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Calcium in PDB 3zyb: Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution

Protein crystallography data

The structure of Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution, PDB code: 3zyb was solved by R.U.Kadam, M.Bergmann, M.Hurley, D.Garg, M.Cacciarini, M.A.Swiderska, C.Nativi, M.Sattler, A.R.Smyth, P.Williams, M.Camara, A.Stocker, T.Darbre, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.26 / 2.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.332, 128.559, 146.063, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 24

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution (pdb code 3zyb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution, PDB code: 3zyb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3zyb

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Calcium binding site 1 out of 8 in the Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 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 Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:22.7
occ:1.00
 OD1 A:ASN108 2.6 22.5 1.0
O4 A:GAL202 2.7 22.1 1.0
O A:THR104 2.7 22.1 1.0
O A:TYR36 2.7 22.5 1.0
OD2 A:ASP100 2.8 21.1 1.0
OD1 A:ASN107 2.8 22.9 1.0
O3 A:GAL202 2.8 21.9 1.0
C A:TYR36 3.5 23.1 1.0
OG1 A:THR104 3.5 21.1 1.0
C A:THR104 3.5 21.5 1.0
C4 A:GAL202 3.6 22.0 1.0
C3 A:GAL202 3.6 22.4 1.0
CG A:ASP100 3.7 21.4 1.0
CG A:ASN108 3.7 22.8 1.0
CB A:THR104 3.7 21.8 1.0
CG A:ASN107 3.8 23.2 1.0
OD1 A:ASP100 3.8 20.7 1.0
CA A:TYR36 3.9 23.0 1.0
CB A:TYR36 4.0 22.2 1.0
ND2 A:ASN108 4.0 21.8 1.0
C2 A:GAL202 4.1 22.3 1.0
O A:HOH307 4.2 22.4 1.0
CA A:THR104 4.3 22.7 1.0
ND2 A:ASN107 4.3 22.4 1.0
N A:TYR105 4.3 22.2 1.0
CA A:TYR105 4.4 22.5 1.0
N A:GLY37 4.4 23.8 1.0
O2 A:GAL202 4.7 22.9 1.0
C A:TYR105 4.8 23.6 1.0
N A:ASN108 4.8 22.9 1.0
CA A:GLY37 4.9 22.6 1.0
C A:ASN107 4.9 22.7 1.0
N A:ASN107 4.9 20.9 1.0
C5 A:GAL202 4.9 22.1 1.0
CB A:ASN108 5.0 22.6 1.0

Calcium binding site 2 out of 8 in 3zyb

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Calcium binding site 2 out of 8 in the Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 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 Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:22.4
occ:1.00
 OD1 B:ASN108 2.6 21.8 1.0
O B:THR104 2.7 24.8 1.0
OD1 B:ASN107 2.7 22.7 1.0
O3 B:GAL202 2.7 21.6 1.0
OD2 B:ASP100 2.8 21.3 1.0
O4 B:GAL202 2.8 20.7 1.0
O B:TYR36 2.8 22.4 1.0
C B:THR104 3.5 22.7 1.0
C3 B:GAL202 3.5 23.2 1.0
OG1 B:THR104 3.5 22.6 1.0
C B:TYR36 3.6 22.8 1.0
C4 B:GAL202 3.6 22.8 1.0
CG B:ASP100 3.6 21.9 1.0
CB B:THR104 3.7 22.0 1.0
CG B:ASN108 3.7 21.9 1.0
CG B:ASN107 3.8 23.2 1.0
OD1 B:ASP100 3.8 22.3 1.0
C2 B:GAL202 3.9 21.8 1.0
CA B:TYR36 4.0 22.1 1.0
CB B:TYR36 4.2 21.4 1.0
ND2 B:ASN108 4.2 20.9 1.0
CA B:THR104 4.2 23.2 1.0
ND2 B:ASN107 4.2 22.2 1.0
N B:TYR105 4.3 21.9 1.0
CA B:TYR105 4.4 22.9 1.0
O2 B:GAL202 4.4 22.0 1.0
N B:GLY37 4.5 22.9 1.0
N B:ASN108 4.7 23.0 1.0
O B:HOH311 4.7 23.3 1.0
C B:TYR105 4.8 23.5 1.0
N B:ASN107 4.8 23.9 1.0
C B:ASN107 4.9 23.4 1.0
CA B:GLY37 4.9 22.0 1.0
CB B:ASN108 4.9 21.8 1.0
C5 B:GAL202 5.0 22.1 1.0

