Sodium in PDB 4ch8: High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex

All present enzymatic activity of High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex:
3.4.21.5;

The structure of High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex, PDB code: 4ch8 was solved by B.C.Lechtenberg, S.M.V.Freund, J.A.Huntington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.14 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.220, 51.330, 150.080, 90.00, 96.13, 90.00
R / Rfree (%)	20.955 / 24.235

The binding sites of Sodium atom in the High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex (pdb code 4ch8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex, PDB code: 4ch8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1578 b:35.4 occ:1.00 O B:HOH2089 2.1 32.1 1.0 O B:LYS556 2.5 34.1 1.0 O B:ARG553 2.7 44.0 1.0 C B:LYS556 3.6 38.0 1.0 C B:ARG553 3.8 45.5 1.0 O B:TYR510 3.9 36.6 1.0 O B:HOH2077 3.9 27.4 1.0 N B:LYS556 4.2 40.2 1.0 C B:ASP552 4.3 45.4 1.0 N B:ARG553 4.4 44.4 1.0 CA B:LYS556 4.4 37.9 1.0 CA B:ASP552 4.5 40.4 1.0 N B:ASP554 4.5 46.8 1.0 OD1 B:ASP552 4.5 37.9 1.0 N B:GLY555 4.5 42.2 1.0 N B:TYR557 4.6 34.6 1.0 CA B:ASP554 4.6 45.1 1.0 O B:ASP552 4.7 43.1 1.0 O B:HOH2078 4.7 32.1 1.0 CA B:ARG553 4.7 45.3 1.0 CA B:TYR557 4.7 32.0 1.0 C B:ASP554 4.8 43.2 1.0 CD2 B:TYR557 4.9 40.6 1.0 CB B:LYS556 4.9 40.2 1.0 O B:GLY518 5.0 32.1 1.0

Sodium binding site 2 out of 4 in the High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1580 b:45.6 occ:1.00 O D:HOH2099 2.0 38.0 1.0 O D:HOH2085 2.2 31.1 1.0 O D:LYS556 2.4 36.8 1.0 O D:ARG553 2.6 39.6 1.0 C D:LYS556 3.5 34.6 1.0 O D:HOH2083 3.6 32.8 1.0 C D:ARG553 3.7 43.9 1.0 O D:TYR510 4.0 39.6 1.0 O D:HOH2086 4.0 31.7 1.0 N D:LYS556 4.1 36.9 1.0 N D:ARG553 4.2 43.8 1.0 C D:ASP552 4.2 46.9 1.0 CA D:LYS556 4.3 36.3 1.0 CA D:ASP552 4.4 45.1 1.0 N D:TYR557 4.5 32.7 1.0 N D:ASP554 4.5 42.4 1.0 N D:GLY555 4.5 38.9 1.0 CA D:ARG553 4.6 44.0 1.0 CA D:ASP554 4.6 43.1 1.0 OD1 D:ASP552 4.6 48.3 1.0 O D:ASP552 4.6 47.3 1.0 CA D:TYR557 4.7 30.5 1.0 CB D:LYS556 4.7 37.0 1.0 CD1 D:TYR557 4.8 35.6 1.0 C D:ASP554 4.8 40.7 1.0 CE1 D:TYR557 4.9 36.7 1.0

Sodium binding site 3 out of 4 in the High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Na1578 b:38.9 occ:1.00 O F:HOH2089 2.3 36.7 1.0 O F:ARG553 2.4 38.2 1.0 O F:HOH2071 2.5 32.1 1.0 O F:LYS556 2.5 30.4 1.0 O F:HOH2072 2.6 29.5 1.0 C F:ARG553 3.4 36.8 1.0 C F:LYS556 3.6 30.5 1.0 O F:HOH2076 3.8 30.6 1.0 N F:LYS556 3.9 32.1 1.0 O F:HOH2075 4.0 35.0 1.0 O F:TYR510 4.0 35.2 1.0 N F:ARG553 4.0 31.9 1.0 C F:ASP552 4.1 31.4 1.0 N F:ASP554 4.2 39.7 1.0 O F:HOH2070 4.3 25.8 1.0 CA F:ASP554 4.3 38.4 1.0 N F:GLY555 4.3 33.4 1.0 CA F:LYS556 4.3 32.2 1.0 CA F:ARG553 4.4 35.5 1.0 CA F:ASP552 4.4 29.8 1.0 O F:ASP552 4.4 35.8 1.0 O F:HOH2077 4.5 30.8 1.0 C F:ASP554 4.5 35.8 1.0 OD1 F:ASP552 4.6 28.8 1.0 N F:TYR557 4.7 31.1 1.0 CB F:LYS556 4.7 33.2 1.0 C F:GLY555 4.9 33.3 1.0 CD1 F:TYR557 5.0 32.6 1.0 CA F:TYR557 5.0 27.4 1.0

Sodium binding site 4 out of 4 in the High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of High-Salt Crystal Structure of A Thrombin-Gpibalpha Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1580 b:45.9 occ:1.00 O H:HOH2084 2.2 34.6 1.0 O H:LYS556 2.2 46.1 1.0 O H:HOH2073 2.2 33.0 1.0 O H:ARG553 2.5 44.4 1.0 C H:LYS556 3.3 45.7 1.0 C H:ARG553 3.6 50.6 1.0 O H:HOH2072 3.9 38.1 1.0 N H:LYS556 3.9 49.2 1.0 N H:ARG553 4.1 50.2 1.0 CA H:LYS556 4.1 47.3 1.0 C H:ASP552 4.1 52.1 1.0 O H:TYR510 4.2 48.3 1.0 N H:TYR557 4.2 42.5 1.0 CA H:ASP552 4.3 52.1 1.0 O H:HOH2075 4.4 34.8 1.0 CA H:TYR557 4.5 40.7 1.0 CA H:ARG553 4.5 51.4 1.0 CB H:LYS556 4.5 49.5 1.0 N H:ASP554 4.5 51.9 1.0 N H:GLY555 4.6 51.9 1.0 O H:ASP552 4.6 53.7 1.0 CD1 H:TYR557 4.7 46.7 1.0 OD1 H:ASP552 4.7 59.1 1.0 CA H:ASP554 4.7 54.2 1.0 C H:ASP554 4.8 53.7 1.0 O H:HOH2082 4.9 38.4 1.0 N H:ASP552 5.0 48.0 1.0 CE1 H:TYR557 5.0 48.5 1.0

B.C.Lechtenberg, S.M.V.Freund, J.A.Huntington. Gpibalpha Interacts Exclusively with Exosite II of Thrombin J.Mol.Biol. V. 426 881 2014.
ISSN: ISSN 0022-2836
PubMed: 24316004
DOI: 10.1016/J.JMB.2013.11.027