Calcium in PDB 4aq1: Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6

The structure of Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6, PDB code: 4aq1 was solved by E.Baranova, H.Remaut, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.81 / 2.42
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	68.500, 88.500, 95.200, 112.50, 101.60, 84.70
R / Rfree (%)	18.301 / 23.567

The binding sites of Calcium atom in the Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6 (pdb code 4aq1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6, PDB code: 4aq1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1923 b:25.3 occ:1.00 OD2 A:ASP781 2.3 36.8 1.0 O A:GLN406 2.3 21.6 1.0 O A:THR440 2.3 28.5 1.0 O A:HOH2063 2.4 19.8 1.0 OE1 A:GLN406 2.5 27.2 1.0 OD1 A:ASP779 2.6 26.2 1.0 OD2 A:ASP779 2.6 23.6 1.0 CG A:ASP779 2.9 25.5 1.0 CG A:ASP781 3.2 36.2 1.0 C A:GLN406 3.4 22.9 1.0 C A:THR440 3.5 29.5 1.0 CB A:ASP781 3.5 36.1 1.0 CD A:GLN406 3.7 27.3 1.0 CA A:GLN406 3.9 24.4 1.0 CB A:GLN406 4.0 25.5 1.0 CA A:LYS441 4.2 32.8 1.0 N A:LYS441 4.3 30.2 1.0 OD1 A:ASP781 4.3 38.7 1.0 CB A:LYS441 4.4 39.1 1.0 O A:HOH2061 4.4 15.8 1.0 CB A:ASP779 4.5 25.7 1.0 N A:ASN407 4.5 20.4 1.0 CG2 A:THR440 4.5 31.2 1.0 CG A:GLN406 4.5 27.1 1.0 CA A:THR440 4.5 29.3 1.0 CB A:ASN407 4.6 19.9 1.0 NE2 A:GLN406 4.7 27.7 1.0 CA A:ASP781 4.7 35.7 1.0 N A:ASP781 4.7 36.1 1.0 CA A:ASN407 4.8 19.4 1.0

Calcium binding site 2 out of 8 in the Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1924 b:23.9 occ:1.00 O A:SER651 2.2 35.4 1.0 O A:ALA646 2.2 23.9 1.0 O A:HOH2154 2.3 23.8 1.0 OG1 A:THR649 2.3 26.5 1.0 O A:HOH2153 2.3 18.0 1.0 O A:THR649 2.4 31.5 1.0 OD1 A:ASP654 2.5 28.2 1.0 C A:THR649 3.3 31.7 1.0 C A:ALA646 3.4 23.3 1.0 CG A:ASP654 3.5 29.9 1.0 C A:SER651 3.5 35.1 1.0 CB A:THR649 3.5 27.9 1.0 OD2 A:ASP654 3.6 32.9 1.0 CA A:THR649 3.7 28.9 1.0 N A:THR649 3.7 28.6 1.0 CA A:ALA646 4.1 21.9 1.0 N A:SER651 4.3 35.6 1.0 CA A:SER651 4.3 35.5 1.0 C A:ALA650 4.4 35.0 1.0 N A:THR652 4.4 34.6 1.0 N A:ALA650 4.4 35.1 1.0 CA A:THR652 4.4 34.3 1.0 N A:PRO647 4.5 24.4 1.0 O A:ALA650 4.5 35.2 1.0 CG2 A:THR649 4.6 26.6 1.0 C A:PRO647 4.6 25.2 1.0 CA A:PRO647 4.6 25.1 1.0 CB A:SER651 4.7 36.0 1.0 O A:ASP654 4.7 25.1 1.0 C A:ASN648 4.7 26.0 1.0 CB A:ALA646 4.7 21.4 1.0 N A:ASN648 4.7 24.6 1.0 O A:HOH2155 4.8 26.1 1.0 CA A:ALA650 4.9 35.2 1.0 CB A:ASP654 4.9 26.5 1.0 C A:THR652 5.0 31.5 1.0

