Atomistry » Calcium » PDB 5cxl-5da8 » 5cyb
Atomistry »
  Calcium »
    PDB 5cxl-5da8 »
      5cyb »

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

Protein crystallography data

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

Calcium Binding Sites:

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 5cyb

Go back to Calcium Binding Sites List in 5cyb
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 5cyb

Go back to Calcium Binding Sites List in 5cyb
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 5cyb

Go back to Calcium Binding Sites List in 5cyb
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 5cyb

Go back to Calcium Binding Sites List in 5cyb
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

Reference:

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.
Page generated: Sat Dec 12 05:20:41 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