Sodium in PDB 9db5: A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker

The structure of A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker, PDB code: 9db5 was solved by M.J.Pedroza Romo, J.C.Averett, A.Keliiliki, E.W.Wilson, C.Smith, D.Hansen, B.Averett, J.Gonzalez, E.Noakes, R.Nickles, T.Doukov, J.D.Moody, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.87 / 1.57
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	97.73, 97.73, 45.816, 90, 90, 120
R / Rfree (%)	16.7 / 19.6

The structure of A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker (pdb code 9db5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker, PDB code: 9db5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker within 5.0Å range: probe atom residue distance (Å) B Occ A:Na314 b:44.0 occ:1.00 O A:HOH491 2.2 24.7 1.0 O A:HOH428 2.4 24.0 1.0 HG12 A:ILE75 3.3 28.1 1.0 HH2 A:TRP27 3.5 23.5 1.0 HD11 A:ILE75 3.6 26.8 1.0 HE1 A:TRP24 3.8 20.5 1.0 HZ3 A:TRP27 3.9 19.7 1.0 CH2 A:TRP27 3.9 19.6 1.0 CG1 A:ILE75 4.0 23.4 1.0 HG13 A:ILE75 4.0 28.1 1.0 CZ3 A:TRP27 4.1 16.5 1.0 CD1 A:ILE75 4.2 22.4 1.0 HD22 A:LEU71 4.3 17.3 1.0 HD13 A:ILE75 4.4 26.8 1.0 HB3 A:LEU71 4.5 14.6 1.0 NE1 A:TRP24 4.6 17.1 1.0 O A:LEU71 4.8 15.8 1.0 CZ2 A:TRP27 4.8 18.5 1.0 HD1 A:TRP24 4.8 22.7 1.0 HB2 A:LEU5 4.9 42.6 1.0

Sodium binding site 2 out of 8 in the A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker within 5.0Å range: probe atom residue distance (Å) B Occ A:Na315 b:42.8 occ:1.00 O A:HOH525 2.0 36.7 1.0 H A:GLY81 2.3 18.2 1.0 CL A:CL322 2.6 39.5 1.0 O A:HOH437 2.8 37.0 1.0 H A:LEU80 3.0 23.1 1.0 N A:GLY81 3.1 15.2 1.0 HA A:ASP79 3.4 20.2 1.0 N A:LEU80 3.4 19.3 1.0 OD1 A:ASP79 3.5 27.2 1.0 HB2 A:LEU80 3.5 22.2 1.0 HA3 A:GLY81 3.6 18.4 1.0 CA A:GLY81 3.9 15.4 1.0 C A:LEU80 4.0 17.6 1.0 C A:ASP79 4.1 19.5 1.0 CA A:LEU80 4.1 16.2 1.0 CA A:ASP79 4.1 16.9 1.0 CB A:LEU80 4.3 18.5 1.0 HA A:ALA104 4.3 18.4 1.0 CG A:ASP79 4.4 23.1 1.0 HA2 A:GLY81 4.4 18.4 1.0 O A:ACY305 4.5 33.4 1.0 H A:LYS82 4.6 17.8 1.0 O A:ALA78 4.6 27.6 1.0 H A:ASP105 4.6 20.8 1.0 HG A:LEU80 4.7 22.0 1.0 CB A:ASP79 4.9 20.7 1.0 HB3 A:LEU80 5.0 22.2 1.0 O A:ASP79 5.0 17.5 1.0 H2 A:ACY305 5.0 29.1 1.0

