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Calcium in PDB 5a6x: Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside

Protein crystallography data

The structure of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside, PDB code: 5a6x was solved by R.Sommer, S.Wagner, A.Varrot, A.Khaledi, S.Haussler, A.Imberty, A.Titz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.84 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.558, 65.585, 109.036, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 15.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside (pdb code 5a6x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside, PDB code: 5a6x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5a6x

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Calcium binding site 1 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca199

b:5.8
occ:1.00
 OD1 A:ASP101 2.3 5.1 1.0
OD1 A:ASP99 2.4 7.9 1.0
OD2 A:ASP104 2.4 5.5 1.0
OE2 A:GLU95 2.4 6.1 1.0
O2 A:MFU201 2.5 6.7 1.0
O3 A:MFU201 2.5 5.7 1.0
OE1 A:GLU95 2.5 5.9 1.0
OD1 A:ASP104 2.6 5.2 1.0
CD A:GLU95 2.8 6.3 1.0
CG A:ASP104 2.9 5.0 1.0
C2 A:MFU201 3.3 6.1 1.0
C3 A:MFU201 3.4 6.0 1.0
CG A:ASP101 3.4 5.2 1.0
CG A:ASP99 3.4 7.0 1.0
CA A:CA200 3.7 5.3 1.0
OD2 A:ASP99 3.8 6.9 1.0
OD2 A:ASP101 4.0 5.0 1.0
N A:ASP101 4.2 6.2 1.0
OD1 A:ASP96 4.3 7.0 1.0
CG A:GLU95 4.3 6.3 1.0
CB A:ASP104 4.3 5.0 1.0
O A:HOH2202 4.4 22.2 1.0
N A:TYR102 4.4 5.8 1.0
N A:ASN100 4.5 6.4 1.0
N A:ASP96 4.5 6.2 1.0
CB A:ASP101 4.6 5.5 1.0
N A:SER97 4.6 7.3 1.0
CB A:SER97 4.7 10.3 1.0
OD1 A:ASN103 4.7 5.0 1.0
C4 A:MFU201 4.7 5.8 1.0
C1 A:MFU201 4.7 6.7 1.0
CA A:GLU95 4.7 5.9 1.0
CA A:ASP101 4.7 5.4 1.0
CB A:ASP99 4.8 6.5 1.0
N A:ASP99 4.8 7.0 1.0
O4 A:MFU201 4.8 5.4 1.0
CB A:GLU95 4.9 6.1 1.0
C A:ASP101 5.0 5.3 1.0

Calcium binding site 2 out of 8 in 5a6x

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Calcium binding site 2 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca200

b:5.3
occ:1.00
 O A:ASN21 2.3 5.4 1.0
OD1 A:ASN103 2.3 5.0 1.0
O B:GLY114 2.4 6.4 1.0
OD1 A:ASP104 2.4 5.2 1.0
OD2 A:ASP101 2.4 5.0 1.0
O3 A:MFU201 2.4 5.7 1.0
O4 A:MFU201 2.5 5.4 1.0
CG A:ASP101 3.1 5.2 1.0
OD1 A:ASP101 3.1 5.1 1.0
C B:GLY114 3.4 6.8 1.0
CG A:ASN103 3.4 5.0 1.0
C3 A:MFU201 3.4 6.0 1.0
C4 A:MFU201 3.4 5.8 1.0
C A:ASN21 3.6 5.5 1.0
CG A:ASP104 3.6 5.0 1.0
OXT B:GLY114 3.7 7.4 1.0
ND2 A:ASN103 3.7 5.4 1.0
CA A:CA199 3.7 5.8 1.0
C2 A:MFU201 3.7 6.1 1.0
CB A:ASN21 4.1 5.5 1.0
CA A:ASP104 4.2 4.9 1.0
N A:ASP104 4.3 5.0 1.0
O2 A:MFU201 4.4 6.7 1.0
O A:HOH2212 4.4 14.5 1.0
N A:SER22 4.4 5.4 1.0
CA A:SER22 4.4 5.7 1.0
CB A:ASP104 4.4 5.0 1.0
OD2 A:ASP104 4.5 5.5 1.0
C A:ASN103 4.5 5.0 1.0
CA A:ASN21 4.5 5.3 1.0
CB A:ASP101 4.6 5.5 1.0
OD2 A:ASP99 4.6 6.9 1.0
CB A:SER22 4.6 5.7 1.0
CB A:ASN103 4.7 5.2 1.0
CA B:GLY114 4.7 6.8 1.0
C5 A:MFU201 4.8 6.2 1.0
O A:ASN103 4.8 5.1 1.0
N A:ASN103 4.9 5.1 1.0
CA A:ASN103 4.9 5.2 1.0

