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Calcium in PDB 4lkd: Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution, PDB code: 4lkd was solved by R.U.Kadam, A.Stocker, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.46 / 2.31
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 159.216, 149.239, 87.018, 90.00, 110.96, 90.00
R / Rfree (%) 21.5 / 24.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution (pdb code 4lkd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution, PDB code: 4lkd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4lkd

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Calcium binding site 1 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution


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 Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:22.8
occ:1.00
 O A:THR104 2.7 22.4 1.0
O A:TYR36 2.7 23.6 1.0
O4 A:GAL201 2.7 26.1 1.0
OD1 A:ASN107 2.8 23.3 1.0
OD1 A:ASN108 2.8 23.5 1.0
OD2 A:ASP100 2.8 26.5 1.0
O3 A:GAL201 2.8 26.4 1.0
C A:TYR36 3.4 16.1 1.0
OG1 A:THR104 3.5 20.9 1.0
C3 A:GAL201 3.6 27.2 1.0
C A:THR104 3.6 19.7 1.0
C4 A:GAL201 3.6 28.4 1.0
CG A:ASP100 3.7 24.4 1.0
CG A:ASN108 3.7 23.1 1.0
CG A:ASN107 3.8 21.3 1.0
OD1 A:ASP100 3.8 22.2 1.0
C2 A:GAL201 3.9 24.5 1.0
CB A:THR104 3.9 25.4 1.0
CA A:TYR36 3.9 19.7 1.0
ND2 A:ASN108 4.0 20.4 1.0
CB A:TYR36 4.1 20.4 1.0
ND2 A:ASN107 4.2 19.5 1.0
N A:GLY37 4.4 15.8 1.0
CA A:THR104 4.4 20.4 1.0
N A:TYR105 4.4 21.5 1.0
CA A:TYR105 4.5 23.9 1.0
O2 A:GAL201 4.5 25.5 1.0
O A:HOH317 4.5 23.7 1.0
CA A:GLY37 4.7 22.2 1.0
N A:ASN108 4.8 19.0 1.0
C A:TYR105 4.9 22.4 1.0
C A:ASN107 4.9 19.5 1.0
CB A:ASN108 4.9 20.9 1.0
N A:ASN107 5.0 20.4 1.0
C5 A:GAL201 5.0 25.6 1.0

Calcium binding site 2 out of 8 in 4lkd

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Calcium binding site 2 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution


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 Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:25.5
occ:1.00
 O B:THR104 2.7 26.1 1.0
OD1 B:ASN108 2.7 22.3 1.0
O B:TYR36 2.7 26.8 1.0
O4 B:GAL201 2.8 23.3 1.0
OD2 B:ASP100 2.8 23.0 1.0
O3 B:GAL201 2.9 28.8 1.0
OD1 B:ASN107 3.0 26.1 1.0
O B:HOH444 3.3 32.9 1.0
C B:TYR36 3.5 27.6 1.0
OG1 B:THR104 3.6 24.0 1.0
C B:THR104 3.7 22.5 1.0
C3 B:GAL201 3.7 27.5 1.0
CG B:ASP100 3.7 24.2 1.0
C4 B:GAL201 3.7 22.6 1.0
CG B:ASN108 3.8 24.1 1.0
OD1 B:ASP100 3.9 19.3 1.0
CA B:TYR36 3.9 21.2 1.0
CB B:THR104 3.9 23.0 1.0
C2 B:GAL201 4.0 24.4 1.0
CG B:ASN107 4.1 29.6 1.0
CB B:TYR36 4.1 19.5 1.0
ND2 B:ASN108 4.3 21.1 1.0
N B:GLY37 4.4 23.8 1.0
CA B:THR104 4.5 25.0 1.0
O B:HOH313 4.5 23.5 1.0
ND2 B:ASN107 4.5 30.5 1.0
N B:TYR105 4.6 23.1 1.0
CA B:TYR105 4.7 22.0 1.0
O2 B:GAL201 4.7 26.6 1.0
CA B:GLY37 4.8 24.8 1.0
N B:ASN108 4.9 23.2 1.0
C B:ASN107 5.0 24.1 1.0

