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Calcium in PDB 4cpb: Crystal Structure of Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium

Protein crystallography data

The structure of Crystal Structure of Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium, PDB code: 4cpb was solved by J.Topin, A.Varrot, A.Imberty, N.Wissinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.97 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.666, 65.393, 159.869, 90.00, 90.00, 90.00
R / Rfree (%) 16.331 / 19.138

Other elements in 4cpb:

The structure of Crystal Structure of Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium (pdb code 4cpb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium, PDB code: 4cpb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4cpb

Go back to Calcium Binding Sites List in 4cpb
Calcium binding site 1 out of 4 in the Crystal Structure of Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium


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 Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1122

b:43.5
occ:1.00
 O4 A:GAL1123 2.1 44.3 1.0
O A:TYR36 2.3 58.0 1.0
O A:THR104 2.3 59.7 1.0
O3 A:GAL1123 2.3 40.7 1.0
OD2 A:ASP100 2.5 50.3 1.0
OD1 A:ASN107 2.5 61.9 1.0
OD1 A:ASN108 2.6 52.5 1.0
C4 A:GAL1123 3.0 50.5 1.0
C3 A:GAL1123 3.1 42.2 1.0
C A:TYR36 3.3 56.2 1.0
C A:THR104 3.4 59.1 1.0
CG A:ASP100 3.5 48.4 1.0
OG1 A:THR104 3.6 58.0 1.0
CG A:ASN108 3.6 47.8 1.0
OD1 A:ASP100 3.6 56.1 1.0
CG A:ASN107 3.6 62.8 1.0
C2 A:GAL1123 3.7 48.6 1.0
CA A:TYR36 3.9 51.5 1.0
CB A:THR104 3.9 61.6 1.0
ND2 A:ASN108 4.0 43.5 1.0
CB A:TYR36 4.0 51.2 1.0
ND2 A:ASN107 4.0 64.5 1.0
CA A:THR104 4.3 61.8 1.0
N A:TYR105 4.4 55.1 1.0
N A:GLY37 4.4 56.1 1.0
CA A:TYR105 4.4 53.6 1.0
C5 A:GAL1123 4.5 46.3 1.0
O2 A:GAL1123 4.5 49.2 1.0
O A:HOH2078 4.6 48.4 1.0
N A:ASN108 4.6 54.3 1.0
CA A:GLY37 4.7 58.8 1.0
CB A:ASP100 4.8 48.0 1.0
C A:TYR105 4.8 56.1 1.0
N A:ASN107 4.9 62.5 1.0
C A:ASN107 4.9 58.2 1.0
CB A:ASN108 4.9 48.3 1.0
O5 A:GAL1123 4.9 48.7 1.0
C1 A:GAL1123 4.9 47.5 1.0
CB A:ASN107 5.0 63.6 1.0

Calcium binding site 2 out of 4 in 4cpb

Go back to Calcium Binding Sites List in 4cpb
Calcium binding site 2 out of 4 in the Crystal Structure of Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium


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 Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1122

b:30.9
occ:1.00
 O B:THR104 2.3 37.9 1.0
O B:TYR36 2.3 34.4 1.0
OD2 B:ASP100 2.4 30.8 1.0
O4 B:GAL1123 2.4 35.5 1.0
O3 B:GAL1123 2.4 28.7 1.0
OD1 B:ASN108 2.4 31.3 1.0
OD1 B:ASN107 2.5 34.2 1.0
C3 B:GAL1123 3.3 28.6 1.0
C4 B:GAL1123 3.3 35.5 1.0
C B:TYR36 3.3 31.8 1.0
CG B:ASP100 3.5 32.5 1.0
CG B:ASN108 3.5 31.7 1.0
C B:THR104 3.5 37.9 1.0
CG B:ASN107 3.6 35.3 1.0
OG1 B:THR104 3.6 38.2 1.0
OD1 B:ASP100 3.8 34.8 1.0
CA B:TYR36 3.9 31.8 1.0
C2 B:GAL1123 3.9 34.5 1.0
ND2 B:ASN108 3.9 31.1 1.0
CB B:THR104 4.0 38.9 1.0
ND2 B:ASN107 4.0 36.5 1.0
CB B:TYR36 4.1 32.2 1.0
CA B:THR104 4.4 39.3 1.0
N B:GLY37 4.4 33.0 1.0
N B:TYR105 4.4 38.1 1.0
CA B:TYR105 4.5 35.0 1.0
N B:ASN108 4.6 33.0 1.0
C5 B:GAL1123 4.7 32.6 1.0
O2 B:GAL1123 4.7 34.4 1.0
CA B:GLY37 4.7 34.2 1.0
CB B:ASN108 4.8 31.5 1.0
C B:ASN107 4.8 35.1 1.0
C B:TYR105 4.8 36.8 1.0
N B:ASN107 4.8 43.2 1.0
CB B:ASP100 4.9 33.0 1.0
CB B:ASN107 4.9 36.6 1.0
CA B:ASN108 4.9 31.3 1.0
O5 B:GAL1123 5.0 35.7 1.0

