Atomistry » Manganese » PDB 4qsh-4u3o » 4rvy
Atomistry »
  Manganese »
    PDB 4qsh-4u3o »
      4rvy »

Manganese 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
Iron (Fe) 6 atoms
Calcium (Ca) 8 atoms
Chlorine (Cl) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 8 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4rvy

Go back to Manganese Binding Sites List in 4rvy
Manganese binding site 1 out of 8 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 Manganese with other atoms in the Mn 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:Mn601

b:22.6
occ:1.00
 MN1 A:OEX601 0.0 22.6 1.0
O3 A:OEX601 1.8 23.3 1.0
O1 A:OEX601 1.9 22.5 1.0
OE2 A:GLU189 1.9 25.1 1.0
NE2 A:HIS332 2.1 20.0 1.0
OD2 A:ASP342 2.3 23.5 1.0
O5 A:OEX601 2.6 24.1 1.0
MN2 A:OEX601 2.8 22.9 1.0
CD A:GLU189 2.9 24.6 1.0
CD2 A:HIS332 3.1 19.9 1.0
CE1 A:HIS332 3.1 22.8 1.0
CG A:ASP342 3.2 22.4 1.0
MN3 A:OEX601 3.3 23.5 1.0
OD1 A:ASP342 3.4 20.7 1.0
OE1 A:GLU189 3.5 26.4 1.0
CA1 A:OEX601 3.5 24.6 1.0
O2 A:OEX601 3.7 25.2 1.0
NE2 A:HIS337 3.9 22.7 1.0
OE1 A:GLU333 4.0 24.2 1.0
CG A:GLU189 4.1 23.9 1.0
ND1 A:HIS332 4.2 19.1 1.0
CG A:HIS332 4.2 20.4 1.0
CG1 A:VAL185 4.5 20.3 1.0
OXT A:ALA344 4.5 25.0 1.0
OE1 C:GLU354 4.5 22.6 1.0
CB A:ASP342 4.5 22.0 1.0
CE1 A:HIS337 4.6 20.6 1.0
OE2 C:GLU354 4.7 23.1 1.0
CD A:GLU333 4.8 21.8 1.0
O A:ALA344 4.9 25.6 1.0
CD2 A:HIS337 5.0 20.5 1.0
MN4 A:OEX601 5.0 26.3 1.0

Manganese binding site 2 out of 8 in 4rvy

Go back to Manganese Binding Sites List in 4rvy
Manganese binding site 2 out of 8 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 Manganese with other atoms in the Mn 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:Mn601

b:22.9
occ:1.00
 MN2 A:OEX601 0.0 22.9 1.0
OXT A:ALA344 2.0 25.0 1.0
O1 A:OEX601 2.1 22.5 1.0
OE1 C:GLU354 2.1 22.6 1.0
O3 A:OEX601 2.1 23.3 1.0
O2 A:OEX601 2.1 25.2 1.0
OD1 A:ASP342 2.1 20.7 1.0
MN1 A:OEX601 2.8 22.6 1.0
MN3 A:OEX601 2.9 23.5 1.0
C A:ALA344 3.0 25.1 1.0
CD C:GLU354 3.0 22.8 1.0
CG A:ASP342 3.1 22.4 1.0
OE2 C:GLU354 3.3 23.1 1.0
OD2 A:ASP342 3.3 23.5 1.0
O A:ALA344 3.3 25.6 1.0
CA1 A:OEX601 3.4 24.6 1.0
O5 A:OEX601 3.8 24.1 1.0
NE2 A:HIS337 3.8 22.7 1.0
CA A:ALA344 4.3 24.7 1.0
N A:ALA344 4.3 24.7 1.0
CD2 A:HIS337 4.3 20.5 1.0
CG C:GLU354 4.4 21.5 1.0
OE2 A:GLU189 4.4 25.1 1.0
CB A:ASP342 4.5 22.0 1.0
O4 A:OEX601 4.5 26.6 1.0
OE1 A:GLU333 4.6 24.2 1.0
NE2 A:HIS332 4.6 20.0 1.0
NH2 C:ARG357 4.7 23.9 1.0
CB C:GLU354 4.8 22.4 1.0
NH1 C:ARG357 4.8 26.4 1.0
CA A:ASP342 4.8 22.5 1.0
C A:ASP342 5.0 22.6 1.0

