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

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4tnk

Go back to Calcium Binding Sites List in 4tnk
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca412

b:0.8
occ:1.00
 CA1 A:OEX412 0.0 0.8 1.0
O1 A:OEX412 2.0 0.4 1.0
O2 A:OEX412 3.0 0.3 1.0
O5 A:OEX412 3.0 0.5 1.0
OD1 A:ASP170 3.0 0.8 1.0
OE1 A:GLU189 3.0 0.9 1.0
MN2 A:OEX412 3.3 0.7 1.0
MN1 A:OEX412 3.4 0.5 1.0
O A:ALA344 3.4 0.7 1.0
CG A:ASP170 3.4 1.0 1.0
OD2 A:ASP170 3.5 0.7 1.0
MN3 A:OEX412 3.5 1.0 1.0
NE2 A:GLN165 3.7 0.6 1.0
MN4 A:OEX412 3.8 1.0 1.0
O4 A:OEX412 3.9 0.7 1.0
CD A:GLU189 4.0 0.3 1.0
O3 A:OEX412 4.1 0.6 1.0
OE2 A:GLU189 4.2 0.1 1.0
OH A:TYR161 4.4 0.3 1.0
C A:ALA344 4.4 0.2 1.0
OXT A:ALA344 4.6 0.7 1.0
CB A:ASP170 4.6 0.7 1.0
CD A:GLN165 4.8 0.0 1.0
NH1 C:ARG357 4.8 0.8 1.0
CG A:GLN165 5.0 0.8 1.0

Calcium binding site 2 out of 6 in 4tnk

Go back to Calcium Binding Sites List in 4tnk
Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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
K:Ca102

b:0.2
occ:1.00
 OD2 K:ASP19 2.5 0.2 1.0
OD2 K:ASP23 3.0 0.1 1.0
OD1 K:ASP23 3.2 0.4 1.0
CG K:ASP23 3.5 0.2 1.0
CG K:ASP19 3.5 0.8 1.0
OD1 K:ASP19 4.1 0.4 1.0
O K:ASP19 4.3 0.2 1.0
NE2 C:HIS74 4.3 0.6 1.0
CB K:ASP19 4.4 0.4 1.0
CE1 C:HIS74 4.5 0.6 1.0
C K:ASP19 4.6 0.9 1.0
O C:ALA73 4.6 0.4 1.0
CD2 C:HIS74 4.8 0.7 1.0
CB C:ALA73 4.9 0.1 1.0
CB K:ASP23 5.0 0.2 1.0

Calcium binding site 3 out of 6 in 4tnk

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Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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
O:Ca301

b:0.1
occ:1.00
 OE1 O:GLU140 2.7 0.2 1.0
NE2 O:HIS257 3.0 0.1 1.0
CD O:GLU140 3.6 0.8 1.0
CD2 O:HIS257 3.7 0.0 1.0
OE2 O:GLU140 3.8 0.5 1.0
CD O:GLU81 4.0 0.9 1.0
CE1 O:HIS257 4.0 0.4 1.0
CG O:GLU81 4.0 0.9 1.0
OE1 O:GLU81 4.2 0.3 1.0
OE2 O:GLU81 4.3 0.7 1.0
SD O:MET136 4.4 0.2 1.0
CE O:MET136 4.8 0.6 1.0
CG O:HIS257 4.9 0.8 1.0
CG O:GLU140 5.0 0.7 1.0

Calcium binding site 4 out of 6 in 4tnk

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Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca 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:Ca411

b:0.5
occ:1.00
 CA1 a:OEX411 0.0 0.5 1.0
O1 a:OEX411 2.0 0.0 1.0
O2 a:OEX411 3.0 0.3 1.0
O5 a:OEX411 3.0 0.5 1.0
OD1 a:ASP170 3.0 0.9 1.0
OE1 a:GLU189 3.1 0.2 1.0
MN2 a:OEX411 3.3 0.1 1.0
OD2 a:ASP170 3.4 0.4 1.0
MN1 a:OEX411 3.4 0.7 1.0
CG a:ASP170 3.4 0.6 1.0
O a:ALA344 3.5 0.6 1.0
MN3 a:OEX411 3.5 0.8 1.0
NE2 a:GLN165 3.6 0.9 1.0
MN4 a:OEX411 3.8 0.6 1.0
O4 a:OEX411 3.9 0.7 1.0
O3 a:OEX411 4.1 0.6 1.0
CD a:GLU189 4.1 0.5 1.0
OH a:TYR161 4.4 0.5 1.0
OE2 a:GLU189 4.4 0.7 1.0
C a:ALA344 4.5 0.5 1.0
CB a:ASP170 4.6 0.9 1.0
OXT a:ALA344 4.6 0.0 1.0
CD a:GLN165 4.6 0.7 1.0
NH1 c:ARG357 4.8 0.1 1.0
CG a:GLN165 4.9 0.4 1.0

Calcium binding site 5 out of 6 in 4tnk

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Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca 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
k:Ca101

b:0.4
occ:1.00
 OD2 k:ASP19 2.7 0.4 1.0
OD2 k:ASP23 2.9 0.7 1.0
OD1 k:ASP23 3.0 0.9 1.0
CG k:ASP23 3.3 0.5 1.0
CG k:ASP19 3.5 0.9 1.0
NE2 c:HIS74 4.0 0.1 1.0
OD1 k:ASP19 4.0 0.1 1.0
CE1 c:HIS74 4.1 0.9 1.0
O k:ASP19 4.2 0.0 1.0
CB k:ASP19 4.5 0.8 1.0
O c:ALA73 4.5 0.3 1.0
CD2 c:HIS74 4.5 0.1 1.0
C k:ASP19 4.6 0.0 1.0
CB c:ALA73 4.7 0.8 1.0
ND1 c:HIS74 4.7 0.6 1.0
CB k:ASP23 4.8 0.7 1.0
CG c:HIS74 5.0 0.7 1.0
CA k:ASP19 5.0 0.5 1.0

Calcium binding site 6 out of 6 in 4tnk

Go back to Calcium Binding Sites List in 4tnk
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca 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
o:Ca301

b:0.3
occ:1.00
 OE1 o:GLU140 2.7 0.5 1.0
NE2 o:HIS257 2.8 0.5 1.0
CD o:GLU140 3.5 0.9 1.0
CD2 o:HIS257 3.6 0.4 1.0
OE2 o:GLU140 3.7 0.9 1.0
CE1 o:HIS257 3.8 0.8 1.0
CD o:GLU81 3.9 0.6 1.0
CG o:GLU81 4.0 0.7 1.0
OE1 o:GLU81 4.0 0.3 1.0
OE2 o:GLU81 4.2 0.7 1.0
SD o:MET136 4.6 0.2 1.0
CG o:HIS257 4.8 0.6 1.0
ND1 o:HIS257 4.9 0.6 1.0
CG o:GLU140 4.9 0.1 1.0
CE o:MET136 5.0 0.4 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: Wed Jul 9 02:07:19 2025

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