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Calcium in PDB 7fio: Leca From Pseudomonas Aeruginosa in Complex with A Synthetic Monovalent Galactosidic Inhibitor

Protein crystallography data

The structure of Leca From Pseudomonas Aeruginosa in Complex with A Synthetic Monovalent Galactosidic Inhibitor, PDB code: 7fio was solved by S.Kuhaudomlarp, E.Siebs, P.Da Silva Figueiredo Celestino Gomes, C.Fortin, D.Rognan, C.Rademacher, A.Imberty, A.Titz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.34 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.597, 52.677, 156.968, 90, 90, 90
R / Rfree (%) 17.7 / 21.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Leca From Pseudomonas Aeruginosa in Complex with A Synthetic Monovalent Galactosidic Inhibitor (pdb code 7fio). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Leca From Pseudomonas Aeruginosa in Complex with A Synthetic Monovalent Galactosidic Inhibitor, PDB code: 7fio:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7fio

Go back to Calcium Binding Sites List in 7fio
Calcium binding site 1 out of 4 in the Leca From Pseudomonas Aeruginosa in Complex with A Synthetic Monovalent Galactosidic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Leca From Pseudomonas Aeruginosa in Complex with A Synthetic Monovalent Galactosidic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:27.6
occ:1.00
 O A:TYR36 2.3 25.9 1.0
O A:THR104 2.3 29.1 1.0
OD1 A:ASN108 2.4 27.0 1.0
O4 A:4VH202 2.4 28.9 1.0
OD2 A:ASP100 2.4 23.2 1.0
OD1 A:ASN107 2.5 35.9 1.0
O3 A:4VH202 2.6 23.7 1.0
C A:TYR36 3.3 26.4 1.0
CG A:ASP100 3.4 17.1 1.0
CG A:ASN108 3.5 23.3 1.0
C A:THR104 3.5 34.8 1.0
CG A:ASN107 3.5 30.3 1.0
C3 A:4VH202 3.6 30.3 1.0
OG1 A:THR104 3.6 34.2 1.0
C4 A:4VH202 3.6 29.7 1.0
OD1 A:ASP100 3.8 24.5 1.0
ND2 A:ASN108 3.9 26.0 1.0
ND2 A:ASN107 3.9 29.9 1.0
CA A:TYR36 3.9 24.5 1.0
CB A:THR104 3.9 36.7 1.0
CB A:TYR36 4.1 23.2 1.0
C2 A:4VH202 4.1 28.5 1.0
CA A:THR104 4.3 31.1 1.0
N A:TYR105 4.4 33.5 1.0
CA A:TYR105 4.4 31.8 1.0
N A:GLY37 4.4 25.7 1.0
N A:ASN108 4.7 30.0 1.0
CA A:GLY37 4.7 24.6 1.0
O2 A:4VH202 4.7 33.3 1.0
C A:TYR105 4.7 32.5 1.0
CB A:ASN108 4.8 24.6 1.0
CB A:ASP100 4.8 21.8 1.0
C A:ASN107 4.8 29.8 1.0
CB A:ASN107 4.9 28.1 1.0
N A:ASN107 4.9 30.6 1.0
CA A:ASN108 5.0 28.4 1.0
C5 A:4VH202 5.0 32.3 1.0
O A:TYR105 5.0 30.0 1.0

Calcium binding site 2 out of 4 in 7fio

Go back to Calcium Binding Sites List in 7fio
Calcium binding site 2 out of 4 in the Leca From Pseudomonas Aeruginosa in Complex with A Synthetic Monovalent Galactosidic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Leca From Pseudomonas Aeruginosa in Complex with A Synthetic Monovalent Galactosidic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:20.8
occ:1.00
 O B:THR104 2.3 23.0 1.0
O B:TYR36 2.4 22.3 1.0
O3 B:4VH202 2.4 22.0 1.0
OD1 B:ASN108 2.4 23.2 1.0
OD2 B:ASP100 2.4 18.3 1.0
OD1 B:ASN107 2.4 26.2 1.0
O4 B:4VH202 2.5 21.0 1.0
C3 B:4VH202 3.4 22.9 1.0
C B:TYR36 3.4 20.6 1.0
C4 B:4VH202 3.4 23.0 1.0
CG B:ASP100 3.4 15.7 1.0
C B:THR104 3.4 23.6 1.0
OG1 B:THR104 3.5 24.5 1.0
CG B:ASN107 3.5 24.8 1.0
CG B:ASN108 3.5 18.9 1.0
OD1 B:ASP100 3.8 19.3 1.0
CB B:THR104 3.9 26.4 1.0
ND2 B:ASN108 3.9 19.9 1.0
CA B:TYR36 3.9 17.7 1.0
ND2 B:ASN107 4.0 25.7 1.0
C2 B:4VH202 4.0 23.2 1.0
CB B:TYR36 4.1 20.0 1.0
CA B:THR104 4.3 23.7 1.0
N B:TYR105 4.3 21.9 1.0
CA B:TYR105 4.4 21.0 1.0
N B:GLY37 4.4 20.6 1.0
O B:HOH329 4.5 25.4 1.0
N B:ASN108 4.6 22.0 1.0
O2 B:4VH202 4.7 26.6 1.0
C5 B:4VH202 4.7 22.6 1.0
CA B:GLY37 4.7 22.1 1.0
C B:TYR105 4.7 23.8 1.0
CB B:ASP100 4.8 16.0 1.0
C B:ASN107 4.8 21.6 1.0
CB B:ASN108 4.8 18.7 1.0
N B:ASN107 4.8 21.8 1.0
CB B:ASN107 4.8 25.2 1.0
CA B:ASN108 5.0 22.2 1.0
O B:TYR105 5.0 23.6 1.0

