Sodium in PDB 6jb8: Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme

All present enzymatic activity of Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme:
3.2.1.17;

The structure of Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme, PDB code: 6jb8 was solved by J.M.M.Caaveiro, H.Tamura, H.Akiba, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.17 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.240, 49.480, 59.280, 90.00, 93.40, 90.00
R / Rfree (%)	16.9 / 20.7

The structure of Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme (pdb code 6jb8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme, PDB code: 6jb8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:43.9 occ:1.00 O A:SER27 2.2 33.8 1.0 OG A:SER30 2.3 33.7 1.0 O A:HOH363 2.4 37.5 1.0 OG A:SER27 2.6 39.5 1.0 O A:HOH406 3.2 34.0 0.6 C A:SER27 3.2 36.8 1.0 N A:SER30 3.2 27.0 1.0 CB A:SER30 3.4 31.3 1.0 CB A:SER27 3.7 40.6 1.0 CA A:SER30 3.7 28.0 1.0 CA A:SER27 3.7 38.9 1.0 N A:SER27 3.7 37.5 1.0 O A:HOH330 3.9 38.7 1.0 OD2 A:ASP29 4.0 35.7 1.0 N A:ILE31 4.0 24.5 1.0 C A:SER30 4.2 25.5 1.0 N A:ASP29 4.2 32.2 1.0 C A:THR28 4.3 32.7 1.0 N A:THR28 4.3 37.0 1.0 C A:ASP29 4.4 27.8 1.0 CG1 A:ILE31 4.5 29.4 1.0 O A:THR28 4.6 32.3 1.0 C A:GLY26 4.6 38.8 1.0 CG A:ASP29 4.6 33.8 1.0 NE A:ARG100 4.7 40.9 1.0 CA A:THR28 4.7 34.9 1.0 CA A:ASP29 4.8 29.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:28.3 occ:1.00 O B:HOH381 2.3 28.7 1.0 O B:ARG73 2.4 27.1 1.0 O B:CYS64 2.4 25.1 1.0 O B:SER60 2.4 23.7 1.0 O B:HOH390 2.5 25.9 1.0 OG B:SER72 2.5 28.7 1.0 C B:ARG73 3.4 27.4 1.0 C B:CYS64 3.4 24.9 1.0 CB B:SER72 3.6 30.2 1.0 C B:SER60 3.6 24.5 1.0 CA B:ASN65 3.8 26.1 1.0 N B:ARG73 3.8 29.2 1.0 N B:ASN65 4.0 25.2 1.0 C B:SER72 4.1 30.3 1.0 CA B:ARG73 4.2 28.2 1.0 N B:ASN74 4.2 26.2 1.0 CA B:SER60 4.3 23.7 1.0 C B:ARG61 4.3 23.4 1.0 O B:ARG61 4.3 23.2 1.0 N B:CYS64 4.4 23.6 1.0 CA B:ASN74 4.4 25.4 1.0 OG1 B:THR69 4.5 40.3 1.0 OD1 B:ASN65 4.5 30.9 1.0 CB B:ASN74 4.5 26.2 1.0 O B:HOH330 4.5 31.1 1.0 CA B:SER72 4.5 32.1 1.0 CA B:CYS64 4.5 23.8 1.0 N B:ARG61 4.6 23.2 1.0 N B:TRP62 4.6 22.7 1.0 O B:SER72 4.6 30.3 1.0 CB B:ASN65 4.6 27.8 1.0 CA B:ARG61 4.7 24.7 1.0 O B:HOH354 4.7 33.1 0.6 CB B:SER60 4.7 24.9 1.0 N B:ASP66 4.7 27.3 1.0 C B:ASN65 4.8 27.3 1.0 N B:TRP63 5.0 21.5 1.0 C B:TRP62 5.0 22.4 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Nanobody D3-L11 in Complex with Hen Egg-White Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:33.2 occ:0.60 O B:HOH341 2.2 25.0 1.0 O B:HOH349 2.3 33.5 1.0 O1 B:GOL201 2.5 27.9 1.0 O B:GLN57 2.5 23.4 1.0 O A:HOH366 3.2 38.6 1.0 C B:GLN57 3.6 22.1 1.0 OE1 B:GLU35 3.7 24.4 1.0 CB B:GLN57 3.7 22.0 1.0 C1 B:GOL201 3.7 25.9 1.0 O2 B:GOL201 3.8 25.5 1.0 CD B:GLU35 4.0 22.4 1.0 OE2 B:GLU35 4.0 24.3 1.0 CD1 B:TRP108 4.1 19.5 1.0 O B:LEU56 4.2 21.6 1.0 CA B:GLN57 4.2 22.2 1.0 O A:HOH408 4.2 35.7 1.0 OD2 B:ASP52 4.3 27.7 1.0 CG B:ASP52 4.4 27.2 1.0 C2 B:GOL201 4.4 25.7 1.0 OD1 B:ASP52 4.6 31.8 1.0 O B:ALA107 4.7 21.8 1.0 N B:ILE58 4.7 22.0 1.0 NE1 B:TRP108 4.7 20.2 1.0 CA B:TRP108 4.9 19.0 1.0 CB B:ASP52 4.9 26.5 1.0 C3 B:GOL201 4.9 26.6 1.0 N B:VAL109 5.0 19.1 1.0 NZ A:LYS101 5.0 37.5 1.0

H.Akiba, H.Tamura, M.Kiyoshi, S.Yanaka, K.Sugase, J.M.M.Caaveiro, K.Tsumoto. Structural and Thermodynamic Basis For the Recognition of the Substrate-Binding Cleft on Hen Egg Lysozyme By A Single-Domain Antibody. Sci Rep V. 9 15481 2019.
ISSN: ESSN 2045-2322
PubMed: 31664051
DOI: 10.1038/S41598-019-50722-Y