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Manganese in PDB 5kaf: Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution

Enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution

All present enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution, PDB code: 5kaf was solved by I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori, F.Fuller, T.Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.-C.Weng, M.S.Hunter, A.Aquila, J.E.Koglin, J.Robinson, M.Liang, S.Boutet, A.Y.Lyubimov, M.Uervirojnangkoorn, N.W.Moriarty, D.Liebschner, P.V.Afonine, D.G.Waterman, G.Evans, H.Dobbek, W.I.Weis, A.T.Brunger, P.H.Zwart, P.D.Adams, A.Zouni, J.Messinger, U.Bergmann, N.K.Sauter, J.Kern, V.K.Yachandra, J.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.12 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.731, 223.815, 330.818, 90.00, 90.00, 90.00
R / Rfree (%) 26.4 / 30.3

Other elements in 5kaf:

The structure of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution (pdb code 5kaf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution, PDB code: 5kaf:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5kaf

Go back to Manganese Binding Sites List in 5kaf
Manganese binding site 1 out of 8 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:37.5
occ:1.00
 MN1 A:OEX601 0.0 37.5 1.0
OE2 A:GLU189 1.8 32.4 1.0
O1 A:OEX601 1.8 40.6 1.0
O3 A:OEX601 1.9 38.7 1.0
NE2 A:HIS332 2.1 39.4 1.0
OD2 A:ASP342 2.2 35.1 1.0
MN2 A:OEX601 2.7 46.2 1.0
O5 A:OEX601 2.7 33.7 1.0
CE1 A:HIS332 2.8 39.0 1.0
CD A:GLU189 3.0 32.0 1.0
CG A:ASP342 3.2 41.7 1.0
MN3 A:OEX601 3.2 38.7 1.0
CD2 A:HIS332 3.3 31.9 1.0
OD1 A:ASP342 3.4 42.3 1.0
CA1 A:OEX601 3.5 45.8 1.0
O2 A:OEX601 3.6 43.1 1.0
OE1 A:GLU189 3.7 41.7 1.0
CG A:GLU189 3.9 34.7 1.0
ND1 A:HIS332 4.0 32.1 1.0
OXT A:ALA344 4.1 33.1 1.0
NE2 A:HIS337 4.1 38.7 1.0
CG A:HIS332 4.2 38.3 1.0
OE1 A:GLU333 4.3 51.5 1.0
OE1 C:GLU354 4.5 36.6 1.0
CB A:ASP342 4.5 41.7 1.0
CE1 A:HIS337 4.6 36.3 1.0
O A:HOH706 4.7 32.0 1.0
OE2 C:GLU354 4.7 41.3 1.0
CG1 A:VAL185 4.8 31.0 1.0
CD A:GLU333 4.8 42.9 1.0
C A:ALA344 4.8 37.7 1.0
O4 A:OEX601 4.9 41.1 1.0
MN4 A:OEX601 4.9 43.9 1.0
O A:ALA344 5.0 44.6 1.0
CD C:GLU354 5.0 36.9 1.0

Manganese binding site 2 out of 8 in 5kaf

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Manganese binding site 2 out of 8 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:46.2
occ:1.00
 MN2 A:OEX601 0.0 46.2 1.0
O1 A:OEX601 1.8 40.6 1.0
O2 A:OEX601 1.8 43.1 1.0
OXT A:ALA344 1.9 33.1 1.0
O3 A:OEX601 2.0 38.7 1.0
OE1 C:GLU354 2.1 36.6 1.0
OD1 A:ASP342 2.2 42.3 1.0
MN1 A:OEX601 2.7 37.5 1.0
MN3 A:OEX601 2.7 38.7 1.0
CD C:GLU354 3.0 36.9 1.0
CG A:ASP342 3.0 41.7 1.0
C A:ALA344 3.0 37.7 1.0
OD2 A:ASP342 3.1 35.1 1.0
OE2 C:GLU354 3.1 41.3 1.0
CA1 A:OEX601 3.3 45.8 1.0
O A:ALA344 3.6 44.6 1.0
NE2 A:HIS337 3.6 38.7 1.0
O5 A:OEX601 3.7 33.7 1.0
OE2 A:GLU189 4.1 32.4 1.0
O4 A:OEX601 4.1 41.1 1.0
CA A:ALA344 4.2 32.2 1.0
N A:ALA344 4.2 38.0 1.0
OE1 A:GLU333 4.3 51.5 1.0
NE2 A:HIS332 4.3 39.4 1.0
CG C:GLU354 4.4 33.6 1.0
CD2 A:HIS337 4.4 38.2 1.0
CB A:ASP342 4.4 41.7 1.0
CE1 A:HIS337 4.7 36.3 1.0
CD A:GLU189 4.9 32.0 1.0
CA A:ASP342 4.9 37.3 1.0
CB C:GLU354 4.9 44.3 1.0
CE1 A:HIS332 5.0 39.0 1.0
C A:ASP342 5.0 35.4 1.0

Manganese binding site 3 out of 8 in 5kaf

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Manganese binding site 3 out of 8 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:38.7
occ:1.00
 MN3 A:OEX601 0.0 38.7 1.0
O2 A:OEX601 1.9 43.1 1.0
O4 A:OEX601 1.9 41.1 1.0
OE1 A:GLU333 2.0 51.5 1.0
O3 A:OEX601 2.1 38.7 1.0
OE2 C:GLU354 2.1 41.3 1.0
O5 A:OEX601 2.2 33.7 1.0
MN2 A:OEX601 2.7 46.2 1.0
CD A:GLU333 2.8 42.9 1.0
OE2 A:GLU333 2.9 34.5 1.0
MN4 A:OEX601 2.9 43.9 1.0
CD C:GLU354 3.1 36.9 1.0
MN1 A:OEX601 3.2 37.5 1.0
OE1 C:GLU354 3.3 36.6 1.0
CA1 A:OEX601 3.4 45.8 1.0
O1 A:OEX601 3.5 40.6 1.0
NE2 A:HIS332 3.8 39.4 1.0
OXT A:ALA344 4.0 33.1 1.0
OD2 A:ASP170 4.0 42.8 1.0
NE2 A:HIS337 4.1 38.7 1.0
CG A:GLU333 4.2 36.2 1.0
O A:HOH702 4.2 47.8 1.0
NH2 C:ARG357 4.2 41.6 1.0
CD2 A:HIS332 4.3 31.9 1.0
CG C:GLU354 4.4 33.6 1.0
OE2 A:GLU189 4.4 32.4 1.0
CE1 A:HIS337 4.5 36.3 1.0
O A:HOH706 4.5 32.0 1.0
O A:HOH709 4.6 27.9 1.0
CB A:GLU333 4.7 36.1 1.0
OD1 A:ASP342 4.7 42.3 1.0
O A:ALA344 4.7 44.6 1.0
OD1 A:ASP170 4.8 55.4 1.0
OD2 A:ASP342 4.8 35.1 1.0
CG A:ASP170 4.8 43.4 1.0
C A:ALA344 4.9 37.7 1.0
CE1 A:HIS332 5.0 39.0 1.0

Manganese binding site 4 out of 8 in 5kaf

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Manganese binding site 4 out of 8 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:43.9
occ:1.00
 MN4 A:OEX601 0.0 43.9 1.0
O A:HOH702 1.9 47.8 1.0
O4 A:OEX601 2.0 41.1 1.0
OD2 A:ASP170 2.0 42.8 1.0
OE2 A:GLU333 2.1 34.5 1.0
O A:HOH709 2.2 27.9 1.0
O5 A:OEX601 2.3 33.7 1.0
MN3 A:OEX601 2.9 38.7 1.0
O A:HOH706 3.1 32.0 1.0
CD A:GLU333 3.2 42.9 1.0
CG A:ASP170 3.2 43.4 1.0
OE1 A:GLU333 3.6 51.5 1.0
CA1 A:OEX601 3.8 45.8 1.0
OD1 A:ASP170 3.8 55.4 1.0
O2 A:OEX601 3.9 43.1 1.0
OD1 A:ASP61 4.3 41.6 1.0
CA A:ASP170 4.4 43.4 1.0
CB A:ASP170 4.4 39.8 1.0
NH2 C:ARG357 4.4 41.6 1.0
CG A:GLU333 4.5 36.2 1.0
OE2 C:GLU354 4.5 41.3 1.0
O3 A:OEX601 4.6 38.7 1.0
O A:SER169 4.7 35.1 1.0
N A:ASP170 4.9 39.7 1.0
MN1 A:OEX601 4.9 37.5 1.0

