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Calcium in PDB 4al9: Crystal Structure of the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose

Protein crystallography data

The structure of Crystal Structure of the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose, PDB code: 4al9 was solved by B.Blanchard, A.Imberty, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.95 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.070, 58.130, 75.940, 101.13, 92.89, 100.98
R / Rfree (%) 16.659 / 21.134

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose (pdb code 4al9). 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 the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose, PDB code: 4al9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4al9

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Calcium binding site 1 out of 8 in the Crystal Structure of the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose


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 the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1122

b:21.3
occ:1.00
O A:TYR36 2.2 19.4 1.0
O A:THR104 2.3 23.0 1.0
O4 A:GLA1123 2.4 25.2 1.0
OD1 A:ASN107 2.4 23.4 1.0
O3 A:GLA1123 2.4 24.7 1.0
OD2 A:ASP100 2.5 18.8 1.0
OD1 A:ASN108 2.5 22.2 1.0
C A:TYR36 3.3 21.1 1.0
C4 A:GLA1123 3.4 29.6 1.0
C3 A:GLA1123 3.4 28.0 1.0
C A:THR104 3.4 26.0 1.0
CG A:ASN107 3.5 23.0 1.0
CG A:ASP100 3.5 18.5 1.0
CG A:ASN108 3.6 19.7 1.0
OG1 A:THR104 3.6 26.5 1.0
OD1 A:ASP100 3.8 20.5 1.0
CB A:THR104 3.9 27.8 1.0
ND2 A:ASN107 3.9 24.2 1.0
C2 A:GLA1123 3.9 30.5 1.0
CA A:TYR36 4.0 20.9 1.0
ND2 A:ASN108 4.0 18.2 1.0
CB A:TYR36 4.2 20.6 1.0
CA A:THR104 4.3 26.2 1.0
N A:TYR105 4.3 26.1 1.0
N A:GLY37 4.3 22.6 1.0
CA A:TYR105 4.4 23.9 1.0
O A:HOH2098 4.4 29.5 1.0
O2 A:GLA1123 4.5 32.7 1.0
O A:HOH2097 4.6 33.0 1.0
N A:ASN108 4.7 22.6 1.0
CA A:GLY37 4.7 24.7 1.0
C A:TYR105 4.7 23.4 1.0
C5 A:GLA1123 4.8 31.2 1.0
N A:ASN107 4.8 24.5 1.0
CB A:ASP100 4.8 18.4 1.0
CB A:ASN107 4.8 22.8 1.0
C A:ASN107 4.8 24.0 1.0
CB A:ASN108 4.9 19.9 1.0
O A:TYR105 4.9 22.2 1.0

Calcium binding site 2 out of 8 in 4al9

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Calcium binding site 2 out of 8 in the Crystal Structure of the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose


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 the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1122

b:18.3
occ:1.00
O B:TYR36 2.3 16.8 1.0
O B:THR104 2.4 21.3 1.0
OD2 B:ASP100 2.4 15.2 1.0
O4 B:GLA1123 2.4 21.5 1.0
O3 B:GLA1123 2.4 21.1 1.0
OD1 B:ASN107 2.5 20.3 1.0
OD1 B:ASN108 2.5 19.9 1.0
C4 B:GLA1123 3.3 24.7 1.0
C3 B:GLA1123 3.3 23.4 1.0
C B:TYR36 3.4 15.7 1.0
CG B:ASP100 3.4 15.9 1.0
C B:THR104 3.5 23.7 1.0
OG1 B:THR104 3.5 27.7 1.0
CG B:ASN107 3.6 20.4 1.0
OD1 B:ASP100 3.6 15.4 1.0
CG B:ASN108 3.6 17.2 1.0
CB B:THR104 3.9 28.4 1.0
ND2 B:ASN107 4.0 20.8 1.0
CA B:TYR36 4.0 15.3 1.0
C2 B:GLA1123 4.0 23.7 1.0
ND2 B:ASN108 4.1 18.3 1.0
CB B:TYR36 4.2 16.6 1.0
CA B:THR104 4.3 25.4 1.0
N B:TYR105 4.4 20.6 1.0
CA B:TYR105 4.4 19.0 1.0
N B:GLY37 4.4 16.2 1.0
O B:HOH2084 4.6 23.5 1.0
O2 B:GLA1123 4.6 25.1 1.0
C5 B:GLA1123 4.7 24.8 1.0
CA B:GLY37 4.7 18.7 1.0
N B:ASN108 4.8 18.0 1.0
CB B:ASP100 4.8 16.3 1.0
C B:ASN107 4.8 18.5 1.0
C B:TYR105 4.8 19.3 1.0
N B:ASN107 4.8 19.3 1.0
CB B:ASN107 4.9 20.0 1.0
CB B:ASN108 4.9 18.4 1.0

Calcium binding site 3 out of 8 in 4al9

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Calcium binding site 3 out of 8 in the Crystal Structure of the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose


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 the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1122

b:26.0
occ:1.00
O C:THR104 2.3 33.2 1.0
O4 C:GLA1123 2.4 31.1 1.0
O C:TYR36 2.4 32.0 1.0
O3 C:GLA1123 2.4 27.9 1.0
OD1 C:ASN107 2.5 30.1 1.0
OD1 C:ASN108 2.5 33.7 1.0
OD2 C:ASP100 2.5 21.3 1.0
C3 C:GLA1123 3.4 31.4 1.0
C4 C:GLA1123 3.4 33.8 1.0
C C:TYR36 3.4 33.2 1.0
C C:THR104 3.5 29.4 1.0
CG C:ASN107 3.5 31.1 1.0
CG C:ASP100 3.6 26.4 1.0
CG C:ASN108 3.6 31.4 1.0
OG1 C:THR104 3.7 24.5 1.0
C2 C:GLA1123 3.8 32.6 1.0
OD1 C:ASP100 3.9 24.4 1.0
CA C:TYR36 3.9 30.9 1.0
CB C:THR104 4.0 27.5 1.0
CB C:TYR36 4.0 32.9 1.0
ND2 C:ASN107 4.0 29.6 1.0
ND2 C:ASN108 4.0 29.7 1.0
CA C:THR104 4.3 29.1 1.0
N C:TYR105 4.4 31.3 1.0
N C:GLY37 4.4 33.2 1.0
CA C:TYR105 4.5 29.3 1.0
O C:HOH2063 4.6 33.8 1.0
O2 C:GLA1123 4.6 32.5 1.0
N C:ASN108 4.7 31.2 1.0
C C:ASN107 4.7 32.1 1.0
CD2 C:TYR36 4.7 34.3 1.0
C5 C:GLA1123 4.8 37.6 1.0
CA C:GLY37 4.8 32.9 1.0
C C:TYR105 4.8 28.8 1.0
CB C:ASN107 4.8 30.9 1.0
N C:ASN107 4.8 30.9 1.0
CG C:TYR36 4.9 32.9 1.0
CB C:ASP100 4.9 25.5 1.0
CB C:ASN108 4.9 31.0 1.0
CA C:ASN107 5.0 30.8 1.0

Calcium binding site 4 out of 8 in 4al9

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Calcium binding site 4 out of 8 in the Crystal Structure of the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose


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 the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1122

b:19.8
occ:1.00
O D:THR104 2.2 21.9 1.0
O D:TYR36 2.4 20.0 1.0
O4 D:GLA1123 2.4 21.0 1.0
OD1 D:ASN108 2.4 16.9 1.0
OD1 D:ASN107 2.5 21.6 1.0
OD2 D:ASP100 2.5 20.1 1.0
O3 D:GLA1123 2.5 22.0 1.0
C4 D:GLA1123 3.3 25.3 1.0
C D:THR104 3.4 19.0 1.0
C D:TYR36 3.4 19.7 1.0
C3 D:GLA1123 3.4 24.2 1.0
CG D:ASP100 3.5 20.9 1.0
CG D:ASN108 3.5 18.7 1.0
CG D:ASN107 3.6 22.4 1.0
OG1 D:THR104 3.6 20.3 1.0
OD1 D:ASP100 3.8 23.6 1.0
CB D:THR104 3.9 21.9 1.0
ND2 D:ASN108 3.9 17.1 1.0
CA D:TYR36 3.9 19.2 1.0
ND2 D:ASN107 4.0 25.7 1.0
C2 D:GLA1123 4.0 26.3 1.0
CB D:TYR36 4.0 20.6 1.0
N D:TYR105 4.3 21.1 1.0
CA D:THR104 4.3 21.3 1.0
CA D:TYR105 4.3 20.1 1.0
N D:GLY37 4.4 23.1 1.0
O D:HOH2081 4.6 29.0 1.0
N D:ASN108 4.7 19.1 1.0
O2 D:GLA1123 4.7 24.8 1.0
C D:TYR105 4.7 20.9 1.0
C5 D:GLA1123 4.7 26.7 1.0
O D:HOH2071 4.7 32.6 1.0
CA D:GLY37 4.8 25.6 1.0
CB D:ASN108 4.8 17.3 1.0
C D:ASN107 4.8 19.2 1.0
N D:ASN107 4.8 19.5 1.0
CB D:ASP100 4.8 19.6 1.0
CB D:ASN107 4.9 21.6 1.0
CD2 D:TYR36 4.9 23.5 1.0
CA D:ASN108 5.0 18.4 1.0
O D:TYR105 5.0 20.4 1.0

