Atomistry » Calcium » PDB 5bu8-5cc4 » 5c9l
Atomistry »
  Calcium »
    PDB 5bu8-5cc4 »
      5c9l »

Calcium in PDB 5c9l: Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution

Protein crystallography data

The structure of Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution, PDB code: 5c9l was solved by A.Kumar, P.Sykorova, G.Demo, P.Dobes, P.Hyrsl, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.15 / 1.65
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 71.120, 87.677, 157.691, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 15.9

Other elements in 5c9l:

The structure of Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution also contains other interesting chemical elements:

Mercury (Hg) 2 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution (pdb code 5c9l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution, PDB code: 5c9l:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5c9l

Go back to Calcium Binding Sites List in 5c9l
Calcium binding site 1 out of 2 in the Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 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 Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:14.2
occ:0.80
O A:HOH704 2.2 26.5 1.0
O A:HOH778 2.3 31.1 1.0
ND1 A:HIS203 2.3 13.4 1.0
OD2 A:ASP132 2.4 10.6 1.0
O A:HIS203 2.5 15.9 1.0
O A:HOH805 2.6 27.0 1.0
CE1 A:HIS203 3.1 12.1 1.0
CG A:HIS203 3.4 13.2 1.0
C A:HIS203 3.6 14.0 1.0
CG A:ASP132 3.6 8.7 1.0
CB A:HIS203 3.7 14.0 1.0
NH2 A:ARG134 4.0 12.7 1.0
CB A:ASP132 4.1 7.7 1.0
CA A:HIS203 4.3 12.8 1.0
NE2 A:HIS203 4.3 14.2 1.0
NE A:ARG134 4.4 8.2 1.0
CD2 A:HIS203 4.4 13.1 1.0
OG1 A:THR204 4.4 17.2 1.0
OD1 A:ASP132 4.6 8.1 1.0
CZ A:ARG134 4.6 9.5 1.0
N A:THR204 4.6 13.8 1.0
O A:ALA202 4.6 12.2 1.0
CA A:THR204 4.9 14.9 1.0

Calcium binding site 2 out of 2 in 5c9l

Go back to Calcium Binding Sites List in 5c9l
Calcium binding site 2 out of 2 in the Crystal Structure of Native Pll Lectin From Photorhabdus Luminescens at 1.65 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 Native Pll Lectin From Photorhabdus Luminescens at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:11.5
occ:0.70
O A:HOH775 2.2 20.4 1.0
O A:HOH790 2.3 29.1 1.0
O A:HOH504 2.3 21.8 1.0
ND1 A:HIS155 2.4 9.7 1.0
OD2 A:ASP84 2.4 8.7 1.0
O A:HIS155 2.5 10.3 1.0
O A:HOH734 2.6 26.0 1.0
CE1 A:HIS155 3.3 10.2 1.0
CG A:HIS155 3.4 8.3 1.0
CG A:ASP84 3.5 8.2 1.0
C A:HIS155 3.6 8.8 1.0
CB A:HIS155 3.7 8.6 1.0
NH2 A:ARG86 4.0 11.9 1.0
CB A:ASP84 4.1 7.4 1.0
CA A:HIS155 4.2 8.3 1.0
NE A:ARG86 4.4 9.4 1.0
NE2 A:HIS155 4.4 9.8 1.0
CD2 A:HIS155 4.5 8.7 1.0
OD1 A:ASP84 4.6 8.1 1.0
O A:HOH859 4.6 28.1 1.0
CZ A:ARG86 4.6 10.2 1.0
N A:THR156 4.6 10.6 1.0
OG1 A:THR156 4.7 14.6 1.0
O A:ALA154 4.7 8.2 1.0
CA A:THR156 4.9 12.1 1.0

Reference:

A.Kumar, P.Sykorova, G.Demo, P.Dobes, P.Hyrsl, M.Wimmerova. A Novel Fucose-Binding Lectin From Photorhabdus Luminescens (Pll) with An Unusual Heptabladed Beta-Propeller Tetrameric Structure. J.Biol.Chem. V. 291 25032 2016.
ISSN: ESSN 1083-351X
PubMed: 27758853
DOI: 10.1074/JBC.M115.693473
Page generated: Sat Dec 12 05:19:20 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy