Calcium in PDB 5ftx: Structure of Surface Layer Protein Sbsc, Domains 4-9

The structure of Structure of Surface Layer Protein Sbsc, Domains 4-9, PDB code: 5ftx was solved by A.Dordic, T.Pavkov-Keller, M.Eder, E.M.Egelseer, K.Davis, D.Mills, U.B.Sleytr, W.Kuehlbrandt, J.Vonck, W.Keller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.04 / 4.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.627, 48.128, 196.136, 90.00, 96.60, 90.00
R / Rfree (%)	20.3 / 26.8

The structure of Structure of Surface Layer Protein Sbsc, Domains 4-9 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Structure of Surface Layer Protein Sbsc, Domains 4-9 (pdb code 5ftx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of Surface Layer Protein Sbsc, Domains 4-9, PDB code: 5ftx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Structure of Surface Layer Protein Sbsc, Domains 4-9


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Surface Layer Protein Sbsc, Domains 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2102 b:98.6 occ:1.00 OD1 A:ASP802 2.3 0.3 1.0 OG1 A:THR806 2.3 0.8 1.0 O A:THR806 2.3 0.5 1.0 O A:SER803 2.4 0.8 1.0 OE1 A:GLU811 2.4 0.4 1.0 O A:THR809 2.5 93.8 1.0 HB A:THR806 2.7 0.8 1.0 CB A:THR806 2.9 99.0 1.0 OE2 A:GLU811 3.1 0.2 1.0 CD A:GLU811 3.1 0.0 1.0 C A:THR806 3.1 99.8 1.0 H A:THR806 3.3 0.0 1.0 H A:SER803 3.3 0.6 1.0 CG A:ASP802 3.4 0.9 1.0 HA A:ASN810 3.4 1.0 1.0 CA A:THR806 3.4 99.0 1.0 C A:SER803 3.5 0.6 1.0 N A:SER803 3.5 84.7 1.0 HA A:ASP802 3.6 0.5 1.0 C A:THR809 3.7 92.5 1.0 N A:THR806 3.8 0.4 1.0 H A:GLU811 3.9 0.8 1.0 C A:ASP802 3.9 0.8 1.0 CA A:SER803 4.0 84.2 1.0 H A:THR809 4.1 0.6 1.0 CA A:ASP802 4.1 99.5 1.0 HG21 A:THR809 4.1 0.8 1.0 HB3 A:SER803 4.1 0.9 1.0 OD2 A:ASP802 4.2 86.1 1.0 CA A:ASN810 4.2 90.8 1.0 CG2 A:THR806 4.3 93.4 1.0 CB A:ASP802 4.3 0.9 1.0 HA A:THR806 4.3 0.9 1.0 N A:PRO807 4.4 98.6 1.0 HG22 A:THR806 4.4 0.1 1.0 N A:ASN810 4.4 93.3 1.0 N A:GLU811 4.4 98.2 1.0 HA A:ALA804 4.5 0.4 1.0 N A:ALA804 4.6 0.3 1.0 CG A:GLU811 4.6 0.1 1.0 HB2 A:ASP802 4.6 0.5 1.0 O A:ASP802 4.6 0.4 1.0 CB A:SER803 4.7 85.8 1.0 HA A:PRO807 4.7 0.5 1.0 HG21 A:THR806 4.7 0.1 1.0 N A:THR809 4.8 0.3 1.0 CA A:THR809 4.8 94.8 1.0 C A:ASN810 4.8 94.3 1.0 HG23 A:THR806 4.9 0.1 1.0 HA A:SER803 4.9 0.0 1.0 CA A:PRO807 4.9 0.4 1.0 HG2 A:GLU811 4.9 0.5 1.0 HB2 A:GLU811 4.9 0.5 1.0 CA A:ALA804 4.9 0.8 1.0

Calcium binding site 2 out of 5 in the Structure of Surface Layer Protein Sbsc, Domains 4-9


