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Calcium in PDB 2ivz: Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain

Protein crystallography data

The structure of Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain, PDB code: 2ivz was solved by S.R.Loftus, D.Walker, M.J.Mate, D.A.Bonsor, R.James, G.R.Moore, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 144.34 / 2.0
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 130.092, 39.933, 154.848, 90.00, 110.62, 90.00
R / Rfree (%) 16.8 / 22.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain (pdb code 2ivz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain, PDB code: 2ivz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2ivz

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Calcium binding site 1 out of 7 in the Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1432

b:18.3
occ:1.00
 OD1 A:ASP337 2.3 12.6 1.0
O A:HOH2216 2.4 13.2 1.0
O A:HOH2212 2.4 18.2 1.0
O A:HOH2213 2.5 22.1 1.0
O A:HOH2214 2.5 12.1 1.0
O A:HOH2253 2.6 29.5 1.0
O A:HOH2044 2.6 28.8 1.0
O A:HOH2217 2.7 19.3 1.0
CG A:ASP337 3.4 10.9 1.0
OD2 A:ASP337 3.9 13.6 1.0
O A:ALA338 4.0 8.0 1.0
O A:HOH2180 4.1 16.2 1.0
O E:HOH2007 4.4 14.7 1.0
O A:HOH2181 4.5 8.1 1.0
O A:HOH2277 4.6 25.2 1.0
O A:ASP337 4.6 9.4 1.0
C A:ASP337 4.6 9.4 1.0
CB A:ASP337 4.6 10.3 1.0
O A:PRO381 4.7 9.2 1.0
CA A:ASP337 4.7 9.2 1.0
CB A:GLU293 4.8 8.0 1.0
C A:ALA338 4.9 8.0 1.0

Calcium binding site 2 out of 7 in 2ivz

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Calcium binding site 2 out of 7 in the Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1433

b:30.6
occ:1.00
 O A:HOH2182 2.2 15.1 1.0
O A:VAL340 2.3 10.8 1.0
O A:HOH2218 2.4 24.5 1.0
O A:HOH2183 2.4 41.8 1.0
O A:HOH2055 2.6 35.7 1.0
OD1 A:ASP339 2.6 16.2 1.0
O A:HOH2221 2.7 31.0 1.0
C A:VAL340 3.5 10.8 1.0
CG A:ASP339 3.8 12.1 1.0
O A:HOH2184 3.9 21.6 1.0
N A:VAL340 3.9 8.6 1.0
OG1 A:THR295 4.2 13.3 1.0
CA A:VAL340 4.2 9.6 1.0
OD2 A:ASP339 4.3 15.0 1.0
O A:TRP296 4.3 9.5 1.0
O A:HOH2048 4.4 31.6 1.0
O A:HOH2066 4.4 16.7 1.0
O A:HOH2255 4.4 34.1 1.0
O A:HOH2185 4.4 5.9 1.0
C A:SER341 4.5 13.9 1.0
N A:SER341 4.5 11.1 1.0
O A:HOH2146 4.6 29.4 1.0
O A:HOH2220 4.6 20.6 1.0
C A:ASP339 4.6 8.6 1.0
CA A:SER341 4.6 12.6 1.0
CB A:VAL340 4.7 9.9 1.0
N A:SER342 4.7 15.1 1.0
O A:SER341 4.7 13.2 1.0
CA A:ASP339 5.0 8.5 1.0
CB A:ASP339 5.0 8.6 1.0

Calcium binding site 3 out of 7 in 2ivz

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Calcium binding site 3 out of 7 in the Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1432

b:16.7
occ:1.00
 O B:HOH2248 2.4 17.5 1.0
OD1 B:ASP337 2.4 14.4 1.0
O B:HOH2282 2.4 27.4 1.0
O B:HOH2250 2.5 7.0 1.0
O B:HOH2281 2.5 9.3 1.0
O B:HOH2048 2.5 18.7 1.0
O B:HOH2247 2.5 22.1 1.0
O B:HOH2249 2.5 15.6 1.0
CG B:ASP337 3.5 12.0 1.0
OD2 B:ASP337 3.9 13.1 1.0
O B:HOH2200 4.0 11.7 1.0
O B:ALA338 4.0 6.8 1.0
O B:HOH2318 4.4 24.6 1.0
O B:HOH2201 4.6 6.9 1.0
O F:HOH2009 4.6 16.6 1.0
C B:ASP337 4.6 8.2 1.0
O B:ASP337 4.7 9.4 1.0
O B:PRO381 4.7 7.2 1.0
CB B:ASP337 4.7 9.0 1.0
CA B:ASP337 4.8 8.5 1.0
O B:HOH2283 4.9 27.4 1.0
CB B:GLU293 4.9 7.1 1.0
C B:ALA338 5.0 6.3 1.0

Calcium binding site 4 out of 7 in 2ivz

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Calcium binding site 4 out of 7 in the Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1432

b:16.9
occ:1.00
 OD1 C:ASP337 2.3 11.5 1.0
O C:HOH2272 2.5 18.1 1.0
O C:HOH2241 2.5 10.2 1.0
O C:HOH2238 2.5 14.8 1.0
O C:HOH2239 2.6 16.6 1.0
O C:HOH2273 2.6 15.4 1.0
O C:HOH2242 2.7 17.8 1.0
O C:HOH2054 2.8 20.7 1.0
CG C:ASP337 3.4 11.1 1.0
OD2 C:ASP337 3.8 13.1 1.0
O C:HOH2200 4.2 16.7 1.0
O C:ALA338 4.2 7.6 1.0
O G:HOH2009 4.4 15.9 1.0
O C:HOH2304 4.5 19.0 1.0
C C:ASP337 4.6 8.4 1.0
CB C:ASP337 4.6 9.1 1.0
O C:HOH2305 4.6 33.3 1.0
O C:ASP337 4.6 8.8 1.0
O C:HOH2199 4.6 9.4 1.0
O C:PRO381 4.6 6.7 1.0
CA C:ASP337 4.7 8.5 1.0
CB C:GLU293 4.8 7.4 1.0
O C:HOH2274 4.9 30.7 1.0