Calcium binding site 3 out of 8 in 3zyb

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Calcium binding site 3 out of 8 in the Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 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 Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:26.5
occ:1.00
 OD1 C:ASN108 2.7 25.9 1.0
O C:THR104 2.7 27.3 1.0
O4 C:GAL202 2.7 26.7 1.0
O C:TYR36 2.8 27.2 1.0
OD2 C:ASP100 2.8 22.8 1.0
O3 C:GAL202 2.8 27.6 1.0
OD1 C:ASN107 2.8 27.2 1.0
C C:TYR36 3.4 26.3 1.0
C3 C:GAL202 3.6 27.4 1.0
C C:THR104 3.6 26.6 1.0
C4 C:GAL202 3.6 26.4 1.0
OG1 C:THR104 3.6 25.6 1.0
CG C:ASP100 3.7 23.3 1.0
CG C:ASN108 3.8 24.8 1.0
CG C:ASN107 3.8 27.7 1.0
CB C:THR104 3.9 26.7 1.0
OD1 C:ASP100 3.9 23.0 1.0
CA C:TYR36 3.9 24.4 1.0
C2 C:GAL202 3.9 27.3 1.0
CB C:TYR36 4.1 24.6 1.0
ND2 C:ASN107 4.1 27.2 1.0
ND2 C:ASN108 4.2 24.0 1.0
N C:GLY37 4.3 26.6 1.0
N C:TYR105 4.4 26.4 1.0
CA C:THR104 4.4 27.1 1.0
CA C:TYR105 4.4 27.0 1.0
O2 C:GAL202 4.5 28.3 1.0
N C:ASN108 4.7 26.0 1.0
CA C:GLY37 4.7 27.5 1.0
C C:TYR105 4.8 26.7 1.0
C C:ASN107 4.8 27.1 1.0
N C:ASN107 4.8 25.8 1.0
O C:HOH327 4.9 27.6 1.0
CB C:ASN108 5.0 24.6 1.0
C5 C:GAL202 5.0 25.8 1.0

Calcium binding site 4 out of 8 in 3zyb

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Calcium binding site 4 out of 8 in the Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 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 Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:24.0
occ:1.00
 O D:THR104 2.7 23.8 1.0
OD2 D:ASP100 2.7 22.1 1.0
OD1 D:ASN107 2.7 23.4 1.0
OD1 D:ASN108 2.7 24.8 1.0
O D:TYR36 2.8 23.6 1.0
O4 D:GAL202 2.8 23.6 1.0
O3 D:GAL202 2.8 23.1 1.0
C D:THR104 3.5 22.5 1.0
OG1 D:THR104 3.5 22.6 1.0
C D:TYR36 3.5 24.1 1.0
CG D:ASP100 3.6 22.2 1.0
C4 D:GAL202 3.6 23.1 1.0
CG D:ASN108 3.6 23.2 1.0
C3 D:GAL202 3.7 23.1 1.0
OD1 D:ASP100 3.7 21.7 1.0
CB D:THR104 3.8 22.6 1.0
CG D:ASN107 3.8 23.8 1.0
CA D:TYR36 4.0 22.3 1.0
ND2 D:ASN108 4.0 23.0 1.0
CB D:TYR36 4.2 22.6 1.0
N D:TYR105 4.2 23.4 1.0
C2 D:GAL202 4.2 21.9 1.0
CA D:THR104 4.3 23.1 1.0
ND2 D:ASN107 4.3 23.1 1.0
CA D:TYR105 4.3 23.1 1.0
O D:HOH306 4.5 20.1 1.0
N D:GLY37 4.5 24.5 1.0
N D:ASN108 4.6 24.0 1.0
C D:TYR105 4.7 23.4 1.0
C D:ASN107 4.8 24.4 1.0
O2 D:GAL202 4.8 21.8 1.0
N D:ASN107 4.8 24.0 1.0
CA D:GLY37 4.9 23.7 1.0
CB D:ASN108 4.9 23.2 1.0
O D:TYR105 5.0 23.6 1.0
CB D:ASP100 5.0 21.0 1.0
CA D:ASN108 5.0 23.4 1.0

