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Calcium in PDB 2jes: Portal Protein (GP6) From Bacteriophage SPP1

Protein crystallography data

The structure of Portal Protein (GP6) From Bacteriophage SPP1, PDB code: 2jes was solved by A.A.Lebedev, M.H.Krause, A.L.Isidro, A.A.Vagin, E.V.Orlova, J.Turner, E.J.Dodson, P.Tavares, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.81 / 3.40
Space group C 2 2 21 1
Cell size a, b, c (Å), α, β, γ (°) 174.314, 221.405, 421.866, 90.00, 90.00, 90.00
R / Rfree (%) 28.8 / 31.9

Other elements in 2jes:

The structure of Portal Protein (GP6) From Bacteriophage SPP1 also contains other interesting chemical elements:

Mercury (Hg) 13 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Portal Protein (GP6) From Bacteriophage SPP1 (pdb code 2jes). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Portal Protein (GP6) From Bacteriophage SPP1, PDB code: 2jes:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in 2jes

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Calcium binding site 1 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:0.2
occ:1.00
 OD1 C:ASP262 2.4 0.2 1.0
OE2 A:GLU60 2.5 0.2 1.0
O A:ARG83 2.6 0.2 1.0
OE1 A:GLU60 2.9 0.2 1.0
CD A:GLU60 3.1 0.2 1.0
CG C:ASP262 3.1 0.2 1.0
OD2 C:ASP262 3.2 0.2 1.0
C A:ARG83 3.8 0.2 1.0
CG A:ARG83 4.4 0.2 1.0
OG A:SER85 4.4 0.2 1.0
CB C:ASP262 4.5 0.2 1.0
CA A:THR84 4.6 0.2 1.0
N A:SER85 4.6 0.2 1.0
CG A:GLU60 4.6 0.2 1.0
N A:THR84 4.6 0.2 1.0
CA A:ARG83 4.8 0.2 1.0

Calcium binding site 2 out of 13 in 2jes

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Calcium binding site 2 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca801

b:0.2
occ:1.00
 OE2 C:GLU60 2.3 0.2 1.0
O C:ARG83 2.5 0.2 1.0
OD1 E:ASP262 2.6 0.2 1.0
OE1 C:GLU60 2.6 0.2 1.0
CD C:GLU60 2.8 0.2 1.0
OD2 E:ASP262 2.8 0.2 1.0
CG E:ASP262 3.1 0.2 1.0
C C:ARG83 3.8 0.2 1.0
OG C:SER85 4.3 0.2 1.0
CG C:GLU60 4.4 0.2 1.0
CG C:ARG83 4.4 0.2 1.0
N C:SER85 4.4 0.2 1.0
CA C:THR84 4.5 0.2 1.0
CB E:ASP262 4.5 0.2 1.0
N C:THR84 4.5 0.2 1.0
CA C:ARG83 4.8 0.2 1.0
C C:THR84 4.9 0.2 1.0
CB C:ARG83 5.0 0.2 1.0

Calcium binding site 3 out of 13 in 2jes

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Calcium binding site 3 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca801

b:0.2
occ:1.00
 O E:ARG83 2.5 0.2 1.0
OD1 G:ASP262 2.5 0.2 1.0
OE2 E:GLU60 2.5 0.2 1.0
OD2 G:ASP262 2.7 0.2 1.0
OE1 E:GLU60 2.9 0.2 1.0
CG G:ASP262 2.9 0.2 1.0
CD E:GLU60 3.1 0.2 1.0
C E:ARG83 3.7 0.2 1.0
OG E:SER85 4.1 0.2 1.0
CG E:ARG83 4.4 0.2 1.0
N E:SER85 4.4 0.2 1.0
CA E:THR84 4.4 0.2 1.0
CB G:ASP262 4.5 0.2 1.0
N E:THR84 4.5 0.2 1.0
CG E:GLU60 4.6 0.2 1.0
CA E:ARG83 4.8 0.2 1.0
C E:THR84 4.9 0.2 1.0
CB E:ARG83 5.0 0.2 1.0

Calcium binding site 4 out of 13 in 2jes

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Calcium binding site 4 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca801

b:0.2
occ:1.00
 OD1 I:ASP262 2.4 0.2 1.0
OE2 G:GLU60 2.4 0.2 1.0
O G:ARG83 2.6 0.2 1.0
OE1 G:GLU60 2.9 0.2 1.0
CD G:GLU60 3.0 0.2 1.0
OD2 I:ASP262 3.1 0.2 1.0
CG I:ASP262 3.1 0.2 1.0
C G:ARG83 3.8 0.2 1.0
OG G:SER85 4.1 0.2 1.0
N G:SER85 4.5 0.2 1.0
CG G:GLU60 4.5 0.2 1.0
CA G:THR84 4.5 0.2 1.0
CG G:ARG83 4.6 0.2 1.0
CB I:ASP262 4.6 0.2 1.0
N G:THR84 4.6 0.2 1.0
CA G:ARG83 4.9 0.2 1.0
C G:THR84 4.9 0.2 1.0

Calcium binding site 5 out of 13 in 2jes

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Calcium binding site 5 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca801

b:0.2
occ:1.00
 OE2 I:GLU60 2.2 0.2 1.0
O I:ARG83 2.5 0.2 1.0
OD1 K:ASP262 2.6 0.2 1.0
OE1 I:GLU60 2.6 0.2 1.0
CD I:GLU60 2.7 0.2 1.0
OD2 K:ASP262 2.9 0.2 1.0
CG K:ASP262 3.1 0.2 1.0
C I:ARG83 3.7 0.2 1.0
OG I:SER85 4.0 0.2 1.0
CG I:GLU60 4.3 0.2 1.0
CG I:ARG83 4.4 0.2 1.0
N I:SER85 4.5 0.2 1.0
CA I:THR84 4.5 0.2 1.0
N I:THR84 4.5 0.2 1.0
CB K:ASP262 4.6 0.2 1.0
CA I:ARG83 4.8 0.2 1.0
C I:THR84 4.9 0.2 1.0
CB I:SER85 5.0 0.2 1.0

Calcium binding site 6 out of 13 in 2jes

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Calcium binding site 6 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca801

b:0.2
occ:1.00
 OE2 K:GLU60 2.4 0.2 1.0
OD1 M:ASP262 2.5 0.2 1.0
O K:ARG83 2.6 0.2 1.0
OE1 K:GLU60 2.8 0.2 1.0
CD K:GLU60 3.0 0.2 1.0
OD2 M:ASP262 3.2 0.2 1.0
CG M:ASP262 3.2 0.2 1.0
C K:ARG83 3.8 0.2 1.0
OG K:SER85 4.0 0.2 1.0
CG K:ARG83 4.5 0.2 1.0
CG K:GLU60 4.5 0.2 1.0
N K:SER85 4.5 0.2 1.0
CA K:THR84 4.5 0.2 1.0
N K:THR84 4.6 0.2 1.0
CB M:ASP262 4.7 0.2 1.0
CA K:ARG83 4.8 0.2 1.0
C K:THR84 5.0 0.2 1.0

Calcium binding site 7 out of 13 in 2jes

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Calcium binding site 7 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca801

b:0.2
occ:1.00
 O M:ARG83 2.5 0.2 1.0
OD1 O:ASP262 2.5 0.2 1.0
OE2 M:GLU60 2.7 0.2 1.0
OE1 M:GLU60 3.1 0.2 1.0
OD2 O:ASP262 3.1 0.2 1.0
CG O:ASP262 3.1 0.2 1.0
CD M:GLU60 3.3 0.2 1.0
C M:ARG83 3.7 0.2 1.0
OG M:SER85 4.2 0.2 1.0
CG M:ARG83 4.4 0.2 1.0
CA M:THR84 4.4 0.2 1.0
N M:THR84 4.5 0.2 1.0
N M:SER85 4.6 0.2 1.0
CB O:ASP262 4.6 0.2 1.0
CA M:ARG83 4.8 0.2 1.0
CG M:GLU60 4.8 0.2 1.0
C M:THR84 5.0 0.2 1.0

