Calcium in PDB 8wdq: Crystal Structure of Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate, PDB code: 8wdq was solved by V.K.Yadav, S.Maji, M.Shukla, S.Bhattacharyya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.75 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.62, 88.69, 97.71, 90, 90, 90
R / Rfree (%) 17.2 / 22

Other elements in 8wdq:

The structure of Crystal Structure of Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate (pdb code 8wdq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate, PDB code: 8wdq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8wdq

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Calcium binding site 1 out of 5 in the Crystal Structure of Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate


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 Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca307

b:39.6
occ:1.00
 OD2 A:ASP89 1.8 16.7 1.0
OD2 A:ASP86 2.2 24.9 1.0
O1 A:IPD301 2.4 28.2 1.0
OD1 A:ASP216 2.4 20.0 1.0
CG A:ASP89 2.4 17.4 1.0
O8 A:IPD301 2.9 26.3 1.0
CB A:ASP89 3.0 15.4 1.0
C1 A:IPD301 3.2 25.3 1.0
P1 A:IPD301 3.3 23.3 1.0
CA A:ASP89 3.4 16.5 1.0
OD1 A:ASP89 3.4 16.5 1.0
CG A:ASP86 3.4 21.1 1.0
CG A:ASP216 3.5 23.2 1.0
O2 A:IPD301 3.6 16.7 1.0
C2 A:IPD301 3.9 19.6 1.0
O A:HOH463 3.9 24.1 1.0
O7 A:IPD301 4.0 18.5 1.0
CA A:CA308 4.1 24.4 1.0
CB A:ASP216 4.1 20.0 1.0
OD1 A:ASP86 4.2 16.1 1.0
CA A:ASP216 4.2 17.9 1.0
C A:ASP89 4.3 15.4 1.0
N A:GLY90 4.4 17.7 1.0
CB A:ASP86 4.5 15.9 1.0
OD2 A:ASP216 4.5 27.1 1.0
C6 A:IPD301 4.5 20.2 1.0
N A:ASP89 4.6 15.8 1.0
O9 A:IPD301 4.6 22.3 1.0
OE1 A:GLU67 4.8 23.5 1.0
O A:LEU88 4.8 14.8 1.0
CD1 A:TRP215 4.9 26.0 1.0
N A:ASP216 4.9 19.9 1.0
O6 A:IPD301 5.0 29.9 1.0

Calcium binding site 2 out of 5 in 8wdq

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Calcium binding site 2 out of 5 in the Crystal Structure of Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate


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 Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca308

b:24.4
occ:1.00
 OD1 A:ASP86 2.3 16.1 1.0
O8 A:IPD301 2.3 26.3 1.0
O A:LEU88 2.3 14.8 1.0
OE1 A:GLU67 2.4 23.5 1.0
O A:HOH415 2.4 18.7 1.0
O A:HOH449 2.5 21.4 1.0
CG A:ASP86 3.0 21.1 1.0
OD2 A:ASP86 3.1 24.9 1.0
C A:LEU88 3.3 17.4 1.0
CD A:GLU67 3.4 30.1 1.0
CA A:CA309 3.8 37.7 1.0
OG1 A:THR91 3.8 21.2 1.0
P1 A:IPD301 3.8 23.3 1.0
OE2 A:GLU67 3.8 27.8 1.0
N A:ASP89 4.0 15.8 1.0
CA A:ASP89 4.0 16.5 1.0
CA A:CA307 4.1 39.6 1.0
N A:LEU88 4.1 16.3 1.0
O A:HOH454 4.1 36.1 1.0
O A:HOH463 4.2 24.1 1.0
CA A:LEU88 4.2 18.8 1.0
OD1 A:ASP44 4.2 31.7 1.0
O7 A:IPD301 4.3 18.5 1.0
O9 A:IPD301 4.5 22.3 1.0
CB A:ASP86 4.5 15.9 1.0
CG A:GLU67 4.5 29.3 1.0
OE2 A:GLU68 4.6 31.9 1.0
O1 A:IPD301 4.7 28.2 1.0
CB A:LEU88 4.7 19.0 1.0
CB A:ASP89 4.8 15.4 1.0
CD A:PRO87 4.9 15.8 1.0
CB A:GLU67 4.9 25.8 1.0
CA A:ASP86 4.9 18.3 1.0

Calcium binding site 3 out of 5 in 8wdq

Go back to Calcium Binding Sites List in 8wdq
Calcium binding site 3 out of 5 in the Crystal Structure of Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate


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 Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca309

b:37.7
occ:1.00
 O9 A:IPD301 2.4 22.3 1.0
OE2 A:GLU67 2.4 27.8 1.0
O A:HOH402 2.4 42.9 1.0
O A:HOH403 2.5 41.4 1.0
O A:HOH463 2.5 24.1 1.0
O A:HOH449 2.6 21.4 1.0
O8 A:IPD301 2.8 26.3 1.0
P1 A:IPD301 3.1 23.3 1.0
OD1 A:ASP38 3.3 80.4 1.0
CD A:GLU67 3.3 30.1 1.0
OE1 A:GLU67 3.5 23.5 1.0
O A:HOH454 3.7 36.1 1.0
CA A:CA308 3.8 24.4 1.0
O1 A:IPD301 4.0 28.2 1.0
O6 A:IPD301 4.1 29.9 1.0
O A:HOH411 4.1 29.7 1.0
O7 A:IPD301 4.4 18.5 1.0
NZ A:LYS34 4.4 46.5 1.0
O A:HOH478 4.4 43.1 1.0
CG A:ASP38 4.4 77.4 1.0
O A:HOH428 4.5 25.3 1.0
CG A:GLU67 4.7 29.3 1.0
O A:HOH450 4.8 53.9 1.0
O A:HOH486 4.8 51.3 1.0
OD2 A:ASP38 4.8 85.7 1.0
O A:TYR39 4.9 43.3 1.0
OG1 A:THR91 5.0 21.2 1.0
NE1 A:TRP215 5.0 23.4 1.0
CE A:LYS34 5.0 52.6 1.0

Calcium binding site 4 out of 5 in 8wdq

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Calcium binding site 4 out of 5 in the Crystal Structure of Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate


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 Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:24.6
occ:1.00
 O9 B:IPD302 2.3 22.6 1.0
OD1 B:ASP86 2.4 27.6 1.0
O B:LEU88 2.4 20.4 1.0
OE1 B:GLU67 2.4 30.1 1.0
O B:HOH487 2.5 25.6 1.0
O B:HOH495 2.5 26.9 1.0
OD2 B:ASP86 2.6 23.4 1.0
CG B:ASP86 2.8 19.9 1.0
C B:LEU88 3.3 17.9 1.0
CD B:GLU67 3.4 37.6 1.0
CA B:CA306 3.6 40.5 1.0
P1 B:IPD302 3.7 23.1 1.0
OE2 B:GLU67 3.7 50.4 1.0
O B:HOH510 3.8 38.4 1.0
N B:ASP89 4.0 14.3 1.0
CA B:ASP89 4.1 16.9 1.0
O7 B:IPD302 4.2 28.3 1.0
N B:LEU88 4.3 16.8 1.0
CG2 B:THR91 4.3 20.9 1.0
CA B:LEU88 4.3 18.6 1.0
CB B:ASP86 4.3 19.5 1.0
O B:HOH407 4.4 37.0 1.0
O8 B:IPD302 4.5 23.9 1.0
O1 B:IPD302 4.7 23.9 1.0
O B:HOH488 4.8 29.3 1.0
CG B:GLU67 4.8 35.7 1.0
CB B:LEU88 4.8 13.6 1.0
OD1 B:ASP44 4.9 27.6 1.0
CD B:PRO87 4.9 18.1 1.0
OE2 B:GLU68 4.9 33.5 1.0
CA B:ASP86 5.0 20.2 1.0

Calcium binding site 5 out of 5 in 8wdq

Go back to Calcium Binding Sites List in 8wdq
Calcium binding site 5 out of 5 in the Crystal Structure of Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate


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 Pseudomonas Aeruginosa Suhb in Complex with D- Myo-Inositol-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:40.5
occ:1.00
 OD2 B:ASP86 2.2 23.4 1.0
OD1 B:ASP216 2.2 28.1 1.0
OD1 B:ASP89 2.4 15.8 1.0
O9 B:IPD302 2.4 22.6 1.0
O1 B:IPD302 2.5 23.9 1.0
O B:HOH510 3.0 38.4 1.0
P1 B:IPD302 3.0 23.1 1.0
CG B:ASP89 3.3 17.4 1.0
CG B:ASP216 3.4 26.3 1.0
CG B:ASP86 3.5 19.9 1.0
CA B:CA305 3.6 24.6 1.0
O6 B:IPD302 3.6 16.3 1.0
CB B:ASP89 3.7 14.8 1.0
CA B:ASP89 3.7 16.9 1.0
C1 B:IPD302 3.8 23.9 1.0
O7 B:IPD302 4.1 28.3 1.0
OD2 B:ASP216 4.1 26.0 1.0
O8 B:IPD302 4.1 23.9 1.0
C6 B:IPD302 4.2 20.8 1.0
C2 B:IPD302 4.3 25.1 1.0
CB B:ASP216 4.3 19.3 1.0
OD1 B:ASP86 4.3 27.6 1.0
OD2 B:ASP89 4.3 19.6 1.0
CA B:ASP216 4.4 19.7 1.0
CB B:ASP86 4.4 19.5 1.0
OE1 B:GLU67 4.5 30.1 1.0
N B:GLY90 4.6 14.6 1.0
O B:HOH418 4.6 27.8 1.0
O B:LEU88 4.6 20.4 1.0
CD1 B:TRP215 4.6 26.6 1.0
C B:ASP89 4.7 13.1 1.0
N B:ASP89 4.7 14.3 1.0
O2 B:IPD302 4.7 24.1 1.0
N B:ASP216 4.9 17.9 1.0
O B:HOH407 4.9 37.0 1.0
O B:HOH495 4.9 26.9 1.0

Reference:

V.K.Yadav, S.Maji, M.Shukla, S.Bhattacharyya. Crystal Structure of Pseudomonas Aeruginosa Suhb in Complex with D-Myo-Inositol-1-Phosphate To Be Published.
Page generated: Sat Sep 28 09:15:34 2024

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