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Calcium in PDB 4lk7: Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Resorufin-B-D-Galactopyranoside at 1.76 A Resolution

Protein crystallography data

The structure of Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Resorufin-B-D-Galactopyranoside at 1.76 A Resolution, PDB code: 4lk7 was solved by R.U.Kadam, A.Stocker, J.L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.31 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.585, 69.576, 158.312, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Resorufin-B-D-Galactopyranoside at 1.76 A Resolution (pdb code 4lk7). 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 Pseudomonas Aeruginosa Lectin Leca Complexed with Resorufin-B-D-Galactopyranoside at 1.76 A Resolution, PDB code: 4lk7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4lk7

Go back to Calcium Binding Sites List in 4lk7
Calcium binding site 1 out of 4 in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Resorufin-B-D-Galactopyranoside at 1.76 A Resolution


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 Pseudomonas Aeruginosa Lectin Leca Complexed with Resorufin-B-D-Galactopyranoside at 1.76 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:19.4
occ:1.00
 O A:THR104 2.4 19.9 1.0
OD1 A:ASN108 2.4 19.7 1.0
O A:TYR36 2.4 19.9 1.0
OD2 A:ASP100 2.5 18.3 1.0
O3 A:GAL203 2.5 19.6 1.0
OD1 A:ASN107 2.5 20.2 1.0
O4 A:GAL203 2.6 16.4 1.0
C A:TYR36 3.4 20.6 1.0
C4 A:GAL203 3.5 20.9 1.0
C3 A:GAL203 3.5 22.2 1.0
CG A:ASP100 3.5 19.9 1.0
CG A:ASN108 3.5 20.1 1.0
OG1 A:THR104 3.5 20.4 1.0
C A:THR104 3.5 20.5 1.0
CG A:ASN107 3.6 20.5 1.0
OD1 A:ASP100 3.8 17.3 1.0
CA A:TYR36 3.9 19.7 1.0
CB A:THR104 3.9 21.1 1.0
ND2 A:ASN108 3.9 19.3 1.0
ND2 A:ASN107 3.9 18.9 1.0
C2 A:GAL203 4.0 22.4 1.0
CB A:TYR36 4.1 18.0 1.0
CA A:THR104 4.4 20.5 1.0
N A:TYR105 4.4 21.0 1.0
CA A:TYR105 4.4 21.1 1.0
N A:GLY37 4.5 19.1 1.0
N A:ASN108 4.6 19.8 1.0
C A:TYR105 4.7 22.4 1.0
O2 A:GAL203 4.7 19.1 1.0
C A:ASN107 4.8 20.8 1.0
N A:ASN107 4.8 19.7 1.0
CB A:ASN108 4.8 17.3 1.0
C5 A:GAL203 4.8 21.5 1.0
CB A:ASP100 4.8 18.6 1.0
CA A:GLY37 4.9 20.1 1.0
CB A:ASN107 4.9 20.4 1.0
CA A:ASN108 5.0 19.4 1.0

Calcium binding site 2 out of 4 in 4lk7

Go back to Calcium Binding Sites List in 4lk7
Calcium binding site 2 out of 4 in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Resorufin-B-D-Galactopyranoside at 1.76 A Resolution


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 Pseudomonas Aeruginosa Lectin Leca Complexed with Resorufin-B-D-Galactopyranoside at 1.76 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:21.5
occ:1.00
 O B:TYR36 2.5 24.1 1.0
O3 B:GAL203 2.5 25.2 1.0
O B:THR104 2.5 22.3 1.0
OD1 B:ASN107 2.5 22.5 1.0
OD1 B:ASN108 2.5 20.2 1.0
OD2 B:ASP100 2.5 19.3 1.0
O4 B:GAL203 2.5 21.5 1.0
C3 B:GAL203 3.3 23.1 1.0
C4 B:GAL203 3.4 20.5 1.0
C B:TYR36 3.4 23.1 1.0
CG B:ASN108 3.5 21.5 1.0
CG B:ASP100 3.6 21.1 1.0
CG B:ASN107 3.6 25.3 1.0
C B:THR104 3.6 25.2 1.0
OG1 B:THR104 3.6 22.5 1.0
C2 B:GAL203 3.8 24.6 1.0
OD1 B:ASP100 3.9 19.6 1.0
CA B:TYR36 3.9 21.8 1.0
ND2 B:ASN108 4.0 18.7 1.0
ND2 B:ASN107 4.0 24.9 1.0
CB B:THR104 4.0 25.3 1.0
CB B:TYR36 4.1 20.5 1.0
CA B:TYR105 4.3 20.7 1.0
N B:TYR105 4.4 21.7 1.0
N B:GLY37 4.4 23.0 1.0
CA B:THR104 4.5 23.9 1.0
O B:HOH310 4.5 29.2 1.0
O2 B:GAL203 4.5 27.4 1.0
N B:ASN108 4.7 21.6 1.0
N B:ASN107 4.7 20.5 1.0
C B:TYR105 4.7 20.8 1.0
C5 B:GAL203 4.7 25.8 1.0
CA B:GLY37 4.7 24.2 1.0
C B:ASN107 4.8 21.8 1.0
CB B:ASN107 4.9 23.0 1.0
CB B:ASN108 4.9 19.8 1.0
CB B:ASP100 4.9 17.3 1.0
CD2 B:TYR36 5.0 22.1 1.0