Manganese binding site 3 out of 8 in 4rvy

Go back to Manganese Binding Sites List in 4rvy
Manganese binding site 3 out of 8 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 Manganese with other atoms in the Mn 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
A:Mn601

b:23.5
occ:1.00
 MN3 A:OEX601 0.0 23.5 1.0
O2 A:OEX601 1.9 25.2 1.0
OE1 A:GLU333 2.1 24.2 1.0
O4 A:OEX601 2.1 26.6 1.0
O3 A:OEX601 2.1 23.3 1.0
OE2 C:GLU354 2.2 23.1 1.0
O5 A:OEX601 2.4 24.1 1.0
MN2 A:OEX601 2.9 22.9 1.0
MN4 A:OEX601 3.0 26.3 1.0
CD A:GLU333 3.0 21.8 1.0
CD C:GLU354 3.1 22.8 1.0
MN1 A:OEX601 3.3 22.6 1.0
OE2 A:GLU333 3.3 22.1 1.0
OE1 C:GLU354 3.4 22.6 1.0
CA1 A:OEX601 3.4 24.6 1.0
O1 A:OEX601 3.5 22.5 1.0
NH2 C:ARG357 4.0 23.9 1.0
NE2 A:HIS337 4.1 22.7 1.0
OD2 A:ASP170 4.2 23.1 1.0
NE2 A:HIS332 4.2 20.0 1.0
CG A:GLU333 4.4 21.6 1.0
OD1 A:ASP170 4.4 23.9 1.0
OXT A:ALA344 4.4 25.0 1.0
CD2 A:HIS332 4.5 19.9 1.0
CG C:GLU354 4.5 21.5 1.0
OD1 A:ASP342 4.7 20.7 1.0
CE1 A:HIS337 4.7 20.6 1.0
CG A:ASP170 4.7 22.6 1.0
CB A:GLU333 4.8 21.0 1.0
O A:ALA344 4.8 25.6 1.0
OD2 A:ASP342 4.9 23.5 1.0
OE2 A:GLU189 4.9 25.1 1.0

Manganese binding site 4 out of 8 in 4rvy

Go back to Manganese Binding Sites List in 4rvy
Manganese binding site 4 out of 8 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 Manganese with other atoms in the Mn 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
A:Mn601

b:26.3
occ:1.00
 MN4 A:OEX601 0.0 26.3 1.0
OD2 A:ASP170 2.1 23.1 1.0
O4 A:OEX601 2.1 26.6 1.0
OE2 A:GLU333 2.2 22.1 1.0
O5 A:OEX601 2.5 24.1 1.0
MN3 A:OEX601 3.0 23.5 1.0
CD A:GLU333 3.1 21.8 1.0
CG A:ASP170 3.2 22.6 1.0
OE1 A:GLU333 3.3 24.2 1.0
OD1 A:ASP170 3.8 23.9 1.0
O2 A:OEX601 3.8 25.2 1.0
CA1 A:OEX601 3.8 24.6 1.0
OD1 A:ASP61 4.1 23.3 1.0
O A:SER169 4.3 20.6 1.0
CB A:ASP170 4.4 21.7 1.0
CG A:GLU333 4.5 21.6 1.0
CA A:ASP170 4.5 21.5 1.0
NH2 C:ARG357 4.7 23.9 1.0
O3 A:OEX601 4.7 23.3 1.0
OE2 C:GLU354 4.9 23.1 1.0
C A:SER169 4.9 20.3 1.0
N A:ASP170 5.0 20.9 1.0
MN1 A:OEX601 5.0 22.6 1.0

