Sodium in PDB 9doc: The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution

The structure of The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution, PDB code: 9doc was solved by P.Samarawickrama, R.Probst, K.Ludlow, T.Doukov, J.D.Moody, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.92 / 1.19
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	101.428, 101.428, 49.239, 90, 90, 120
R / Rfree (%)	18.9 / 19.7

The structure of The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Sodium atom in the The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution (pdb code 9doc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution, PDB code: 9doc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:30.5 occ:1.00 O A:HOH555 2.8 24.4 1.0 ND1 A:HIS12 2.9 35.5 1.0 HA A:HIS12 3.3 37.5 1.0 CE1 A:HIS12 3.8 32.2 1.0 CG A:HIS12 4.0 31.3 1.0 CA A:HIS12 4.1 31.2 1.0 H A:SER13 4.2 35.6 1.0 CB A:HIS12 4.2 29.3 1.0 HE1 A:PHE43 4.2 22.0 1.0 O A:HOH473 4.3 25.7 1.0 O A:HIS11 4.6 34.1 1.0 N A:SER13 4.9 29.7 1.0 CD2 A:HIS11 4.9 38.9 1.0 O A:HOH476 4.9 29.3 1.0 N A:HIS12 4.9 32.6 1.0 NE2 A:HIS12 5.0 33.2 1.0

Sodium binding site 2 out of 5 in the The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na312 b:36.5 occ:1.00 OD2 A:ASP95 2.7 34.1 1.0 OG A:SER192 2.8 34.6 1.0 OH A:TYR97 2.8 32.2 1.0 HE1 A:TYR97 2.8 31.7 1.0 HA A:ILE182 2.9 39.1 1.0 HB3 A:ALA185 3.0 46.7 1.0 HB2 A:ASP95 3.1 33.1 1.0 HG12 A:ILE182 3.1 37.1 1.0 HG A:SER192 3.2 41.5 1.0 HG21 A:THR190 3.3 51.8 1.0 HB A:THR190 3.3 48.3 1.0 HB3 A:ASP95 3.4 33.1 1.0 HH A:TYR97 3.5 38.6 1.0 CG A:ASP95 3.5 29.4 1.0 CB A:ASP95 3.5 27.6 1.0 CE1 A:TYR97 3.5 26.4 1.0 HG23 A:ILE182 3.5 44.8 1.0 CZ A:TYR97 3.6 27.4 1.0 HB1 A:ALA185 3.6 46.7 1.0 CB A:ALA185 3.6 38.9 1.0 HD22 A:LEU146 3.6 43.5 1.0 HB2 A:ALA185 3.8 46.7 1.0 OG1 A:THR190 3.8 38.9 1.0 CB A:THR190 3.8 40.3 1.0 CA A:ILE182 3.9 32.6 1.0 HD21 A:LEU146 3.9 43.5 1.0 CG1 A:ILE182 3.9 31.0 1.0 HB3 A:SER192 3.9 37.7 1.0 CB A:SER192 3.9 31.4 1.0 CG2 A:THR190 4.0 43.1 1.0 HG13 A:ILE182 4.1 37.1 1.0 HH21 A:ARG130 4.2 48.0 1.0 CD2 A:LEU146 4.2 36.2 1.0 CB A:ILE182 4.2 32.6 1.0 CG2 A:ILE182 4.3 37.3 1.0 HA A:SER192 4.4 33.5 1.0 HG1 A:THR190 4.5 46.7 1.0 HG22 A:THR190 4.5 51.8 1.0 O A:ILE182 4.6 39.2 1.0 HB2 A:SER192 4.6 37.7 1.0 N A:ILE182 4.6 34.0 1.0 OD1 A:ASP95 4.6 30.8 1.0 HG23 A:THR190 4.7 51.8 1.0 O A:GLN181 4.7 38.7 1.0 HD23 A:LEU146 4.7 43.5 1.0 HG21 A:ILE182 4.7 44.8 1.0 C A:ILE182 4.7 36.3 1.0 CA A:SER192 4.7 28.0 1.0 O A:HOH516 4.8 34.1 1.0 NH2 A:ARG130 4.8 40.0 1.0 CD1 A:TYR97 4.9 23.6 1.0 HH22 A:ARG130 4.9 48.0 1.0 CE2 A:TYR97 4.9 27.0 1.0 CA A:ASP95 5.0 26.7 1.0 C A:GLN181 5.0 35.5 1.0

