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Calcium in PDB 5whv: Crystal Structure of Artb

Protein crystallography data

The structure of Crystal Structure of Artb, PDB code: 5whv was solved by X.Gao, J.E.Galan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.12 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.872, 94.231, 125.230, 90.00, 103.62, 90.00
R / Rfree (%) 16.7 / 21.3

Other elements in 5whv:

The structure of Crystal Structure of Artb also contains other interesting chemical elements:

Chlorine (Cl) 11 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Artb (pdb code 5whv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Artb, PDB code: 5whv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 5whv

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Calcium binding site 1 out of 9 in the Crystal Structure of Artb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:21.9
occ:1.00
 O A:CYS128 2.3 19.6 1.0
O H:HOH374 2.3 23.1 1.0
O D:HOH319 2.3 20.1 1.0
O A:HOH321 2.3 32.3 1.0
O A:HOH303 2.4 17.5 1.0
OD1 H:ASP132 2.4 21.1 1.0
OD2 H:ASP132 2.5 22.0 1.0
CG H:ASP132 2.8 26.5 1.0
C A:CYS128 3.5 26.7 1.0
OH D:TYR93 4.1 21.8 1.0
N A:CYS128 4.2 24.8 1.0
OE2 A:GLU97 4.2 17.5 1.0
O H:HOH325 4.3 18.1 1.0
CB H:ASP132 4.3 19.9 1.0
N A:THR129 4.4 31.5 1.0
CA A:CYS128 4.4 22.7 1.0
CA A:THR129 4.5 34.6 1.0
O A:ASP98 4.5 27.6 1.0
O H:HOH314 4.6 33.8 1.0
OD1 D:ASN37 4.8 26.3 1.0
CB H:SER131 5.0 33.9 1.0
CB A:THR127 5.0 16.1 1.0

Calcium binding site 2 out of 9 in 5whv

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Calcium binding site 2 out of 9 in the Crystal Structure of Artb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca205

b:64.9
occ:1.00
 O B:HOH319 2.4 43.5 1.0
O B:CYS128 2.5 41.2 1.0
O B:HOH305 2.9 29.7 1.0
C B:CYS128 3.7 29.9 1.0
O B:HOH341 4.0 37.4 1.0
O B:HOH301 4.1 41.3 1.0
OH C:TYR93 4.3 26.3 1.0
CA B:THR129 4.4 54.1 1.0
N B:THR129 4.5 52.6 1.0
OE2 B:GLU97 4.6 22.3 1.0
N B:CYS128 4.6 29.5 1.0
CA B:CYS128 4.8 27.5 1.0
C B:THR129 4.9 61.5 1.0
O B:THR129 4.9 67.9 1.0
O B:ASP98 4.9 26.8 1.0

Calcium binding site 3 out of 9 in 5whv

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Calcium binding site 3 out of 9 in the Crystal Structure of Artb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca206

b:49.3
occ:1.00
 O E:HOH352 2.3 55.2 1.0
O E:CYS128 2.5 30.7 1.0
O E:HOH304 2.5 30.9 1.0
O E:HOH324 2.6 47.3 1.0
O B:HOH310 2.6 29.7 1.0
O B:HOH343 2.7 42.9 1.0
C E:CYS128 3.6 33.2 1.0
OH B:TYR93 4.0 20.5 1.0
O E:HOH345 4.0 36.5 1.0
OE2 E:GLU97 4.1 21.1 1.0
CA E:THR129 4.3 45.8 1.0
N E:THR129 4.4 40.9 1.0
N E:CYS128 4.4 29.4 1.0
CA E:CYS128 4.6 30.4 1.0
O E:ASP98 4.8 23.4 1.0
CG2 E:THR129 5.0 45.6 1.0
O E:HOH350 5.0 34.5 1.0

Calcium binding site 4 out of 9 in 5whv

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Calcium binding site 4 out of 9 in the Crystal Structure of Artb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca207

b:54.9
occ:1.00
 O E:HOH323 2.7 14.1 1.0
O E:THR95 2.7 18.6 1.0
O F:HOH322 2.8 19.4 1.0
O F:HOH332 2.9 22.9 1.0
CB F:PRO64 3.1 15.3 1.0
CA F:PRO64 3.5 20.6 1.0
C E:THR95 3.5 18.7 1.0
CA E:THR95 3.7 17.5 1.0
NE F:ARG59 3.8 36.5 1.0
CD F:ARG59 3.8 28.3 1.0
CG F:PRO64 4.2 23.7 1.0
H42 E:PEG202 4.3 82.7 1.0
CB E:THR95 4.3 18.4 1.0
N F:PRO64 4.3 20.5 1.0
H41 E:PEG202 4.3 82.7 1.0
O4 E:PEG202 4.4 68.2 1.0
O E:ALA94 4.4 24.1 1.0
CD F:PRO64 4.5 18.7 1.0
C4 E:PEG202 4.6 69.0 1.0
OE1 F:GLN30 4.6 31.6 1.0
CB F:ARG59 4.6 16.1 1.0
O F:HOH357 4.6 20.1 1.0
C F:PRO64 4.7 25.3 1.0
N F:ASN65 4.7 24.7 1.0
CG F:ARG59 4.8 17.2 1.0
O F:HOH329 4.8 34.4 1.0
N E:GLY96 4.8 24.1 1.0
O F:HOH374 4.8 31.9 1.0
N E:THR95 4.9 18.6 1.0
HO4 E:PEG202 4.9 81.9 1.0
CZ F:ARG59 4.9 31.2 1.0
O F:HOH342 5.0 40.9 1.0