Calcium binding site 5 out of 8 in 3zyb

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Calcium binding site 5 out of 8 in the Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:27.3
occ:1.00
 OD1 E:ASN108 2.7 25.7 1.0
O4 E:GAL202 2.7 26.2 1.0
OD1 E:ASN107 2.8 26.0 1.0
O E:THR104 2.8 28.0 1.0
O E:TYR36 2.8 27.4 1.0
OD2 E:ASP100 2.8 24.7 1.0
O3 E:GAL202 2.8 26.4 1.0
C E:TYR36 3.5 26.2 1.0
OG1 E:THR104 3.5 24.7 1.0
C E:THR104 3.5 25.8 1.0
C4 E:GAL202 3.6 27.3 1.0
C3 E:GAL202 3.6 28.1 1.0
CG E:ASP100 3.6 25.2 1.0
CB E:THR104 3.7 26.1 1.0
OD1 E:ASP100 3.8 24.3 1.0
CG E:ASN108 3.8 24.4 1.0
CG E:ASN107 3.8 26.1 1.0
CA E:TYR36 4.0 24.9 1.0
C2 E:GAL202 4.0 27.9 1.0
CB E:TYR36 4.1 24.8 1.0
CA E:THR104 4.3 26.8 1.0
ND2 E:ASN107 4.3 25.2 1.0
N E:TYR105 4.3 26.4 1.0
ND2 E:ASN108 4.3 23.4 1.0
CA E:TYR105 4.4 26.3 1.0
N E:GLY37 4.4 26.0 1.0
O2 E:GAL202 4.6 28.7 1.0
N E:ASN108 4.7 26.3 1.0
C E:TYR105 4.8 26.5 1.0
CA E:GLY37 4.8 27.2 1.0
C E:ASN107 4.8 26.7 1.0
N E:ASN107 4.9 26.6 1.0
C5 E:GAL202 5.0 26.6 1.0

Calcium binding site 6 out of 8 in 3zyb

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Calcium binding site 6 out of 8 in the Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:24.2
occ:1.00
 OD1 F:ASN108 2.7 23.2 1.0
O F:THR104 2.7 24.2 1.0
O4 F:GAL202 2.8 22.9 1.0
OD2 F:ASP100 2.8 22.7 1.0
O F:TYR36 2.8 23.4 1.0
O3 F:GAL202 2.8 24.7 1.0
OD1 F:ASN107 2.8 23.3 1.0
OG1 F:THR104 3.4 22.8 1.0
C F:THR104 3.5 23.1 1.0
C F:TYR36 3.6 23.6 1.0
C3 F:GAL202 3.6 24.2 1.0
CG F:ASP100 3.6 22.9 1.0
C4 F:GAL202 3.6 23.7 1.0
CB F:THR104 3.7 23.8 1.0
OD1 F:ASP100 3.7 21.8 1.0
CG F:ASN108 3.7 23.0 1.0
CG F:ASN107 3.9 23.8 1.0
C2 F:GAL202 3.9 24.8 1.0
CA F:TYR36 4.0 23.6 1.0
CB F:TYR36 4.1 22.9 1.0
ND2 F:ASN108 4.2 23.3 1.0
CA F:THR104 4.2 23.7 1.0
N F:TYR105 4.3 23.8 1.0
ND2 F:ASN107 4.3 24.1 1.0
CA F:TYR105 4.5 22.9 1.0
O2 F:GAL202 4.5 24.9 1.0
N F:GLY37 4.6 24.4 1.0
N F:ASN108 4.8 23.3 1.0
C F:TYR105 4.9 23.5 1.0
O F:HOH342 4.9 25.1 1.0
CA F:GLY37 5.0 22.9 1.0
CB F:ASP100 5.0 21.5 1.0
N F:ASN107 5.0 23.2 1.0
CB F:ASN108 5.0 22.5 1.0