Calcium binding site 3 out of 8 in the Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1925 b:23.0 occ:1.00 OE1 A:GLU837 2.3 27.9 1.0 O A:GLY822 2.3 21.8 1.0 OE2 A:GLU784 2.3 24.6 1.0 OE1 A:GLU836 2.3 23.5 1.0 OD1 A:ASN824 2.4 25.1 1.0 OD1 A:ASP835 2.4 21.3 1.0 CD A:GLU837 3.3 30.4 1.0 CD A:GLU784 3.3 26.7 1.0 CG A:ASN824 3.4 24.6 1.0 C A:GLY822 3.4 20.1 1.0 CD A:GLU836 3.5 24.8 1.0 OE2 A:GLU837 3.6 31.8 1.0 CG A:ASP835 3.6 22.1 1.0 CG A:GLU784 3.8 26.3 1.0 N A:ASN824 4.0 21.7 1.0 ND2 A:ASN824 4.0 26.5 1.0 N A:GLU836 4.0 22.2 1.0 OE2 A:GLU836 4.2 24.8 1.0 OE1 A:GLU784 4.3 29.6 1.0 CA A:GLY822 4.3 19.3 1.0 C A:LEU823 4.3 20.6 1.0 OD2 A:ASP835 4.3 22.0 1.0 N A:LEU823 4.3 19.3 1.0 CB A:GLU836 4.3 24.3 1.0 CA A:ASN824 4.5 24.3 1.0 N A:GLU837 4.5 24.4 1.0 CA A:LEU823 4.5 18.9 1.0 CG A:GLU836 4.5 24.4 1.0 CB A:ASN824 4.5 24.3 1.0 CG A:GLU837 4.6 29.8 1.0 C A:ASP835 4.7 21.2 1.0 CA A:ASP835 4.7 20.9 1.0 CA A:GLU836 4.7 23.0 1.0 CB A:ASP835 4.7 21.4 1.0 CB A:GLU784 5.0 25.6 1.0 O A:LEU823 5.0 21.1 1.0

Calcium binding site 4 out of 8 in the Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1926 b:27.8 occ:1.00 OE2 A:GLU518 2.3 35.4 1.0 O A:VAL625 2.3 34.3 1.0 OD1 A:ASP592 2.4 39.7 1.0 O A:HOH2125 2.4 19.0 1.0 OD1 A:ASN624 2.4 30.7 1.0 OD2 A:ASP517 2.5 29.7 1.0 OD1 A:ASP517 3.0 28.5 1.0 CG A:ASP517 3.1 29.5 1.0 CD A:GLU518 3.3 36.5 1.0 C A:VAL625 3.5 34.8 1.0 CG A:ASN624 3.6 35.0 1.0 CG A:ASP592 3.6 42.0 1.0 CG A:GLU518 3.8 35.8 1.0 N A:VAL625 4.0 32.8 1.0 OD2 A:ASP592 4.3 44.9 1.0 N A:LYS626 4.4 37.4 1.0 OE1 A:GLU518 4.4 36.3 1.0 ND2 A:ASN624 4.4 37.1 1.0 CA A:VAL625 4.4 32.5 1.0 CA A:LYS626 4.4 40.2 1.0 N A:ASP592 4.5 41.0 1.0 CB A:ASP517 4.5 29.7 1.0 CA A:ASP592 4.6 42.3 1.0 NZ A:LYS591 4.7 50.2 1.0 CB A:ASP592 4.7 42.1 1.0 CB A:ASN624 4.7 34.0 1.0 C A:ASN624 4.8 32.7 1.0 CA A:ASN624 4.8 33.3 1.0

