Calcium in PDB 5cyb: Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae

The structure of Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae, PDB code: 5cyb was solved by C.Carrasco-Lopez, M.R.Abdullah, S.Hammerschmidt, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.10 / 2.10
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	107.485, 107.485, 63.870, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 21.7

The binding sites of Calcium atom in the Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae (pdb code 5cyb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae, PDB code: 5cyb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:0.9 occ:1.00 OD1 A:ASP81 2.4 0.9 1.0 O A:HOH304 2.4 1.0 1.0 OD2 A:ASP81 2.8 0.0 1.0 CG A:ASP81 2.9 0.8 1.0 OD1 A:ASP146 3.5 0.4 1.0 HA A:ASP146 3.6 85.1 1.0 O A:SER145 3.7 94.3 1.0 OD1 A:ASP80 3.8 75.4 1.0 O A:HOH359 4.3 0.2 1.0 CB A:ASP81 4.4 0.4 1.0 CA A:ASP146 4.6 70.9 1.0 CG A:ASP146 4.6 0.5 1.0 C A:SER145 4.8 82.2 1.0 H A:ASP81 4.8 97.3 1.0 HB3 A:ASP81 4.8 0.5 1.0 HB2 A:ASP81 4.9 0.5 1.0 CG A:ASP80 5.0 76.5 1.0 HA A:ASP81 5.0 0.6 1.0

Calcium binding site 2 out of 4 in the Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:92.0 occ:1.00 OD2 A:ASP104 2.2 72.1 1.0 O A:HOH341 2.4 95.7 1.0 OD2 A:ASP102 2.4 74.5 1.0 OE2 A:GLU100 2.9 59.7 0.4 OE1 A:GLU100 3.0 76.3 0.4 HB2 A:ASP104 3.2 63.4 1.0 CG A:ASP104 3.2 60.5 1.0 CD A:GLU100 3.3 68.2 0.4 CG A:ASP102 3.4 68.9 1.0 OD1 A:ASP102 3.5 70.7 1.0 CB A:ASP104 3.6 52.8 1.0 HB3 A:ASP104 3.9 63.4 1.0 OD1 A:ASP104 4.3 54.1 1.0 HG2 A:GLU100 4.4 0.3 0.6 HB2 A:GLU100 4.5 77.9 0.4 HB3 A:GLU100 4.6 78.0 0.6 CG A:GLU100 4.6 69.2 0.4 HB2 A:GLU100 4.6 78.0 0.6 HB3 A:GLU100 4.8 77.9 0.4 H A:ASP104 4.8 58.0 1.0 CB A:ASP102 4.8 51.8 1.0 CB A:GLU100 4.9 64.9 0.4 HG3 A:GLU100 4.9 83.0 0.4 CB A:GLU100 5.0 65.0 0.6

Calcium binding site 3 out of 4 in the Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:1.0 occ:1.00 OD2 A:ASP141 2.4 0.1 1.0 O A:HOH303 2.5 81.4 1.0 HB2 A:ASP143 3.1 0.8 1.0 CG A:ASP141 3.2 0.2 1.0 OD1 A:ASP141 3.2 91.7 1.0 HB3 A:ASP143 3.5 0.8 1.0 OD2 A:ASP143 3.6 0.9 1.0 CB A:ASP143 3.7 87.4 1.0 OD2 A:ASP146 4.0 0.9 1.0 OD2 A:ASP139 4.0 0.2 1.0 CG A:ASP143 4.1 0.1 1.0 HB3 A:ASP139 4.3 89.5 1.0 O A:HOH353 4.5 59.7 1.0 H A:ASP143 4.6 88.8 1.0 CB A:ASP141 4.7 85.3 1.0 HB2 A:ASP139 4.7 89.5 1.0 CG A:ASP139 4.8 92.0 1.0 CB A:ASP139 4.9 74.5 1.0 HB3 A:ASP141 4.9 0.4 1.0 HB2 A:ASP141 5.0 0.4 1.0

Calcium binding site 4 out of 4 in the Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:88.8 occ:1.00 OXT A:ACT202 3.0 0.1 1.0 O A:LYS152 3.8 73.1 1.0 HD22 A:ASN133 4.0 52.9 1.0 C A:ACT202 4.2 0.6 1.0 OXT A:LYS152 4.4 69.6 1.0 C A:LYS152 4.6 56.9 1.0 O A:ACT202 4.6 0.1 1.0 ND2 A:ASN133 4.7 44.0 1.0 HG22 A:THR151 4.8 59.6 1.0 HD21 A:ASN133 4.9 52.9 1.0

M.R.Abdullah, C.Carrasco-Lopez, M.Saleh, A.Gomez, L.Petruschka, F.Vob, T.Pribyl, J.A.Hermoso, S.Hammerschmidt. Unraveling the Function and Structure of A Lipocalin Lipoprotein Affecting Virulence in Streptococcus Pneumoniae To Be Published.