Atomistry » Manganese » PDB 4ima-4k28 » 4ixq
Atomistry »
  Manganese »
    PDB 4ima-4k28 »
      4ixq »

Manganese in PDB 4ixq: Rt Fs X-Ray Diffraction of Photosystem II, Dark State

Enzymatic activity of Rt Fs X-Ray Diffraction of Photosystem II, Dark State

All present enzymatic activity of Rt Fs X-Ray Diffraction of Photosystem II, Dark State:
1.10.3.9;

Protein crystallography data

The structure of Rt Fs X-Ray Diffraction of Photosystem II, Dark State, PDB code: 4ixq was solved by J.Kern, R.Alonso-Mori, R.Tran, J.Hattne, R.J.Gildea, N.Echols, C.Gloeckner, J.Hellmich, H.Laksmono, R.G.Sierra, B.Lassalle-Kaiser, S.Koroidov, A.Lampe, G.Han, S.Gul, D.Difiore, D.Milathianaki, A.R.Fry, A.Miahnahri, D.W.Schafer, M.Messerschmidt, M.M.Seibert, J.E.Koglin, D.Sokaras, T.-C.Weng, J.Sellberg, M.J.Latimer, R.W.Grosse-Kunstleve, P.H.Zwart, W.E.White, P.Glatzel, P.D.Adams, M.J.Bogan, G.J.Williams, S.Boutet, J.Messinger, A.Zouni, N.K.Sauter, V.K.Yachandra, U.Bergmann, J.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.94 / 5.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 131.864, 227.511, 307.219, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 31.4

Other elements in 4ixq:

The structure of Rt Fs X-Ray Diffraction of Photosystem II, Dark State 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 Fs X-Ray Diffraction of Photosystem II, Dark State (pdb code 4ixq). 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 Fs X-Ray Diffraction of Photosystem II, Dark State, PDB code: 4ixq:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 1 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn409

b:36.0
occ:1.00
 MN1 A:OEC409 0.0 36.0 1.0
OE2 A:GLU189 1.8 61.9 1.0
NE2 A:HIS332 2.4 57.7 1.0
OD2 A:ASP342 2.5 63.1 1.0
MN2 A:OEC409 2.6 45.6 1.0
CD A:GLU189 2.8 65.1 1.0
CD2 A:HIS332 3.2 61.6 1.0
MN3 A:OEC409 3.3 44.6 1.0
OE1 A:GLU189 3.3 63.2 1.0
CA1 A:OEC409 3.4 46.3 1.0
CG A:ASP342 3.4 70.1 1.0
CE1 A:HIS332 3.5 57.2 1.0
OD1 A:ASP342 3.6 68.3 1.0
OE1 A:GLU333 3.8 65.5 1.0
CG A:GLU189 4.0 60.9 1.0
NE2 A:HIS337 4.1 62.0 1.0
OE2 C:GLU354 4.3 68.1 1.0
CG A:HIS332 4.4 58.8 1.0
ND1 A:HIS332 4.5 55.4 1.0
CE1 A:HIS337 4.5 62.8 1.0
OE1 C:GLU354 4.6 64.5 1.0
CG1 A:VAL185 4.6 60.7 1.0
CD A:GLU333 4.6 68.8 1.0
O A:ALA344 4.7 75.4 1.0
CB A:ASP342 4.8 74.2 1.0
C A:ALA344 4.9 78.8 1.0
CD C:GLU354 4.9 69.6 1.0

Manganese binding site 2 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 2 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn409

b:45.6
occ:1.00
 MN2 A:OEC409 0.0 45.6 1.0
OD1 A:ASP342 2.3 68.3 1.0
C A:ALA344 2.3 78.8 1.0
O A:ALA344 2.6 75.4 1.0
MN1 A:OEC409 2.6 36.0 1.0
MN3 A:OEC409 2.7 44.6 1.0
OE2 C:GLU354 3.0 68.1 1.0
CG A:ASP342 3.1 70.1 1.0
OD2 A:ASP342 3.2 63.1 1.0
OE1 C:GLU354 3.2 64.5 1.0
CA1 A:OEC409 3.3 46.3 1.0
OE2 A:GLU189 3.4 61.9 1.0
CD C:GLU354 3.5 69.6 1.0
CA A:ALA344 3.6 85.6 1.0
N A:ALA344 3.8 80.8 1.0
NE2 A:HIS337 4.2 62.0 1.0
OE1 A:GLU333 4.3 65.5 1.0
CB A:ALA344 4.3 87.5 1.0
CD A:GLU189 4.3 65.1 1.0
OE1 A:GLU189 4.3 63.2 1.0
CB A:ASP342 4.6 74.2 1.0
OD1 A:ASP170 4.7 83.0 1.0
NE2 A:HIS332 4.8 57.7 1.0
CG C:GLU354 4.9 72.2 1.0

