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Calcium in PDB 4blo: P4 Protein From Bacteriophage PHI6 in Complex with Adp

Enzymatic activity of P4 Protein From Bacteriophage PHI6 in Complex with Adp

All present enzymatic activity of P4 Protein From Bacteriophage PHI6 in Complex with Adp:
3.6.1.15;

Protein crystallography data

The structure of P4 Protein From Bacteriophage PHI6 in Complex with Adp, PDB code: 4blo was solved by K.El Omari, C.Meier, D.Kainov, G.Sutton, J.M.Grimes, M.M.Poranen, D.H.Bamford, R.Tuma, D.I.Stuart, E.J.Mancini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 93.840, 95.260, 98.330, 82.46, 86.17, 64.85
R / Rfree (%) 21.7 / 24.41

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the P4 Protein From Bacteriophage PHI6 in Complex with Adp (pdb code 4blo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the P4 Protein From Bacteriophage PHI6 in Complex with Adp, PDB code: 4blo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 4blo

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Calcium binding site 1 out of 12 in the P4 Protein From Bacteriophage PHI6 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of P4 Protein From Bacteriophage PHI6 in Complex with Adp 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
O1A 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
O2A 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 12 in 4blo

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Calcium binding site 2 out of 12 in the P4 Protein From Bacteriophage PHI6 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of P4 Protein From Bacteriophage PHI6 in Complex with Adp 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
O1A 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
CG B:GLU150 4.9 45.4 1.0
CD B:GLU153 4.9 63.9 1.0
O1B B:ADP401 4.9 27.9 1.0

Calcium binding site 3 out of 12 in 4blo

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Calcium binding site 3 out of 12 in the P4 Protein From Bacteriophage PHI6 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of P4 Protein From Bacteriophage PHI6 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca400

b:68.2
occ:1.00
 OG C:SER133 2.3 75.4 1.0
O2B C:ADP401 2.4 70.5 1.0
CB C:SER133 3.3 69.4 1.0
PB C:ADP401 3.5 73.6 1.0
O3B C:ADP401 3.5 72.1 1.0
O1A C:ADP401 3.5 79.8 1.0
OE1 C:GLU150 3.5 88.3 1.0
OE2 C:GLU153 3.6 74.7 1.0
O3A C:ADP401 4.2 78.1 1.0
OD1 C:ASP187 4.2 71.3 1.0
CD C:GLU150 4.3 76.5 1.0
PA C:ADP401 4.4 81.5 1.0
N C:SER133 4.4 68.9 1.0
CA C:SER133 4.4 67.7 1.0
CD C:GLU153 4.5 93.3 1.0
OE1 C:GLU153 4.5 99.3 1.0
OD2 C:ASP187 4.6 81.2 1.0
OE2 C:GLU150 4.7 30.5 1.0
O1B C:ADP401 4.7 73.7 1.0
O2A C:ADP401 4.7 82.4 1.0
NH2 C:ARG147 4.8 57.5 1.0
CG C:ASP187 4.9 71.1 1.0

Calcium binding site 4 out of 12 in 4blo

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Calcium binding site 4 out of 12 in the P4 Protein From Bacteriophage PHI6 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of P4 Protein From Bacteriophage PHI6 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca400

b:70.9
occ:1.00
 OG D:SER133 2.2 64.2 1.0
O2B D:ADP401 2.6 82.0 1.0
OE1 D:GLU150 3.0 79.6 1.0
CB D:SER133 3.3 61.2 1.0
OE2 D:GLU153 3.6 60.7 1.0
O3B D:ADP401 3.8 82.1 1.0
PB D:ADP401 3.8 84.1 1.0
O1A D:ADP401 3.8 95.7 1.0
OD2 D:ASP187 4.1 71.1 1.0
CD D:GLU150 4.1 84.5 1.0
OD1 D:ASP187 4.1 54.7 1.0
CA D:SER133 4.4 59.0 1.0
N D:SER133 4.5 58.5 1.0
CG D:ASP187 4.5 59.0 1.0
CD D:GLU153 4.5 0.5 1.0
NH2 D:ARG147 4.5 78.6 1.0
O3A D:ADP401 4.6 91.8 1.0
OE1 D:GLU153 4.7 0.1 1.0
PA D:ADP401 4.7 97.4 1.0
OE2 D:GLU150 4.8 72.2 1.0
CG D:GLU150 4.9 64.8 1.0
O1B D:ADP401 4.9 82.6 1.0
O2A D:ADP401 5.0 97.0 1.0

Calcium binding site 5 out of 12 in 4blo

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Calcium binding site 5 out of 12 in the P4 Protein From Bacteriophage PHI6 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of P4 Protein From Bacteriophage PHI6 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca400

b:76.6
occ:1.00
 OG E:SER133 2.1 60.9 1.0
O2B E:ADP401 2.4 63.0 1.0
CB E:SER133 3.3 53.3 1.0
OE1 E:GLU150 3.3 65.5 1.0
PB E:ADP401 3.6 65.3 1.0
O3B E:ADP401 3.7 65.8 1.0
OD1 E:ASP187 3.9 46.4 1.0
OE2 E:GLU153 3.9 60.7 1.0
O1A E:ADP401 4.0 77.9 1.0
CD E:GLU150 4.1 72.5 1.0
OD2 E:ASP187 4.1 57.4 1.0
N E:SER133 4.3 49.6 1.0
CA E:SER133 4.3 49.6 1.0
CG E:ASP187 4.5 50.6 1.0
O3A E:ADP401 4.5 72.4 1.0
NH2 E:ARG147 4.7 53.2 1.0
O1B E:ADP401 4.7 64.4 1.0
OE2 E:GLU150 4.7 74.6 1.0
PA E:ADP401 4.8 77.0 1.0
CD E:GLU153 4.8 87.1 1.0
CG E:GLU150 4.9 48.4 1.0
OE1 E:GLU153 4.9 88.2 1.0

Calcium binding site 6 out of 12 in 4blo

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Calcium binding site 6 out of 12 in the P4 Protein From Bacteriophage PHI6 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of P4 Protein From Bacteriophage PHI6 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca400

b:70.9
occ:1.00
 O2B F:ADP401 2.5 63.0 1.0
OG F:SER133 2.6 57.2 1.0
O3B F:ADP401 3.4 65.4 1.0
OE1 F:GLU150 3.5 70.0 1.0
PB F:ADP401 3.5 66.0 1.0
CB F:SER133 3.8 54.7 1.0
OE2 F:GLU153 4.0 52.2 1.0
CD F:GLU150 4.0 68.6 1.0
OD1 F:ASP187 4.1 55.8 1.0
O1A F:ADP401 4.1 82.4 1.0
OD2 F:ASP187 4.4 68.4 1.0
OE2 F:GLU150 4.4 34.7 1.0
O3A F:ADP401 4.5 74.1 1.0
CG F:ASP187 4.7 58.2 1.0
O1B F:ADP401 4.7 63.1 1.0
N F:SER133 4.7 52.5 1.0
CG F:GLU150 4.7 47.5 1.0
CA F:SER133 4.8 51.9 1.0
PA F:ADP401 4.9 81.5 1.0
CD F:GLU153 4.9 76.3 1.0

Calcium binding site 7 out of 12 in 4blo

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Calcium binding site 7 out of 12 in the P4 Protein From Bacteriophage PHI6 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of P4 Protein From Bacteriophage PHI6 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca400

b:80.8
occ:1.00
 O2B G:ADP401 2.3 63.6 1.0
OG G:SER133 2.5 71.8 1.0
O3B G:ADP401 3.2 64.3 1.0
PB G:ADP401 3.3 66.0 1.0
OE1 G:GLU150 3.5 95.4 1.0
CB G:SER133 3.6 61.1 1.0
O1A G:ADP401 3.7 72.1 1.0
OE2 G:GLU153 3.9 30.5 1.0
O3A G:ADP401 4.2 69.8 1.0
OD1 G:ASP187 4.3 62.2 1.0
CD G:GLU150 4.3 86.6 1.0
O1B G:ADP401 4.5 65.1 1.0
N G:SER133 4.5 56.5 1.0
PA G:ADP401 4.5 73.8 1.0
CA G:SER133 4.6 56.7 1.0
OD2 G:ASP187 4.6 65.2 1.0
OE2 G:GLU150 4.8 66.0 1.0
CD G:GLU153 4.8 64.0 1.0
OE1 G:GLU153 4.9 74.9 1.0
O2A G:ADP401 4.9 74.9 1.0
CG G:ASP187 4.9 60.2 1.0

Calcium binding site 8 out of 12 in 4blo

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Calcium binding site 8 out of 12 in the P4 Protein From Bacteriophage PHI6 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of P4 Protein From Bacteriophage PHI6 in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca400

b:68.2
occ:1.00
 OG H:SER133 2.1 53.7 1.0
O2B H:ADP401 2.4 78.9 1.0
CB H:SER133 3.1 52.9 1.0
O1A H:ADP401 3.4 0.8 1.0
OE2 H:GLU153 3.5 42.5 1.0
OE1 H:GLU150 3.5 64.6 1.0
PB H:ADP401 3.5 81.8 1.0
O3B H:ADP401 3.6 77.9 1.0
OD2 H:ASP187 4.0 59.8 1.0
O3A H:ADP401 4.2 93.4 1.0
CA H:SER133 4.3 51.4 1.0
N H:SER133 4.3 52.1 1.0
PA H:ADP401 4.3 0.9 1.0
CD H:GLU153 4.4 65.1 1.0
OE1 H:GLU153 4.4 60.6 1.0
OD1 H:ASP187 4.4 53.0 1.0
CD H:GLU150 4.5 69.6 1.0
O2A H:ADP401 4.6 0.7 1.0
NH2 H:ARG147 4.7 77.7 1.0
CG H:ASP187 4.7 52.5 1.0
O1B H:ADP401 4.8 80.8 1.0

Calcium binding site 9 out of 12 in 4blo

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Calcium binding site 9 out of 12 in the P4 Protein From Bacteriophage PHI6 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of P4 Protein From Bacteriophage PHI6 in Complex with Adp 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
O1A 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
O2A 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 10 out of 12 in 4blo

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Calcium binding site 10 out of 12 in the P4 Protein From Bacteriophage PHI6 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of P4 Protein From Bacteriophage PHI6 in Complex with Adp 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
O1A 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

Reference:

K.El Omari, C.Meier, D.Kainov, G.Sutton, J.M.Grimes, M.M.Poranen, D.H.Bamford, R.Tuma, D.I.Stuart, E.J.Mancini. Tracking in Atomic Detail the Functional Specializations in Viral Reca Helicases That Occur During Evolution. Nucleic Acids Res. V. 41 9396 2013.
ISSN: ISSN 0305-1048
PubMed: 23939620
DOI: 10.1093/NAR/GKT713
Page generated: Sat Dec 12 04:41:12 2020

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