Calcium binding site 7 out of 8 in 3zyb

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Calcium binding site 7 out of 8 in the Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:28.8
occ:1.00
 OD1 G:ASN108 2.7 26.0 1.0
OD2 G:ASP100 2.7 25.3 1.0
O G:THR104 2.8 28.6 1.0
O4 G:GAL202 2.8 27.0 1.0
O G:TYR36 2.8 27.7 1.0
OD1 G:ASN107 2.8 28.0 1.0
O3 G:GAL202 2.8 27.0 1.0
C G:TYR36 3.5 27.5 1.0
C G:THR104 3.5 26.8 1.0
OG1 G:THR104 3.6 26.4 1.0
C3 G:GAL202 3.6 28.2 1.0
C4 G:GAL202 3.7 27.2 1.0
CG G:ASP100 3.7 25.3 1.0
CG G:ASN108 3.7 26.5 1.0
CG G:ASN107 3.9 28.1 1.0
OD1 G:ASP100 3.9 23.7 1.0
CB G:THR104 3.9 27.2 1.0
CA G:TYR36 3.9 26.6 1.0
ND2 G:ASN108 4.1 25.9 1.0
C2 G:GAL202 4.1 28.8 1.0
CB G:TYR36 4.1 26.4 1.0
N G:TYR105 4.3 26.8 1.0
ND2 G:ASN107 4.3 29.1 1.0
CA G:TYR105 4.4 26.9 1.0
CA G:THR104 4.4 27.3 1.0
N G:GLY37 4.4 27.6 1.0
O2 G:GAL202 4.7 28.9 1.0
C G:TYR105 4.7 26.2 1.0
CA G:GLY37 4.8 28.3 1.0
C G:ASN107 4.9 28.6 1.0
N G:ASN107 4.9 27.8 1.0
N G:ASN108 4.9 27.9 1.0
O G:HOH322 5.0 28.8 1.0

Calcium binding site 8 out of 8 in 3zyb

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Calcium binding site 8 out of 8 in the Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Pa-Il Lectin Complexed with GALAG0 at 2.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca201

b:28.8
occ:1.00
 OD1 H:ASN108 2.7 27.4 1.0
O H:THR104 2.7 28.9 1.0
OD2 H:ASP100 2.8 26.3 1.0
O3 H:GAL202 2.8 28.3 1.0
OD1 H:ASN107 2.8 28.0 1.0
O H:TYR36 2.8 27.7 1.0
O4 H:GAL202 2.8 27.4 1.0
C H:TYR36 3.5 27.4 1.0
OG1 H:THR104 3.6 26.8 1.0
C H:THR104 3.6 26.9 1.0
CG H:ASP100 3.6 27.0 1.0
C3 H:GAL202 3.6 28.9 1.0
C4 H:GAL202 3.7 27.8 1.0
OD1 H:ASP100 3.7 25.0 1.0
CG H:ASN108 3.7 26.9 1.0
CG H:ASN107 3.8 28.9 1.0
CB H:THR104 3.8 27.7 1.0
CA H:TYR36 3.9 25.9 1.0
C2 H:GAL202 4.0 29.9 1.0
CB H:TYR36 4.0 25.6 1.0
ND2 H:ASN107 4.2 28.8 1.0
ND2 H:ASN108 4.2 26.1 1.0
CA H:THR104 4.4 27.8 1.0
N H:TYR105 4.4 27.3 1.0
N H:GLY37 4.4 28.2 1.0
CA H:TYR105 4.5 26.9 1.0
O H:HOH315 4.6 30.9 1.0
O2 H:GAL202 4.7 30.3 1.0
N H:ASN108 4.8 27.9 1.0
CA H:GLY37 4.8 28.1 1.0
C H:TYR105 4.9 27.3 1.0
C H:ASN107 5.0 29.2 1.0
N H:ASN107 5.0 28.6 1.0
CB H:ASN108 5.0 27.2 1.0
CB H:ASP100 5.0 25.1 1.0

Reference:

R.U.Kadam, M.Bergmann, M.Hurley, D.Garg, M.Cacciarini, M.A.Swiderska, C.Nativi, M.Sattler, A.R.Smyth, P.Williams, M.Camara, A.Stocker, T.Darbre, J.-L.Reymond. A Glycopeptide Dendrimer Inhibitor of the Galactose-Specific Lectin Leca and of Pseudomonas Aeruginosa Biofilms. Angew.Chem.Int.Ed.Engl. V. 50 10631 2011.
ISSN: ISSN 1433-7851
PubMed: 21919164
DOI: 10.1002/ANIE.201104342
Page generated: Tue Jul 8 18:19:53 2025

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