Manganese binding site 3 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 3 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn409

b:44.6
occ:1.00
 MN3 A:OEC409 0.0 44.6 1.0
OE1 A:GLU333 2.2 65.5 1.0
OE2 C:GLU354 2.3 68.1 1.0
MN2 A:OEC409 2.7 45.6 1.0
CD A:GLU333 3.2 68.8 1.0
MN4 A:OEC409 3.2 62.1 1.0
MN1 A:OEC409 3.3 36.0 1.0
CA1 A:OEC409 3.3 46.3 1.0
CD C:GLU354 3.5 69.6 1.0
OE2 A:GLU333 3.6 69.8 1.0
OD2 A:ASP170 3.7 73.9 1.0
OD1 A:ASP170 3.8 83.0 1.0
C A:ALA344 4.0 78.8 1.0
O A:ALA344 4.0 75.4 1.0
OE1 C:GLU354 4.0 64.5 1.0
CG A:ASP170 4.2 78.6 1.0
NH2 C:ARG357 4.3 70.2 1.0
CG A:GLU333 4.5 66.0 1.0
OE2 A:GLU189 4.6 61.9 1.0
CG C:GLU354 4.7 72.2 1.0
OD1 A:ASP342 4.7 68.3 1.0
NE2 A:HIS332 4.8 57.7 1.0
NE2 A:HIS337 4.8 62.0 1.0
OD2 A:ASP342 5.0 63.1 1.0
CD2 A:HIS332 5.0 61.6 1.0

Manganese binding site 4 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 4 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn409

b:62.1
occ:1.00
 MN4 A:OEC409 0.0 62.1 1.0
OD2 A:ASP170 2.3 73.9 1.0
OE2 A:GLU333 2.4 69.8 1.0
CD A:GLU333 3.1 68.8 1.0
MN3 A:OEC409 3.2 44.6 1.0
OE1 A:GLU333 3.4 65.5 1.0
CG A:ASP170 3.5 78.6 1.0
OD1 A:ASP170 4.2 83.0 1.0
OD1 A:ASP61 4.3 60.3 1.0
CG A:GLU333 4.3 66.0 1.0
O A:SER169 4.4 71.3 1.0
CA A:ASP170 4.5 66.5 1.0
CA1 A:OEC409 4.6 46.3 1.0
CB A:ASP170 4.7 72.7 1.0
C A:SER169 5.0 66.8 1.0

Manganese binding site 5 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 5 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn411

b:36.0
occ:1.00
 MN1 a:OEC411 0.0 36.0 1.0
OE2 a:GLU189 1.8 59.9 1.0
NE2 a:HIS332 2.5 52.8 1.0
MN2 a:OEC411 2.6 45.6 1.0
OD2 a:ASP342 2.6 60.5 1.0
CD a:GLU189 2.7 68.3 1.0
OE1 a:GLU189 3.0 75.2 1.0
CD2 a:HIS332 3.2 55.0 1.0
MN3 a:OEC411 3.3 44.6 1.0
CA1 a:OEC411 3.4 62.4 1.0
CG a:ASP342 3.5 64.2 1.0
CE1 a:HIS332 3.6 52.6 1.0
OD1 a:ASP342 3.6 65.2 1.0
OE1 a:GLU333 3.7 61.0 1.0
CG a:GLU189 3.9 68.1 1.0
NE2 a:HIS337 4.2 71.7 1.0
OE2 c:GLU354 4.4 67.8 1.0
CG a:HIS332 4.4 50.8 1.0
CG1 a:VAL185 4.6 57.6 1.0
ND1 a:HIS332 4.6 48.4 1.0
CE1 a:HIS337 4.6 72.0 1.0
CD a:GLU333 4.6 67.0 1.0
OE1 c:GLU354 4.7 72.9 1.0
O a:ALA344 4.8 83.7 1.0
CB a:ASP342 4.9 62.9 1.0
C a:ALA344 4.9 87.0 1.0
CD c:GLU354 5.0 72.2 1.0

