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Calcium in PDB 5whu: Crystal Structure of 3'Sl Bound Artb

Protein crystallography data

The structure of Crystal Structure of 3'Sl Bound Artb, PDB code: 5whu 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) 50.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.915, 94.213, 123.964, 90.00, 102.60, 90.00
R / Rfree (%) 17.4 / 23

Other elements in 5whu:

The structure of Crystal Structure of 3'Sl Bound Artb also contains other interesting chemical elements:

Chlorine (Cl) 23 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 7 in 5whu

Go back to Calcium Binding Sites List in 5whu
Calcium binding site 1 out of 7 in the Crystal Structure of 3'Sl Bound 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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca206

b:44.8
occ:1.00
 O E:HOH341 2.4 33.5 1.0
O E:CYS128 2.4 38.0 1.0
O B:HOH329 2.5 30.1 1.0
O E:HOH307 2.5 23.4 1.0
O E:HOH321 3.1 33.5 1.0
C E:CYS128 3.6 40.3 1.0
O E:HOH331 4.0 41.6 1.0
OE2 E:GLU97 4.1 22.2 1.0
OH B:TYR93 4.1 26.4 1.0
CA E:THR129 4.3 44.7 1.0
N E:THR129 4.4 44.1 1.0
N E:CYS128 4.5 28.9 1.0
CA E:CYS128 4.7 30.5 1.0
O E:ASP98 4.8 21.6 1.0
C E:THR129 4.9 49.7 1.0
CD E:GLU97 5.0 21.0 1.0
O E:THR129 5.0 54.0 1.0

Calcium binding site 2 out of 7 in 5whu

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Calcium binding site 2 out of 7 in the Crystal Structure of 3'Sl Bound 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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:32.3
occ:1.00
 O F:HOH344 2.2 22.9 1.0
O F:CYS128 2.3 31.6 1.0
O F:HOH308 2.4 16.6 1.0
O I:HOH314 2.5 20.4 1.0
C F:CYS128 3.5 23.9 1.0
OH I:TYR93 4.0 18.7 1.0
CA F:THR129 4.1 32.7 1.0
OE2 F:GLU97 4.2 18.5 1.0
N F:THR129 4.3 31.7 1.0
O F:HOH334 4.3 26.4 1.0
N F:CYS128 4.4 20.7 1.0
CA F:CYS128 4.5 19.5 1.0
O F:ASP98 4.6 20.0 1.0
C F:THR129 4.8 35.3 1.0
CG2 F:THR129 4.9 44.4 1.0
CB F:GLU97 5.0 20.3 1.0

Calcium binding site 3 out of 7 in 5whu

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Calcium binding site 3 out of 7 in the Crystal Structure of 3'Sl Bound 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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca202

b:32.3
occ:1.00
 O G:CYS128 2.4 21.8 1.0
O H:HOH332 2.5 17.8 1.0
O G:HOH302 2.5 22.4 1.0
O G:HOH337 2.8 34.3 1.0
C G:CYS128 3.5 21.6 1.0
OH H:TYR93 4.1 23.6 1.0
CA G:THR129 4.2 35.4 1.0
N G:THR129 4.3 29.3 1.0
OE2 G:GLU97 4.3 20.0 1.0
N G:CYS128 4.4 19.4 1.0
O G:ASP98 4.5 15.9 1.0
CA G:CYS128 4.5 20.6 1.0
O G:HOH346 4.6 37.4 1.0
CG2 G:THR129 4.8 31.8 1.0
CB G:GLU97 4.9 18.1 1.0

Calcium binding site 4 out of 7 in 5whu

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Calcium binding site 4 out of 7 in the Crystal Structure of 3'Sl Bound 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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca205

b:18.9
occ:1.00
 O D:HOH325 2.3 11.1 1.0
O A:CYS128 2.3 19.4 1.0
O H:HOH345 2.3 22.0 1.0
O H:HOH320 2.3 19.0 1.0
O A:HOH312 2.3 9.3 1.0
OD1 H:ASP132 2.5 22.7 1.0
OD2 H:ASP132 2.5 22.6 1.0
CG H:ASP132 2.8 22.3 1.0
C A:CYS128 3.5 29.3 1.0
OH D:TYR93 4.1 13.6 1.0
O H:HOH313 4.2 14.5 1.0
OE2 A:GLU97 4.3 13.2 1.0
N A:CYS128 4.3 22.7 1.0
CB H:ASP132 4.3 21.3 1.0
CA A:THR129 4.4 20.9 1.0
N A:THR129 4.4 19.5 1.0
CA A:CYS128 4.5 25.9 1.0
O H:HOH304 4.5 20.9 1.0
O A:ASP98 4.6 18.8 1.0
O A:HOH341 4.7 25.9 1.0
CG2 A:THR129 4.7 25.6 1.0
CB H:SER131 4.9 31.3 1.0
OD1 D:ASN37 4.9 19.8 1.0
CB A:THR127 5.0 16.7 1.0

Calcium binding site 5 out of 7 in 5whu

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Calcium binding site 5 out of 7 in the Crystal Structure of 3'Sl Bound 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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca206

b:25.3
occ:1.00
 O H:CYS128 2.3 18.3 1.0
O F:HOH304 2.5 14.5 1.0
O H:HOH305 2.5 17.5 1.0
O H:HOH335 2.5 24.1 1.0
C H:CYS128 3.5 16.5 1.0
OH F:TYR93 4.0 23.6 1.0
O F:HOH335 4.1 28.7 1.0
N H:CYS128 4.2 14.5 1.0
CA H:THR129 4.4 25.9 1.0
N H:THR129 4.4 25.3 1.0
OE2 H:GLU97 4.4 18.1 1.0
CA H:CYS128 4.5 17.8 1.0
O H:ASP98 4.5 14.1 1.0
OD1 F:ASN37 4.7 24.6 1.0
O H:THR129 4.8 40.7 1.0
C H:THR129 4.8 33.2 1.0
CB H:THR127 5.0 16.1 1.0

Calcium binding site 6 out of 7 in 5whu

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Calcium binding site 6 out of 7 in the Crystal Structure of 3'Sl Bound 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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca206

b:39.8
occ:1.00
 O I:CYS128 2.3 28.7 1.0
O I:HOH304 2.4 14.8 1.0
O J:HOH328 2.4 28.3 1.0
O I:HOH321 2.5 40.4 1.0
C I:CYS128 3.5 19.8 1.0
OH J:TYR93 4.0 18.6 1.0
OE2 I:GLU97 4.0 26.9 1.0
CL I:CL209 4.1 47.9 1.0
CA I:THR129 4.2 35.1 1.0
N I:CYS128 4.3 17.0 1.0
N I:THR129 4.3 21.2 1.0
CA I:CYS128 4.5 17.9 1.0
O I:HOH339 4.6 28.9 1.0
O I:ASP98 4.6 23.3 1.0
CG2 I:THR129 4.8 36.0 1.0
CD I:GLU97 4.9 25.7 1.0
CB I:GLU97 4.9 22.7 1.0
CB I:THR127 5.0 26.2 1.0

Calcium binding site 7 out of 7 in 5whu

Go back to Calcium Binding Sites List in 5whu
Calcium binding site 7 out of 7 in the Crystal Structure of 3'Sl Bound 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 3'Sl Bound Artb within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca205

b:39.3
occ:1.00
 O G:HOH333 2.2 38.7 1.0
O G:HOH334 2.2 21.7 1.0
O J:CYS128 2.3 31.6 1.0
O J:HOH306 2.5 18.2 1.0
C J:CYS128 3.5 26.0 1.0
O J:HOH349 3.8 50.5 1.0
O J:HOH341 4.1 19.1 1.0
OE2 J:GLU97 4.2 26.4 1.0
CA J:THR129 4.2 30.9 1.0
OH G:TYR93 4.3 17.2 1.0
N J:THR129 4.3 19.6 1.0
N J:CYS128 4.3 22.1 1.0
CA J:CYS128 4.5 17.9 1.0
O J:ASP98 4.6 17.3 1.0
CG2 J:THR129 4.7 29.9 1.0
CB J:THR127 4.9 15.1 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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