Calcium binding site 5 out of 7 in 2ivz

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Calcium binding site 5 out of 7 in the Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1433

b:29.2
occ:1.00
 O C:HOH2201 2.2 12.1 1.0
O C:HOH2070 2.3 30.4 1.0
O C:HOH2203 2.3 38.7 1.0
O C:VAL340 2.4 10.1 1.0
O C:HOH2244 2.5 26.2 1.0
OD1 C:ASP339 2.5 10.0 1.0
O C:HOH2243 2.9 35.8 1.0
C C:VAL340 3.5 9.8 1.0
CG C:ASP339 3.6 11.6 1.0
O C:HOH2099 3.7 35.9 1.0
N C:VAL340 3.8 9.0 1.0
OD2 C:ASP339 4.1 11.7 1.0
O C:HOH2245 4.1 25.3 1.0
OG1 C:THR295 4.2 10.6 1.0
CA C:VAL340 4.2 9.7 1.0
O C:HOH2085 4.4 25.4 1.0
O C:TRP296 4.5 7.7 1.0
O C:HOH2202 4.5 6.8 1.0
C C:ASP339 4.5 8.3 1.0
C C:SER341 4.6 12.9 1.0
O C:HOH2160 4.6 28.8 1.0
N C:SER341 4.6 10.7 1.0
O C:HOH2276 4.7 12.1 1.0
CB C:VAL340 4.7 9.4 1.0
CA C:SER341 4.7 11.7 1.0
O C:SER341 4.7 11.4 1.0
N C:SER342 4.8 14.6 1.0
CB C:ASP339 4.9 8.5 1.0
CA C:ASP339 4.9 8.3 1.0

Calcium binding site 6 out of 7 in 2ivz

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Calcium binding site 6 out of 7 in the Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1432

b:20.0
occ:1.00
 OD1 D:ASP337 2.4 16.1 1.0
O D:HOH2201 2.5 28.2 1.0
O D:HOH2204 2.5 15.2 1.0
O D:HOH2200 2.5 17.7 1.0
O D:HOH2234 2.6 49.2 1.0
O D:HOH2043 2.7 31.7 1.0
O D:HOH2203 2.7 22.3 1.0
O D:HOH2235 2.7 14.9 1.0
CG D:ASP337 3.4 12.3 1.0
OD2 D:ASP337 3.9 15.7 1.0
O D:HOH2165 4.0 16.5 1.0
O D:ALA338 4.2 10.3 1.0
O D:HOH2268 4.2 28.8 1.0
O H:HOH2009 4.4 19.0 1.0
O D:HOH2164 4.4 11.2 1.0
O D:HOH2269 4.6 17.9 1.0
C D:ASP337 4.6 9.9 1.0
O D:ASP337 4.6 10.1 1.0
CB D:ASP337 4.7 10.7 1.0
O D:PRO381 4.7 7.9 1.0
CA D:ASP337 4.8 10.4 1.0
CB D:GLU293 4.8 7.7 1.0
O D:HOH2236 4.9 34.4 1.0

Calcium binding site 7 out of 7 in 2ivz

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Calcium binding site 7 out of 7 in the Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Tolb in Complex with A Peptide of the Colicin E9 T-Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1433

b:28.5
occ:1.00
 O D:HOH2205 2.2 27.9 1.0
O D:VAL340 2.3 10.6 1.0
O D:HOH2167 2.3 37.0 1.0
O D:HOH2166 2.3 12.8 1.0
OD1 D:ASP339 2.4 17.6 1.0
O D:HOH2207 2.9 26.0 1.0
C D:VAL340 3.4 10.7 1.0
CG D:ASP339 3.6 13.9 1.0
N D:VAL340 3.8 9.6 1.0
O D:HOH2168 4.0 28.3 1.0
OD2 D:ASP339 4.1 13.4 1.0
CA D:VAL340 4.2 10.1 1.0
OG1 D:THR295 4.3 13.6 1.0
O D:TRP296 4.3 9.1 1.0
O D:HOH2078 4.4 31.8 1.0
N D:SER341 4.4 11.6 1.0
C D:SER341 4.5 14.1 1.0
O D:HOH2046 4.5 21.9 1.0
O D:HOH2069 4.5 21.4 1.0
C D:ASP339 4.5 9.5 1.0
O D:HOH2238 4.5 12.0 1.0
O D:HOH2169 4.6 9.5 1.0
CB D:VAL340 4.6 10.4 1.0
CA D:SER341 4.6 12.7 1.0
O D:SER341 4.7 12.8 1.0
N D:SER342 4.7 15.7 1.0
CB D:ASP339 4.8 10.6 1.0
CA D:ASP339 4.9 10.2 1.0
O D:HOH2137 5.0 30.2 1.0

Reference:

S.R.Loftus, D.Walker, M.J.Mate, D.A.Bonsor, R.James, G.R.Moore, C.Kleanthous. Competitive Recruitment of the Periplasmic Translocation Portal Tolb By A Natively Disordered Domain of Colicin E9 Proc.Natl.Acad.Sci.Usa V. 103 12353 2006.
ISSN: ISSN 0027-8424
PubMed: 16894158
DOI: 10.1073/PNAS.0603433103
Page generated: Tue Jul 8 06:18:03 2025

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