Calcium binding site 3 out of 8 in 5a6x

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Calcium binding site 3 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca199

b:6.1
occ:1.00
 OD1 B:ASP101 2.4 6.3 1.0
OD1 B:ASP99 2.4 7.8 1.0
OE2 B:GLU95 2.4 6.7 1.0
OD2 B:ASP104 2.4 5.1 1.0
O2 B:MFU201 2.5 7.3 1.0
O3 B:MFU201 2.5 6.6 1.0
OE1 B:GLU95 2.5 5.6 1.0
OD1 B:ASP104 2.7 5.4 1.0
CD B:GLU95 2.8 6.1 1.0
CG B:ASP104 2.9 5.3 1.0
C2 B:MFU201 3.3 6.8 1.0
CG B:ASP99 3.4 8.1 1.0
C3 B:MFU201 3.4 6.6 1.0
CG B:ASP101 3.5 6.3 1.0
OD2 B:ASP99 3.7 7.7 1.0
CA B:CA200 3.8 5.8 1.0
OD2 B:ASP101 4.0 6.0 1.0
N B:ASP101 4.2 6.4 1.0
CG B:GLU95 4.3 6.1 1.0
OD1 B:ASP96 4.3 6.9 1.0
CB B:ASP104 4.4 5.1 1.0
N B:ASN100 4.5 6.8 1.0
N B:ASP96 4.5 6.0 1.0
N B:TYR102 4.5 6.4 1.0
N B:SER97 4.6 7.6 1.0
CB B:ASP101 4.6 6.3 1.0
CB B:SER97 4.6 9.7 1.0
CA B:GLU95 4.7 5.9 1.0
C4 B:MFU201 4.7 6.7 1.0
CB B:ASP99 4.7 8.2 1.0
CA B:ASP101 4.7 6.3 1.0
OD1 B:ASN103 4.7 5.3 1.0
C1 B:MFU201 4.8 6.9 1.0
O4 B:MFU201 4.8 6.4 1.0
N B:ASP99 4.8 8.2 1.0
CB B:GLU95 4.9 6.1 1.0
CG B:ASP96 5.0 6.6 1.0

Calcium binding site 4 out of 8 in 5a6x

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Calcium binding site 4 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca200

b:5.8
occ:1.00
 O B:ASN21 2.4 5.4 1.0
OD1 B:ASN103 2.4 5.3 1.0
OD1 B:ASP104 2.4 5.4 1.0
O A:GLY114 2.4 6.8 1.0
OD2 B:ASP101 2.4 6.0 1.0
O3 B:MFU201 2.5 6.6 1.0
O4 B:MFU201 2.5 6.4 1.0
CG B:ASP101 3.1 6.3 1.0
OD1 B:ASP101 3.1 6.3 1.0
C A:GLY114 3.4 7.8 1.0
CG B:ASN103 3.4 5.3 1.0
C3 B:MFU201 3.4 6.6 1.0
C4 B:MFU201 3.5 6.7 1.0
C B:ASN21 3.6 5.2 1.0
CG B:ASP104 3.6 5.3 1.0
OXT A:GLY114 3.7 8.5 1.0
ND2 B:ASN103 3.7 5.7 1.0
CA B:CA199 3.8 6.1 1.0
C2 B:MFU201 3.8 6.8 1.0
CB B:ASN21 4.1 5.3 1.0
CA B:ASP104 4.3 5.0 1.0
N B:ASP104 4.3 5.1 1.0
O2 B:MFU201 4.4 7.3 1.0
O A:HOH2216 4.4 13.8 1.0
CA B:SER22 4.4 5.9 1.0
N B:SER22 4.4 5.4 1.0
OD2 B:ASP104 4.4 5.1 1.0
CB B:ASP104 4.5 5.1 1.0
C B:ASN103 4.5 5.3 1.0
CB B:ASP101 4.5 6.3 1.0
CA B:ASN21 4.5 5.3 1.0
OD2 B:ASP99 4.6 7.7 1.0
CB B:SER22 4.7 6.1 1.0
CB B:ASN103 4.7 5.4 1.0
C5 B:MFU201 4.8 6.7 1.0
CA A:GLY114 4.8 7.3 1.0
O B:ASN103 4.8 5.7 1.0
N B:ASN103 4.9 5.3 1.0
CA B:ASN103 5.0 5.3 1.0

