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

Manganese in PDB 4tnk: Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 A Resolution

Enzymatic activity of Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 A Resolution

All present enzymatic activity of Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 A Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 A Resolution, PDB code: 4tnk was solved by J.Kern, R.Tran, R.Alonso-Mori, S.Koroidov, N.Echols, J.Hattne, M.Ibrahim, S.Gul, H.Laksmono, R.G.Sierra, R.J.Gildea, G.Han, J.Hellmich, B.Lassalle-Kaiser, R.Chatterjee, A.Brewster, C.A.Stan, C.Gloeckner, A.Lampe, D.Difiore, D.Milathianaki, A.R.Fry, M.M.Seibert, J.E.Koglin, E.Gallo, J.Uhlig, D.Sokaras, T.-C.Weng, P.H.Zwart, D.E.Skinner, M.J.Bogan, M.Messerschmidt, P.Glatzel, G.J.Williams, S.Boutet, P.D.Adams, A.Zouni, J.Messinger, N.K.Sauter, U.Bergmann, J.Yano, V.K.Yachandra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.41 / 5.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 132.615, 229.296, 306.825, 90.00, 90.00, 90.00
R / Rfree (%) 27.1 / 28.9

Other elements in 4tnk:

The structure of Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 A Resolution also contains other interesting chemical elements:

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

Manganese Binding Sites:

The binding sites of Manganese atom in the Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 A Resolution (pdb code 4tnk). 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 250 Microsec After the Third Illumination at 5.2 A Resolution, PDB code: 4tnk:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4tnk

Go back to Manganese Binding Sites List in 4tnk
Manganese binding site 1 out of 8 in the Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 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 250 Microsec After the Third Illumination at 5.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:0.5
occ:1.00
 MN1 A:OEX412 0.0 0.5 1.0
O3 A:OEX412 1.9 0.6 1.0
O1 A:OEX412 1.9 0.4 1.0
O5 A:OEX412 1.9 0.5 1.0
OE2 A:GLU189 2.5 0.1 1.0
NE2 A:HIS332 2.6 0.4 1.0
MN3 A:OEX412 2.7 1.0 1.0
MN2 A:OEX412 2.7 0.7 1.0
OD2 A:ASP342 2.8 0.9 1.0
CD2 A:HIS332 3.1 0.4 1.0
CD A:GLU189 3.3 0.3 1.0
CA1 A:OEX412 3.4 0.8 1.0
OE1 A:GLU189 3.4 0.9 1.0
O2 A:OEX412 3.5 0.3 1.0
CG A:ASP342 3.8 0.4 1.0
CE1 A:HIS332 3.8 0.8 1.0
MN4 A:OEX412 3.8 1.0 1.0
OD1 A:ASP342 4.0 0.5 1.0
NE2 A:HIS337 4.2 1.0 1.0
O4 A:OEX412 4.2 0.7 1.0
OE1 A:GLU333 4.4 0.2 1.0
CG A:HIS332 4.4 0.3 1.0
OE1 C:GLU354 4.5 0.2 1.0
CG1 A:VAL185 4.6 0.1 1.0
OE2 C:GLU354 4.6 0.3 1.0
CG A:GLU189 4.6 0.6 1.0
CE1 A:HIS337 4.6 0.2 1.0
CD A:GLU333 4.7 0.9 1.0
ND1 A:HIS332 4.7 0.9 1.0
CG A:GLU333 4.9 0.4 1.0

