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Calcium in PDB 6pfy: Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A

Enzymatic activity of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A

All present enzymatic activity of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A:
1.97.1.12;

Protein crystallography data

The structure of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A, PDB code: 6pfy was solved by R.Fromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.87 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 278.496, 165.126, 283.427, 90.00, 119.42, 90.00
R / Rfree (%) 30.3 / 34.3

Other elements in 6pfy:

The structure of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A also contains other interesting chemical elements:

Magnesium (Mg) 285 atoms
Iron (Fe) 36 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A (pdb code 6pfy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A, PDB code: 6pfy:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6pfy

Go back to Calcium Binding Sites List in 6pfy
Calcium binding site 1 out of 3 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca203

b:56.0
occ:1.00
O h:PHE153 2.3 32.4 1.0
OD2 L:ASP70 2.5 42.2 1.0
O L:PRO67 2.6 31.1 1.0
OD1 L:ASP70 3.1 40.5 1.0
OD2 A:ASP473 3.1 34.6 1.0
CG L:ASP70 3.2 41.5 1.0
C h:PHE153 3.5 33.5 1.0
CB h:ASN154 3.5 37.3 1.0
C L:PRO67 3.6 30.8 1.0
NE2 A:GLN472 3.7 24.2 1.0
ND2 h:ASN154 3.8 33.5 1.0
CA L:PRO67 3.9 29.8 1.0
CG A:ASP473 4.0 31.7 1.0
OD1 A:ASP473 4.0 31.1 1.0
CG h:ASN154 4.2 35.8 1.0
CA h:ASN154 4.2 38.1 1.0
N h:ASN154 4.3 35.6 1.0
CB L:PRO67 4.3 29.8 1.0
C h:ASN154 4.4 44.0 1.0
OXT h:ASN154 4.5 49.9 1.0
CA h:PHE153 4.6 32.8 1.0
CB L:ASP70 4.6 39.7 1.0
CB h:PHE153 4.6 32.8 1.0
NH2 A:ARG470 4.7 27.5 1.0
NE A:ARG470 4.8 28.9 1.0
N L:LEU68 4.8 32.7 1.0
CD A:GLN472 4.9 25.8 1.0

Calcium binding site 2 out of 3 in 6pfy

Go back to Calcium Binding Sites List in 6pfy
Calcium binding site 2 out of 3 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Ca1001

b:37.1
occ:1.00
O L:PHE153 2.1 35.8 1.0
OD1 U:ASP70 2.2 46.5 1.0
OD2 U:ASP70 2.5 44.8 1.0
O U:PRO67 2.5 33.7 1.0
CG U:ASP70 2.7 43.3 1.0
C L:PHE153 3.3 35.9 1.0
C U:PRO67 3.6 34.2 1.0
OD1 Y:ASP473 4.0 43.8 1.0
CB L:ASN154 4.0 43.3 1.0
CA L:PHE153 4.1 35.4 1.0
CB L:PHE153 4.2 34.6 1.0
NE2 Y:GLN472 4.2 38.0 1.0
CB U:ASP70 4.2 37.3 1.0
OXT L:ASN154 4.3 41.5 1.0
N L:ASN154 4.3 37.9 1.0
N U:LEU68 4.5 34.1 1.0
CA U:PRO67 4.5 33.1 1.0
OD2 Y:ASP473 4.5 43.8 1.0
CA L:ASN154 4.6 39.9 1.0
CA U:LEU68 4.6 32.6 1.0
CG Y:ASP473 4.7 40.1 1.0
C L:ASN154 4.8 38.8 1.0
N U:ASP70 4.9 36.5 1.0
CG L:ASN154 4.9 46.0 1.0
CB U:PRO67 5.0 34.3 1.0
CA U:ASP70 5.0 37.1 1.0

Calcium binding site 3 out of 3 in 6pfy

Go back to Calcium Binding Sites List in 6pfy
Calcium binding site 3 out of 3 in the Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Membrane Protein Megahertz Crystallography at the European Xfel, Photosystem I at Synchrotron to 2.9 A within 5.0Å range:
probe atom residue distance (Å) B Occ
h:Ca203

b:65.7
occ:1.00
O U:PHE153 2.0 30.8 1.0
OD2 h:ASP70 2.1 32.4 1.0
OD1 h:ASP70 2.6 33.4 1.0
CG h:ASP70 2.7 33.7 1.0
O h:PRO67 2.8 33.1 1.0
C U:PHE153 3.2 31.9 1.0
CB U:ASN154 3.8 34.6 1.0
C h:PRO67 3.9 31.6 1.0
OD2 G:ASP473 4.0 26.5 1.0
CA U:PHE153 4.0 32.4 1.0
NE2 G:GLN472 4.1 28.1 1.0
OXT U:ASN154 4.1 34.6 1.0
N U:ASN154 4.1 33.4 1.0
CB h:ASP70 4.1 33.9 1.0
CB U:PHE153 4.2 31.4 1.0
CG U:ASN154 4.4 36.4 1.0
CA U:ASN154 4.4 33.0 1.0
CA h:PRO67 4.4 31.4 1.0
OD1 G:ASP473 4.6 28.6 1.0
CG G:ASP473 4.7 27.2 1.0
C U:ASN154 4.7 32.8 1.0
OD1 U:ASN154 4.9 38.0 1.0
ND2 U:ASN154 4.9 36.8 1.0
N h:LEU68 4.9 29.9 1.0
CB h:PRO67 5.0 31.3 1.0

Reference:

C.Gisriel, J.Coe, R.Letrun, O.M.Yefanov, C.Luna-Chavez, N.E.Stander, S.Lisova, V.Mariani, M.Kuhn, S.Aplin, T.D.Grant, K.Dorner, T.Sato, A.Echelmeier, J.Cruz Villarreal, M.S.Hunter, M.O.Wiedorn, J.Knoska, V.Mazalova, S.Roy-Chowdhury, J.H.Yang, A.Jones, R.Bean, J.Bielecki, Y.Kim, G.Mills, B.Weinhausen, J.D.Meza, N.Al-Qudami, S.Bajt, G.Brehm, S.Botha, D.Boukhelef, S.Brockhauser, B.D.Bruce, M.A.Coleman, C.Danilevski, E.Discianno, Z.Dobson, H.Fangohr, J.M.Martin-Garcia, Y.Gevorkov, S.Hauf, A.Hosseinizadeh, F.Januschek, G.K.Ketawala, C.Kupitz, L.Maia, M.Manetti, M.Messerschmidt, T.Michelat, J.Mondal, A.Ourmazd, G.Previtali, I.Sarrou, S.Schon, P.Schwander, M.L.Shelby, A.Silenzi, J.Sztuk-Dambietz, J.Szuba, M.Turcato, T.A.White, K.Wrona, C.Xu, M.H.Abdellatif, J.D.Zook, J.C.H.Spence, H.N.Chapman, A.Barty, R.A.Kirian, M.Frank, A.Ros, M.Schmidt, R.Fromme, A.P.Mancuso, P.Fromme, N.A.Zatsepin. Membrane Protein Megahertz Crystallography at the European Xfel. Nat Commun V. 10 5021 2019.
ISSN: ESSN 2041-1723
PubMed: 31685819
DOI: 10.1038/S41467-019-12955-3
Page generated: Tue Jul 16 12:51:35 2024

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