Manganese binding site 5 out of 8 in 4rvy

Go back to Manganese Binding Sites List in 4rvy
Manganese binding site 5 out of 8 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 Manganese with other atoms in the Mn 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
a:Mn601

b:22.6
occ:1.00
 MN1 a:OEX601 0.0 22.6 1.0
O3 a:OEX601 1.8 23.3 1.0
O1 a:OEX601 1.9 22.5 1.0
OE2 a:GLU189 1.9 25.1 1.0
NE2 a:HIS332 2.1 20.0 1.0
OD2 a:ASP342 2.3 23.5 1.0
O5 a:OEX601 2.6 24.1 1.0
MN2 a:OEX601 2.8 22.9 1.0
CD a:GLU189 2.9 24.6 1.0
CD2 a:HIS332 3.1 19.9 1.0
CE1 a:HIS332 3.1 22.8 1.0
CG a:ASP342 3.2 22.4 1.0
MN3 a:OEX601 3.3 23.5 1.0
OD1 a:ASP342 3.4 20.7 1.0
OE1 a:GLU189 3.5 26.4 1.0
CA1 a:OEX601 3.5 24.6 1.0
O2 a:OEX601 3.7 25.2 1.0
NE2 a:HIS337 3.9 22.7 1.0
OE1 a:GLU333 4.0 24.2 1.0
CG a:GLU189 4.1 23.9 1.0
ND1 a:HIS332 4.2 19.1 1.0
CG a:HIS332 4.2 20.4 1.0
CG1 a:VAL185 4.5 20.3 1.0
OXT a:ALA344 4.5 25.0 1.0
OE1 c:GLU354 4.5 22.6 1.0
CB a:ASP342 4.5 22.0 1.0
CE1 a:HIS337 4.6 20.6 1.0
OE2 c:GLU354 4.7 23.1 1.0
CD a:GLU333 4.8 21.8 1.0
O a:ALA344 4.9 25.6 1.0
CD2 a:HIS337 5.0 20.5 1.0
MN4 a:OEX601 5.0 26.3 1.0

Manganese binding site 6 out of 8 in 4rvy

Go back to Manganese Binding Sites List in 4rvy
Manganese binding site 6 out of 8 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 Manganese with other atoms in the Mn 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
a:Mn601

b:22.9
occ:1.00
 MN2 a:OEX601 0.0 22.9 1.0
OXT a:ALA344 2.0 25.0 1.0
O1 a:OEX601 2.1 22.5 1.0
OE1 c:GLU354 2.1 22.6 1.0
O3 a:OEX601 2.1 23.3 1.0
O2 a:OEX601 2.1 25.2 1.0
OD1 a:ASP342 2.1 20.7 1.0
MN1 a:OEX601 2.8 22.6 1.0
MN3 a:OEX601 2.9 23.5 1.0
C a:ALA344 3.0 25.1 1.0
CD c:GLU354 3.0 22.8 1.0
CG a:ASP342 3.1 22.4 1.0
OE2 c:GLU354 3.3 23.1 1.0
OD2 a:ASP342 3.3 23.5 1.0
O a:ALA344 3.3 25.6 1.0
CA1 a:OEX601 3.4 24.6 1.0
O5 a:OEX601 3.8 24.1 1.0
NE2 a:HIS337 3.8 22.7 1.0
CA a:ALA344 4.3 24.7 1.0
N a:ALA344 4.3 24.7 1.0
CD2 a:HIS337 4.3 20.5 1.0
CG c:GLU354 4.4 21.5 1.0
OE2 a:GLU189 4.4 25.1 1.0
CB a:ASP342 4.5 22.0 1.0
O4 a:OEX601 4.5 26.6 1.0
OE1 a:GLU333 4.6 24.2 1.0
NE2 a:HIS332 4.6 20.0 1.0
NH2 c:ARG357 4.7 23.9 1.0
CB c:GLU354 4.8 22.4 1.0
NH1 c:ARG357 4.8 26.4 1.0
CA a:ASP342 4.8 22.5 1.0
C a:ASP342 5.0 22.6 1.0

