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Chlorine 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
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5kai

Go back to Chlorine Binding Sites List in 5kai
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl604

b:39.2
occ:1.00
 N A:GLU333 3.1 46.2 1.0
NZ D:LYS317 3.3 46.0 1.0
CA A:HIS332 3.4 42.2 1.0
CB A:HIS332 3.5 42.2 1.0
C A:HIS332 3.7 48.7 1.0
ND2 A:ASN181 3.8 37.8 1.0
O A:HOH708 3.8 37.7 1.0
CG A:GLU333 3.9 44.7 1.0
CE D:LYS317 4.0 40.6 1.0
CA A:GLU333 4.1 49.8 1.0
CG2 A:VAL185 4.5 32.4 1.0
CG A:HIS332 4.6 47.8 1.0
CB A:GLU333 4.6 46.6 1.0
CD1 D:LEU321 4.6 37.3 1.0
CD2 D:LEU321 4.6 39.5 1.0
OD1 A:ASN181 4.7 39.8 1.0
CG A:ASN181 4.7 40.0 1.0
N A:HIS332 4.7 47.9 1.0
CB D:LYS317 4.7 34.8 1.0
CG D:LEU321 4.8 43.2 1.0
CD2 A:HIS332 4.9 45.1 1.0
O A:MET331 4.9 49.8 1.0
O D:LYS317 4.9 49.1 1.0
O A:HIS332 4.9 50.5 1.0

Chlorine binding site 2 out of 4 in 5kai

Go back to Chlorine Binding Sites List in 5kai
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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:Cl605

b:51.2
occ:1.00
 N A:ASN338 3.1 46.3 1.0
CD2 A:PHE339 3.3 49.6 1.0
N A:PHE339 3.6 45.5 1.0
O A:HOH706 3.6 41.3 1.0
CA A:HIS337 3.7 48.1 1.0
N C:GLU354 3.8 51.0 1.0
CA C:GLY353 3.8 48.8 1.0
C A:HIS337 3.8 49.3 1.0
CA A:ASN338 4.0 41.1 1.0
CG A:PHE339 4.1 52.6 1.0
CB A:PHE339 4.1 48.4 1.0
CE2 A:PHE339 4.1 41.2 1.0
C A:ASN338 4.2 41.6 1.0
O A:ALA336 4.2 54.4 1.0
CB A:ASN338 4.3 40.9 1.0
C C:GLY353 4.3 53.7 1.0
CB A:HIS337 4.4 53.8 1.0
CA A:PHE339 4.4 44.6 1.0
O A:PHE339 4.6 48.5 1.0
CB C:GLU354 4.7 50.5 1.0
N A:HIS337 4.7 51.5 1.0
CA C:GLU354 4.8 50.3 1.0
C A:ALA336 4.9 51.5 1.0
C A:PHE339 5.0 49.4 1.0
CG A:ASN338 5.0 45.7 1.0

Chlorine binding site 3 out of 4 in 5kai

Go back to Chlorine Binding Sites List in 5kai
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl 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:Cl704

b:59.5
occ:0.92
 NZ d:LYS317 3.0 42.8 1.0
ND2 a:ASN181 3.5 37.9 1.0
N a:GLU333 3.5 49.9 1.0
CA a:HIS332 3.6 44.5 1.0
CE d:LYS317 3.8 48.4 1.0
CB a:HIS332 3.8 44.1 1.0
C a:HIS332 4.1 50.5 1.0
CD2 d:LEU321 4.2 42.7 1.0
CB d:LYS317 4.3 42.3 1.0
CD1 d:LEU321 4.4 42.7 1.0
CG a:GLU333 4.4 37.0 1.0
O d:LYS317 4.5 50.1 1.0
CG d:LEU321 4.5 40.8 1.0
CG a:ASN181 4.5 44.5 1.0
CA a:GLU333 4.6 47.2 1.0
CG2 a:VAL185 4.6 42.5 1.0
OD1 a:ASN181 4.7 51.7 1.0
CG d:LYS317 4.7 49.7 1.0
N a:HIS332 4.9 35.0 1.0
CD d:LYS317 4.9 55.3 1.0
C d:LYS317 5.0 48.6 1.0
CG a:HIS332 5.0 44.9 1.0

Chlorine binding site 4 out of 4 in 5kai

Go back to Chlorine Binding Sites List in 5kai
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl 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:Cl705

b:50.4
occ:1.00
 N a:ASN338 2.9 49.4 1.0
CA a:HIS337 3.5 43.5 1.0
CD2 a:PHE339 3.5 52.6 1.0
N a:PHE339 3.6 48.3 1.0
N c:GLU354 3.6 46.1 1.0
C a:HIS337 3.7 47.8 1.0
CA a:ASN338 3.8 49.3 1.0
CA c:GLY353 3.9 50.8 1.0
CB a:HIS337 4.0 50.9 1.0
C a:ASN338 4.1 47.6 1.0
CB a:ASN338 4.1 42.5 1.0
CB a:PHE339 4.2 53.9 1.0
CG a:PHE339 4.2 50.4 1.0
O a:ALA336 4.2 52.2 1.0
CE2 a:PHE339 4.3 47.9 1.0
C c:GLY353 4.3 51.1 1.0
CA a:PHE339 4.4 54.6 1.0
CB c:GLU354 4.5 43.7 1.0
CA c:GLU354 4.6 48.5 1.0
N a:HIS337 4.6 42.7 1.0
O a:PHE339 4.7 55.6 1.0
CG a:HIS337 4.7 52.5 1.0
CD2 a:HIS337 4.8 51.4 1.0
O a:HIS337 4.9 46.0 1.0
C a:ALA336 4.9 45.8 1.0
CG a:ASN338 4.9 48.5 1.0
O c:GLY352 4.9 54.0 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: Fri Jul 26 10:34:28 2024

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