Calcium binding site 3 out of 8 in 4lkd

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Calcium binding site 3 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution


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 Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:31.3
occ:1.00
 O C:THR104 2.7 31.6 1.0
OD1 C:ASN108 2.8 34.6 1.0
OD2 C:ASP100 2.8 28.0 1.0
O4 C:GAL201 2.8 31.0 1.0
O C:TYR36 2.8 35.6 1.0
O3 C:GAL201 2.8 34.5 1.0
OD1 C:ASN107 2.8 35.2 1.0
OG1 C:THR104 3.5 31.8 1.0
C C:TYR36 3.5 28.8 1.0
C C:THR104 3.6 29.8 1.0
CG C:ASN108 3.6 31.6 1.0
C3 C:GAL201 3.6 34.3 1.0
C4 C:GAL201 3.6 32.8 1.0
CG C:ASP100 3.6 31.3 1.0
OD1 C:ASP100 3.8 31.2 1.0
CG C:ASN107 3.8 29.8 1.0
ND2 C:ASN108 3.9 28.8 1.0
CB C:THR104 4.0 31.9 1.0
CA C:TYR36 4.0 27.5 1.0
C2 C:GAL201 4.1 35.1 1.0
CB C:TYR36 4.2 27.6 1.0
ND2 C:ASN107 4.2 28.9 1.0
N C:TYR105 4.3 27.6 1.0
CA C:TYR105 4.3 29.7 1.0
CA C:THR104 4.4 31.2 1.0
N C:GLY37 4.5 28.3 1.0
O C:HOH333 4.6 33.8 1.0
O2 C:GAL201 4.7 34.5 1.0
C C:TYR105 4.7 30.8 1.0
N C:ASN108 4.8 28.9 1.0
C C:ASN107 4.8 29.2 1.0
CA C:GLY37 4.8 30.4 1.0
N C:ASN107 4.9 32.6 1.0
CB C:ASN108 4.9 30.8 1.0
CB C:ASP100 5.0 23.7 1.0

Calcium binding site 4 out of 8 in 4lkd

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Calcium binding site 4 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution


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 Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:32.9
occ:1.00
 OD1 D:ASN108 2.7 31.2 1.0
O4 D:GAL201 2.7 26.3 1.0
O D:TYR36 2.8 32.8 1.0
O D:THR104 2.8 38.0 1.0
OD1 D:ASN107 2.8 29.6 1.0
O3 D:GAL201 2.8 28.8 1.0
OD2 D:ASP100 2.8 23.9 1.0
OG1 D:THR104 3.3 29.7 1.0
C D:THR104 3.5 33.0 1.0
CG D:ASN108 3.5 26.5 1.0
C D:TYR36 3.6 28.9 1.0
C3 D:GAL201 3.6 40.5 1.0
C4 D:GAL201 3.6 30.3 1.0
CG D:ASP100 3.6 25.8 1.0
ND2 D:ASN108 3.7 22.2 1.0
CB D:THR104 3.7 31.9 1.0
OD1 D:ASP100 3.8 20.8 1.0
CG D:ASN107 3.9 30.1 1.0
C2 D:GAL201 4.0 26.5 1.0
CA D:TYR36 4.1 23.9 1.0
O D:HOH311 4.1 29.5 1.0
CB D:TYR36 4.2 24.4 1.0
N D:TYR105 4.2 28.8 1.0
CA D:THR104 4.3 28.5 1.0
ND2 D:ASN107 4.3 30.6 1.0
CA D:TYR105 4.4 30.5 1.0
N D:GLY37 4.6 27.6 1.0
O2 D:GAL201 4.7 22.8 1.0
C D:TYR105 4.8 30.8 1.0
CB D:ASN108 4.9 24.8 1.0
N D:ASN108 4.9 30.6 1.0
CA D:GLY37 5.0 27.5 1.0
N D:ASN107 5.0 25.9 1.0
CB D:ASP100 5.0 27.2 1.0

Calcium binding site 5 out of 8 in 4lkd

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Calcium binding site 5 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution


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 Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca202

b:27.0
occ:1.00
 O E:THR104 2.6 27.7 1.0
O E:TYR36 2.7 26.4 1.0
O4 E:GAL201 2.7 24.9 1.0
OD2 E:ASP100 2.7 23.5 1.0
OD1 E:ASN107 2.7 23.5 1.0
OD1 E:ASN108 2.7 22.8 1.0
O3 E:GAL201 2.8 30.9 1.0
OG1 E:THR104 3.4 28.1 1.0
C E:TYR36 3.5 24.6 1.0
C E:THR104 3.5 28.2 1.0
C4 E:GAL201 3.6 23.8 1.0
C3 E:GAL201 3.6 27.7 1.0
CG E:ASP100 3.6 29.6 1.0
CG E:ASN108 3.7 26.4 1.0
CG E:ASN107 3.8 25.6 1.0
OD1 E:ASP100 3.9 23.1 1.0
CB E:THR104 3.9 28.4 1.0
ND2 E:ASN108 4.0 25.9 1.0
CA E:TYR36 4.0 22.6 1.0
C2 E:GAL201 4.0 23.9 1.0
ND2 E:ASN107 4.2 20.7 1.0
CB E:TYR36 4.2 22.7 1.0
N E:TYR105 4.3 26.0 1.0
CA E:THR104 4.4 29.4 1.0
CA E:TYR105 4.4 27.7 1.0
N E:GLY37 4.5 22.1 1.0
O2 E:GAL201 4.6 24.8 1.0
N E:ASN108 4.8 27.2 1.0
C E:TYR105 4.8 30.3 1.0
N E:ASN107 4.8 27.4 1.0
CA E:GLY37 4.9 22.2 1.0
C E:ASN107 4.9 26.4 1.0
CB E:ASN108 5.0 24.5 1.0
C5 E:GAL201 5.0 24.8 1.0
CB E:ASP100 5.0 26.0 1.0

Calcium binding site 6 out of 8 in 4lkd

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Calcium binding site 6 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution


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 Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca202

b:26.4
occ:1.00
 O F:THR104 2.7 33.1 1.0
OD2 F:ASP100 2.7 27.3 1.0
O4 F:GAL201 2.8 27.8 1.0
OD1 F:ASN107 2.8 29.8 1.0
O F:TYR36 2.8 25.6 1.0
OD1 F:ASN108 2.8 29.1 1.0
O3 F:GAL201 2.8 28.9 1.0
OG1 F:THR104 3.3 24.9 1.0
C F:THR104 3.5 29.8 1.0
CG F:ASP100 3.6 24.9 1.0
C4 F:GAL201 3.6 28.2 1.0
C3 F:GAL201 3.6 27.9 1.0
CG F:ASN108 3.6 27.2 1.0
C F:TYR36 3.6 26.2 1.0
CB F:THR104 3.7 31.7 1.0
OD1 F:ASP100 3.8 23.2 1.0
ND2 F:ASN108 3.9 26.8 1.0
CG F:ASN107 3.9 26.5 1.0
C2 F:GAL201 4.1 26.5 1.0
CA F:TYR36 4.1 25.9 1.0
N F:TYR105 4.2 27.6 1.0
CA F:THR104 4.3 32.3 1.0
CA F:TYR105 4.3 29.6 1.0
CB F:TYR36 4.3 24.5 1.0
ND2 F:ASN107 4.3 23.8 1.0
O F:HOH317 4.5 29.0 1.0
N F:GLY37 4.6 26.3 1.0
C F:TYR105 4.7 28.2 1.0
O2 F:GAL201 4.8 29.2 1.0
N F:ASN108 4.8 25.3 1.0
CB F:ASP100 4.9 21.4 1.0
N F:ASN107 4.9 26.7 1.0
C F:ASN107 5.0 25.8 1.0
CB F:ASN108 5.0 25.2 1.0

Calcium binding site 7 out of 8 in 4lkd

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Calcium binding site 7 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution


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 Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca202

b:31.4
occ:1.00
 OD2 G:ASP100 2.7 27.7 1.0
OD1 G:ASN108 2.7 33.8 1.0
O G:THR104 2.7 30.2 1.0
O4 G:GAL201 2.8 28.3 1.0
O G:TYR36 2.8 34.9 1.0
O3 G:GAL201 2.8 31.5 1.0
OD1 G:ASN107 2.8 28.8 1.0
OG1 G:THR104 3.3 30.9 1.0
C G:THR104 3.6 25.0 1.0
C G:TYR36 3.6 28.1 1.0
C4 G:GAL201 3.6 28.6 1.0
C3 G:GAL201 3.6 34.3 1.0
CG G:ASP100 3.6 33.0 1.0
CG G:ASN108 3.7 30.4 1.0
CB G:THR104 3.8 28.9 1.0
OD1 G:ASP100 3.8 28.4 1.0
CG G:ASN107 3.9 32.7 1.0
CA G:TYR36 4.1 26.0 1.0
C2 G:GAL201 4.1 33.7 1.0
ND2 G:ASN108 4.1 27.6 1.0
CB G:TYR36 4.2 26.7 1.0
O G:HOH322 4.3 36.6 1.0
ND2 G:ASN107 4.3 36.6 1.0
CA G:THR104 4.3 28.9 1.0
N G:TYR105 4.4 27.6 1.0
CA G:TYR105 4.5 26.6 1.0
N G:GLY37 4.6 28.6 1.0
O2 G:GAL201 4.7 32.0 1.0
N G:ASN108 4.9 30.2 1.0
C G:TYR105 4.9 27.2 1.0
CA G:GLY37 4.9 29.3 1.0
C G:ASN107 5.0 26.8 1.0
CB G:ASP100 5.0 23.3 1.0
N G:ASN107 5.0 27.4 1.0

Calcium binding site 8 out of 8 in 4lkd

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Calcium binding site 8 out of 8 in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution


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 Pseudomonas Aeruginosa Lectin Leca Complexed with Gala-Qrs at 2.31 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca202

b:33.1
occ:1.00
 OD1 H:ASN108 2.7 27.3 1.0
O4 H:GAL201 2.7 28.2 1.0
O H:TYR36 2.7 31.4 1.0
OD2 H:ASP100 2.8 27.3 1.0
O H:THR104 2.8 37.9 1.0
OD1 H:ASN107 2.8 27.1 1.0
O3 H:GAL201 2.8 29.9 1.0
OG1 H:THR104 3.4 31.3 1.0
C H:TYR36 3.5 30.0 1.0
C H:THR104 3.5 34.1 1.0
C4 H:GAL201 3.6 28.9 1.0
C3 H:GAL201 3.6 32.6 1.0
CG H:ASP100 3.6 25.9 1.0
CG H:ASN108 3.7 29.1 1.0
CB H:THR104 3.7 35.5 1.0
OD1 H:ASP100 3.7 20.8 1.0
CG H:ASN107 3.9 27.8 1.0
CA H:TYR36 4.0 23.9 1.0
ND2 H:ASN108 4.0 24.9 1.0
C2 H:GAL201 4.1 28.7 1.0
CB H:TYR36 4.1 22.5 1.0
CA H:THR104 4.3 35.6 1.0
ND2 H:ASN107 4.3 28.1 1.0
N H:TYR105 4.3 31.6 1.0
CA H:TYR105 4.5 29.9 1.0
N H:GLY37 4.6 27.9 1.0
O2 H:GAL201 4.7 27.9 1.0
C H:ASN107 4.8 31.3 1.0
O H:ASN107 4.8 33.9 1.0
C H:TYR105 4.9 30.1 1.0
CA H:GLY37 4.9 26.5 1.0
C5 H:GAL201 5.0 28.9 1.0
N H:ASN108 5.0 31.2 1.0
N H:ASN107 5.0 30.7 1.0
CB H:ASP100 5.0 27.1 1.0

Reference:

R.U.Kadam, M.Bergmann, D.Garg, G.Gabrieli, A.Stocker, T.Darbre, J.-L.Reymond. Structure-Based Optimization of the Terminal Tripeptide in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Leca. Chemistry V. 19 17054 2013.
ISSN: ISSN 0947-6539
PubMed: 24307364
DOI: 10.1002/CHEM.201302587
Page generated: Sun Jul 14 09:33:41 2024

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