Sodium binding site 3 out of 5 in the The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na313 b:40.1 occ:1.00 O A:HOH554 2.6 35.1 1.0 HA2 A:GLY156 2.6 35.4 1.0 OD2 A:ASP159 2.9 43.7 1.0 O A:ILE143 2.9 35.8 1.0 CA A:GLY156 3.4 29.5 1.0 HA A:LEU144 3.4 34.1 1.0 HG3 A:LYS155 3.5 47.3 1.0 HA3 A:GLY156 3.6 35.4 1.0 HB2 A:LEU144 3.6 33.7 1.0 HD13 A:LEU144 3.6 40.6 1.0 N A:GLY156 3.7 30.5 1.0 HD12 A:LEU144 3.8 40.6 1.0 HG22 A:ILE143 3.9 38.7 1.0 C A:ILE143 3.9 30.9 1.0 CG A:ASP159 3.9 41.6 1.0 HB2 A:ASP159 3.9 40.6 1.0 HG23 A:ILE143 3.9 38.7 1.0 H A:GLY156 4.0 36.6 1.0 CA A:LEU144 4.1 28.4 1.0 C A:LYS155 4.2 33.0 1.0 CD1 A:LEU144 4.2 33.8 1.0 O A:LYS155 4.3 32.5 1.0 CB A:LEU144 4.3 28.1 1.0 HZ2 A:LYS155 4.3 63.0 1.0 O A:HOH642 4.4 39.5 1.0 CG2 A:ILE143 4.4 32.3 1.0 HB3 A:LYS155 4.4 43.3 1.0 N A:LEU144 4.4 31.2 1.0 CG A:LYS155 4.4 39.4 1.0 O A:HOH640 4.4 48.3 1.0 CB A:ASP159 4.4 33.9 1.0 O A:LYS152 4.6 32.0 1.0 C A:GLY156 4.7 28.8 1.0 HD3 A:PRO145 4.7 47.5 1.0 HG2 A:LYS155 4.7 47.3 1.0 HB3 A:ASP159 4.7 40.6 1.0 HZ3 A:LYS155 4.8 63.0 1.0 CB A:LYS155 4.9 36.1 1.0 HD2 A:PRO145 4.9 47.5 1.0 CG A:LEU144 4.9 29.5 1.0 O A:GLY156 4.9 27.4 1.0 OD1 A:ASP159 4.9 47.7 1.0 HD11 A:LEU144 4.9 40.6 1.0 NZ A:LYS155 5.0 52.5 1.0

Sodium binding site 4 out of 5 in the The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na314 b:55.6 occ:1.00 H A:SER192 2.9 36.5 1.0 O A:GLY221 3.0 35.5 1.0 HA A:SER191 3.2 42.1 1.0 O A:SER192 3.6 29.6 1.0 HA A:ALA222 3.6 35.7 1.0 N A:SER192 3.6 30.4 1.0 O A:HOH495 3.7 36.5 1.0 CA A:SER191 4.1 35.1 0.7 CA A:SER191 4.1 35.1 0.3 C A:GLY221 4.1 36.3 1.0 H A:SER223 4.1 35.5 1.0 HD13 A:ILE193 4.2 37.9 1.0 HG A:SER191 4.2 39.6 0.3 OG A:SER191 4.2 33.0 0.3 HB2 A:SER223 4.2 39.6 1.0 C A:SER191 4.3 35.1 1.0 C A:SER192 4.4 27.6 1.0 CA A:ALA222 4.4 29.8 1.0 HB3 A:SER191 4.4 37.6 0.7 N A:SER223 4.5 29.6 1.0 HE1 A:PHE94 4.5 64.7 1.0 CA A:SER192 4.6 28.0 1.0 HD11 A:ILE193 4.6 37.9 1.0 C A:ALA222 4.6 29.3 1.0 O A:THR190 4.7 39.9 1.0 CB A:SER191 4.7 31.4 0.7 N A:ALA222 4.7 33.5 1.0 CB A:SER191 4.7 31.4 0.3 HB3 A:GLN267 4.8 42.1 1.0 HB2 A:SER192 4.8 37.7 1.0 OE1 A:GLN267 4.8 39.0 1.0 CD1 A:ILE193 4.9 31.6 1.0 OG A:SER191 4.9 39.0 0.7 HA3 A:GLY221 5.0 43.1 1.0 CB A:SER223 5.0 33.0 1.0

Sodium binding site 5 out of 5 in the The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Von Willebrand Factor A Domain of Human Capillary Morphogenesis Gene II, Flexibly Fused to the 1TEL Crystallization Chaperone, Thr- Val Linker Variant, at 1.2 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na315 b:57.1 occ:1.00 HA A:ARG239 2.9 36.8 1.0 HG2 A:ARG239 3.0 40.5 1.0 O A:HOH430 3.2 27.0 1.0 CA A:ARG239 3.8 30.7 1.0 CG A:ARG239 3.9 33.8 1.0 HB3 A:ARG239 4.0 37.6 1.0 CB A:ARG239 4.1 31.3 1.0 O A:HOH583 4.1 50.8 1.0 O A:HOH461 4.2 46.3 1.0 O A:GLU238 4.3 32.8 1.0 O A:ARG239 4.3 35.9 1.0 HG3 A:ARG239 4.4 40.5 1.0 C A:ARG239 4.6 28.4 1.0 HD2 A:ARG239 4.6 44.9 1.0 N A:ARG239 4.7 29.1 1.0 CD A:ARG239 4.8 37.5 1.0 C A:GLU238 4.9 28.9 1.0 HD3 A:ARG239 4.9 44.9 1.0

P.Samarawickrama, K.Ludlow, R.Probst, W.Abiodun, J.Averett, D.Hansen, T.Doukov, J.D.Moody. 1TEL Fusions Outperform 2TEL and 3TEL Fusions in Controlled Comparisons To Be Published.