Sodium binding site 3 out of 8 in the A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker within 5.0Å range: probe atom residue distance (Å) B Occ A:Na316 b:36.1 occ:1.00 HG A:SER17 2.6 18.3 1.0 OG A:SER17 2.8 15.3 1.0 HB3 A:ASP19 3.1 20.0 1.0 O A:HOH440 3.3 31.7 1.0 HB3 A:SER17 3.4 17.4 1.0 CB A:SER17 3.5 14.5 1.0 HB2 A:SER17 3.7 17.4 1.0 O A:HOH432 3.7 27.1 1.0 CB A:ASP19 4.0 16.7 1.0 OD1 A:ASP20 4.0 15.1 1.0 HB2 A:ASP19 4.2 20.0 1.0 H A:ASP20 4.2 13.8 1.0 O A:HOH508 4.3 20.4 1.0 OD2 A:ASP19 4.3 24.4 1.0 H A:ASP19 4.4 14.7 1.0 CG A:ASP20 4.5 12.7 1.0 OD2 A:ASP20 4.5 15.9 1.0 CG A:ASP19 4.7 22.3 1.0 N A:ASP20 4.7 11.5 1.0 H A:SER17 4.8 14.0 1.0 CA A:ASP19 5.0 14.2 1.0 CA A:SER17 5.0 11.6 1.0

Sodium binding site 4 out of 8 in the A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker within 5.0Å range: probe atom residue distance (Å) B Occ A:Na317 b:38.9 occ:1.00 HD22 A:ASN45 2.4 17.6 1.0 O A:HOH550 2.9 38.5 1.0 ND2 A:ASN45 3.2 14.7 1.0 HA A:SER17 3.2 13.9 1.0 HB3 A:ASN45 3.4 13.0 1.0 HB2 A:ASN45 3.5 13.0 1.0 HD21 A:ASN45 3.7 17.6 1.0 CB A:ASN45 3.8 10.9 1.0 CG A:ASN45 3.9 12.6 1.0 O A:HOH417 4.1 42.1 1.0 CA A:SER17 4.2 11.6 1.0 O A:HOH462 4.3 14.3 1.0 HB2 A:SER17 4.4 17.4 1.0 H A:ARG18 4.4 13.9 1.0 O A:TRP16 4.4 11.5 1.0 HB3 A:SER17 4.4 17.4 1.0 CB A:SER17 4.6 14.5 1.0 N A:SER17 4.9 11.7 1.0 N A:ARG18 5.0 11.7 1.0

Sodium binding site 5 out of 8 in the A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker within 5.0Å range: probe atom residue distance (Å) B Occ A:Na318 b:44.5 occ:1.00 O A:THR41 2.7 33.3 1.0 HA A:THR41 2.9 28.4 1.0 HH12 A:ARG60 3.2 24.2 1.0 HH11 A:ARG60 3.2 24.2 1.0 NH1 A:ARG60 3.3 20.2 1.0 C A:THR41 3.4 31.7 1.0 HG2 A:ARG60 3.5 18.9 1.0 CA A:THR41 3.6 23.7 1.0 O A:ASN40 3.9 39.0 1.0 CZ A:ARG60 4.1 19.4 1.0 HG22 A:THR41 4.4 45.0 1.0 HB3 A:ARG60 4.4 18.1 1.0 CG A:ARG60 4.4 15.8 1.0 HB A:THR41 4.4 27.6 1.0 N A:PHE42 4.5 22.7 1.0 CB A:THR41 4.6 23.0 1.0 HA A:PHE42 4.6 18.0 1.0 N A:THR41 4.6 22.9 1.0 HD3 A:ARG60 4.7 15.3 1.0 C A:ASN40 4.7 32.1 1.0 HH22 A:ARG60 4.7 20.8 1.0 H A:GLU43 4.7 15.2 1.0 HA A:ARG60 4.7 16.6 1.0 NH2 A:ARG60 4.8 17.4 1.0 NE A:ARG60 4.8 15.1 1.0 CB A:ARG60 4.9 15.2 1.0 CD A:ARG60 4.9 12.8 1.0 CG2 A:THR41 5.0 37.6 1.0