Manganese binding site 6 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 6 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn411

b:45.6
occ:1.00
 MN2 a:OEC411 0.0 45.6 1.0
OD1 a:ASP342 2.3 65.2 1.0
C a:ALA344 2.4 87.0 1.0
MN1 a:OEC411 2.6 36.0 1.0
O a:ALA344 2.7 83.7 1.0
MN3 a:OEC411 2.7 44.6 1.0
OE2 c:GLU354 3.1 67.8 1.0
CG a:ASP342 3.1 64.2 1.0
OE1 c:GLU354 3.2 72.9 1.0
CA1 a:OEC411 3.2 62.4 1.0
OD2 a:ASP342 3.3 60.5 1.0
OE2 a:GLU189 3.3 59.9 1.0
CD c:GLU354 3.5 72.2 1.0
CA a:ALA344 3.7 90.9 1.0
N a:ALA344 3.9 88.2 1.0
OE1 a:GLU189 4.0 75.2 1.0
CD a:GLU189 4.1 68.3 1.0
OE1 a:GLU333 4.3 61.0 1.0
NE2 a:HIS337 4.3 71.7 1.0
CB a:ALA344 4.4 86.8 1.0
CB a:ASP342 4.6 62.9 1.0
OD1 a:ASP170 4.8 72.0 1.0
NE2 a:HIS332 4.8 52.8 1.0
CG c:GLU354 5.0 70.6 1.0
C a:ASP342 5.0 65.8 1.0

Manganese binding site 7 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 7 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn411

b:44.6
occ:1.00
 MN3 a:OEC411 0.0 44.6 1.0
OE1 a:GLU333 2.2 61.0 1.0
OE2 c:GLU354 2.3 67.8 1.0
MN2 a:OEC411 2.7 45.6 1.0
MN4 a:OEC411 3.2 62.1 1.0
MN1 a:OEC411 3.3 36.0 1.0
CD a:GLU333 3.3 67.0 1.0
CA1 a:OEC411 3.3 62.4 1.0
CD c:GLU354 3.4 72.2 1.0
OD2 a:ASP170 3.6 65.1 1.0
OE2 a:GLU333 3.7 66.7 1.0
OD1 a:ASP170 3.8 72.0 1.0
OE1 c:GLU354 4.0 72.9 1.0
C a:ALA344 4.0 87.0 1.0
O a:ALA344 4.0 83.7 1.0
NH2 c:ARG357 4.0 82.3 1.0
CG a:ASP170 4.1 69.3 1.0
CG a:GLU333 4.6 65.0 1.0
CG c:GLU354 4.6 70.6 1.0
OE2 a:GLU189 4.7 59.9 1.0
OD1 a:ASP342 4.7 65.2 1.0
CZ c:ARG357 4.9 77.7 1.0
OE1 a:GLU189 4.9 75.2 1.0
NE2 a:HIS332 5.0 52.8 1.0

Manganese binding site 8 out of 8 in 4ixq

Go back to Manganese Binding Sites List in 4ixq
Manganese binding site 8 out of 8 in the Rt Fs X-Ray Diffraction of Photosystem II, Dark State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Rt Fs X-Ray Diffraction of Photosystem II, Dark State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn411

b:62.1
occ:1.00
 MN4 a:OEC411 0.0 62.1 1.0
OD2 a:ASP170 2.3 65.1 1.0
OE2 a:GLU333 2.4 66.7 1.0
CD a:GLU333 3.1 67.0 1.0
MN3 a:OEC411 3.2 44.6 1.0
OE1 a:GLU333 3.2 61.0 1.0
CG a:ASP170 3.5 69.3 1.0
OD1 a:ASP61 4.2 58.0 1.0
O a:SER169 4.2 60.2 1.0
OD1 a:ASP170 4.2 72.0 1.0
CG a:GLU333 4.4 65.0 1.0
CA a:ASP170 4.4 58.9 1.0
CB a:ASP170 4.6 65.4 1.0
CA1 a:OEC411 4.6 62.4 1.0
C a:SER169 4.8 60.1 1.0
NH2 c:ARG357 4.8 82.3 1.0
N a:ASP170 4.9 59.4 1.0
OG a:SER169 4.9 70.4 1.0
OE2 c:GLU354 4.9 67.8 1.0

Reference:

J.Kern, R.Alonso-Mori, R.Tran, J.Hattne, R.J.Gildea, N.Echols, C.Glockner, J.Hellmich, H.Laksmono, R.G.Sierra, B.Lassalle-Kaiser, S.Koroidov, A.Lampe, G.Han, S.Gul, D.Difiore, D.Milathianaki, A.R.Fry, A.Miahnahri, D.W.Schafer, M.Messerschmidt, M.M.Seibert, J.E.Koglin, D.Sokaras, T.C.Weng, J.Sellberg, M.J.Latimer, R.W.Grosse-Kunstleve, P.H.Zwart, W.E.White, P.Glatzel, P.D.Adams, M.J.Bogan, G.J.Williams, S.Boutet, J.Messinger, A.Zouni, N.K.Sauter, V.K.Yachandra, U.Bergmann, J.Yano. Simultaneous Femtosecond X-Ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. Science V. 340 491 2013.
ISSN: ISSN 0036-8075
PubMed: 23413188
DOI: 10.1126/SCIENCE.1234273
Page generated: Sat Oct 5 19:55:32 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