Calcium binding site 5 out of 8 in 4al9

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Calcium binding site 5 out of 8 in the Crystal Structure of the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose


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 the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1122

b:19.5
occ:1.00
O4 E:GLA1123 2.3 20.5 1.0
O E:TYR36 2.4 18.5 1.0
O E:THR104 2.4 20.1 1.0
OD2 E:ASP100 2.4 12.9 1.0
OD1 E:ASN108 2.4 18.1 1.0
O3 E:GLA1123 2.5 17.7 1.0
OD1 E:ASN107 2.5 22.2 1.0
C4 E:GLA1123 3.2 22.0 1.0
C3 E:GLA1123 3.3 20.0 1.0
CG E:ASP100 3.4 15.0 1.0
C E:TYR36 3.4 19.0 1.0
C E:THR104 3.5 21.9 1.0
CG E:ASN108 3.5 17.2 1.0
OG1 E:THR104 3.6 22.1 1.0
CG E:ASN107 3.6 20.8 1.0
OD1 E:ASP100 3.7 15.4 1.0
CB E:THR104 3.9 22.7 1.0
C2 E:GLA1123 3.9 22.2 1.0
ND2 E:ASN108 4.0 16.1 1.0
CA E:TYR36 4.0 16.6 1.0
ND2 E:ASN107 4.0 20.4 1.0
CB E:TYR36 4.1 16.7 1.0
CA E:THR104 4.3 21.9 1.0
N E:TYR105 4.4 20.1 1.0
CA E:TYR105 4.4 19.5 1.0
N E:GLY37 4.5 19.6 1.0
C5 E:GLA1123 4.6 22.4 1.0
O E:HOH2108 4.6 25.3 1.0
O2 E:GLA1123 4.7 22.4 1.0
N E:ASN108 4.7 19.9 1.0
CB E:ASP100 4.8 14.7 1.0
C E:TYR105 4.8 21.4 1.0
CB E:ASN108 4.8 17.3 1.0
CA E:GLY37 4.8 19.4 1.0
C E:ASN107 4.9 20.0 1.0
N E:ASN107 4.9 20.8 1.0
CB E:ASN107 5.0 20.9 1.0
CA E:ASN108 5.0 17.6 1.0

Calcium binding site 6 out of 8 in 4al9

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Calcium binding site 6 out of 8 in the Crystal Structure of the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose


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 the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1123

b:11.7
occ:1.00
O F:THR104 2.2 12.3 1.0
O F:TYR36 2.3 10.7 1.0
OD1 F:ASN107 2.4 12.5 1.0
O3 F:GLA1124 2.4 11.1 1.0
OD1 F:ASN108 2.4 12.0 1.0
OD2 F:ASP100 2.5 10.6 1.0
O4 F:GLA1124 2.6 11.8 1.0
C3 F:GLA1124 3.3 11.8 1.0
C F:TYR36 3.4 10.8 1.0
C4 F:GLA1124 3.4 13.2 1.0
C F:THR104 3.4 13.8 1.0
CG F:ASN107 3.5 12.2 1.0
CG F:ASN108 3.5 11.8 1.0
CG F:ASP100 3.5 11.7 1.0
OG1 F:THR104 3.6 14.6 1.0
OD1 F:ASP100 3.9 12.3 1.0
ND2 F:ASN108 3.9 10.9 1.0
ND2 F:ASN107 3.9 12.1 1.0
CA F:TYR36 3.9 10.7 1.0
C2 F:GLA1124 4.0 12.5 1.0
CB F:THR104 4.0 14.6 1.0
CB F:TYR36 4.1 10.8 1.0
N F:TYR105 4.3 13.9 1.0
CA F:TYR105 4.3 13.0 1.0
CA F:THR104 4.3 14.7 1.0
O F:HOH2088 4.4 13.0 1.0
N F:GLY37 4.5 11.7 1.0
N F:ASN108 4.6 10.9 1.0
O2 F:GLA1124 4.6 13.0 1.0
C F:TYR105 4.7 13.1 1.0
C F:ASN107 4.7 12.0 1.0
CB F:ASN107 4.8 12.4 1.0
C5 F:GLA1124 4.8 13.5 1.0
CA F:GLY37 4.8 11.8 1.0
CB F:ASN108 4.8 11.2 1.0
N F:ASN107 4.8 12.7 1.0
CB F:ASP100 4.9 11.6 1.0
CA F:ASN108 4.9 11.8 1.0
CA F:ASN107 5.0 12.1 1.0
O F:TYR105 5.0 14.4 1.0

Calcium binding site 7 out of 8 in 4al9

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Calcium binding site 7 out of 8 in the Crystal Structure of the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose


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 the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1122

b:22.2
occ:1.00
O G:TYR36 2.2 22.4 1.0
O G:THR104 2.3 25.2 1.0
O4 G:GLA1123 2.3 23.4 1.0
OD1 G:ASN108 2.4 23.5 1.0
O3 G:GLA1123 2.4 23.9 1.0
OD1 G:ASN107 2.5 25.5 1.0
OD2 G:ASP100 2.5 17.0 1.0
C4 G:GLA1123 3.3 25.6 1.0
C3 G:GLA1123 3.3 25.0 1.0
C G:TYR36 3.3 19.5 1.0
C G:THR104 3.5 26.3 1.0
CG G:ASN108 3.5 21.4 1.0
CG G:ASP100 3.6 17.6 1.0
CG G:ASN107 3.6 24.4 1.0
OG1 G:THR104 3.7 25.7 1.0
C2 G:GLA1123 3.9 27.0 1.0
CA G:TYR36 3.9 19.4 1.0
ND2 G:ASN108 3.9 22.2 1.0
OD1 G:ASP100 4.0 18.9 1.0
CB G:THR104 4.1 27.2 1.0
ND2 G:ASN107 4.1 25.7 1.0
CB G:TYR36 4.1 19.6 1.0
CA G:TYR105 4.3 22.9 1.0
N G:TYR105 4.3 23.8 1.0
N G:GLY37 4.3 21.6 1.0
CA G:THR104 4.4 25.9 1.0
O2 G:GLA1123 4.5 30.1 1.0
O G:HOH2087 4.5 30.1 1.0
C G:TYR105 4.6 24.0 1.0
N G:ASN108 4.6 23.5 1.0
CA G:GLY37 4.7 25.3 1.0
C5 G:GLA1123 4.7 27.6 1.0
CB G:ASN108 4.7 22.2 1.0
C G:ASN107 4.8 23.7 1.0
N G:ASN107 4.8 25.6 1.0
O G:TYR105 4.9 24.6 1.0
CB G:ASN107 4.9 24.5 1.0
CB G:ASP100 4.9 17.3 1.0
CA G:ASN108 4.9 21.5 1.0

Calcium binding site 8 out of 8 in 4al9

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Calcium binding site 8 out of 8 in the Crystal Structure of the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose


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 the Lectin Pa-Il From Pseudomonas Aeruginoas in Complex with Melibiose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1123

b:11.0
occ:1.00
OD1 H:ASN108 2.3 11.0 1.0
O H:THR104 2.3 11.1 1.0
O H:TYR36 2.4 10.5 1.0
O3 H:GLA1124 2.4 11.5 1.0
OD2 H:ASP100 2.5 8.2 1.0
OD1 H:ASN107 2.5 12.4 1.0
O4 H:GLA1124 2.5 11.4 1.0
C3 H:GLA1124 3.3 12.8 1.0
C4 H:GLA1124 3.3 13.4 1.0
CG H:ASN108 3.4 10.6 1.0
C H:TYR36 3.4 9.8 1.0
CG H:ASP100 3.5 8.9 1.0
C H:THR104 3.5 11.8 1.0
CG H:ASN107 3.6 11.4 1.0
OG1 H:THR104 3.7 13.6 1.0
OD1 H:ASP100 3.8 9.4 1.0
ND2 H:ASN108 3.8 9.5 1.0
CA H:TYR36 3.9 10.4 1.0
C2 H:GLA1124 3.9 13.2 1.0
ND2 H:ASN107 4.0 11.2 1.0
CB H:THR104 4.1 13.5 1.0
CB H:TYR36 4.1 11.1 1.0
N H:TYR105 4.4 11.7 1.0
CA H:TYR105 4.4 11.7 1.0
CA H:THR104 4.4 13.1 1.0
O H:HOH2106 4.5 16.9 1.0
N H:GLY37 4.5 9.7 1.0
N H:ASN108 4.6 11.7 1.0
O2 H:GLA1124 4.6 13.0 1.0
CB H:ASN108 4.7 11.1 1.0
C H:TYR105 4.7 12.1 1.0
C H:ASN107 4.7 12.4 1.0
C5 H:GLA1124 4.8 13.2 1.0
N H:ASN107 4.8 12.2 1.0
CA H:GLY37 4.8 9.9 1.0
CB H:ASP100 4.8 9.4 1.0
CB H:ASN107 4.9 11.6 1.0
CA H:ASN108 4.9 12.0 1.0

Reference:

B.Blanchard, A.Imberty, A.Varrot. Secondary Sugar Binding Site Identified For Leca Lectin From Pseudomonas Aeruginosa. Proteins V. 82 1060 2014.
ISSN: ISSN 0887-3585
PubMed: 24123124
DOI: 10.1002/PROT.24430
Page generated: Sat Dec 12 04:39:05 2020

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