Sodium in PDB 4af8: The Structural Basis For Metacaspase Substrate Specificity and Activation

The structure of The Structural Basis For Metacaspase Substrate Specificity and Activation, PDB code: 4af8 was solved by K.Mcluskey, J.Rudolf, N.W.Isaacs, G.H.Coombs, C.X.Moss, J.C.Mottram, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.03 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.372, 50.115, 85.400, 90.00, 117.09, 90.00
R / Rfree (%)	15.3 / 17.8

The structure of The Structural Basis For Metacaspase Substrate Specificity and Activation also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the The Structural Basis For Metacaspase Substrate Specificity and Activation (pdb code 4af8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Structural Basis For Metacaspase Substrate Specificity and Activation, PDB code: 4af8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the The Structural Basis For Metacaspase Substrate Specificity and Activation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structural Basis For Metacaspase Substrate Specificity and Activation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1348 b:39.6 occ:1.00 O A:HOH2115 2.8 14.8 1.0 OE1 A:GLN98 2.9 8.4 1.0 O A:HOH2240 3.0 39.6 1.0 O A:LEU23 3.0 13.1 1.0 CD A:GLN98 3.7 6.8 1.0 CG A:GLN98 3.7 6.2 1.0 CB A:GLN98 3.8 5.5 1.0 O A:HOH2026 3.9 23.0 1.0 O A:HOH2025 3.9 28.7 1.0 C A:LEU23 4.0 10.7 1.0 O A:HOH2242 4.3 25.0 1.0 CA A:LEU23 4.4 9.3 1.0 O A:TRP22 4.5 7.1 1.0 OG1 A:THR102 4.5 5.9 1.0 CA A:GLN98 4.6 5.0 1.0 O A:HOH2036 4.7 22.5 1.0 OG1 A:THR289 4.7 6.4 1.0 CD1 A:LEU23 4.8 10.6 1.0 CB A:SER28 4.8 8.1 1.0 OE1 A:GLN286 4.9 8.5 1.0 NE2 A:GLN286 4.9 7.4 1.0 O A:GLN98 4.9 4.7 1.0

Sodium binding site 2 out of 4 in the The Structural Basis For Metacaspase Substrate Specificity and Activation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structural Basis For Metacaspase Substrate Specificity and Activation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1349 b:42.8 occ:1.00 OE1 A:GLN29 2.6 15.8 1.0 O A:LYS314 2.7 9.7 1.0 O A:HOH2037 3.2 11.3 1.0 NH1 A:ARG315 3.3 9.7 0.3 C A:LYS314 3.4 9.1 1.0 CD A:GLN29 3.7 13.0 1.0 CA A:LYS314 3.8 9.5 1.0 CD A:PRO30 4.0 5.4 1.0 CG A:ARG315 4.1 10.8 0.7 CB A:ARG315 4.1 8.9 0.7 CD A:ARG315 4.1 14.4 0.7 CB A:ARG315 4.2 8.7 0.3 CG A:ARG315 4.2 9.2 0.3 CD A:ARG315 4.3 10.0 0.3 CB A:LYS314 4.3 10.3 1.0 N A:ARG315 4.4 9.1 1.0 CZ A:ARG315 4.5 10.1 0.3 NE2 A:GLN29 4.5 15.1 1.0 CG A:PRO30 4.7 5.6 1.0 CG A:GLN29 4.8 10.2 1.0 NE A:ARG315 4.8 17.9 0.7 CB A:GLN29 4.8 7.9 1.0 CA A:ARG315 4.8 8.9 0.7 CA A:ARG315 4.8 8.8 0.3 O A:ARG313 4.8 8.9 0.3 NE A:ARG315 4.9 10.7 0.3 O A:HOH2039 4.9 7.2 1.0 O A:HOH2038 4.9 25.3 1.0 O A:ARG313 4.9 10.9 0.7

Sodium binding site 3 out of 4 in the The Structural Basis For Metacaspase Substrate Specificity and Activation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structural Basis For Metacaspase Substrate Specificity and Activation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1350 b:31.9 occ:1.00 OD2 A:ASP247 2.8 15.9 1.0 O A:HOH2174 3.5 30.7 0.5 CG A:ASP247 3.6 12.8 1.0 CB A:ASP247 3.7 11.0 1.0 OG A:SER198 3.9 14.7 1.0 CB A:SER198 3.9 11.3 1.0 O A:ASP247 4.7 11.2 1.0 OD1 A:ASP247 4.8 14.9 1.0 CA A:SER198 5.0 10.6 1.0

Sodium binding site 4 out of 4 in the The Structural Basis For Metacaspase Substrate Specificity and Activation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structural Basis For Metacaspase Substrate Specificity and Activation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1352 b:34.3 occ:1.00 ND1 A:HIS158 2.8 6.5 1.0 O A:HOH2149 2.9 13.0 1.0 O A:GLY159 3.0 10.0 1.0 N A:LEU36 3.4 16.8 1.0 O A:GLN34 3.5 15.5 1.0 CE1 A:HIS158 3.6 6.4 1.0 CA A:ALA35 3.8 15.9 1.0 CG A:HIS158 3.8 5.5 1.0 C A:ALA35 4.0 16.5 1.0 CB A:LEU36 4.0 16.8 0.5 CB A:LEU36 4.1 17.2 0.5 C A:GLY159 4.1 8.7 1.0 CG1 A:VAL33 4.1 9.7 1.0 CD2 A:HIS214 4.1 30.1 1.0 CB A:HIS158 4.2 6.4 1.0 CB A:HIS214 4.2 28.2 1.0 N A:GLY159 4.2 6.6 1.0 CA A:LEU36 4.3 17.0 0.5 CA A:LEU36 4.3 17.2 0.5 C A:GLN34 4.4 14.5 1.0 CG A:LEU36 4.4 17.4 0.5 CA A:HIS158 4.4 6.0 1.0 CG A:HIS214 4.5 29.2 1.0 N A:ALA35 4.5 15.2 1.0 NE2 A:HIS158 4.7 7.7 1.0 C A:HIS158 4.8 6.3 1.0 CB A:THR160 4.8 10.1 1.0 CB A:ALA35 4.8 16.2 1.0 CA A:GLY159 4.8 7.8 1.0 N A:HIS214 4.9 25.3 1.0 CD2 A:HIS158 4.9 6.3 1.0

K.Mcluskey, J.Rudolf, W.R.Proto, N.W.Isaacs, G.H.Coombs, C.X.Moss, J.C.Mottram. Crystal Structure of A Trypanosoma Brucei Metacaspase. Proc.Natl.Acad.Sci.Usa V. 109 7469 2012.
ISSN: ISSN 0027-8424
PubMed: 22529389
DOI: 10.1073/PNAS.1200885109