Atomistry » Calcium » PDB 3zq9-4a41 » 3zyf
Atomistry »
  Calcium »
    PDB 3zq9-4a41 »
      3zyf »

Calcium in PDB 3zyf: Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 A Resolution

Protein crystallography data

The structure of Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 A Resolution, PDB code: 3zyf 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) 48.284 / 1.94
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.562, 84.562, 163.709, 90.00, 90.00, 90.00
R / Rfree (%) 18.55 / 21

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 A Resolution (pdb code 3zyf). 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 Pa-Il Lectin Complexed with Npg at 1.9 A Resolution, PDB code: 3zyf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3zyf

Go back to Calcium Binding Sites List in 3zyf
Calcium binding site 1 out of 4 in the Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 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 Npg at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:31.4
occ:1.00
OD2 A:ASP100 2.5 20.4 1.0
O A:TYR36 2.6 28.6 1.0
OD1 A:ASN108 2.6 30.9 1.0
O3 A:1471001 2.6 22.2 1.0
O A:THR104 2.6 32.4 1.0
O4 A:1471001 2.6 30.7 1.0
OD1 A:ASN107 2.7 39.7 1.0
C A:TYR36 3.4 25.6 1.0
CG A:ASP100 3.5 24.1 1.0
C3 A:1471001 3.5 27.3 1.0
OG1 A:THR104 3.5 32.8 1.0
C4 A:1471001 3.6 28.1 1.0
C A:THR104 3.6 31.7 1.0
CG A:ASN108 3.7 29.4 1.0
CG A:ASN107 3.7 38.7 1.0
OD1 A:ASP100 3.7 24.8 1.0
CB A:THR104 3.9 36.1 1.0
CA A:TYR36 3.9 23.4 1.0
C2 A:1471001 4.0 31.4 1.0
ND2 A:ASN107 4.1 35.9 1.0
CB A:TYR36 4.1 22.6 1.0
ND2 A:ASN108 4.1 24.5 1.0
CA A:THR104 4.4 35.3 1.0
N A:TYR105 4.4 31.4 1.0
N A:GLY37 4.4 32.5 1.0
CA A:TYR105 4.5 31.2 1.0
O A:HOH2119 4.6 38.0 1.0
O2 A:1471001 4.7 33.5 1.0
N A:ASN108 4.7 35.8 1.0
CA A:GLY37 4.8 34.7 1.0
C A:TYR105 4.8 33.4 1.0
CB A:ASP100 4.9 21.1 1.0
C5 A:1471001 4.9 28.3 1.0
O A:HOH2116 4.9 40.6 1.0
C A:ASN107 4.9 36.7 1.0
N A:ASN107 5.0 37.2 1.0
CB A:ASN108 5.0 28.7 1.0
CD2 A:TYR36 5.0 23.4 1.0

Calcium binding site 2 out of 4 in 3zyf

Go back to Calcium Binding Sites List in 3zyf
Calcium binding site 2 out of 4 in the Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 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 Npg at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:26.1
occ:1.00
OD1 B:ASN108 2.5 20.6 1.0
O B:THR104 2.5 27.2 1.0
O3 B:1471002 2.6 22.5 1.0
O B:TYR36 2.6 24.3 1.0
O4 B:1471002 2.6 24.5 1.0
OD2 B:ASP100 2.6 23.6 1.0
OD1 B:ASN107 2.6 27.7 1.0
C B:TYR36 3.4 20.1 1.0
C4 B:1471002 3.5 24.6 1.0
C3 B:1471002 3.5 24.7 1.0
CG B:ASN108 3.6 26.3 1.0
C B:THR104 3.6 26.9 1.0
CG B:ASP100 3.6 23.5 1.0
CG B:ASN107 3.7 29.6 1.0
OG1 B:THR104 3.7 22.6 1.0
CA B:TYR36 3.9 21.1 1.0
OD1 B:ASP100 3.9 22.9 1.0
CB B:THR104 4.0 26.7 1.0
CB B:TYR36 4.0 19.4 1.0
C2 B:1471002 4.0 27.3 1.0
ND2 B:ASN108 4.1 26.3 1.0
ND2 B:ASN107 4.2 27.9 1.0
N B:GLY37 4.4 32.9 1.0
CA B:THR104 4.4 27.2 1.0
N B:TYR105 4.5 26.1 1.0
CA B:TYR105 4.5 25.9 1.0
N B:ASN108 4.6 30.2 1.0
O B:HOH2090 4.6 38.3 1.0
O2 B:1471002 4.7 26.1 1.0
C B:ASN107 4.8 31.1 1.0
CA B:GLY37 4.8 35.3 1.0
C B:TYR105 4.8 26.9 1.0
CB B:ASN108 4.8 26.8 1.0
C5 B:1471002 4.8 22.4 1.0
N B:ASN107 4.8 31.4 1.0
CA B:ASN108 4.9 26.7 1.0
CB B:ASP100 4.9 17.6 1.0
CB B:ASN107 5.0 31.6 1.0