Manganese binding site 5 out of 8 in 5kaf

Go back to Manganese Binding Sites List in 5kaf
Manganese binding site 5 out of 8 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:40.4
occ:1.00
 MN1 a:OEX601 0.0 40.4 1.0
OE2 a:GLU189 1.8 35.2 1.0
O1 a:OEX601 1.8 51.1 1.0
O3 a:OEX601 1.9 48.8 1.0
NE2 a:HIS332 2.1 34.0 1.0
OD2 a:ASP342 2.2 51.0 1.0
MN2 a:OEX601 2.7 40.8 1.0
O5 a:OEX601 2.7 45.9 1.0
CD a:GLU189 2.7 37.5 1.0
CE1 a:HIS332 2.9 40.9 1.0
OE1 a:GLU189 3.1 58.7 1.0
MN3 a:OEX601 3.2 44.2 1.0
CD2 a:HIS332 3.2 38.4 1.0
CG a:ASP342 3.3 55.1 1.0
CA1 a:OEX601 3.5 49.0 1.0
O2 a:OEX601 3.6 41.6 1.0
OD1 a:ASP342 3.7 56.2 1.0
ND1 a:HIS332 4.0 42.8 1.0
OXT a:ALA344 4.0 52.8 1.0
CG a:GLU189 4.1 36.4 1.0
CG a:HIS332 4.2 38.2 1.0
OE1 a:GLU333 4.2 50.1 1.0
NE2 a:HIS337 4.3 44.9 1.0
OE1 c:GLU354 4.4 31.6 1.0
O a:HOH711 4.5 34.7 1.0
CB a:ASP342 4.6 51.2 1.0
CG1 a:VAL185 4.7 29.4 1.0
OE2 c:GLU354 4.7 40.9 1.0
CD a:GLU333 4.8 37.2 1.0
C a:ALA344 4.8 54.5 1.0
CE1 a:HIS337 4.8 43.0 1.0
O4 a:OEX601 4.9 46.8 1.0
O a:ALA344 4.9 54.6 1.0
MN4 a:OEX601 4.9 43.7 1.0
CD c:GLU354 5.0 38.7 1.0

Manganese binding site 6 out of 8 in 5kaf

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Manganese binding site 6 out of 8 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:40.8
occ:1.00
 MN2 a:OEX601 0.0 40.8 1.0
O1 a:OEX601 1.8 51.1 1.0
O2 a:OEX601 1.8 41.6 1.0
OXT a:ALA344 1.9 52.8 1.0
O3 a:OEX601 2.0 48.8 1.0
OE1 c:GLU354 2.1 31.6 1.0
OD1 a:ASP342 2.2 56.2 1.0
MN1 a:OEX601 2.7 40.4 1.0
MN3 a:OEX601 2.7 44.2 1.0
OD2 a:ASP342 2.8 51.0 1.0
CG a:ASP342 2.8 55.1 1.0
CD c:GLU354 3.0 38.7 1.0
C a:ALA344 3.1 54.5 1.0
OE2 c:GLU354 3.2 40.9 1.0
CA1 a:OEX601 3.3 49.0 1.0
O a:ALA344 3.6 54.6 1.0
O5 a:OEX601 3.7 45.9 1.0
NE2 a:HIS337 4.0 44.9 1.0
O4 a:OEX601 4.1 46.8 1.0
OE2 a:GLU189 4.2 35.2 1.0
CA a:ALA344 4.3 51.9 1.0
OE1 a:GLU333 4.3 50.1 1.0
N a:ALA344 4.3 50.3 1.0
NE2 a:HIS332 4.3 34.0 1.0
CB a:ASP342 4.3 51.2 1.0
OE1 a:GLU189 4.4 58.7 1.0
CG c:GLU354 4.4 44.3 1.0
CD2 a:HIS337 4.7 38.8 1.0
CD a:GLU189 4.7 37.5 1.0
CB c:GLU354 4.9 42.0 1.0
CA a:ASP342 4.9 50.2 1.0