Calcium binding site 5 out of 8 in the Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1922 b:28.0 occ:1.00 OE2 C:GLU784 2.2 31.9 1.0 OD1 C:ASN824 2.2 35.4 1.0 OD1 C:ASP835 2.2 29.7 1.0 O C:GLY822 2.3 29.1 1.0 OE1 C:GLU837 2.4 34.6 1.0 OE1 C:GLU836 2.5 29.9 1.0 CD C:GLU784 3.1 35.0 1.0 CG C:ASN824 3.3 33.7 1.0 C C:GLY822 3.4 28.3 1.0 CG C:ASP835 3.5 30.8 1.0 CD C:GLU837 3.5 36.8 1.0 CD C:GLU836 3.5 34.4 1.0 CG C:GLU784 3.7 34.8 1.0 ND2 C:ASN824 3.9 31.6 1.0 OE2 C:GLU837 4.0 36.2 1.0 N C:ASN824 4.0 31.4 1.0 N C:GLU836 4.0 27.1 1.0 OE1 C:GLU784 4.0 39.5 1.0 OD2 C:ASP835 4.1 32.9 1.0 CA C:GLY822 4.2 27.8 1.0 OE2 C:GLU836 4.2 35.7 1.0 C C:LEU823 4.3 30.1 1.0 N C:LEU823 4.3 29.6 1.0 CB C:GLU836 4.3 31.0 1.0 O C:HOH2142 4.4 35.2 1.0 CA C:ASN824 4.4 31.9 1.0 CB C:ASN824 4.4 32.4 1.0 N C:GLU837 4.4 31.0 1.0 CG C:GLU836 4.5 32.6 1.0 CA C:LEU823 4.5 29.5 1.0 CB C:ASP835 4.6 27.9 1.0 CA C:ASP835 4.6 26.0 1.0 C C:ASP835 4.7 25.8 1.0 CA C:GLU836 4.7 29.6 1.0 CB C:GLU784 4.7 33.1 1.0 CG C:GLU837 4.8 35.0 1.0 O C:LEU823 4.9 29.7 1.0

Calcium binding site 6 out of 8 in the Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1923 b:29.1 occ:1.00 OD2 C:ASP781 2.3 38.5 1.0 O C:GLN406 2.3 26.1 1.0 O C:THR440 2.3 29.8 1.0 OE1 C:GLN406 2.5 32.7 1.0 O C:HOH2028 2.5 12.9 1.0 OD2 C:ASP779 2.5 30.6 1.0 OD1 C:ASP779 2.6 33.1 1.0 CG C:ASP779 2.9 32.0 1.0 CG C:ASP781 3.3 40.4 1.0 C C:THR440 3.4 30.2 1.0 C C:GLN406 3.4 27.5 1.0 CD C:GLN406 3.7 33.9 1.0 CB C:ASP781 3.7 40.0 1.0 CA C:GLN406 4.0 30.1 1.0 CB C:GLN406 4.1 31.3 1.0 CA C:LYS441 4.1 33.5 1.0 N C:LYS441 4.1 31.8 1.0 CB C:LYS441 4.2 37.5 1.0 CA C:THR440 4.4 29.9 1.0 CB C:ASP779 4.4 32.2 1.0 OD1 C:ASP781 4.5 41.8 1.0 N C:ASN407 4.5 24.6 1.0 CG C:GLN406 4.5 32.9 1.0 CB C:ASN407 4.6 24.1 1.0 CB C:THR440 4.6 31.2 1.0 NE2 C:GLN406 4.6 35.9 1.0 O C:HOH2026 4.7 24.8 1.0 CA C:ASN407 4.8 23.3 1.0 N C:ASP781 4.8 39.8 1.0 CA C:ASP781 4.9 40.2 1.0

