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Manganese in PDB 5kai: NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution

Enzymatic activity of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution

All present enzymatic activity of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution:
1.10.3.9;

Protein crystallography data

The structure of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution, PDB code: 5kai 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) 43.57 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.911, 224.268, 330.996, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 30

Other elements in 5kai:

The structure of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 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 NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution (pdb code 5kai). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution, PDB code: 5kai:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5kai

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Manganese binding site 1 out of 8 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:54.3
occ:1.00
 MN1 A:OEX601 0.0 54.3 1.0
OE2 A:GLU189 1.8 49.8 1.0
O1 A:OEX601 1.8 56.5 1.0
O3 A:OEX601 1.9 56.4 1.0
NE2 A:HIS332 2.1 48.5 1.0
OD2 A:ASP342 2.2 50.2 1.0
MN2 A:OEX601 2.7 51.3 1.0
O5 A:OEX601 2.7 56.4 1.0
CD A:GLU189 3.0 47.3 1.0
CD2 A:HIS332 3.0 45.1 1.0
CE1 A:HIS332 3.1 46.0 1.0
MN3 A:OEX601 3.2 59.5 1.0
CG A:ASP342 3.3 48.4 1.0
CA1 A:OEX601 3.5 42.4 1.0
O2 A:OEX601 3.6 48.5 1.0
OD1 A:ASP342 3.6 50.4 1.0
OE1 A:GLU189 3.8 47.5 1.0
CG A:GLU189 4.1 41.9 1.0
NE2 A:HIS337 4.1 48.9 1.0
CG A:HIS332 4.2 47.8 1.0
ND1 A:HIS332 4.2 46.8 1.0
OXT A:ALA344 4.2 48.8 1.0
OE1 A:GLU333 4.3 54.6 1.0
O A:HOH703 4.3 41.1 1.0
CG1 A:VAL185 4.5 34.6 1.0
CB A:ASP342 4.6 45.5 1.0
OE2 C:GLU354 4.6 55.9 1.0
OE1 C:GLU354 4.6 51.0 1.0
O A:HOH710 4.6 47.8 1.0
CE1 A:HIS337 4.8 48.3 1.0
O A:ALA344 4.8 55.8 1.0
C A:ALA344 4.8 47.6 1.0
CD A:GLU333 4.9 53.6 1.0
O4 A:OEX601 4.9 52.8 1.0
MN4 A:OEX601 4.9 60.4 1.0
CD C:GLU354 5.0 48.7 1.0

Manganese binding site 2 out of 8 in 5kai

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Manganese binding site 2 out of 8 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:51.3
occ:1.00
 MN2 A:OEX601 0.0 51.3 1.0
O1 A:OEX601 1.8 56.5 1.0
O2 A:OEX601 1.8 48.5 1.0
OXT A:ALA344 1.9 48.8 1.0
O3 A:OEX601 2.0 56.4 1.0
OE1 C:GLU354 2.1 51.0 1.0
OD1 A:ASP342 2.2 50.4 1.0
MN1 A:OEX601 2.7 54.3 1.0
MN3 A:OEX601 2.7 59.5 1.0
CD C:GLU354 2.9 48.7 1.0
CG A:ASP342 2.9 48.4 1.0
OD2 A:ASP342 2.9 50.2 1.0
OE2 C:GLU354 2.9 55.9 1.0
C A:ALA344 2.9 47.6 1.0
O A:ALA344 3.3 55.8 1.0
CA1 A:OEX601 3.3 42.4 1.0
O5 A:OEX601 3.7 56.4 1.0
NE2 A:HIS337 3.8 48.9 1.0
OE2 A:GLU189 3.9 49.8 1.0
O4 A:OEX601 4.1 52.8 1.0
CA A:ALA344 4.2 45.6 1.0
CG C:GLU354 4.3 47.6 1.0
N A:ALA344 4.3 52.1 1.0
OE1 A:GLU333 4.3 54.6 1.0
CB A:ASP342 4.3 45.5 1.0
NE2 A:HIS332 4.4 48.5 1.0
CD2 A:HIS337 4.4 48.2 1.0
O A:HOH710 4.8 47.8 1.0
CD A:GLU189 4.8 47.3 1.0
CA A:ASP342 4.9 44.7 1.0
CB C:GLU354 4.9 50.5 1.0
CE1 A:HIS337 4.9 48.3 1.0
OD1 A:ASP170 5.0 54.0 1.0