Calcium binding site 3 out of 4 in 4lk7

Go back to Calcium Binding Sites List in 4lk7
Calcium binding site 3 out of 4 in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Resorufin-B-D-Galactopyranoside at 1.76 A Resolution


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 Pseudomonas Aeruginosa Lectin Leca Complexed with Resorufin-B-D-Galactopyranoside at 1.76 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:19.7
occ:1.00
 O C:TYR36 2.4 20.1 1.0
O C:THR104 2.4 21.2 1.0
OD1 C:ASN108 2.4 21.1 1.0
OD2 C:ASP100 2.5 17.9 1.0
O4 C:GAL203 2.5 18.4 1.0
OD1 C:ASN107 2.5 21.3 1.0
O3 C:GAL203 2.6 18.1 1.0
C C:TYR36 3.4 21.3 1.0
CG C:ASP100 3.5 21.7 1.0
C4 C:GAL203 3.5 21.8 1.0
OG1 C:THR104 3.5 22.0 1.0
C3 C:GAL203 3.5 21.1 1.0
CG C:ASN108 3.5 20.2 1.0
C C:THR104 3.5 21.3 1.0
CG C:ASN107 3.6 20.9 1.0
OD1 C:ASP100 3.7 19.9 1.0
CA C:TYR36 3.9 18.1 1.0
ND2 C:ASN108 4.0 18.8 1.0
CB C:THR104 4.0 22.0 1.0
C2 C:GAL203 4.0 20.5 1.0
ND2 C:ASN107 4.0 20.3 1.0
CB C:TYR36 4.1 20.1 1.0
CA C:THR104 4.4 21.3 1.0
N C:TYR105 4.4 20.6 1.0
CA C:TYR105 4.4 20.8 1.0
N C:GLY37 4.5 18.1 1.0
N C:ASN108 4.6 17.6 1.0
C C:TYR105 4.7 21.7 1.0
C C:ASN107 4.8 21.3 1.0
N C:ASN107 4.8 19.4 1.0
CB C:ASN108 4.8 19.1 1.0
C5 C:GAL203 4.8 22.5 1.0
CA C:GLY37 4.8 17.9 1.0
O2 C:GAL203 4.8 21.1 1.0
CB C:ASP100 4.8 18.4 1.0
CB C:ASN107 4.9 20.9 1.0
CA C:ASN108 4.9 19.8 1.0

Calcium binding site 4 out of 4 in 4lk7

Go back to Calcium Binding Sites List in 4lk7
Calcium binding site 4 out of 4 in the Crystal Structure of Pseudomonas Aeruginosa Lectin Leca Complexed with Resorufin-B-D-Galactopyranoside at 1.76 A Resolution


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 Pseudomonas Aeruginosa Lectin Leca Complexed with Resorufin-B-D-Galactopyranoside at 1.76 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:25.6
occ:1.00
 O D:TYR36 2.3 25.4 1.0
OD1 D:ASN108 2.4 25.8 1.0
O D:THR104 2.4 22.5 1.0
O3 D:GAL203 2.5 25.1 1.0
OD2 D:ASP100 2.5 22.5 1.0
OD1 D:ASN107 2.6 28.2 1.0
O4 D:GAL203 2.7 25.1 1.0
C D:TYR36 3.3 27.1 1.0
C3 D:GAL203 3.4 29.9 1.0
OG1 D:THR104 3.5 26.7 1.0
CG D:ASN108 3.5 24.2 1.0
C4 D:GAL203 3.5 29.1 1.0
CG D:ASP100 3.5 27.1 1.0
C D:THR104 3.6 25.7 1.0
CG D:ASN107 3.6 28.4 1.0
OD1 D:ASP100 3.8 23.4 1.0
CA D:TYR36 3.9 25.2 1.0
C2 D:GAL203 3.9 31.2 1.0
CB D:THR104 3.9 27.1 1.0
ND2 D:ASN108 4.0 23.6 1.0
CB D:TYR36 4.0 23.7 1.0
ND2 D:ASN107 4.1 27.2 1.0
N D:GLY37 4.4 27.1 1.0
CA D:THR104 4.4 26.4 1.0
N D:TYR105 4.5 26.2 1.0
CA D:TYR105 4.5 24.2 1.0
N D:ASN108 4.6 26.7 1.0
O2 D:GAL203 4.6 30.8 1.0
O D:HOH345 4.7 32.5 1.0
CA D:GLY37 4.7 27.7 1.0
C D:ASN107 4.7 28.3 1.0
CB D:ASN108 4.8 23.4 1.0
C D:TYR105 4.8 25.9 1.0
N D:ASN107 4.9 25.0 1.0
C5 D:GAL203 4.9 32.6 1.0
CB D:ASP100 4.9 21.5 1.0
CB D:ASN107 4.9 30.8 1.0
CA D:ASN108 4.9 27.5 1.0
CD2 D:TYR36 5.0 29.4 1.0

Reference:

R.U.Kadam, D.Garg, J.Schwartz, R.Visini, M.Sattler, A.Stocker, T.Darbre, J.L.Reymond. Ch-Pi "T-Shape" Interaction with Histidine Explains Binding of Aromatic Galactosides to Pseudomonas Aeruginosa Lectin Leca Acs Chem.Biol. V. 8 1925 2013.
ISSN: ISSN 1554-8929
PubMed: 23869965
DOI: 10.1021/CB400303W
Page generated: Sun Jul 14 09:32:35 2024

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