Calcium binding site 5 out of 8 in 5a6x

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Calcium binding site 5 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca199

b:6.9
occ:1.00
 OD1 C:ASP101 2.3 7.0 1.0
OD1 C:ASP99 2.4 9.6 1.0
OD2 C:ASP104 2.4 6.2 1.0
OE2 C:GLU95 2.4 7.7 1.0
O2 C:MFU201 2.5 7.4 1.0
OE1 C:GLU95 2.5 6.8 1.0
O3 C:MFU201 2.5 6.2 1.0
OD1 C:ASP104 2.6 6.2 1.0
CD C:GLU95 2.8 7.3 1.0
CG C:ASP104 2.9 6.2 1.0
C2 C:MFU201 3.3 6.8 1.0
CG C:ASP99 3.4 9.2 1.0
C3 C:MFU201 3.4 6.8 1.0
CG C:ASP101 3.4 7.5 1.0
OD2 C:ASP99 3.7 9.0 1.0
CA C:CA200 3.8 6.4 1.0
OD2 C:ASP101 4.0 6.8 1.0
N C:ASP101 4.2 8.6 1.0
CG C:GLU95 4.3 6.5 1.0
OD1 C:ASP96 4.3 7.4 1.0
CB C:ASP104 4.4 5.8 1.0
N C:ASP96 4.5 6.5 1.0
N C:TYR102 4.5 7.5 1.0
CB C:ASP101 4.6 7.6 1.0
N C:SER97 4.6 8.8 1.0
N C:ASN100 4.6 10.2 1.0
CB C:SER97 4.6 10.2 1.0
CA C:GLU95 4.7 6.0 1.0
OD1 C:ASN103 4.7 6.2 1.0
CA C:ASP101 4.7 7.8 1.0
CB C:ASP99 4.7 9.3 1.0
C4 C:MFU201 4.7 6.8 1.0
C1 C:MFU201 4.8 6.9 1.0
O4 C:MFU201 4.8 7.3 1.0
N C:ASP99 4.8 10.1 1.0
CB C:GLU95 4.9 6.2 1.0
CG C:ASP96 5.0 7.1 1.0

Calcium binding site 6 out of 8 in 5a6x

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Calcium binding site 6 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca200

b:6.4
occ:1.00
 OD1 C:ASN103 2.3 6.2 1.0
O C:ASN21 2.4 6.0 1.0
OD1 C:ASP104 2.4 6.2 1.0
O D:GLY114 2.4 6.1 1.0
OD2 C:ASP101 2.4 6.8 1.0
O3 C:MFU201 2.5 6.2 1.0
O4 C:MFU201 2.5 7.3 1.0
CG C:ASP101 3.1 7.5 1.0
OD1 C:ASP101 3.1 7.0 1.0
CG C:ASN103 3.4 6.0 1.0
C D:GLY114 3.4 6.4 1.0
C3 C:MFU201 3.4 6.8 1.0
C4 C:MFU201 3.5 6.8 1.0
C C:ASN21 3.6 5.8 1.0
CG C:ASP104 3.6 6.2 1.0
OXT D:GLY114 3.6 6.5 1.0
CA C:CA199 3.8 6.9 1.0
ND2 C:ASN103 3.8 6.0 1.0
C2 C:MFU201 3.8 6.8 1.0
CB C:ASN21 4.1 5.5 1.0
CA C:ASP104 4.2 5.6 1.0
N C:ASP104 4.3 5.2 1.0
O2 C:MFU201 4.3 7.4 1.0
CA C:SER22 4.4 6.0 1.0
C C:ASN103 4.4 5.3 1.0
N C:SER22 4.5 5.7 1.0
OD2 C:ASP104 4.5 6.2 1.0
O C:HOH2184 4.5 13.3 1.0
CB C:ASP104 4.5 5.8 1.0
CA C:ASN21 4.5 5.3 1.0
CB C:ASP101 4.5 7.6 1.0
OD2 C:ASP99 4.6 9.0 1.0
CB C:ASN103 4.7 5.5 1.0
CB C:SER22 4.7 6.4 1.0
CA D:GLY114 4.8 6.2 1.0
O C:ASN103 4.8 5.8 1.0
C5 C:MFU201 4.8 6.9 1.0
N C:ASN103 4.8 5.8 1.0
CA C:ASN103 4.9 5.5 1.0