Manganese binding site 3 out of 8 in 5kai

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Manganese binding site 3 out of 8 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:59.5
occ:1.00
 MN3 A:OEX601 0.0 59.5 1.0
O2 A:OEX601 1.9 48.5 1.0
O4 A:OEX601 1.9 52.8 1.0
OE1 A:GLU333 2.0 54.6 1.0
O3 A:OEX601 2.1 56.4 1.0
OE2 C:GLU354 2.1 55.9 1.0
O5 A:OEX601 2.2 56.4 1.0
MN2 A:OEX601 2.7 51.3 1.0
CD A:GLU333 2.8 53.6 1.0
MN4 A:OEX601 2.9 60.4 1.0
OE2 A:GLU333 3.0 55.7 1.0
CD C:GLU354 3.1 48.7 1.0
MN1 A:OEX601 3.2 54.3 1.0
CA1 A:OEX601 3.4 42.4 1.0
OE1 C:GLU354 3.5 51.0 1.0
O1 A:OEX601 3.5 56.5 1.0
OD2 A:ASP170 4.1 52.0 1.0
OXT A:ALA344 4.1 48.8 1.0
NE2 A:HIS337 4.2 48.9 1.0
OD1 A:ASP170 4.2 54.0 1.0
NE2 A:HIS332 4.2 48.5 1.0
CG A:GLU333 4.2 44.7 1.0
NH2 C:ARG357 4.2 51.1 1.0
O A:HOH701 4.3 44.3 1.0
CD2 A:HIS332 4.4 45.1 1.0
CG C:GLU354 4.5 47.6 1.0
OE2 A:GLU189 4.5 49.8 1.0
CG A:ASP170 4.6 50.0 1.0
O A:ALA344 4.6 55.8 1.0
O A:HOH707 4.6 47.7 1.0
CB A:GLU333 4.7 46.6 1.0
OD1 A:ASP342 4.7 50.4 1.0
OD2 A:ASP342 4.7 50.2 1.0
CE1 A:HIS337 4.7 48.3 1.0
C A:ALA344 4.8 47.6 1.0

Manganese binding site 4 out of 8 in 5kai

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Manganese binding site 4 out of 8 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:60.4
occ:1.00
 MN4 A:OEX601 0.0 60.4 1.0
O4 A:OEX601 2.0 52.8 1.0
OD2 A:ASP170 2.0 52.0 1.0
O A:HOH707 2.1 47.7 1.0
OE2 A:GLU333 2.1 55.7 1.0
O A:HOH701 2.2 44.3 1.0
O5 A:OEX601 2.3 56.4 1.0
MN3 A:OEX601 2.9 59.5 1.0
CG A:ASP170 3.0 50.0 1.0
CD A:GLU333 3.1 53.6 1.0
OD1 A:ASP170 3.3 54.0 1.0
OE1 A:GLU333 3.5 54.6 1.0
CA1 A:OEX601 3.8 42.4 1.0
O2 A:OEX601 3.9 48.5 1.0
O A:HOH703 4.2 41.1 1.0
CB A:ASP170 4.2 44.1 1.0
O A:HOH711 4.3 40.3 1.0
CG A:GLU333 4.4 44.7 1.0
CA A:ASP170 4.4 43.1 1.0
O A:SER169 4.6 53.5 1.0
OE2 C:GLU354 4.6 55.9 1.0
O3 A:OEX601 4.6 56.4 1.0
OD1 A:ASP61 4.7 41.2 1.0
NH2 C:ARG357 4.8 51.1 1.0
N A:ASP170 4.9 39.3 1.0
MN1 A:OEX601 4.9 54.3 1.0
C A:SER169 5.0 46.3 1.0

Manganese binding site 5 out of 8 in 5kai

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Manganese binding site 5 out of 8 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn702

b:48.3
occ:1.00
 MN1 a:OEX702 0.0 48.3 1.0
OE2 a:GLU189 1.8 53.5 1.0
O1 a:OEX702 1.8 60.2 1.0
O3 a:OEX702 1.9 58.2 1.0
NE2 a:HIS332 2.1 49.8 1.0
OD2 a:ASP342 2.2 52.4 1.0
CD a:GLU189 2.6 46.9 1.0
MN2 a:OEX702 2.7 59.4 1.0
O5 a:OEX702 2.7 52.6 1.0
OE1 a:GLU189 3.0 55.3 1.0
CD2 a:HIS332 3.0 46.5 1.0
CE1 a:HIS332 3.1 45.7 1.0
MN3 a:OEX702 3.2 51.0 1.0
CG a:ASP342 3.3 51.0 1.0
CA1 a:OEX702 3.5 47.9 1.0
O2 a:OEX702 3.6 53.0 1.0
OD1 a:ASP342 3.6 61.2 1.0
CG a:GLU189 4.0 47.6 1.0
OXT a:ALA344 4.2 50.5 1.0
ND1 a:HIS332 4.2 46.1 1.0
NE2 a:HIS337 4.2 56.8 1.0
CG a:HIS332 4.2 44.9 1.0
OE1 a:GLU333 4.4 62.4 1.0
CG1 a:VAL185 4.4 42.4 1.0
OE2 c:GLU354 4.5 52.5 1.0
O a:HOH808 4.5 49.7 1.0
OE1 c:GLU354 4.6 50.0 1.0
CB a:ASP342 4.6 43.7 1.0
O a:HOH803 4.6 48.8 1.0
CE1 a:HIS337 4.7 54.1 1.0
O a:ALA344 4.8 58.6 1.0
C a:ALA344 4.8 51.8 1.0
O4 a:OEX702 4.9 44.7 1.0
CD a:GLU333 4.9 46.4 1.0
CD c:GLU354 4.9 52.2 1.0
MN4 a:OEX702 4.9 56.0 1.0

Manganese binding site 6 out of 8 in 5kai

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Manganese binding site 6 out of 8 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn702

b:59.4
occ:1.00
 MN2 a:OEX702 0.0 59.4 1.0
O1 a:OEX702 1.8 60.2 1.0
O2 a:OEX702 1.8 53.0 1.0
OXT a:ALA344 1.9 50.5 1.0
O3 a:OEX702 2.0 58.2 1.0
OE1 c:GLU354 2.1 50.0 1.0
OD1 a:ASP342 2.2 61.2 1.0
MN1 a:OEX702 2.7 48.3 1.0
MN3 a:OEX702 2.7 51.0 1.0
CD c:GLU354 2.8 52.2 1.0
OD2 a:ASP342 2.9 52.4 1.0
CG a:ASP342 2.9 51.0 1.0
OE2 c:GLU354 2.9 52.5 1.0
C a:ALA344 3.0 51.8 1.0
CA1 a:OEX702 3.3 47.9 1.0
O a:ALA344 3.4 58.6 1.0
O5 a:OEX702 3.7 52.6 1.0
NE2 a:HIS337 3.7 56.8 1.0
OE2 a:GLU189 3.9 53.5 1.0
O4 a:OEX702 4.1 44.7 1.0
CA a:ALA344 4.2 46.9 1.0
OE1 a:GLU333 4.3 62.4 1.0
CG c:GLU354 4.3 45.8 1.0
NE2 a:HIS332 4.3 49.8 1.0
CB a:ASP342 4.3 43.7 1.0
N a:ALA344 4.4 54.5 1.0
OE1 a:GLU189 4.4 55.3 1.0
CD2 a:HIS337 4.4 51.4 1.0
CD a:GLU189 4.6 46.9 1.0
CE1 a:HIS337 4.7 54.1 1.0
O a:HOH803 4.8 48.8 1.0
CB c:GLU354 4.9 43.7 1.0
CA a:ASP342 4.9 49.4 1.0
C a:ASP342 5.0 49.7 1.0

Manganese binding site 7 out of 8 in 5kai

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Manganese binding site 7 out of 8 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn702

b:51.0
occ:1.00
 MN3 a:OEX702 0.0 51.0 1.0
O2 a:OEX702 1.9 53.0 1.0
O4 a:OEX702 1.9 44.7 1.0
OE1 a:GLU333 2.1 62.4 1.0
O3 a:OEX702 2.1 58.2 1.0
OE2 c:GLU354 2.1 52.5 1.0
O5 a:OEX702 2.2 52.6 1.0
MN2 a:OEX702 2.7 59.4 1.0
CD a:GLU333 2.7 46.4 1.0
OE2 a:GLU333 2.9 45.9 1.0
MN4 a:OEX702 2.9 56.0 1.0
CD c:GLU354 3.2 52.2 1.0
MN1 a:OEX702 3.2 48.3 1.0
CA1 a:OEX702 3.4 47.9 1.0
O1 a:OEX702 3.5 60.2 1.0
OE1 c:GLU354 3.5 50.0 1.0
OD2 a:ASP170 3.9 54.2 1.0
NE2 a:HIS332 4.1 49.8 1.0
CG a:GLU333 4.1 37.0 1.0
OXT a:ALA344 4.1 50.5 1.0
CD2 a:HIS332 4.2 46.5 1.0
NE2 a:HIS337 4.3 56.8 1.0
O a:HOH807 4.3 47.5 1.0
NH2 c:ARG357 4.3 45.0 1.0
O a:HOH801 4.5 65.3 1.0
CG c:GLU354 4.5 45.8 1.0
OD1 a:ASP170 4.5 56.5 1.0
OD2 a:ASP342 4.6 52.4 1.0
CE1 a:HIS337 4.6 54.1 1.0
CG a:ASP170 4.6 49.1 1.0
CB a:GLU333 4.7 44.2 1.0
OD1 a:ASP342 4.7 61.2 1.0
O a:ALA344 4.7 58.6 1.0
C a:ALA344 4.9 51.8 1.0
OE2 a:GLU189 4.9 53.5 1.0

Manganese binding site 8 out of 8 in 5kai

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Manganese binding site 8 out of 8 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn702

b:56.0
occ:1.00
 MN4 a:OEX702 0.0 56.0 1.0
O4 a:OEX702 2.0 44.7 1.0
OD2 a:ASP170 2.0 54.2 1.0
OE2 a:GLU333 2.1 45.9 1.0
O a:HOH801 2.1 65.3 1.0
O a:HOH807 2.3 47.5 1.0
O5 a:OEX702 2.3 52.6 1.0
MN3 a:OEX702 2.9 51.0 1.0
CD a:GLU333 3.2 46.4 1.0
CG a:ASP170 3.2 49.1 1.0
OE1 a:GLU333 3.6 62.4 1.0
CA1 a:OEX702 3.8 47.9 1.0
OD1 a:ASP170 3.8 56.5 1.0
O2 a:OEX702 3.9 53.0 1.0
CA a:ASP170 4.3 48.6 1.0
CB a:ASP170 4.3 44.2 1.0
CG a:GLU333 4.4 37.0 1.0
OD1 a:ASP61 4.4 41.5 1.0
O a:SER169 4.5 48.2 1.0
O3 a:OEX702 4.6 58.2 1.0
OE2 c:GLU354 4.7 52.5 1.0
O a:HOH808 4.7 49.7 1.0
NH2 c:ARG357 4.8 45.0 1.0
N a:ASP170 4.9 52.0 1.0
MN1 a:OEX702 4.9 48.3 1.0
C a:SER169 5.0 46.3 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: Sun Oct 6 01:36:38 2024

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