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Calcium in PDB 5mih: Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside

Protein crystallography data

The structure of Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside, PDB code: 5mih was solved by S.Wagner, D.Hauk, M.Hofmann, I.Joachim, R.Sommer, R.Muller, A.Imberty, A.Varrot, A.Titz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.30 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 27.343, 73.771, 101.454, 90.00, 93.36, 90.00
R / Rfree (%) 14.9 / 19.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside (pdb code 5mih). 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 the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside, PDB code: 5mih:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5mih

Go back to Calcium Binding Sites List in 5mih
Calcium binding site 1 out of 4 in the Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside


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 Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca200

b:14.8
occ:1.00
O A:TYR36 2.3 14.7 1.0
O A:THR104 2.3 12.9 1.0
OD1 A:ASN108 2.4 15.5 1.0
OD2 A:ASP100 2.4 10.7 1.0
O3 A:7NU201 2.5 15.2 1.0
OD1 A:ASN107 2.5 18.8 1.0
O4 A:7NU201 2.5 17.2 1.0
C A:TYR36 3.4 16.5 1.0
C3 A:7NU201 3.4 16.3 1.0
CG A:ASP100 3.5 12.2 1.0
CG A:ASN108 3.5 14.5 1.0
C4 A:7NU201 3.5 16.2 1.0
C A:THR104 3.5 14.2 1.0
CG A:ASN107 3.5 17.1 1.0
OG1 A:THR104 3.7 14.9 1.0
OD1 A:ASP100 3.8 11.0 1.0
ND2 A:ASN107 3.9 15.0 1.0
CA A:TYR36 3.9 14.9 1.0
C2 A:7NU201 4.0 16.5 1.0
ND2 A:ASN108 4.0 13.7 1.0
CB A:THR104 4.0 16.4 1.0
CB A:TYR36 4.2 13.9 1.0
N A:TYR105 4.4 13.2 1.0
CA A:THR104 4.4 15.0 1.0
N A:GLY37 4.4 16.9 1.0
CA A:TYR105 4.4 14.6 1.0
O A:HOH304 4.5 22.8 1.0
N A:ASN108 4.6 15.9 1.0
CA A:GLY37 4.7 17.1 1.0
O2 A:7NU201 4.7 16.6 1.0
C A:TYR105 4.8 18.2 1.0
CB A:ASN108 4.8 15.3 1.0
C A:ASN107 4.8 15.8 1.0
C5 A:7NU201 4.8 16.1 1.0
N A:ASN107 4.8 15.1 1.0
CB A:ASP100 4.8 11.4 1.0
CB A:ASN107 4.9 16.2 1.0
O A:HOH419 4.9 24.0 1.0
CA A:ASN108 4.9 15.4 1.0

Calcium binding site 2 out of 4 in 5mih

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Calcium binding site 2 out of 4 in the Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside


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 Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca200

b:16.0
occ:1.00
O B:THR104 2.3 16.7 1.0
O B:TYR36 2.4 18.7 1.0
OD1 B:ASN108 2.4 14.3 1.0
O3 B:7NU201 2.4 14.5 1.0
OD2 B:ASP100 2.4 15.4 1.0
O4 B:7NU201 2.5 19.0 1.0
OD1 B:ASN107 2.5 17.5 1.0
C3 B:7NU201 3.2 18.7 1.0
C4 B:7NU201 3.3 20.1 1.0
C B:TYR36 3.4 14.5 1.0
C B:THR104 3.4 15.3 1.0
CG B:ASP100 3.5 16.2 1.0
CG B:ASN108 3.5 14.1 1.0
CG B:ASN107 3.6 18.3 1.0
OG1 B:THR104 3.6 18.1 1.0
OD1 B:ASP100 3.8 16.5 1.0
CB B:THR104 3.9 18.1 1.0
C2 B:7NU201 3.9 21.3 1.0
ND2 B:ASN108 3.9 14.7 1.0
ND2 B:ASN107 4.0 17.4 1.0
CA B:TYR36 4.0 12.4 1.0
CB B:TYR36 4.2 13.4 1.0
CA B:THR104 4.3 17.4 1.0
N B:TYR105 4.3 16.1 1.0
CA B:TYR105 4.4 15.0 1.0
O B:HOH305 4.4 28.2 1.0
N B:GLY37 4.5 15.7 1.0
N B:ASN108 4.6 13.5 1.0
O2 B:7NU201 4.6 22.8 1.0
C5 B:7NU201 4.7 18.0 1.0
C B:TYR105 4.7 16.4 1.0
CA B:GLY37 4.8 16.4 1.0
CB B:ASN108 4.8 13.5 1.0
C B:ASN107 4.8 14.7 1.0
CB B:ASP100 4.8 16.3 1.0
N B:ASN107 4.8 15.6 1.0
CB B:ASN107 4.9 16.6 1.0
CA B:ASN108 4.9 14.2 1.0
O B:TYR105 5.0 14.7 1.0

Calcium binding site 3 out of 4 in 5mih

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Calcium binding site 3 out of 4 in the Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside


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 Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca200

b:15.2
occ:1.00
O C:TYR36 2.3 13.2 1.0
O C:THR104 2.4 18.5 1.0
O4 C:7NU201 2.4 14.9 1.0
OD1 C:ASN108 2.4 13.4 1.0
OD1 C:ASN107 2.4 15.5 1.0
O3 C:7NU201 2.4 14.0 1.0
OD2 C:ASP100 2.5 12.1 1.0
C3 C:7NU201 3.3 15.4 1.0
C C:TYR36 3.3 13.8 1.0
C4 C:7NU201 3.4 16.2 1.0
CG C:ASN107 3.5 15.1 1.0
CG C:ASN108 3.5 12.7 1.0
C C:THR104 3.5 19.2 1.0
CG C:ASP100 3.5 11.2 1.0
OG1 C:THR104 3.7 17.3 1.0
OD1 C:ASP100 3.9 11.9 1.0
ND2 C:ASN107 3.9 16.2 1.0
C2 C:7NU201 3.9 15.4 1.0
CA C:TYR36 4.0 12.2 1.0
CB C:THR104 4.0 18.7 1.0
ND2 C:ASN108 4.0 13.6 1.0
CB C:TYR36 4.2 12.0 1.0
N C:GLY37 4.4 14.1 1.0
O C:HOH306 4.4 24.5 1.0
CA C:THR104 4.4 18.0 1.0
N C:TYR105 4.4 17.6 1.0
CA C:TYR105 4.5 16.3 1.0
O2 C:7NU201 4.6 13.9 1.0
N C:ASN108 4.6 14.2 1.0
CA C:GLY37 4.7 15.4 1.0
O C:HOH409 4.7 26.5 1.0
C5 C:7NU201 4.7 17.4 1.0
C C:ASN107 4.8 14.6 1.0
C C:TYR105 4.8 17.4 1.0
N C:ASN107 4.8 14.3 1.0
CB C:ASN108 4.8 13.8 1.0
CB C:ASN107 4.8 15.4 1.0
CB C:ASP100 4.9 11.9 1.0
CA C:ASN108 4.9 13.9 1.0

Calcium binding site 4 out of 4 in 5mih

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Calcium binding site 4 out of 4 in the Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside


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 Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca200

b:11.1
occ:1.00
O D:TYR36 2.3 10.2 1.0
O D:THR104 2.3 11.4 1.0
OD1 D:ASN108 2.4 12.3 1.0
O4 D:7NU201 2.4 10.3 1.0
O3 D:7NU201 2.4 10.1 1.0
OD1 D:ASN107 2.5 12.9 1.0
OD2 D:ASP100 2.5 10.4 1.0
C3 D:7NU201 3.3 10.9 1.0
C D:TYR36 3.4 10.9 1.0
C4 D:7NU201 3.4 10.8 1.0
C D:THR104 3.5 11.0 1.0
CG D:ASP100 3.5 10.6 1.0
CG D:ASN107 3.5 13.9 1.0
CG D:ASN108 3.5 12.5 1.0
OG1 D:THR104 3.6 10.8 1.0
OD1 D:ASP100 3.8 9.9 1.0
ND2 D:ASN107 3.9 13.9 1.0
C2 D:7NU201 3.9 11.0 1.0
CB D:THR104 4.0 12.0 1.0
ND2 D:ASN108 4.0 11.9 1.0
CA D:TYR36 4.0 11.2 1.0
CB D:TYR36 4.2 11.3 1.0
CA D:THR104 4.4 11.0 1.0
N D:TYR105 4.4 9.9 1.0
N D:GLY37 4.4 11.7 1.0
CA D:TYR105 4.4 10.3 1.0
N D:ASN108 4.6 11.4 1.0
CA D:GLY37 4.7 13.3 1.0
O2 D:7NU201 4.7 11.1 1.0
C5 D:7NU201 4.7 11.3 1.0
C D:TYR105 4.8 11.0 1.0
C D:ASN107 4.8 11.6 1.0
CB D:ASN108 4.8 12.7 1.0
O D:HOH392 4.8 18.3 1.0
N D:ASN107 4.8 12.5 1.0
CB D:ASN107 4.8 12.9 1.0
CB D:ASP100 4.8 8.8 1.0
CA D:ASN108 5.0 12.1 1.0

Reference:

S.Wagner, D.Hauck, M.Hoffmann, R.Sommer, I.Joachim, R.Muller, A.Imberty, A.Varrot, A.Titz. Covalent Lectin Inhibition and Application in Bacterial Biofilm Imaging. Angew. Chem. Int. Ed. Engl. V. 56 16559 2017.
ISSN: ESSN 1521-3773
PubMed: 28960731
DOI: 10.1002/ANIE.201709368
Page generated: Mon Jul 15 08:26:20 2024

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