Sodium in PDB 3gcd: Structure of the V. Cholerae Rtx Cysteine Protease Domain in Complex with An Aza-Leucine Peptide Inhibitor

The structure of Structure of the V. Cholerae Rtx Cysteine Protease Domain in Complex with An Aza-Leucine Peptide Inhibitor, PDB code: 3gcd was solved by P.J.Lupardus, K.C.Garcia, A.Shen, M.Bogyo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.560, 65.854, 254.880, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 26.5

The binding sites of Sodium atom in the Structure of the V. Cholerae Rtx Cysteine Protease Domain in Complex with An Aza-Leucine Peptide Inhibitor (pdb code 3gcd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the V. Cholerae Rtx Cysteine Protease Domain in Complex with An Aza-Leucine Peptide Inhibitor, PDB code: 3gcd:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the V. Cholerae Rtx Cysteine Protease Domain in Complex with An Aza-Leucine Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the V. Cholerae Rtx Cysteine Protease Domain in Complex with An Aza-Leucine Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na215 b:36.8 occ:1.00 O31 A:IHP214 2.0 41.6 1.0 O A:GLU27 2.0 38.8 1.0 O32 A:IHP214 2.3 40.0 1.0 O A:HOH252 2.7 31.9 1.0 C A:GLU27 3.2 38.4 1.0 P1 A:IHP214 3.4 37.6 1.0 P2 A:IHP214 3.7 36.1 1.0 O11 A:IHP214 3.9 39.8 1.0 O21 A:IHP214 4.0 40.2 1.0 N A:GLU27 4.1 40.0 1.0 N A:THR28 4.1 36.8 1.0 CA A:GLU27 4.1 39.4 1.0 CA A:THR28 4.2 35.2 1.0 O A:HOH257 4.2 34.3 1.0 O42 A:IHP214 4.4 39.5 1.0 O41 A:IHP214 4.5 41.7 1.0 C2 A:IHP214 4.5 36.8 1.0 CB A:GLU27 4.5 39.6 1.0 O22 A:IHP214 4.6 38.0 1.0 C A:GLY26 4.6 40.4 1.0 NZ A:LYS54 4.6 26.3 1.0 O12 A:IHP214 4.7 38.6 1.0 O A:HOH229 4.7 29.5 1.0 O A:GLY25 4.7 41.3 1.0 C1 A:IHP214 4.7 37.2 1.0 CB A:THR28 4.9 34.6 1.0 CE1 A:HIS55 4.9 27.6 1.0 O A:HOH248 5.0 38.6 1.0

Sodium binding site 2 out of 4 in the Structure of the V. Cholerae Rtx Cysteine Protease Domain in Complex with An Aza-Leucine Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the V. Cholerae Rtx Cysteine Protease Domain in Complex with An Aza-Leucine Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na215 b:67.9 occ:1.00 O32 B:IHP214 2.2 63.8 1.0 O31 B:IHP214 2.3 65.4 1.0 O B:GLU27 2.4 75.2 1.0 P1 B:IHP214 3.2 66.2 1.0 O21 B:IHP214 3.2 68.5 1.0 C B:GLU27 3.4 75.2 1.0 P2 B:IHP214 3.6 62.2 1.0 O11 B:IHP214 3.7 63.7 1.0 N B:GLU27 4.0 77.8 1.0 C2 B:IHP214 4.2 60.6 1.0 O42 B:IHP214 4.2 62.8 1.0 CA B:GLU27 4.3 77.2 1.0 N B:THR28 4.3 73.2 1.0 CA B:THR28 4.4 70.9 1.0 C1 B:IHP214 4.4 61.0 1.0 O12 B:IHP214 4.4 61.4 1.0 O41 B:IHP214 4.6 66.3 1.0 O22 B:IHP214 4.6 62.3 1.0 CB B:GLU27 4.9 78.5 1.0

Sodium binding site 3 out of 4 in the Structure of the V. Cholerae Rtx Cysteine Protease Domain in Complex with An Aza-Leucine Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the V. Cholerae Rtx Cysteine Protease Domain in Complex with An Aza-Leucine Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Na215 b:58.4 occ:1.00 O31 C:IHP214 1.9 46.1 1.0 O C:HOH254 2.3 33.3 1.0 O32 C:IHP214 2.3 44.8 1.0 O C:GLU27 2.3 55.8 1.0 O C:HOH240 3.0 35.3 1.0 C C:GLU27 3.2 55.6 1.0 P1 C:IHP214 3.4 44.8 1.0 P2 C:IHP214 3.8 43.2 1.0 O11 C:IHP214 4.0 43.3 1.0 N C:THR28 4.0 56.0 1.0 O21 C:IHP214 4.1 45.7 1.0 N C:GLU27 4.1 54.5 1.0 CA C:THR28 4.1 55.5 1.0 CA C:GLU27 4.1 55.7 1.0 O42 C:IHP214 4.4 45.3 1.0 O41 C:IHP214 4.4 46.5 1.0 C2 C:IHP214 4.4 42.4 1.0 CB C:GLU27 4.5 56.8 1.0 O12 C:IHP214 4.6 44.3 1.0 O22 C:IHP214 4.6 43.9 1.0 O C:GLY25 4.7 51.4 1.0 C1 C:IHP214 4.7 41.5 1.0 CB C:THR28 4.9 55.0 1.0 C C:GLY26 4.9 53.2 1.0

Sodium binding site 4 out of 4 in the Structure of the V. Cholerae Rtx Cysteine Protease Domain in Complex with An Aza-Leucine Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the V. Cholerae Rtx Cysteine Protease Domain in Complex with An Aza-Leucine Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Na215 b:81.0 occ:1.00 O31 D:IHP214 2.1 72.3 1.0 O D:GLU27 2.3 86.6 1.0 O32 D:IHP214 2.3 69.6 1.0 C D:GLU27 3.3 87.6 1.0 P1 D:IHP214 3.5 72.6 1.0 P2 D:IHP214 3.8 66.0 1.0 N D:GLU27 3.8 93.0 1.0 O D:GLY25 3.8 95.9 1.0 O11 D:IHP214 4.0 68.8 1.0 O21 D:IHP214 4.1 73.6 1.0 N D:THR28 4.2 84.8 1.0 CA D:GLU27 4.2 91.2 1.0 CA D:THR28 4.2 82.0 1.0 O22 D:IHP214 4.4 68.9 1.0 OD2 B:ASP81 4.4 74.5 1.0 O42 D:IHP214 4.6 64.5 1.0 O41 D:IHP214 4.6 74.5 1.0 C D:GLY26 4.6 94.9 1.0 C2 D:IHP214 4.7 65.4 1.0 O12 D:IHP214 4.7 65.6 1.0 CA D:GLY26 4.8 96.6 1.0 C1 D:IHP214 4.9 66.4 1.0 CE1 D:HIS55 4.9 73.3 1.0 C D:GLY25 4.9 96.8 1.0 NZ D:LYS54 5.0 72.6 1.0

A.Shen, P.J.Lupardus, V.E.Albrow, A.Guzzetta, J.C.Powers, K.C.Garcia, M.Bogyo. Mechanistic and Structural Insights Into the Proteolytic Activation of Vibrio Cholerae Martx Toxin. Nat.Chem.Biol. V. 5 469 2009.
ISSN: ISSN 1552-4450
PubMed: 19465933
DOI: 10.1038/NCHEMBIO.178