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Surface Layer Protein Sbsc, Domains 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2103 b:92.8 occ:1.00 O A:SER666 2.2 0.3 1.0 HD22 A:ASN674 2.2 0.0 1.0 OD1 A:ASN674 2.3 0.0 1.0 O A:ASP664 2.3 96.7 1.0 OE2 A:GLU669 2.3 0.1 1.0 OE1 A:GLU669 2.4 0.0 1.0 CD A:GLU669 2.6 1.0 1.0 ND2 A:ASN674 2.8 94.2 1.0 CG A:ASN674 2.8 0.0 1.0 C A:SER666 3.4 0.5 1.0 C A:ASP664 3.4 0.7 1.0 HA A:LYS665 3.5 0.3 1.0 HD21 A:ASN674 3.6 0.0 1.0 HB3 A:ASP664 3.7 0.2 1.0 HA A:ALA667 3.8 0.3 1.0 N A:SER666 3.8 0.9 1.0 H A:SER666 3.9 0.9 1.0 C A:LYS665 3.9 0.8 1.0 CA A:LYS665 4.0 0.9 1.0 CG A:GLU669 4.0 94.8 1.0 N A:LYS665 4.2 0.8 1.0 HG3 A:GLU669 4.2 0.8 1.0 H A:GLU669 4.2 0.5 1.0 CA A:SER666 4.3 0.0 1.0 CB A:ASN674 4.3 92.4 1.0 N A:ALA667 4.3 0.5 1.0 CA A:ALA667 4.4 0.6 1.0 HB3 A:GLU669 4.4 0.9 1.0 HA A:ASN674 4.5 97.2 1.0 CB A:ASP664 4.5 0.2 1.0 O A:LYS665 4.5 0.4 1.0 CA A:ASP664 4.5 0.7 1.0 HG2 A:GLU669 4.6 0.8 1.0 HB3 A:SER666 4.7 0.3 1.0 H A:ASP664 4.7 0.2 1.0 HB3 A:ASN674 4.8 0.8 1.0 HB2 A:ASN674 4.8 0.8 1.0 C A:ALA667 4.8 96.1 1.0 CB A:GLU669 4.8 0.1 1.0 CA A:ASN674 4.9 81.0 1.0 O A:ASN673 4.9 80.5 1.0 H A:THR668 4.9 0.6 1.0 HA A:SER666 5.0 0.5 1.0

Calcium binding site 3 out of 5 in the Structure of Surface Layer Protein Sbsc, Domains 4-9


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Surface Layer Protein Sbsc, Domains 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2104 b:68.1 occ:1.00 OD1 A:ASN673 2.2 84.3 1.0 OD2 A:ASP659 2.3 96.0 1.0 O A:ASP675 2.4 77.4 1.0 OD1 A:ASP660 2.4 91.8 1.0 HB2 A:ASP659 2.8 0.8 1.0 O A:LYS662 3.2 80.4 1.0 CG A:ASP659 3.2 90.4 1.0 OD1 A:ASP675 3.3 96.1 1.0 CB A:ASP659 3.4 89.0 1.0 CG A:ASN673 3.4 94.7 1.0 CG A:ASP660 3.5 81.3 1.0 H A:ASP660 3.5 0.3 1.0 C A:ASP675 3.5 81.2 1.0 H A:ASP675 3.7 0.0 1.0 HA A:VAL676 3.7 0.5 1.0 HB3 A:ASP659 3.7 0.8 1.0 H A:LYS662 3.8 95.9 1.0 HE21 A:GLN677 3.8 0.6 1.0 OD2 A:ASP660 3.9 71.2 1.0 HA A:ASN673 3.9 0.8 1.0 HD22 A:ASN673 4.0 0.1 1.0 H A:GLY661 4.2 0.7 1.0 HG23 A:VAL676 4.2 99.2 1.0 ND2 A:ASN673 4.2 1.0 1.0 HE22 A:GLN677 4.2 0.6 1.0 N A:ASP660 4.2 0.4 1.0 NE2 A:GLN677 4.2 0.9 1.0 OD1 A:ASP659 4.4 83.5 1.0 N A:ASP675 4.4 92.5 1.0 C A:LYS662 4.4 82.2 1.0 N A:VAL676 4.4 80.1 1.0 CA A:VAL676 4.5 87.0 1.0 CA A:ASP675 4.5 94.1 1.0 CG A:ASP675 4.5 0.5 1.0 CB A:ASN673 4.5 88.0 1.0 CA A:ASN673 4.5 94.0 1.0 N A:LYS662 4.6 79.9 1.0 HG21 A:VAL676 4.7 99.2 1.0 CB A:ASP660 4.7 86.8 1.0 CA A:ASP659 4.7 95.2 1.0 C A:ASN673 4.8 82.9 1.0 N A:GLY661 4.8 94.7 1.0 HA A:ILE663 4.8 99.2 1.0 CG2 A:VAL676 4.8 82.7 1.0 HB2 A:ASN673 4.8 0.6 1.0 HB3 A:ASP660 4.9 0.2 1.0 C A:ASP659 4.9 0.9 1.0 HG12 A:ILE663 5.0 0.5 1.0 CA A:ASP660 5.0 0.3 1.0

Calcium binding site 4 out of 5 in the Structure of Surface Layer Protein Sbsc, Domains 4-9


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Surface Layer Protein Sbsc, Domains 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2105 b:0.8 occ:1.00 OE2 A:GLU702 2.3 0.1 1.0 OD1 A:ASN707 2.3 0.9 1.0 OE2 A:GLU737 2.4 89.9 1.0 OE1 A:GLU737 2.4 0.6 1.0 OD1 A:ASP705 2.4 0.3 1.0 O A:VAL709 2.6 0.7 1.0 CD A:GLU737 2.7 97.2 1.0 H A:THR706 2.9 0.1 1.0 HA A:ASP705 3.1 0.6 1.0 H A:ASN707 3.2 0.5 1.0 H A:VAL709 3.3 0.1 1.0 CG A:ASN707 3.4 0.5 1.0 CG A:ASP705 3.4 0.8 1.0 CD A:GLU702 3.5 0.5 1.0 C A:VAL709 3.5 99.3 1.0 HB A:VAL709 3.6 0.6 1.0 N A:THR706 3.7 0.1 1.0 HD22 A:ASN707 3.8 0.4 1.0 HG2 A:GLU702 3.9 0.5 1.0 CA A:ASP705 3.9 1.0 1.0 HG1 A:THR706 3.9 0.8 1.0 ND2 A:ASN707 4.0 1.0 1.0 N A:ASN707 4.0 0.6 1.0 N A:VAL709 4.0 0.4 1.0 HG12 A:ILE710 4.0 0.4 1.0 CB A:ASP705 4.1 0.7 1.0 HA A:ILE710 4.1 0.4 1.0 HB2 A:ASP705 4.1 0.4 1.0 CG A:GLU737 4.2 86.1 1.0 CG A:GLU702 4.2 0.6 1.0 CA A:VAL709 4.2 95.4 1.0 H A:GLY708 4.3 0.7 1.0 OD2 A:ASP705 4.3 0.1 1.0 HG3 A:GLU702 4.3 0.5 1.0 C A:ASP705 4.4 0.5 1.0 HB2 A:GLU737 4.4 0.2 1.0 CB A:VAL709 4.4 98.0 1.0 HG2 A:GLU737 4.5 0.4 1.0 CB A:ASN707 4.5 0.8 1.0 OE1 A:GLU702 4.5 0.1 1.0 N A:ILE710 4.5 98.0 1.0 HG13 A:ILE710 4.6 0.4 1.0 N A:GLY708 4.6 0.7 1.0 OG1 A:THR706 4.6 0.3 1.0 CA A:ASN707 4.6 0.2 1.0 HG3 A:GLU737 4.7 0.4 1.0 HB3 A:ASN707 4.7 1.0 1.0 CG1 A:ILE710 4.7 0.7 1.0 CA A:ILE710 4.8 0.7 1.0 HD21 A:ASN707 4.8 0.4 1.0 CA A:THR706 4.8 0.1 1.0 CB A:GLU737 4.8 94.3 1.0 C A:THR706 4.9 0.3 1.0 C A:ASN707 4.9 1.0 1.0 HB3 A:ASP705 5.0 0.4 1.0

Calcium binding site 5 out of 5 in the Structure of Surface Layer Protein Sbsc, Domains 4-9


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Surface Layer Protein Sbsc, Domains 4-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2108 b:43.5 occ:1.00 OD1 A:ASP892 2.4 45.1 1.0 OD2 A:ASP892 2.4 63.5 1.0 CG A:ASP892 2.8 62.5 1.0 OE1 A:GLU979 3.1 85.2 1.0 OD1 A:ASP982 3.3 96.0 1.0 OD2 A:ASP982 3.5 84.8 1.0 H A:LEU893 3.7 0.0 1.0 CG A:ASP982 3.8 92.1 1.0 CD A:GLU979 4.2 92.0 1.0 CB A:ASP892 4.3 67.7 1.0 HB2 A:LEU893 4.5 0.6 1.0 N A:LEU893 4.5 90.0 1.0 O A:LEU893 4.6 0.9 1.0 HB3 A:ASP892 4.7 81.3 1.0 HB2 A:ASP892 4.7 81.3 1.0 OE2 A:GLU979 4.8 0.0 1.0 HA A:ASP892 4.9 0.3 1.0

T.Pavkov-Keller, A.Dordic, M.Eder, E.M.Egelseer, K.Davis, D.Mills, U.B.Sleytr, W.Kuehlbrandt, J.Vonck, W.Keller. Structure of Surface Layer Protein Sbsc To Be Published.