Calcium binding site 3 out of 4 in 7fio

Go back to Calcium Binding Sites List in 7fio
Calcium binding site 3 out of 4 in the Leca From Pseudomonas Aeruginosa in Complex with A Synthetic Monovalent Galactosidic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Leca From Pseudomonas Aeruginosa in Complex with A Synthetic Monovalent Galactosidic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:18.5
occ:1.00
 O C:THR104 2.4 17.5 1.0
OD1 C:ASN108 2.4 18.3 1.0
OD1 C:ASN107 2.4 18.9 1.0
O C:TYR36 2.4 17.7 1.0
O3 C:4VH202 2.4 19.1 1.0
OD2 C:ASP100 2.4 17.0 1.0
O4 C:4VH202 2.5 18.4 1.0
C C:TYR36 3.3 17.4 1.0
C3 C:4VH202 3.4 20.1 1.0
C C:THR104 3.5 16.6 1.0
CG C:ASN108 3.5 18.0 1.0
CG C:ASN107 3.5 18.0 1.0
C4 C:4VH202 3.5 20.4 1.0
CG C:ASP100 3.5 16.4 1.0
OG1 C:THR104 3.6 20.1 1.0
OD1 C:ASP100 3.8 16.9 1.0
ND2 C:ASN108 3.9 16.9 1.0
CA C:TYR36 3.9 14.9 1.0
ND2 C:ASN107 4.0 20.1 1.0
CB C:THR104 4.0 21.3 1.0
C2 C:4VH202 4.0 21.2 1.0
CB C:TYR36 4.2 16.9 1.0
CA C:THR104 4.3 20.6 1.0
N C:TYR105 4.4 17.4 1.0
N C:GLY37 4.4 19.8 1.0
CA C:TYR105 4.4 17.9 1.0
O C:HOH338 4.6 23.5 1.0
N C:ASN108 4.6 19.9 1.0
O2 C:4VH202 4.7 19.4 1.0
CA C:GLY37 4.7 20.3 1.0
C C:ASN107 4.8 20.1 1.0
C C:TYR105 4.8 18.0 1.0
CB C:ASN108 4.8 17.5 1.0
N C:ASN107 4.8 18.7 1.0
CB C:ASP100 4.8 16.7 1.0
CB C:ASN107 4.8 17.3 1.0
C5 C:4VH202 4.8 20.1 1.0
CA C:ASN108 5.0 19.8 1.0
O C:HOH393 5.0 30.5 1.0

Calcium binding site 4 out of 4 in 7fio

Go back to Calcium Binding Sites List in 7fio
Calcium binding site 4 out of 4 in the Leca From Pseudomonas Aeruginosa in Complex with A Synthetic Monovalent Galactosidic Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Leca From Pseudomonas Aeruginosa in Complex with A Synthetic Monovalent Galactosidic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:16.1
occ:1.00
 O D:THR104 2.3 16.1 1.0
OD2 D:ASP100 2.4 14.5 1.0
O D:TYR36 2.4 15.4 1.0
O4 D:4VH202 2.4 17.1 1.0
OD1 D:ASN108 2.4 14.9 1.0
O3 D:4VH202 2.5 16.5 1.0
OD1 D:ASN107 2.5 16.8 1.0
C4 D:4VH202 3.4 15.7 1.0
C3 D:4VH202 3.4 16.3 1.0
C D:TYR36 3.4 16.1 1.0
C D:THR104 3.4 16.5 1.0
CG D:ASP100 3.4 13.8 1.0
CG D:ASN108 3.5 13.1 1.0
OG1 D:THR104 3.5 18.6 1.0
CG D:ASN107 3.5 17.1 1.0
OD1 D:ASP100 3.8 15.4 1.0
ND2 D:ASN107 3.9 17.6 1.0
CA D:TYR36 3.9 14.0 1.0
ND2 D:ASN108 4.0 14.4 1.0
CB D:THR104 4.0 19.2 1.0
C2 D:4VH202 4.0 17.6 1.0
CB D:TYR36 4.1 15.6 1.0
N D:TYR105 4.3 16.1 1.0
CA D:THR104 4.3 17.6 1.0
CA D:TYR105 4.3 16.8 1.0
N D:GLY37 4.5 15.8 1.0
O D:HOH306 4.5 23.7 1.0
N D:ASN108 4.6 15.6 1.0
O2 D:4VH202 4.7 17.6 1.0
C D:ASN107 4.7 16.1 1.0
CA D:GLY37 4.7 16.1 1.0
C D:TYR105 4.8 15.1 1.0
C5 D:4VH202 4.8 15.5 1.0
CB D:ASP100 4.8 14.6 1.0
CB D:ASN108 4.8 15.3 1.0
N D:ASN107 4.8 17.4 1.0
CB D:ASN107 4.9 16.9 1.0
CA D:ASN108 5.0 14.6 1.0

Reference:

E.Siebs, E.Shanina, S.Kuhaudomlarp, P.Da Silva Figueiredo Celestino Gomes, C.Fortin, P.H.Seeberger, D.Rognan, C.Rademacher, A.Imberty, A.Titz. Targeting the Central Pocket of the Pseudomonas Aeruginosa Lectin Leca. Chembiochem V. 23 00563 2022.
ISSN: ESSN 1439-7633
PubMed: 34788491
DOI: 10.1002/CBIC.202100563
Page generated: Fri Jul 19 00:56:50 2024

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