Calcium binding site 8 out of 13 in 2jes

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Calcium binding site 8 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca801

b:0.2
occ:1.00
 OD1 Q:ASP262 2.5 0.2 1.0
OE2 O:GLU60 2.6 0.2 1.0
O O:ARG83 2.6 0.2 1.0
OE1 O:GLU60 2.9 0.2 1.0
OD2 Q:ASP262 2.9 0.2 1.0
CG Q:ASP262 3.1 0.2 1.0
CD O:GLU60 3.1 0.2 1.0
C O:ARG83 3.8 0.2 1.0
CG O:ARG83 4.3 0.2 1.0
OG O:SER85 4.3 0.2 1.0
CB Q:ASP262 4.6 0.2 1.0
CG O:GLU60 4.7 0.2 1.0
CA O:THR84 4.7 0.2 1.0
N O:THR84 4.7 0.2 1.0
N O:SER85 4.8 0.2 1.0
CA O:ARG83 4.8 0.2 1.0

Calcium binding site 9 out of 13 in 2jes

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Calcium binding site 9 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ca801

b:0.2
occ:1.00
 OE2 Q:GLU60 2.4 0.2 1.0
O Q:ARG83 2.4 0.2 1.0
OD2 S:ASP262 2.5 0.2 1.0
OE1 Q:GLU60 2.8 0.2 1.0
OD1 S:ASP262 2.8 0.2 1.0
CD Q:GLU60 2.9 0.2 1.0
CG S:ASP262 3.0 0.2 1.0
C Q:ARG83 3.6 0.2 1.0
CG Q:ARG83 4.3 0.2 1.0
OG Q:SER85 4.3 0.2 1.0
CA Q:THR84 4.4 0.2 1.0
N Q:THR84 4.4 0.2 1.0
CG Q:GLU60 4.5 0.2 1.0
CB S:ASP262 4.6 0.2 1.0
N Q:SER85 4.6 0.2 1.0
CA Q:ARG83 4.7 0.2 1.0
C Q:THR84 4.9 0.2 1.0
CB Q:ARG83 4.9 0.2 1.0

Calcium binding site 10 out of 13 in 2jes

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Calcium binding site 10 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ca801

b:0.2
occ:1.00
 OD1 U:ASP262 2.5 0.2 1.0
OE2 S:GLU60 2.6 0.2 1.0
O S:ARG83 2.6 0.2 1.0
OE1 S:GLU60 2.7 0.2 1.0
OD2 U:ASP262 2.8 0.2 1.0
CD S:GLU60 3.0 0.2 1.0
CG U:ASP262 3.0 0.2 1.0
C S:ARG83 3.8 0.2 1.0
CG S:ARG83 4.5 0.2 1.0
CB U:ASP262 4.5 0.2 1.0
CG S:GLU60 4.6 0.2 1.0
CA S:THR84 4.6 0.2 1.0
N S:THR84 4.7 0.2 1.0
OG S:SER85 4.7 0.2 1.0
N S:SER85 4.8 0.2 1.0
CA S:ARG83 4.9 0.2 1.0

Reference:

A.A.Lebedev, M.H.Krause, A.L.Isidro, A.A.Vagin, E.V.Orlova, J.Turner, E.J.Dodson, P.Tavares, A.A.Antson. Structural Framework For Dna Translocation Via the Viral Portal Protein Embo J. V. 26 1984 2007.
ISSN: ISSN 0261-4189
PubMed: 17363899
DOI: 10.1038/SJ.EMBOJ.7601643
Page generated: Fri Jul 12 13:44:23 2024

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