Calcium binding site 5 out of 9 in 5whv

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Calcium binding site 5 out of 9 in the Crystal Structure of Artb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca207

b:38.9
occ:1.00
 O F:CYS128 2.4 30.5 1.0
O F:HOH310 2.4 16.0 1.0
O I:HOH336 2.4 23.4 1.0
O F:HOH376 2.6 40.3 1.0
O I:HOH330 2.6 47.2 1.0
O F:HOH373 3.0 49.6 1.0
C F:CYS128 3.6 27.2 1.0
O F:HOH352 3.8 25.7 1.0
OH I:TYR93 4.1 19.8 1.0
OE2 F:GLU97 4.3 27.6 1.0
N F:CYS128 4.4 22.7 1.0
N F:THR129 4.5 36.1 1.0
CA F:THR129 4.5 43.0 1.0
CA F:CYS128 4.5 24.8 1.0
O F:ASP98 4.6 20.6 1.0
CB F:GLU97 4.9 16.9 1.0
O F:HOH331 5.0 42.5 1.0

Calcium binding site 6 out of 9 in 5whv

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Calcium binding site 6 out of 9 in the Crystal Structure of Artb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca205

b:43.4
occ:1.00
 O G:HOH349 2.0 56.7 1.0
O G:CYS128 2.4 31.8 1.0
O G:HOH310 2.5 15.6 1.0
O H:HOH333 2.7 26.0 1.0
O G:HOH357 3.0 38.1 1.0
C G:CYS128 3.5 25.1 1.0
OH H:TYR93 3.8 20.4 1.0
CA G:THR129 4.1 30.5 1.0
O G:HOH321 4.2 26.2 1.0
N G:THR129 4.2 29.9 1.0
OE2 G:GLU97 4.3 23.5 1.0
N G:CYS128 4.3 22.5 1.0
CA G:CYS128 4.5 21.5 1.0
CG2 G:THR129 4.6 21.6 1.0
O G:ASP98 4.8 18.1 1.0
CB G:THR127 4.9 16.7 1.0
C G:THR129 5.0 32.8 1.0

Calcium binding site 7 out of 9 in 5whv

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Calcium binding site 7 out of 9 in the Crystal Structure of Artb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca205

b:25.9
occ:1.00
 O H:CYS128 2.3 25.8 1.0
O H:HOH306 2.6 15.0 1.0
O H:HOH322 2.6 27.3 1.0
C H:CYS128 3.5 26.1 1.0
O F:HOH334 3.8 28.2 1.0
N H:CYS128 4.1 19.4 1.0
OH F:TYR93 4.2 8.9 1.0
CA H:THR129 4.2 30.5 1.0
OE2 H:GLU97 4.3 13.9 1.0
N H:THR129 4.3 32.0 1.0
CA H:CYS128 4.4 23.2 1.0
O H:ASP98 4.5 12.8 1.0
O H:THR129 4.6 33.1 1.0
C H:THR129 4.6 30.0 1.0
OD1 F:ASN37 4.7 14.5 1.0
CB H:THR127 4.9 16.4 1.0
O H:HOH344 5.0 19.6 1.0

Calcium binding site 8 out of 9 in 5whv

Go back to Calcium Binding Sites List in 5whv
Calcium binding site 8 out of 9 in the Crystal Structure of Artb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca206

b:43.2
occ:1.00
 O I:HOH311 2.1 39.7 1.0
O I:CYS128 2.3 38.1 1.0
O J:HOH351 2.5 31.1 1.0
O I:HOH309 2.5 18.2 1.0
O I:HOH366 2.5 41.7 1.0
O I:HOH364 3.0 38.7 1.0
C I:CYS128 3.5 25.2 1.0
OH J:TYR93 4.0 20.0 1.0
OE2 I:GLU97 4.1 24.0 1.0
CA I:THR129 4.2 38.7 1.0
N I:CYS128 4.2 20.7 1.0
N I:THR129 4.3 33.2 1.0
CA I:CYS128 4.5 23.7 1.0
O I:HOH343 4.5 19.7 1.0
O J:HOH384 4.5 52.6 1.0
O I:ASP98 4.7 20.0 1.0
CG2 I:THR129 4.9 29.2 1.0
CB I:THR127 5.0 21.7 1.0
CD I:GLU97 5.0 24.5 1.0
ND2 J:ASN37 5.0 16.1 1.0

Calcium binding site 9 out of 9 in 5whv

Go back to Calcium Binding Sites List in 5whv
Calcium binding site 9 out of 9 in the Crystal Structure of Artb


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca204

b:44.1
occ:1.00
 O J:HOH374 2.3 29.0 1.0
O G:HOH339 2.3 35.6 1.0
O J:HOH328 2.5 40.0 1.0
O J:CYS128 2.5 27.2 1.0
O J:HOH308 2.5 21.1 1.0
C J:CYS128 3.7 27.0 1.0
O J:HOH335 4.1 26.3 1.0
OH G:TYR93 4.3 26.5 1.0
OE2 J:GLU97 4.4 20.5 1.0
N J:CYS128 4.4 26.1 1.0
CA J:THR129 4.5 33.0 1.0
N J:THR129 4.5 37.2 1.0
CA J:CYS128 4.7 25.8 1.0
O J:ASP98 4.7 17.1 1.0
O J:HOH334 5.0 38.7 1.0

Reference:

X.Gao, L.Deng, G.Stack, H.Yu, X.Chen, Y.Naito-Matsui, A.Varki, J.E.Galan. Evolution of Host Adaptation in the Salmonella Typhoid Toxin. Nat Microbiol V. 2 1592 2017.
ISSN: ESSN 2058-5276
PubMed: 28993610
DOI: 10.1038/S41564-017-0033-2
Page generated: Mon Jul 15 13:11:11 2024

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