Manganese binding site 2 out of 8 in 4tnk

Go back to Manganese Binding Sites List in 4tnk
Manganese binding site 2 out of 8 in the Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 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 250 Microsec After the Third Illumination at 5.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:0.7
occ:1.00
 MN2 A:OEX412 0.0 0.7 1.0
O1 A:OEX412 1.9 0.4 1.0
O3 A:OEX412 1.9 0.6 1.0
O2 A:OEX412 2.0 0.3 1.0
OD1 A:ASP342 2.6 0.5 1.0
OXT A:ALA344 2.6 0.7 1.0
MN1 A:OEX412 2.7 0.5 1.0
MN3 A:OEX412 2.8 1.0 1.0
OE1 C:GLU354 2.8 0.2 1.0
O A:ALA344 2.9 0.7 1.0
C A:ALA344 3.0 0.2 1.0
OD2 A:ASP342 3.2 0.9 1.0
CG A:ASP342 3.3 0.4 1.0
CA1 A:OEX412 3.3 0.8 1.0
OE2 C:GLU354 3.4 0.3 1.0
CD C:GLU354 3.4 0.3 1.0
O5 A:OEX412 3.5 0.5 1.0
CA A:ALA344 4.2 0.1 1.0
N A:ALA344 4.2 0.8 1.0
OE2 A:GLU189 4.3 0.1 1.0
O4 A:OEX412 4.3 0.7 1.0
NE2 A:HIS337 4.4 1.0 1.0
CB A:ASP342 4.7 0.6 1.0
OD1 A:ASP170 4.7 0.8 1.0
OE1 A:GLU189 4.7 0.9 1.0
CG C:GLU354 4.9 0.7 1.0
OE1 A:GLU333 4.9 0.2 1.0
NE2 A:HIS332 4.9 0.4 1.0
CD A:GLU189 4.9 0.3 1.0
CB A:ALA344 4.9 0.9 1.0

Manganese binding site 3 out of 8 in 4tnk

Go back to Manganese Binding Sites List in 4tnk
Manganese binding site 3 out of 8 in the Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 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 250 Microsec After the Third Illumination at 5.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:1.0
occ:1.00
 MN3 A:OEX412 0.0 1.0 1.0
O5 A:OEX412 1.8 0.5 1.0
O4 A:OEX412 1.9 0.7 1.0
O2 A:OEX412 1.9 0.3 1.0
O3 A:OEX412 1.9 0.6 1.0
OE1 A:GLU333 2.6 0.2 1.0
MN4 A:OEX412 2.6 1.0 1.0
OE2 C:GLU354 2.7 0.3 1.0
MN1 A:OEX412 2.7 0.5 1.0
MN2 A:OEX412 2.8 0.7 1.0
O1 A:OEX412 3.0 0.4 1.0
CD A:GLU333 3.2 0.9 1.0
CA1 A:OEX412 3.5 0.8 1.0
OE2 A:GLU333 3.6 0.1 1.0
CD C:GLU354 3.6 0.3 1.0
OE1 C:GLU354 3.8 0.2 1.0
OD1 A:ASP170 4.0 0.8 1.0
OD2 A:ASP170 4.0 0.7 1.0
CG A:GLU333 4.1 0.4 1.0
OXT A:ALA344 4.3 0.7 1.0
CG A:ASP170 4.4 1.0 1.0
NE2 A:HIS332 4.5 0.4 1.0
NH2 C:ARG357 4.6 0.6 1.0
CD2 A:HIS332 4.6 0.4 1.0
NE2 A:HIS337 4.7 1.0 1.0
O A:ALA344 4.8 0.7 1.0
OD2 A:ASP342 4.8 0.9 1.0
CE1 A:HIS337 4.9 0.2 1.0
OD1 A:ASP342 4.9 0.5 1.0
CB A:GLU333 4.9 0.1 1.0
CG C:GLU354 5.0 0.7 1.0
C A:ALA344 5.0 0.2 1.0

Manganese binding site 4 out of 8 in 4tnk

Go back to Manganese Binding Sites List in 4tnk
Manganese binding site 4 out of 8 in the Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 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 250 Microsec After the Third Illumination at 5.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn412

b:1.0
occ:1.00
 MN4 A:OEX412 0.0 1.0 1.0
O4 A:OEX412 1.9 0.7 1.0
O5 A:OEX412 1.9 0.5 1.0
MN3 A:OEX412 2.6 1.0 1.0
OD2 A:ASP170 2.7 0.7 1.0
OE2 A:GLU333 2.8 0.1 1.0
CD A:GLU333 3.2 0.9 1.0
OE1 A:GLU333 3.6 0.2 1.0
CG A:ASP170 3.7 1.0 1.0
MN1 A:OEX412 3.8 0.5 1.0
CA1 A:OEX412 3.8 0.8 1.0
O2 A:OEX412 3.9 0.3 1.0
CG A:GLU333 4.0 0.4 1.0
OD1 A:ASP170 4.1 0.8 1.0
O3 A:OEX412 4.2 0.6 1.0
O1 A:OEX412 4.3 0.4 1.0
CG1 A:VAL185 4.3 0.1 1.0
CD2 A:HIS332 4.6 0.4 1.0