Sodium binding site 6 out of 8 in the A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker within 5.0Å range: probe atom residue distance (Å) B Occ A:Na319 b:27.6 occ:1.00 OXT A:ACY305 2.1 30.1 1.0 H A:THR109 2.7 19.6 1.0 HA A:ALA108 3.0 15.5 1.0 C A:ACY305 3.2 35.2 1.0 O A:HOH416 3.3 42.0 1.0 N A:THR109 3.4 16.4 1.0 O A:HOH458 3.4 24.1 1.0 HB A:THR109 3.4 25.3 1.0 HG1 A:THR109 3.6 24.3 1.0 O A:ACY305 3.7 33.4 1.0 CA A:ALA108 3.9 12.9 1.0 O A:ASN107 4.0 18.4 1.0 CB A:THR109 4.1 21.1 1.0 C A:ALA108 4.1 17.9 1.0 OD2 A:ASP105 4.1 34.5 1.0 OG1 A:THR109 4.2 20.3 1.0 O A:THR109 4.2 19.8 1.0 CA A:THR109 4.2 12.0 1.0 O A:HOH531 4.3 34.2 1.0 CH3 A:ACY305 4.5 24.3 1.0 H3 A:ACY305 4.5 29.1 1.0 N A:ALA108 4.6 11.7 1.0 C A:ASN107 4.7 14.9 1.0 HB1 A:ALA108 4.7 20.0 1.0 C A:THR109 4.8 13.9 1.0 H1 A:ACY305 4.8 29.1 1.0 CB A:ALA108 4.9 16.7 1.0

Sodium binding site 7 out of 8 in the A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker within 5.0Å range: probe atom residue distance (Å) B Occ A:Na320 b:41.2 occ:1.00 O A:HOH527 2.3 28.5 1.0 HA A:THR53 3.0 14.1 1.0 HH A:TYR69 3.1 25.1 1.0 O A:HOH488 3.4 39.5 1.0 HG22 A:THR53 3.5 19.5 1.0 OH A:TYR69 3.6 20.9 1.0 HE2 A:TYR69 3.7 17.9 1.0 O A:LEU52 3.9 14.5 1.0 O A:HOH465 3.9 22.8 1.0 O A:HOH402 3.9 30.9 1.0 CA A:THR53 4.0 11.8 1.0 O A:HOH436 4.0 39.5 1.0 HA A:ASN102 4.2 19.4 1.0 HB A:THR53 4.3 15.9 1.0 CG2 A:THR53 4.4 16.3 1.0 H A:LYS54 4.4 16.4 1.0 OD1 A:ASN102 4.4 23.1 1.0 CE2 A:TYR69 4.4 15.0 1.0 O A:ALA101 4.5 20.4 1.0 CB A:THR53 4.5 13.3 1.0 CZ A:TYR69 4.5 14.3 1.0 C A:LEU52 4.5 12.0 1.0 N A:THR53 4.6 11.1 1.0 HG23 A:THR53 4.8 19.5 1.0 N A:LYS54 4.9 13.7 1.0 C A:THR53 4.9 11.5 1.0

Sodium binding site 8 out of 8 in the A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of A Darpin Fused to the 1TEL Crystallization Chaperone Via A Proline- Alanine Linker within 5.0Å range: probe atom residue distance (Å) B Occ A:Na321 b:48.7 occ:1.00 O A:HOH539 2.3 28.5 1.0 NE2 A:HIS158 3.0 20.4 1.0 O A:HOH469 3.7 29.8 1.0 HE1 A:HIS158 3.7 19.7 1.0 CE1 A:HIS158 3.8 16.5 1.0 HA3 A:GLY124 3.9 22.3 1.0 O A:HOH490 3.9 40.8 1.0 O A:ASN123 4.0 17.3 1.0 CD2 A:HIS158 4.1 18.6 1.0 HD2 A:HIS158 4.3 22.2 1.0 C A:ASN123 4.5 12.9 1.0 HA A:ASN123 4.7 16.1 1.0 CA A:GLY124 4.8 18.6 1.0 N A:GLY124 5.0 16.2 1.0 ND1 A:HIS158 5.0 17.5 1.0

M.J.Pedroza Romo, J.C.Averett, A.Keliiliki, E.W.Wilson, C.Smith, D.Hansen, B.Averett, J.Gonzalez, E.Noakes, R.Nickles, T.Doukov, J.D.Moody. Optimal Telsam-Target Protein Linker Character Is Target Protein Dependent To Be Published.