Sodium in PDB 4boh: Madanins (Merops I53) Are Cleaved By Thrombin and Factor Xa

All present enzymatic activity of Madanins (Merops I53) Are Cleaved By Thrombin and Factor Xa:
3.4.21.5;

The structure of Madanins (Merops I53) Are Cleaved By Thrombin and Factor Xa, PDB code: 4boh was solved by A.C.Figueiredo, D.Desanctis, P.J.B.Pereira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.980 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.071, 78.578, 155.156, 90.00, 90.00, 90.00
R / Rfree (%)	19.08 / 23.86

The binding sites of Sodium atom in the Madanins (Merops I53) Are Cleaved By Thrombin and Factor Xa (pdb code 4boh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Madanins (Merops I53) Are Cleaved By Thrombin and Factor Xa, PDB code: 4boh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Madanins (Merops I53) Are Cleaved By Thrombin and Factor Xa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Madanins (Merops I53) Are Cleaved By Thrombin and Factor Xa within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1579 b:38.3 occ:1.00 O A:ARG553 2.4 47.5 1.0 O A:HOH2040 2.4 43.2 1.0 O A:HOH2027 2.4 42.4 1.0 O A:HOH2037 2.4 33.3 1.0 O A:LYS556 2.4 40.7 1.0 O A:HOH2029 2.5 43.2 1.0 C A:ARG553 3.5 49.8 1.0 C A:LYS556 3.5 40.0 1.0 O A:HOH2025 3.8 33.1 1.0 N A:ARG553 3.8 45.6 1.0 C A:ASP552 4.0 44.6 1.0 N A:LYS556 4.0 45.8 1.0 O A:TYR510 4.1 40.2 1.0 O A:HOH2028 4.2 33.6 1.0 CA A:ASP552 4.2 44.0 1.0 CA A:LYS556 4.3 43.1 1.0 CA A:ARG553 4.3 48.9 1.0 N A:ASP554 4.4 51.8 1.0 O A:HOH2034 4.5 30.4 1.0 N A:GLY555 4.5 48.9 1.0 O A:ASP552 4.5 42.4 1.0 N A:TYR557 4.5 37.9 1.0 OD1 A:ASP552 4.5 46.5 1.0 CA A:ASP554 4.5 51.2 1.0 CB A:LYS556 4.6 41.6 1.0 CA A:TYR557 4.7 37.2 1.0 O A:HOH2038 4.7 45.5 1.0 C A:ASP554 4.8 49.7 1.0 CD2 A:TYR557 5.0 43.0 1.0 N A:ASP552 5.0 45.2 1.0

Sodium binding site 2 out of 2 in the Madanins (Merops I53) Are Cleaved By Thrombin and Factor Xa


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Madanins (Merops I53) Are Cleaved By Thrombin and Factor Xa within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1581 b:46.5 occ:1.00 O H:LYS556 2.3 44.0 1.0 O H:ARG553 2.4 55.9 1.0 O H:HOH2036 2.4 31.9 1.0 O H:HOH2042 2.4 38.8 1.0 O H:HOH2031 2.4 59.6 1.0 O H:HOH2033 2.5 29.1 1.0 C H:LYS556 3.4 50.2 1.0 C H:ARG553 3.5 55.5 1.0 O H:HOH2029 3.6 35.8 1.0 N H:ARG553 3.7 51.0 1.0 C H:ASP552 3.9 50.5 1.0 O H:HOH2032 4.0 35.0 1.0 N H:LYS556 4.0 54.4 1.0 CA H:ASP552 4.1 47.4 1.0 CA H:LYS556 4.1 52.0 1.0 CA H:ARG553 4.2 54.4 1.0 O H:HOH2035 4.2 44.6 1.0 N H:TYR557 4.3 42.8 1.0 O H:TYR510 4.3 45.2 1.0 CA H:TYR557 4.4 44.0 1.0 N H:ASP554 4.5 58.9 1.0 CB H:LYS556 4.5 47.5 1.0 O H:ASP552 4.5 51.9 1.0 O H:HOH2037 4.5 42.5 1.0 OD1 H:ASP552 4.5 53.9 1.0 N H:GLY555 4.6 58.1 1.0 CA H:ASP554 4.7 62.4 1.0 N H:ASP552 4.8 44.5 1.0 C H:ASP554 4.9 62.3 1.0 CD2 H:TYR557 4.9 48.7 1.0

A.C.Figueiredo, D.De Sanctis, P.J.Pereira. The Tick-Derived Anticoagulant Madanin Is Processed By Thrombin and Factor Xa. Plos One V. 8 71866 2013.
ISSN: ISSN 1932-6203
PubMed: 23951260
DOI: 10.1371/JOURNAL.PONE.0071866