Manganese binding site 5 out of 8 in 4tnk

Go back to Manganese Binding Sites List in 4tnk
Manganese binding site 5 out of 8 in the Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 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 250 Microsec After the Third Illumination at 5.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn411

b:0.7
occ:1.00
 MN1 a:OEX411 0.0 0.7 1.0
O1 a:OEX411 1.9 0.0 1.0
O3 a:OEX411 1.9 0.6 1.0
O5 a:OEX411 1.9 0.5 1.0
OE2 a:GLU189 2.5 0.7 1.0
NE2 a:HIS332 2.6 0.2 1.0
MN3 a:OEX411 2.7 0.8 1.0
MN2 a:OEX411 2.7 0.1 1.0
OD2 a:ASP342 2.9 0.3 1.0
CD2 a:HIS332 3.1 0.4 1.0
CD a:GLU189 3.2 0.5 1.0
OE1 a:GLU189 3.3 0.2 1.0
CA1 a:OEX411 3.4 0.5 1.0
O2 a:OEX411 3.5 0.3 1.0
CE1 a:HIS332 3.8 0.1 1.0
CG a:ASP342 3.8 0.6 1.0
MN4 a:OEX411 3.8 0.6 1.0
OD1 a:ASP342 4.0 0.7 1.0
O4 a:OEX411 4.2 0.7 1.0
NE2 a:HIS337 4.3 0.9 1.0
OE1 a:GLU333 4.4 0.2 1.0
CG a:HIS332 4.4 0.0 1.0
CG1 a:VAL185 4.5 0.1 1.0
CG a:GLU189 4.6 0.0 1.0
OE2 c:GLU354 4.6 0.7 1.0
OE1 c:GLU354 4.6 0.3 1.0
ND1 a:HIS332 4.7 0.3 1.0
CD a:GLU333 4.7 0.2 1.0
CE1 a:HIS337 4.7 0.8 1.0
CG a:GLU333 4.9 0.1 1.0

Manganese binding site 6 out of 8 in 4tnk

Go back to Manganese Binding Sites List in 4tnk
Manganese binding site 6 out of 8 in the Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 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 250 Microsec After the Third Illumination at 5.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn411

b:0.1
occ:1.00
 MN2 a:OEX411 0.0 0.1 1.0
O1 a:OEX411 1.9 0.0 1.0
O3 a:OEX411 1.9 0.6 1.0
O2 a:OEX411 2.0 0.3 1.0
OD1 a:ASP342 2.6 0.7 1.0
OXT a:ALA344 2.7 0.0 1.0
MN1 a:OEX411 2.7 0.7 1.0
MN3 a:OEX411 2.8 0.8 1.0
OE1 c:GLU354 2.8 0.3 1.0
C a:ALA344 3.1 0.5 1.0
O a:ALA344 3.1 0.6 1.0
OD2 a:ASP342 3.3 0.3 1.0
CG a:ASP342 3.3 0.6 1.0
CA1 a:OEX411 3.3 0.5 1.0
OE2 c:GLU354 3.3 0.7 1.0
CD c:GLU354 3.4 0.3 1.0
O5 a:OEX411 3.5 0.5 1.0
CA a:ALA344 4.2 0.3 1.0
N a:ALA344 4.2 0.4 1.0
OE2 a:GLU189 4.3 0.7 1.0
O4 a:OEX411 4.3 0.7 1.0
NE2 a:HIS337 4.4 0.9 1.0
OE1 a:GLU189 4.6 0.2 1.0
OD1 a:ASP170 4.7 0.9 1.0
CB a:ASP342 4.7 0.5 1.0
CG c:GLU354 4.9 0.5 1.0
CD a:GLU189 4.9 0.5 1.0
OE1 a:GLU333 4.9 0.2 1.0
NE2 a:HIS332 4.9 0.2 1.0
CB a:ALA344 5.0 0.8 1.0

Manganese binding site 7 out of 8 in 4tnk

Go back to Manganese Binding Sites List in 4tnk
Manganese binding site 7 out of 8 in the Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 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 250 Microsec After the Third Illumination at 5.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn411

b:0.8
occ:1.00
 MN3 a:OEX411 0.0 0.8 1.0
O5 a:OEX411 1.9 0.5 1.0
O4 a:OEX411 1.9 0.7 1.0
O2 a:OEX411 1.9 0.3 1.0
O3 a:OEX411 1.9 0.6 1.0
OE1 a:GLU333 2.6 0.2 1.0
MN4 a:OEX411 2.6 0.6 1.0
MN1 a:OEX411 2.7 0.7 1.0
OE2 c:GLU354 2.7 0.7 1.0
MN2 a:OEX411 2.8 0.1 1.0
O1 a:OEX411 3.0 0.0 1.0
CD a:GLU333 3.2 0.2 1.0
CA1 a:OEX411 3.5 0.5 1.0
OE2 a:GLU333 3.6 0.3 1.0
CD c:GLU354 3.7 0.3 1.0
OE1 c:GLU354 3.9 0.3 1.0
OD2 a:ASP170 4.0 0.4 1.0
OD1 a:ASP170 4.0 0.9 1.0
CG a:GLU333 4.1 0.1 1.0
OXT a:ALA344 4.3 0.0 1.0
CG a:ASP170 4.4 0.6 1.0
NE2 a:HIS332 4.5 0.2 1.0
NH2 c:ARG357 4.6 0.3 1.0
CD2 a:HIS332 4.6 0.4 1.0
NE2 a:HIS337 4.8 0.9 1.0
OD2 a:ASP342 4.8 0.3 1.0
O a:ALA344 4.9 0.6 1.0
CB a:GLU333 5.0 0.7 1.0
CE1 a:HIS337 5.0 0.8 1.0
OD1 a:ASP342 5.0 0.7 1.0

Manganese binding site 8 out of 8 in 4tnk

Go back to Manganese Binding Sites List in 4tnk
Manganese binding site 8 out of 8 in the Rt Xfel Structure of Photosystem II 250 Microsec After the Third Illumination at 5.2 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 250 Microsec After the Third Illumination at 5.2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn411

b:0.6
occ:1.00
 MN4 a:OEX411 0.0 0.6 1.0
O4 a:OEX411 1.9 0.7 1.0
O5 a:OEX411 1.9 0.5 1.0
MN3 a:OEX411 2.6 0.8 1.0
OD2 a:ASP170 2.6 0.4 1.0
OE2 a:GLU333 2.8 0.3 1.0
CD a:GLU333 3.3 0.2 1.0
OE1 a:GLU333 3.6 0.2 1.0
CG a:ASP170 3.7 0.6 1.0
MN1 a:OEX411 3.8 0.7 1.0
CA1 a:OEX411 3.8 0.5 1.0
O2 a:OEX411 3.9 0.3 1.0
CG a:GLU333 4.1 0.1 1.0
OD1 a:ASP170 4.1 0.9 1.0
O3 a:OEX411 4.2 0.6 1.0
O1 a:OEX411 4.3 0.0 1.0
CG1 a:VAL185 4.4 0.1 1.0
CD2 a:HIS332 4.7 0.4 1.0
CB a:ASP170 5.0 0.9 1.0

Reference:

J.Kern, R.Tran, R.Alonso-Mori, S.Koroidov, N.Echols, J.Hattne, M.Ibrahim, S.Gul, H.Laksmono, R.G.Sierra, R.J.Gildea, G.Han, J.Hellmich, B.Lassalle-Kaiser, R.Chatterjee, A.S.Brewster, C.A.Stan, C.Glockner, A.Lampe, D.Difiore, D.Milathianaki, A.R.Fry, M.M.Seibert, J.E.Koglin, E.Gallo, J.Uhlig, D.Sokaras, T.C.Weng, P.H.Zwart, D.E.Skinner, M.J.Bogan, M.Messerschmidt, P.Glatzel, G.J.Williams, S.Boutet, P.D.Adams, A.Zouni, J.Messinger, N.K.Sauter, U.Bergmann, J.Yano, V.K.Yachandra. Taking Snapshots of Photosynthetic Water Oxidation Using Femtosecond X-Ray Diffraction and Spectroscopy. Nat Commun V. 5 4371 2014.
ISSN: ESSN 2041-1723
PubMed: 25006873
DOI: 10.1038/NCOMMS5371
Page generated: Sat Oct 5 21:15:11 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy