Atomistry » Sodium » PDB 3fvs-3gdg » 3gcd
Atomistry »
  Sodium »
    PDB 3fvs-3gdg »
      3gcd »

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

Protein crystallography data

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

Sodium Binding Sites:

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 3gcd

Go back to Sodium Binding Sites List in 3gcd
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 3gcd

Go back to Sodium Binding Sites List in 3gcd
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 3gcd

Go back to Sodium Binding Sites List in 3gcd
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 3gcd

Go back to Sodium Binding Sites List in 3gcd
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

Reference:

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
Page generated: Tue Dec 15 06:12:21 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy