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Calcium in PDB 5muw: Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex

Enzymatic activity of Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex

All present enzymatic activity of Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex:
3.6.1.15;

Calcium Binding Sites:

The binding sites of Calcium atom in the Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex (pdb code 5muw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex, PDB code: 5muw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5muw

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Calcium binding site 1 out of 6 in the Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca400

b:65.1
occ:1.00
 OG A:SER133 2.2 40.5 1.0
O2B A:ADP401 2.2 38.8 1.0
OE1 A:GLU150 3.3 66.8 1.0
CB A:SER133 3.3 34.1 1.0
PB A:ADP401 3.4 37.3 1.0
O3B A:ADP401 3.4 33.4 1.0
O2A A:ADP401 3.9 45.9 1.0
OD1 A:ASP187 4.0 34.6 1.0
OE2 A:GLU153 4.1 37.5 1.0
N A:SER133 4.1 31.9 1.0
OD2 A:ASP187 4.2 49.4 1.0
CA A:SER133 4.2 32.3 1.0
O3A A:ADP401 4.3 43.5 1.0
CD A:GLU150 4.3 59.4 1.0
O1B A:ADP401 4.5 37.7 1.0
CG A:ASP187 4.6 36.8 1.0
PA A:ADP401 4.6 49.0 1.0
O1A A:ADP401 4.8 50.1 1.0
OE2 A:GLU150 4.9 22.3 1.0
NH2 A:ARG147 5.0 74.1 1.0

Calcium binding site 2 out of 6 in 5muw

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Calcium binding site 2 out of 6 in the Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca400

b:55.1
occ:1.00
 OG B:SER133 2.3 36.2 1.0
O2B B:ADP401 2.6 29.5 1.0
OE1 B:GLU150 3.2 52.2 1.0
CB B:SER133 3.5 27.2 1.0
OD1 B:ASP187 3.8 37.4 1.0
O3B B:ADP401 3.8 24.1 1.0
PB B:ADP401 3.8 29.3 1.0
OE2 B:GLU153 3.9 42.7 1.0
CD B:GLU150 4.0 61.3 1.0
OD2 B:ASP187 4.1 35.7 1.0
O2A B:ADP401 4.2 44.9 1.0
CG B:ASP187 4.4 36.2 1.0
N B:SER133 4.5 27.9 1.0
OE2 B:GLU150 4.5 26.6 1.0
CA B:SER133 4.5 26.8 1.0
NH2 B:ARG147 4.6 49.2 1.0
O3A B:ADP401 4.8 37.5 1.0
CD B:GLU153 4.9 63.9 1.0
CG B:GLU150 4.9 45.4 1.0
O1B B:ADP401 4.9 27.9 1.0

Calcium binding site 3 out of 6 in 5muw

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Calcium binding site 3 out of 6 in the Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca400

b:49.8
occ:1.00
 OG I:SER133 2.4 36.7 1.0
O2B I:ADP401 2.5 33.5 1.0
CB I:SER133 3.1 31.1 1.0
OE1 I:GLU150 3.1 40.9 1.0
OE2 I:GLU153 3.3 42.5 1.0
O2A I:ADP401 3.5 52.8 1.0
PB I:ADP401 3.7 38.5 1.0
O3B I:ADP401 3.9 37.8 1.0
CD I:GLU153 4.2 71.6 1.0
OE1 I:GLU153 4.2 71.9 1.0
O3A I:ADP401 4.3 48.4 1.0
CD I:GLU150 4.4 59.2 1.0
PA I:ADP401 4.4 54.2 1.0
OD1 I:ASP187 4.4 27.1 1.0
CA I:SER133 4.4 29.0 1.0
N I:SER133 4.5 28.5 1.0
OD2 I:ASP187 4.5 38.2 1.0
NH2 I:ARG147 4.6 69.6 1.0
O1A I:ADP401 4.6 54.3 1.0
CG I:ASP187 4.9 30.1 1.0
O1B I:ADP401 5.0 38.1 1.0

Calcium binding site 4 out of 6 in 5muw

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Calcium binding site 4 out of 6 in the Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca400

b:48.8
occ:1.00
 OG J:SER133 2.4 45.7 1.0
O2B J:ADP401 2.6 52.2 1.0
OE1 J:GLU150 3.4 45.1 1.0
CB J:SER133 3.5 33.5 1.0
O3B J:ADP401 3.6 52.5 1.0
PB J:ADP401 3.7 51.3 1.0
OE2 J:GLU153 3.7 36.3 1.0
O2A J:ADP401 3.8 54.6 1.0
OD1 J:ASP187 4.1 22.7 1.0
OD2 J:ASP187 4.2 28.8 1.0
CD J:GLU150 4.3 46.0 1.0
O3A J:ADP401 4.5 52.8 1.0
N J:SER133 4.5 30.0 1.0
CA J:SER133 4.6 30.5 1.0
CG J:ASP187 4.6 26.1 1.0
CD J:GLU153 4.6 54.6 1.0
PA J:ADP401 4.7 54.6 1.0
NH2 J:ARG147 4.7 52.5 1.0
OE1 J:GLU153 4.8 56.8 1.0
O1B J:ADP401 4.8 48.3 1.0
OE2 J:GLU150 5.0 22.1 1.0

Calcium binding site 5 out of 6 in 5muw

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Calcium binding site 5 out of 6 in the Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca400

b:61.6
occ:1.00
 OG K:SER133 2.4 43.8 1.0
O2B K:ADP401 2.6 49.2 1.0
OE1 K:GLU150 3.1 61.4 1.0
O3B K:ADP401 3.5 51.2 1.0
OE2 K:GLU153 3.5 47.1 1.0
CB K:SER133 3.6 39.5 1.0
PB K:ADP401 3.7 50.6 1.0
O2A K:ADP401 3.8 65.1 1.0
CD K:GLU150 4.1 54.0 1.0
OD1 K:ASP187 4.2 29.9 1.0
OD2 K:ASP187 4.4 45.1 1.0
CD K:GLU153 4.5 72.7 1.0
O3A K:ADP401 4.5 57.5 1.0
NH2 K:ARG147 4.6 39.8 1.0
OE1 K:GLU153 4.6 80.8 1.0
N K:SER133 4.6 38.2 1.0
CA K:SER133 4.7 38.0 1.0
PA K:ADP401 4.7 65.5 1.0
CG K:ASP187 4.7 34.6 1.0
OE2 K:GLU150 4.7 52.6 1.0
O1B K:ADP401 4.9 50.1 1.0
CG K:GLU150 4.9 31.3 1.0

Calcium binding site 6 out of 6 in 5muw

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Calcium binding site 6 out of 6 in the Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Atomic Structure of P4 Packaging Enzyme Fitted Into A Localized Reconstruction of Bacteriophage PHI6 Vertex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca400

b:50.2
occ:1.00
 OG L:SER133 2.3 30.6 1.0
O2B L:ADP401 2.5 45.1 1.0
CB L:SER133 3.2 29.6 1.0
OE2 L:GLU153 3.5 24.8 1.0
OE1 L:GLU150 3.5 53.5 1.0
O2A L:ADP401 3.5 57.3 1.0
O3B L:ADP401 3.5 39.8 1.0
PB L:ADP401 3.6 44.4 1.0
O3A L:ADP401 4.3 49.4 1.0
CD L:GLU153 4.3 59.1 1.0
OE1 L:GLU153 4.4 65.6 1.0
OD2 L:ASP187 4.4 51.4 1.0
PA L:ADP401 4.4 56.3 1.0
OD1 L:ASP187 4.4 30.4 1.0
CA L:SER133 4.4 29.4 1.0
N L:SER133 4.5 29.1 1.0
CD L:GLU150 4.5 52.9 1.0
NH2 L:ARG147 4.6 48.4 1.0
O1A L:ADP401 4.8 55.5 1.0
O1B L:ADP401 4.8 42.8 1.0
CG L:ASP187 4.9 37.4 1.0

Reference:

Z.Sun, K.El Omari, X.Sun, S.L.Ilca, A.Kotecha, D.I.Stuart, M.M.Poranen, J.T.Huiskonen. Double-Stranded Rna Virus Outer Shell Assembly By Bona Fide Domain-Swapping. Nat Commun V. 8 14814 2017.
ISSN: ESSN 2041-1723
PubMed: 28287099
DOI: 10.1038/NCOMMS14814
Page generated: Mon Jul 15 08:38:34 2024

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