Manganese binding site 7 out of 8 in 5kaf

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Manganese binding site 7 out of 8 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:44.2
occ:1.00
 MN3 a:OEX601 0.0 44.2 1.0
O2 a:OEX601 1.9 41.6 1.0
O4 a:OEX601 1.9 46.8 1.0
OE1 a:GLU333 2.1 50.1 1.0
O3 a:OEX601 2.1 48.8 1.0
OE2 c:GLU354 2.1 40.9 1.0
O5 a:OEX601 2.2 45.9 1.0
MN2 a:OEX601 2.7 40.8 1.0
CD a:GLU333 2.8 37.2 1.0
MN4 a:OEX601 2.9 43.7 1.0
OE2 a:GLU333 2.9 36.0 1.0
CD c:GLU354 3.0 38.7 1.0
MN1 a:OEX601 3.2 40.4 1.0
OE1 c:GLU354 3.3 31.6 1.0
CA1 a:OEX601 3.4 49.0 1.0
O1 a:OEX601 3.5 51.1 1.0
NE2 a:HIS332 3.8 34.0 1.0
O a:HOH701 4.0 40.7 1.0
OXT a:ALA344 4.1 52.8 1.0
OD2 a:ASP170 4.1 46.5 1.0
CG a:GLU333 4.2 33.7 1.0
CD2 a:HIS332 4.2 38.4 1.0
NH2 c:ARG357 4.3 33.6 1.0
NE2 a:HIS337 4.4 44.9 1.0
CG c:GLU354 4.4 44.3 1.0
OD2 a:ASP342 4.6 51.0 1.0
CB a:GLU333 4.7 34.1 1.0
OE2 a:GLU189 4.7 35.2 1.0
OD1 a:ASP342 4.7 56.2 1.0
OD1 a:ASP170 4.8 41.9 1.0
O a:ALA344 4.8 54.6 1.0
CG a:ASP170 4.9 45.2 1.0
CE1 a:HIS337 4.9 43.0 1.0
C a:ALA344 4.9 54.5 1.0
O a:HOH707 5.0 38.6 1.0

Manganese binding site 8 out of 8 in 5kaf

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Manganese binding site 8 out of 8 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn601

b:43.7
occ:1.00
 MN4 a:OEX601 0.0 43.7 1.0
O4 a:OEX601 2.0 46.8 1.0
OD2 a:ASP170 2.0 46.5 1.0
OE2 a:GLU333 2.1 36.0 1.0
O a:HOH701 2.1 40.7 1.0
O5 a:OEX601 2.3 45.9 1.0
O a:HOH707 2.4 38.6 1.0
MN3 a:OEX601 2.9 44.2 1.0
CD a:GLU333 3.2 37.2 1.0
CG a:ASP170 3.2 45.2 1.0
OE1 a:GLU333 3.6 50.1 1.0
CA1 a:OEX601 3.8 49.0 1.0
OD1 a:ASP170 3.8 41.9 1.0
O2 a:OEX601 3.9 41.6 1.0
O a:HOH711 4.2 34.7 1.0
OD1 a:ASP61 4.2 33.6 1.0
CA a:ASP170 4.3 34.9 1.0
CB a:ASP170 4.3 40.7 1.0
CG a:GLU333 4.4 33.7 1.0
OE2 c:GLU354 4.5 40.9 1.0
O3 a:OEX601 4.6 48.8 1.0
NH2 c:ARG357 4.6 33.6 1.0
O a:SER169 4.8 42.2 1.0
N a:ASP170 4.8 33.1 1.0
MN1 a:OEX601 4.9 40.4 1.0

Reference:

I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, F.D.Fuller, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori, T.Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, R.Hussein, M.Zhang, L.Douthit, M.Kubin, C.De Lichtenberg, L.Vo Pham, H.Nilsson, M.H.Cheah, D.Shevela, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.C.Weng, E.Pastor, C.Weninger, T.Fransson, L.Lassalle, P.Brauer, P.Aller, P.T.Docker, B.Andi, A.M.Orville, J.M.Glownia, S.Nelson, M.Sikorski, D.Zhu, M.S.Hunter, T.J.Lane, A.Aquila, J.E.Koglin, J.Robinson, M.Liang, S.Boutet, A.Y.Lyubimov, M.Uervirojnangkoorn, N.W.Moriarty, D.Liebschner, P.V.Afonine, D.G.Waterman, G.Evans, P.Wernet, H.Dobbek, W.I.Weis, A.T.Brunger, P.H.Zwart, P.D.Adams, A.Zouni, J.Messinger, U.Bergmann, N.K.Sauter, J.Kern, V.K.Yachandra, J.Yano. Structure of Photosystem II and Substrate Binding at Room Temperature. Nature V. 540 453 2016.
ISSN: ESSN 1476-4687
PubMed: 27871088
DOI: 10.1038/NATURE20161
Page generated: Tue Dec 15 04:42:45 2020

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