Calcium binding site 7 out of 8 in the Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1924 b:24.8 occ:1.00 O C:HOH2093 2.2 23.5 1.0 O C:SER651 2.2 45.4 1.0 O C:ALA646 2.3 27.1 1.0 O C:THR649 2.3 39.4 1.0 O C:HOH2092 2.3 20.8 1.0 OG1 C:THR649 2.5 35.5 1.0 OD1 C:ASP654 2.5 34.7 1.0 C C:THR649 3.2 40.8 1.0 C C:SER651 3.4 46.7 1.0 CG C:ASP654 3.4 34.1 1.0 C C:ALA646 3.4 27.4 1.0 CB C:THR649 3.6 35.2 1.0 OD2 C:ASP654 3.7 34.3 1.0 CA C:THR649 3.7 36.9 1.0 N C:THR649 3.7 34.8 1.0 CA C:ALA646 4.1 25.9 1.0 N C:SER651 4.2 46.4 1.0 CA C:SER651 4.3 47.8 1.0 C C:ALA650 4.4 47.4 1.0 N C:THR652 4.4 46.6 1.0 N C:ALA650 4.4 44.8 1.0 O C:ASP654 4.4 30.0 1.0 CA C:THR652 4.5 45.2 1.0 N C:PRO647 4.5 27.3 1.0 O C:ALA650 4.6 49.0 1.0 C C:PRO647 4.7 30.4 1.0 CG2 C:THR649 4.7 32.0 1.0 CB C:ALA646 4.7 25.4 1.0 CB C:SER651 4.7 48.9 1.0 CA C:PRO647 4.7 29.2 1.0 C C:ASN648 4.8 34.3 1.0 O C:PRO647 4.8 32.3 1.0 CB C:ASP654 4.8 33.1 1.0 N C:ASP654 4.9 34.0 1.0 CA C:ALA650 4.9 47.0 1.0 N C:ASN648 5.0 30.6 1.0 C C:THR652 5.0 43.2 1.0

Calcium binding site 8 out of 8 in the Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Sbsb S-Layer Protein of Geobacillus Stearothermophilus PV72P2 in Complex with Nanobody KB6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1925 b:33.8 occ:1.00 OE2 C:GLU518 2.2 45.3 1.0 OD1 C:ASN624 2.3 40.2 1.0 OD2 C:ASP517 2.3 44.6 1.0 O C:VAL625 2.3 45.4 1.0 OD1 C:ASP592 2.5 48.2 1.0 O C:HOH2072 2.7 28.2 1.0 CG C:ASP517 3.1 42.1 1.0 OD1 C:ASP517 3.1 41.0 1.0 CD C:GLU518 3.3 46.9 1.0 CG C:ASN624 3.3 42.6 1.0 C C:VAL625 3.6 44.6 1.0 CG C:ASP592 3.6 49.6 1.0 CG C:GLU518 3.7 45.5 1.0 ND2 C:ASN624 3.8 44.7 1.0 N C:VAL625 4.0 41.7 1.0 OD2 C:ASP592 4.2 52.0 1.0 OE1 C:GLU518 4.4 46.1 1.0 CA C:VAL625 4.5 41.8 1.0 N C:LYS626 4.5 46.3 1.0 CB C:ASP517 4.5 41.9 1.0 CB C:ASN624 4.5 42.5 1.0 N C:ASP592 4.5 42.6 1.0 CA C:LYS626 4.5 49.1 1.0 CA C:ASP592 4.6 45.3 1.0 CA C:ASN624 4.7 42.6 1.0 C C:ASN624 4.7 41.3 1.0 CB C:ASP592 4.7 47.6 1.0 NZ C:LYS591 4.9 52.2 1.0 CB C:GLU518 4.9 45.1 1.0 CG2 C:VAL625 5.0 40.2 1.0

E.Baranova, R.Fronzes, A.Garcia-Pino, N.Van Gerven, D.Papapostolou, G.Pehau-Arnaudet, E.Pardon, J.Steyaert, S.Howorka, H.Remaut. Sbsb Structure and Lattice Reconstruction Unveil CA21 Triggered S-Layer Assembly Nature V. 487 119 2012.
ISSN: ISSN 0028-0836
PubMed: 22722836
DOI: 10.1038/NATURE11155