Calcium binding site 3 out of 4 in 3zyf

Go back to Calcium Binding Sites List in 3zyf
Calcium binding site 3 out of 4 in the Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 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 Npg at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca903

b:28.3
occ:1.00
O C:TYR36 2.5 30.8 1.0
O C:THR104 2.5 34.4 1.0
OD2 C:ASP100 2.6 24.5 1.0
OD1 C:ASN108 2.6 28.5 1.0
O3 C:1471003 2.6 25.9 1.0
OD1 C:ASN107 2.6 35.0 1.0
O4 C:1471003 2.6 30.9 1.0
C C:TYR36 3.4 30.4 1.0
C3 C:1471003 3.5 30.8 1.0
C4 C:1471003 3.5 32.7 1.0
CG C:ASP100 3.6 27.9 1.0
C C:THR104 3.7 34.1 1.0
CG C:ASN108 3.7 27.7 1.0
CG C:ASN107 3.7 33.0 1.0
OG1 C:THR104 3.7 28.8 1.0
OD1 C:ASP100 3.8 26.4 1.0
CA C:TYR36 3.9 27.1 1.0
C2 C:1471003 4.0 30.9 1.0
CB C:TYR36 4.1 25.3 1.0
ND2 C:ASN107 4.1 31.9 1.0
CB C:THR104 4.1 32.0 1.0
ND2 C:ASN108 4.1 26.1 1.0
N C:GLY37 4.4 27.2 1.0
CA C:TYR105 4.5 34.2 1.0
N C:TYR105 4.5 34.0 1.0
CA C:THR104 4.5 34.5 1.0
O2 C:1471003 4.7 29.9 1.0
N C:ASN108 4.7 28.6 1.0
CA C:GLY37 4.8 29.0 1.0
C C:ASN107 4.8 30.6 1.0
C C:TYR105 4.8 32.3 1.0
C5 C:1471003 4.9 31.9 1.0
O C:HOH2096 4.9 37.8 1.0
N C:ASN107 4.9 34.0 1.0
CB C:ASP100 4.9 24.8 1.0
CD1 C:TYR36 5.0 28.5 1.0
CB C:ASN108 5.0 26.8 1.0
CB C:ASN107 5.0 34.0 1.0

Calcium binding site 4 out of 4 in 3zyf

Go back to Calcium Binding Sites List in 3zyf
Calcium binding site 4 out of 4 in the Crystal Structure of Pa-Il Lectin Complexed with Npg at 1.9 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 Npg at 1.9 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca904

b:36.0
occ:1.00
OD1 D:ASN108 2.5 34.4 1.0
OD2 D:ASP100 2.5 30.2 1.0
O3 D:1471004 2.6 32.6 1.0
O D:THR104 2.6 42.4 1.0
O D:TYR36 2.6 43.4 1.0
O4 D:1471004 2.7 35.5 1.0
OD1 D:ASN107 2.7 44.2 1.0
C D:TYR36 3.4 41.5 1.0
CG D:ASP100 3.5 33.8 1.0
C3 D:1471004 3.5 34.9 1.0
C D:THR104 3.5 43.5 1.0
OG1 D:THR104 3.6 34.2 1.0
CG D:ASN108 3.6 35.2 1.0
C4 D:1471004 3.6 37.1 1.0
CG D:ASN107 3.8 45.0 1.0
OD1 D:ASP100 3.8 31.6 1.0
CA D:TYR36 3.9 35.4 1.0
C2 D:1471004 3.9 37.5 1.0
CB D:THR104 4.0 39.9 1.0
ND2 D:ASN108 4.1 33.9 1.0
CB D:TYR36 4.1 32.1 1.0
ND2 D:ASN107 4.2 46.2 1.0
N D:TYR105 4.4 44.7 1.0
CA D:THR104 4.4 41.2 1.0
CA D:TYR105 4.4 43.1 1.0
N D:GLY37 4.4 42.6 1.0
O2 D:1471004 4.5 40.3 1.0
N D:ASN108 4.7 38.8 1.0
C D:TYR105 4.8 44.6 1.0
CA D:GLY37 4.8 43.5 1.0
N D:ASN107 4.8 44.4 1.0
C D:ASN107 4.8 39.4 1.0
CB D:ASP100 4.9 29.4 1.0
C5 D:1471004 4.9 37.1 1.0
CB D:ASN108 4.9 36.4 1.0
O D:HOH2086 4.9 35.1 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: Sat Dec 12 04:37:44 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy