Sodium in PDB 2fbb: Crystal Structure Analysis of Hexagonal Lysozyme

All present enzymatic activity of Crystal Structure Analysis of Hexagonal Lysozyme:
3.2.1.17;

The structure of Crystal Structure Analysis of Hexagonal Lysozyme, PDB code: 2fbb was solved by C.Brinkmann, M.S.Weiss, E.Weckert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.00 / 1.46
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	85.637, 85.637, 67.932, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 19.8

The binding sites of Sodium atom in the Crystal Structure Analysis of Hexagonal Lysozyme (pdb code 2fbb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure Analysis of Hexagonal Lysozyme, PDB code: 2fbb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure Analysis of Hexagonal 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 Analysis of Hexagonal Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na131 b:27.4 occ:1.00 OG A:SER72 2.2 34.8 1.0 O A:ARG73 2.2 33.3 1.0 O A:SER60 2.3 29.6 1.0 O A:CYS64 2.3 29.6 1.0 O3 A:NO3156 2.6 35.8 1.0 O A:HOH1038 2.6 34.1 1.0 CB A:SER72 3.2 38.5 1.0 O1 A:NO3156 3.2 42.8 1.0 N A:NO3156 3.3 38.7 1.0 C A:ARG73 3.4 33.6 1.0 C A:CYS64 3.4 27.1 1.0 C A:SER60 3.5 28.9 1.0 N A:ARG73 3.6 36.2 1.0 CA A:ASN65 3.9 26.9 1.0 C A:SER72 4.0 38.3 1.0 N A:ASN65 4.1 29.8 1.0 CA A:ARG73 4.1 34.9 1.0 CA A:SER60 4.2 30.9 1.0 C A:ARG61 4.2 30.2 1.0 CA A:SER72 4.2 38.2 1.0 O A:ARG61 4.3 32.8 1.0 N A:ASN74 4.3 30.4 1.0 N A:CYS64 4.4 29.2 1.0 CB A:SER60 4.4 30.4 1.0 N A:ARG61 4.5 30.4 1.0 N A:TRP62 4.5 29.3 1.0 CA A:ARG61 4.5 31.2 1.0 CB A:THR69 4.6 33.7 1.0 O2 A:NO3156 4.6 36.6 1.0 CA A:CYS64 4.6 29.2 1.0 CA A:ASN74 4.6 30.5 1.0 O A:SER72 4.7 42.1 1.0 N A:ASP66 4.8 28.4 1.0 CB A:ASN65 4.8 28.9 1.0 CB A:ASN74 4.8 30.9 1.0 ND2 A:ASN65 4.8 31.9 1.0 CG2 A:THR69 4.9 35.7 1.0 C A:TRP62 4.9 29.0 1.0 C A:ASN65 4.9 26.9 1.0 O A:THR69 5.0 35.0 1.0 N A:TRP63 5.0 29.2 1.0

Sodium binding site 2 out of 5 in the Crystal Structure Analysis of Hexagonal 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 Analysis of Hexagonal Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na132 b:21.7 occ:0.50 OE1 A:GLN41 2.3 27.2 1.0 O A:LEU84 2.5 26.8 1.0 O2 A:NO3150 2.5 21.4 1.0 O1 A:NO3150 2.6 26.8 1.0 N A:NO3150 2.8 20.3 0.5 C A:LEU84 3.3 28.4 1.0 CD A:GLN41 3.4 27.2 1.0 CB A:LEU84 3.8 28.6 1.0 N A:SER85 4.0 27.6 1.0 CA A:SER85 4.0 28.4 1.0 CG A:GLN41 4.0 26.6 1.0 O3 A:NO3150 4.2 21.0 0.5 CA A:LEU84 4.2 28.7 1.0 OG1 A:THR40 4.5 27.9 1.0 NE2 A:GLN41 4.5 27.4 1.0 C A:SER85 4.6 28.6 1.0 N A:SER86 4.8 27.9 1.0

Sodium binding site 3 out of 5 in the Crystal Structure Analysis of Hexagonal 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 Analysis of Hexagonal Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na133 b:37.8 occ:0.50 O A:HOH1126 2.1 36.2 1.0 O2 A:NO3153 2.1 38.6 1.0 O A:HOH1095 2.2 29.9 0.5 O3 A:NO3153 2.4 37.6 1.0 N A:NO3153 2.8 33.1 1.0 O1 A:NO3153 4.1 30.6 1.0 OH A:TYR53 4.3 30.1 1.0 CB A:ASP66 4.3 29.4 1.0 O A:ASP66 4.4 30.2 1.0 O1 A:NO3162 4.6 44.6 1.0 CE2 A:TYR53 4.8 29.0 1.0 CA A:ASP66 4.9 28.8 1.0 NH1 A:ARG68 4.9 30.1 1.0

Sodium binding site 4 out of 5 in the Crystal Structure Analysis of Hexagonal Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure Analysis of Hexagonal Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na134 b:33.3 occ:1.00 O3 A:NO3152 2.2 34.9 1.0 O A:ARG114 2.3 31.8 1.0 O A:HOH1128 2.4 35.3 1.0 O A:HOH1015 2.5 28.0 1.0 O1 A:NO3152 2.6 34.6 1.0 N A:NO3152 2.7 33.7 1.0 C A:ARG114 3.6 30.3 1.0 CG2 A:THR118 4.1 37.2 1.0 O2 A:NO3152 4.1 34.5 1.0 OG1 A:THR118 4.2 35.8 1.0 NE1 A:TRP123 4.3 32.4 1.0 CA A:ARG114 4.4 29.9 1.0 SG A:CYS30 4.4 27.1 1.0 CB A:THR118 4.4 34.6 1.0 O A:HOH1018 4.5 26.2 1.0 N A:CYS115 4.5 28.7 1.0 CB A:ARG114 4.5 29.4 1.0 CE2 A:PHE34 4.5 29.9 1.0 CA A:CYS115 4.6 29.1 1.0 CZ2 A:TRP123 4.9 30.9 1.0 CZ A:PHE34 5.0 27.6 1.0 O A:HOH1119 5.0 40.3 1.0

Sodium binding site 5 out of 5 in the Crystal Structure Analysis of Hexagonal Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure Analysis of Hexagonal Lysozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Na135 b:36.4 occ:1.00 O3 A:NO3161 2.3 38.5 1.0 NE A:ARG14 3.0 29.6 1.0 N A:NO3161 3.4 35.7 1.0 CE1 A:HIS15 3.5 30.3 1.0 ND1 A:HIS15 3.7 34.8 1.0 NH1 A:ARG14 3.7 31.7 1.0 CZ A:ARG14 3.8 29.9 1.0 CD A:ARG14 3.8 26.1 1.0 O2 A:NO3161 3.9 37.5 1.0 CB A:ARG14 4.1 27.6 1.0 CB A:ALA11 4.1 29.1 1.0 CA A:ALA11 4.1 27.7 1.0 O A:ALA11 4.4 27.6 1.0 CG A:ARG14 4.5 27.5 1.0 O A:HOH1120 4.6 46.6 1.0 O1 A:NO3161 4.6 33.1 1.0 NE2 A:HIS15 4.7 36.8 1.0 C A:ALA11 4.7 27.8 1.0 CG A:HIS15 5.0 30.1 1.0

C.Brinkmann, M.S.Weiss, E.Weckert. The Structure of the Hexagonal Crystal Form of Hen Egg-White Lysozyme. Acta Crystallogr.,Sect.D V. 62 349 2006.
ISSN: ISSN 0907-4449
PubMed: 16552135
DOI: 10.1107/S0907444906000825