Calcium binding site 3 out of 4 in 4cpb

Go back to Calcium Binding Sites List in 4cpb
Calcium binding site 3 out of 4 in the Crystal Structure of Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium


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 Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1122

b:28.0
occ:1.00
 OD2 C:ASP100 2.3 27.7 1.0
O C:TYR36 2.3 28.7 1.0
O C:THR104 2.4 32.2 1.0
O4 C:GAL1123 2.4 28.0 1.0
O3 C:GAL1123 2.4 28.9 1.0
OD1 C:ASN107 2.4 29.9 1.0
OD1 C:ASN108 2.5 30.2 1.0
C3 C:GAL1123 3.3 25.8 1.0
C4 C:GAL1123 3.3 29.6 1.0
C C:TYR36 3.4 28.1 1.0
CG C:ASP100 3.4 29.4 1.0
C C:THR104 3.5 33.8 1.0
OG1 C:THR104 3.5 34.3 1.0
CG C:ASN107 3.5 32.1 1.0
CG C:ASN108 3.5 30.3 1.0
OD1 C:ASP100 3.7 29.1 1.0
CB C:THR104 3.9 34.3 1.0
C2 C:GAL1123 4.0 30.2 1.0
CA C:TYR36 4.0 26.6 1.0
ND2 C:ASN107 4.0 31.8 1.0
ND2 C:ASN108 4.0 29.8 1.0
CB C:TYR36 4.1 26.2 1.0
CA C:THR104 4.3 35.4 1.0
N C:TYR105 4.4 33.5 1.0
CA C:TYR105 4.4 33.0 1.0
N C:GLY37 4.5 28.7 1.0
C5 C:GAL1123 4.7 28.5 1.0
N C:ASN108 4.7 31.1 1.0
CB C:ASP100 4.8 28.1 1.0
C C:TYR105 4.8 33.2 1.0
CA C:GLY37 4.8 31.0 1.0
C C:ASN107 4.8 32.2 1.0
O2 C:GAL1123 4.8 31.7 1.0
N C:ASN107 4.9 33.3 1.0
CB C:ASN107 4.9 32.4 1.0
CB C:ASN108 4.9 28.5 1.0

Calcium binding site 4 out of 4 in 4cpb

Go back to Calcium Binding Sites List in 4cpb
Calcium binding site 4 out of 4 in the Crystal Structure of Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium


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 Leca in Complex with A Divalent Galactoside at 1.57 Angstrom in Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1123

b:27.0
occ:1.00
 O D:TYR36 2.3 29.6 1.0
O D:THR104 2.3 30.8 1.0
OD1 D:ASN107 2.4 30.9 1.0
OD1 D:ASN108 2.4 27.1 1.0
O3 D:GAL1124 2.4 29.7 1.0
OD2 D:ASP100 2.4 26.4 1.0
O4 D:GAL1124 2.6 28.5 1.0
C3 D:GAL1124 3.3 28.9 1.0
C D:TYR36 3.4 29.3 1.0
C4 D:GAL1124 3.4 29.9 1.0
CG D:ASN107 3.5 31.6 1.0
C D:THR104 3.5 30.9 1.0
CG D:ASP100 3.5 27.4 1.0
CG D:ASN108 3.5 26.2 1.0
OG1 D:THR104 3.6 31.9 1.0
OD1 D:ASP100 3.8 28.0 1.0
ND2 D:ASN107 3.9 33.5 1.0
CA D:TYR36 3.9 28.4 1.0
C2 D:GAL1124 4.0 31.1 1.0
CB D:THR104 4.0 31.5 1.0
ND2 D:ASN108 4.0 25.5 1.0
CB D:TYR36 4.2 27.3 1.0
CA D:TYR105 4.3 29.0 1.0
N D:TYR105 4.3 30.3 1.0
CA D:THR104 4.4 32.1 1.0
N D:GLY37 4.4 31.5 1.0
O D:HOH2090 4.6 38.1 1.0
N D:ASN108 4.6 28.8 1.0
O2 D:GAL1124 4.6 34.9 1.0
CA D:GLY37 4.7 32.6 1.0
C D:ASN107 4.7 30.2 1.0
O D:HOH2088 4.7 45.6 1.0
C D:TYR105 4.7 29.4 1.0
N D:ASN107 4.7 30.2 1.0
CB D:ASN107 4.8 32.2 1.0
CB D:ASN108 4.8 27.3 1.0
C5 D:GAL1124 4.8 30.8 1.0
CB D:ASP100 4.8 26.6 1.0
CA D:ASN107 5.0 31.8 1.0
CA D:ASN108 5.0 27.2 1.0

Reference:

A.Novoa, T.Eierhoff, J.Topin, A.Varrot, S.Barluenga, A.Imberty, W.Romer, N.Winssinger. A Leca Ligand Identified From A Galactoside-Conjugate Array Inhibits Host Cell Invasion By Pseudomonas Aeruginosa. Angew.Chem.Int.Ed.Engl. V. 53 8885 2014.
ISSN: ISSN 1433-7851
PubMed: 25044671
DOI: 10.1002/ANIE.201402831
Page generated: Tue Jul 8 19:15:45 2025

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