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Calcium in PDB 4ixr: Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State

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

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

Protein crystallography data

The structure of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State, PDB code: 4ixr 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) 82.97 / 5.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 131.976, 227.568, 306.994, 90.00, 90.00, 90.00
R / Rfree (%) 28.5 / 31.3

Other elements in 4ixr:

The structure of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State (pdb code 4ixr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State, PDB code: 4ixr:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4ixr

Go back to Calcium Binding Sites List in 4ixr
Calcium binding site 1 out of 6 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:57.8
occ:1.00
CA1 A:OEC409 0.0 57.8 1.0
OE1 A:GLU189 2.3 66.7 1.0
OD1 A:ASP170 2.9 90.2 1.0
O A:ALA344 3.1 77.2 1.0
MN2 A:OEC409 3.2 45.6 1.0
CD A:GLU189 3.2 63.5 1.0
MN3 A:OEC409 3.3 44.6 1.0
MN1 A:OEC409 3.4 36.0 1.0
OE2 A:GLU189 3.4 59.5 1.0
CG A:ASP170 3.6 83.6 1.0
OD2 A:ASP170 3.8 80.5 1.0
C A:ALA344 4.0 80.8 1.0
NE2 A:GLN165 4.0 58.4 1.0
OH A:TYR161 4.4 52.1 1.0
CG A:GLU189 4.6 60.6 1.0
MN4 A:OEC409 4.6 62.1 1.0
CB A:ASP170 4.8 72.7 1.0
CG1 A:VAL185 4.9 64.1 1.0

Calcium binding site 2 out of 6 in 4ixr

Go back to Calcium Binding Sites List in 4ixr
Calcium binding site 2 out of 6 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca101

b:86.6
occ:1.00
OD2 K:ASP19 2.7 0.5 1.0
OD2 K:ASP23 2.8 92.3 1.0
OD1 K:ASP23 3.1 92.2 1.0
CG K:ASP23 3.3 92.0 1.0
CG K:ASP19 3.5 0.0 1.0
O K:ASP19 4.0 93.1 1.0
OD1 K:ASP19 4.1 99.5 1.0
CB K:ASP19 4.3 92.4 1.0
C K:ASP19 4.4 95.5 1.0
NE2 C:HIS74 4.6 84.4 1.0
CE1 C:HIS74 4.7 84.8 1.0
CA K:ASP19 4.8 91.5 1.0
CB K:ASP23 4.8 93.3 1.0
O C:ALA73 4.9 96.2 1.0
N K:PRO20 5.0 100.0 1.0

Calcium binding site 3 out of 6 in 4ixr

Go back to Calcium Binding Sites List in 4ixr
Calcium binding site 3 out of 6 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:0.4
occ:1.00
OE1 O:GLU140 2.6 93.9 1.0
NE2 O:HIS257 2.7 77.9 1.0
CD O:GLU140 3.4 90.0 1.0
OE2 O:GLU140 3.4 88.1 1.0
CD O:GLU81 3.7 0.6 1.0
CE1 O:HIS257 3.7 73.2 1.0
CD2 O:HIS257 3.7 72.0 1.0
OE1 O:GLU81 3.7 0.2 1.0
OE2 O:GLU81 4.0 1.0 1.0
CG O:GLU81 4.0 0.6 1.0
ND1 O:HIS257 4.8 65.4 1.0
CG O:GLU140 4.8 88.5 1.0
CG O:HIS257 4.9 63.6 1.0

Calcium binding site 4 out of 6 in 4ixr

Go back to Calcium Binding Sites List in 4ixr
Calcium binding site 4 out of 6 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca411

b:68.3
occ:1.00
CA1 a:OEC411 0.0 68.3 1.0
OE1 a:GLU189 2.4 83.0 1.0
OD1 a:ASP170 2.9 68.0 1.0
O a:ALA344 3.1 83.2 1.0
MN2 a:OEC411 3.3 45.6 1.0
MN3 a:OEC411 3.3 44.6 1.0
MN1 a:OEC411 3.4 36.0 1.0
CD a:GLU189 3.4 75.8 1.0
CG a:ASP170 3.5 66.7 1.0
OE2 a:GLU189 3.6 64.5 1.0
OD2 a:ASP170 3.7 65.1 1.0
NE2 a:GLN165 3.9 60.6 1.0
C a:ALA344 4.0 83.2 1.0
OH a:TYR161 4.5 57.1 1.0
MN4 a:OEC411 4.6 62.1 1.0
CG a:GLU189 4.8 76.2 1.0
CB a:ASP170 4.8 62.5 1.0
CD a:GLN165 4.9 55.1 1.0
OE1 a:GLU333 5.0 65.9 1.0

Calcium binding site 5 out of 6 in 4ixr

Go back to Calcium Binding Sites List in 4ixr
Calcium binding site 5 out of 6 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Ca101

b:0.2
occ:1.00
OD2 k:ASP19 2.6 0.4 1.0
OD2 k:ASP23 3.0 98.4 1.0
OD1 k:ASP23 3.1 98.6 1.0
CG k:ASP19 3.3 0.8 1.0
CG k:ASP23 3.4 97.0 1.0
OD1 k:ASP19 4.0 0.7 1.0
O k:ASP19 4.1 88.8 1.0
CB k:ASP19 4.1 0.3 1.0
C k:ASP19 4.4 91.2 1.0
NE2 c:HIS74 4.6 89.5 1.0
CE1 c:HIS74 4.7 88.0 1.0
O c:ALA73 4.7 82.2 1.0
CA k:ASP19 4.7 95.8 1.0
CB c:ALA73 4.9 83.2 1.0
CB k:ASP23 5.0 96.5 1.0
N k:PRO20 5.0 90.1 1.0

Calcium binding site 6 out of 6 in 4ixr

Go back to Calcium Binding Sites List in 4ixr
Calcium binding site 6 out of 6 in the Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Rt Fs X-Ray Diffraction of Photosystem II, First Illuminated State within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca301

b:98.7
occ:1.00
OE1 o:GLU140 2.5 83.5 1.0
NE2 o:HIS257 2.8 78.2 1.0
CD o:GLU140 3.2 85.8 1.0
OE2 o:GLU140 3.2 87.4 1.0
CE1 o:HIS257 3.7 69.7 1.0
CD2 o:HIS257 3.7 73.9 1.0
CD o:GLU81 3.8 0.3 1.0
OE1 o:GLU81 3.9 0.2 1.0
OE2 o:GLU81 4.1 0.5 1.0
CG o:GLU81 4.2 0.3 1.0
CG o:GLU140 4.6 83.3 1.0
SD o:MET136 4.8 87.1 1.0
ND1 o:HIS257 4.9 61.5 1.0
CG o:HIS257 4.9 64.1 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 Dec 12 04:52:32 2020

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