Calcium binding site 7 out of 8 in 5a6x

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Calcium binding site 7 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca199

b:7.1
occ:1.00
 OD1 D:ASP101 2.4 7.5 1.0
OD1 D:ASP99 2.4 9.5 1.0
OD2 D:ASP104 2.4 6.2 1.0
OE2 D:GLU95 2.4 8.0 1.0
O2 D:MFU201 2.4 6.9 1.0
O3 D:MFU201 2.5 7.2 1.0
OE1 D:GLU95 2.5 6.7 1.0
OD1 D:ASP104 2.6 6.3 1.0
CD D:GLU95 2.8 7.3 1.0
CG D:ASP104 2.9 5.8 1.0
C2 D:MFU201 3.3 6.7 1.0
C3 D:MFU201 3.3 7.1 1.0
CG D:ASP99 3.4 9.2 1.0
CG D:ASP101 3.4 7.3 1.0
CA D:CA200 3.7 6.4 1.0
OD2 D:ASP99 3.8 9.0 1.0
OD2 D:ASP101 4.0 7.0 1.0
N D:ASP101 4.2 9.5 1.0
CG D:GLU95 4.3 7.4 1.0
OD1 D:ASP96 4.3 7.8 1.0
CB D:ASP104 4.4 5.5 1.0
N D:ASP96 4.5 7.4 1.0
N D:TYR102 4.5 7.8 1.0
N D:ASN100 4.5 9.8 1.0
CB D:ASP101 4.6 8.5 1.0
N D:SER97 4.6 9.3 1.0
C4 D:MFU201 4.7 7.1 1.0
C1 D:MFU201 4.7 7.3 1.0
CA D:GLU95 4.7 6.7 1.0
OD1 D:ASN103 4.7 5.5 1.0
CA D:ASP101 4.7 8.7 1.0
CB D:ASP99 4.7 10.2 1.0
CB D:SER97 4.8 12.9 1.0
O4 D:MFU201 4.8 6.8 1.0
N D:ASP99 4.8 11.6 1.0
O D:HOH2136 4.8 21.2 1.0
CB D:GLU95 4.9 7.0 1.0
O1 D:MFU201 5.0 8.2 1.0

Calcium binding site 8 out of 8 in 5a6x

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Calcium binding site 8 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Alpha-Methyl-Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca200

b:6.4
occ:1.00
 OD1 D:ASN103 2.3 5.5 1.0
O D:ASN21 2.4 5.6 1.0
OD1 D:ASP104 2.4 6.3 1.0
O3 D:MFU201 2.4 7.2 1.0
O C:GLY114 2.4 6.8 1.0
OD2 D:ASP101 2.4 7.0 1.0
O4 D:MFU201 2.5 6.8 1.0
OD1 D:ASP101 3.1 7.5 1.0
CG D:ASP101 3.1 7.3 1.0
C3 D:MFU201 3.4 7.1 1.0
CG D:ASN103 3.4 6.2 1.0
C C:GLY114 3.4 8.1 1.0
C4 D:MFU201 3.4 7.1 1.0
C D:ASN21 3.6 5.3 1.0
CG D:ASP104 3.6 5.8 1.0
OXT C:GLY114 3.7 9.1 1.0
CA D:CA199 3.7 7.1 1.0
ND2 D:ASN103 3.7 6.4 1.0
C2 D:MFU201 3.8 6.7 1.0
CB D:ASN21 4.2 5.4 1.0
CA D:ASP104 4.2 5.4 1.0
N D:ASP104 4.3 5.7 1.0
O2 D:MFU201 4.3 6.9 1.0
CA D:SER22 4.4 5.8 1.0
N D:SER22 4.4 5.3 1.0
OD2 D:ASP104 4.4 6.2 1.0
CB D:ASP104 4.5 5.5 1.0
O C:HOH2186 4.5 14.2 1.0
C D:ASN103 4.5 5.8 1.0
CB D:ASP101 4.5 8.5 1.0
OD2 D:ASP99 4.6 9.0 1.0
CA D:ASN21 4.6 5.0 1.0
CB D:SER22 4.6 5.5 1.0
CB D:ASN103 4.7 6.2 1.0
CA C:GLY114 4.8 8.0 1.0
C5 D:MFU201 4.8 7.1 1.0
O D:ASN103 4.8 5.8 1.0
N D:ASN103 4.8 5.8 1.0
O C:HOH2101 4.9 32.8 1.0
CA D:ASN103 4.9 5.8 1.0

Reference:

R.Sommer, S.Wagner, A.Varrot, C.M.Nycholat, A.Khaledi, S.Haussler, J.C.Paulson, A.Imberty, A.Titz. The Virulence Factor Lecb Varies in Clinical Isolates: Consequences For Ligand Binding and Drug Discovery. Chem Sci V. 7 4990 2016.
ISSN: ISSN 2041-6520
PubMed: 30155149
DOI: 10.1039/C6SC00696E
Page generated: Sun Jul 14 16:21:48 2024

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