Manganese binding site 7 out of 8 in 4rvy

Go back to Manganese Binding Sites List in 4rvy
Manganese binding site 7 out of 8 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 Manganese with other atoms in the Mn binding site number 7 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:Mn601

b:23.5
occ:1.00
 MN3 a:OEX601 0.0 23.5 1.0
O2 a:OEX601 1.9 25.2 1.0
OE1 a:GLU333 2.1 24.2 1.0
O4 a:OEX601 2.1 26.6 1.0
O3 a:OEX601 2.1 23.3 1.0
OE2 c:GLU354 2.2 23.1 1.0
O5 a:OEX601 2.4 24.1 1.0
MN2 a:OEX601 2.9 22.9 1.0
MN4 a:OEX601 3.0 26.3 1.0
CD a:GLU333 3.0 21.8 1.0
CD c:GLU354 3.1 22.8 1.0
MN1 a:OEX601 3.3 22.6 1.0
OE2 a:GLU333 3.3 22.1 1.0
OE1 c:GLU354 3.4 22.6 1.0
CA1 a:OEX601 3.4 24.6 1.0
O1 a:OEX601 3.5 22.5 1.0
NH2 c:ARG357 4.0 23.9 1.0
NE2 a:HIS337 4.1 22.7 1.0
OD2 a:ASP170 4.2 23.1 1.0
NE2 a:HIS332 4.2 20.0 1.0
CG a:GLU333 4.4 21.6 1.0
OD1 a:ASP170 4.4 23.9 1.0
OXT a:ALA344 4.4 25.0 1.0
CD2 a:HIS332 4.5 19.9 1.0
CG c:GLU354 4.5 21.5 1.0
OD1 a:ASP342 4.7 20.7 1.0
CE1 a:HIS337 4.7 20.6 1.0
CG a:ASP170 4.7 22.6 1.0
CB a:GLU333 4.8 21.0 1.0
O a:ALA344 4.8 25.6 1.0
OD2 a:ASP342 4.9 23.5 1.0
OE2 a:GLU189 4.9 25.1 1.0

Manganese binding site 8 out of 8 in 4rvy

Go back to Manganese Binding Sites List in 4rvy
Manganese binding site 8 out of 8 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 Manganese with other atoms in the Mn binding site number 8 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:Mn601

b:26.3
occ:1.00
 MN4 a:OEX601 0.0 26.3 1.0
OD2 a:ASP170 2.1 23.1 1.0
O4 a:OEX601 2.1 26.6 1.0
OE2 a:GLU333 2.2 22.1 1.0
O5 a:OEX601 2.5 24.1 1.0
MN3 a:OEX601 3.0 23.5 1.0
CD a:GLU333 3.1 21.8 1.0
CG a:ASP170 3.2 22.6 1.0
OE1 a:GLU333 3.3 24.2 1.0
OD1 a:ASP170 3.8 23.9 1.0
O2 a:OEX601 3.8 25.2 1.0
CA1 a:OEX601 3.8 24.6 1.0
OD1 a:ASP61 4.1 23.3 1.0
O a:SER169 4.3 20.6 1.0
CB a:ASP170 4.5 21.7 1.0
CG a:GLU333 4.5 21.6 1.0
CA a:ASP170 4.5 21.5 1.0
NH2 c:ARG357 4.7 23.9 1.0
O3 a:OEX601 4.7 23.3 1.0
OE2 c:GLU354 4.9 23.1 1.0
C a:SER169 4.9 20.3 1.0
N a:ASP170 5.0 20.9 1.0
MN1 a:OEX601 5.0 22.6 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: Tue Dec 15 04:29:04 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