.4 1.0

Calcium binding site 6 out of 9 in 4pbu

Go back to Calcium Binding Sites List in 4pbu
Calcium binding site 6 out of 9 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca601

b:77.2
occ:1.00
OD1 b:ASN438 2.6 31.5 1.0
CG b:ASN438 3.8 28.2 1.0
ND2 b:ASN438 4.6 28.8 1.0
OE1 o:GLU181 4.7 46.0 1.0
CA b:ASN438 4.7 25.8 1.0
O b:SER439 4.7 23.8 1.0
CB b:ASN438 4.8 25.9 1.0
C b:ASN438 5.0 25.1 1.0

Calcium binding site 7 out of 9 in 4pbu

Go back to Calcium Binding Sites List in 4pbu
Calcium binding site 7 out of 9 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca901

b:46.5
occ:1.00
O c:THR24 2.4 44.6 1.0
OE1 c:GLU29 2.4 41.9 1.0
OG c:SER30 2.4 38.9 1.0
O c:PHE22 2.4 49.6 1.0
OD2 c:ASP27 2.5 39.6 1.0
OD1 c:ASP27 2.6 38.1 1.0
CG c:ASP27 2.9 39.4 1.0
C c:PHE22 3.5 49.7 1.0
CB c:SER30 3.5 37.8 1.0
CD c:GLU29 3.6 41.0 1.0
C c:THR24 3.6 44.4 1.0
N c:SER30 4.0 38.0 1.0
CA c:PHE22 4.1 50.5 1.0
OE2 c:GLU29 4.2 42.0 1.0
CB c:PHE22 4.2 50.6 1.0
N c:THR24 4.3 46.5 1.0
CA c:SER30 4.3 37.6 1.0
CA c:ASN25 4.4 42.4 1.0
C c:ALA23 4.4 47.4 1.0
CB c:ASP27 4.4 39.8 1.0
N c:ASN25 4.4 43.2 1.0
N c:ALA23 4.5 48.8 1.0
CA c:THR24 4.6 45.3 1.0
CB c:GLU29 4.7 39.4 1.0
CG c:GLU29 4.7 40.7 1.0
O c:ALA23 4.7 47.6 1.0
C c:ASN25 4.8 41.9 1.0
CA c:ALA23 4.8 48.1 1.0
C c:GLU29 4.9 38.5 1.0

Calcium binding site 8 out of 9 in 4pbu

Go back to Calcium Binding Sites List in 4pbu
Calcium binding site 8 out of 9 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Ca102

b:58.4
occ:1.00
OXT f:ARG45 2.5 38.0 1.0
O f:ARG45 3.0 38.5 1.0
C f:ARG45 3.2 38.3 1.0
OE2 v:GLU23 3.3 53.4 1.0
CD v:GLU23 4.3 52.6 1.0
OE1 v:GLU23 4.5 53.2 1.0
O a:ALA309 4.6 34.1 1.0
CA f:ARG45 4.7 38.2 1.0

Calcium binding site 9 out of 9 in 4pbu

Go back to Calcium Binding Sites List in 4pbu
Calcium binding site 9 out of 9 in the Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca301

b:51.6
occ:1.00
O o:THR138 2.3 48.8 1.0
O o:VAL201 2.5 43.4 1.0
OD1 o:ASN200 2.6 44.1 1.0
C o:THR138 3.3 49.0 1.0
CG o:ASN200 3.6 43.8 1.0
C o:VAL201 3.7 43.3 1.0
ND2 o:ASN200 4.1 44.4 1.0
N o:SER139 4.1 48.8 1.0
CA o:SER139 4.1 48.5 1.0
CA o:THR138 4.3 49.1 1.0
N o:VAL201 4.4 42.7 1.0
O o:THR140 4.5 46.8 1.0
N o:ALA202 4.6 43.8 1.0
CA o:VAL201 4.6 42.7 1.0
CA o:ALA202 4.6 44.5 1.0
C o:SER139 4.6 48.2 1.0
CB o:THR138 4.6 49.1 1.0
C o:ASN200 4.7 42.1 1.0
CB o:ASN200 5.0 41.9 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: ESSN 1476-4687
PubMed: 25043005
DOI: 10.1038/NATURE13453
Page generated: Sat Dec 12 05:03:52 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy