Atomistry » Chlorine » PDB 5k9d-5kga » 5kai
Atomistry »
  Chlorine »
    PDB 5k9d-5kga »
      5kai »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy