Atomistry » Sodium » PDB 6u7p-6v1q » 6uai
Atomistry »
  Sodium »
    PDB 6u7p-6v1q »
      6uai »

Sodium in PDB 6uai: Imidazole-Triggered Ras-Specific Subtilisin SUBT_BACAM Complexed with Ysam Peptide

Protein crystallography data

The structure of Imidazole-Triggered Ras-Specific Subtilisin SUBT_BACAM Complexed with Ysam Peptide, PDB code: 6uai was solved by E.A.Toth, P.N.Bryan, J.Orban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.50 / 1.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.640, 58.640, 125.170, 90.00, 90.00, 90.00
R / Rfree (%) 10.9 / 12.5

Other elements in 6uai:

The structure of Imidazole-Triggered Ras-Specific Subtilisin SUBT_BACAM Complexed with Ysam Peptide also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Imidazole-Triggered Ras-Specific Subtilisin SUBT_BACAM Complexed with Ysam Peptide (pdb code 6uai). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Imidazole-Triggered Ras-Specific Subtilisin SUBT_BACAM Complexed with Ysam Peptide, PDB code: 6uai:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6uai

Go back to Sodium Binding Sites List in 6uai
Sodium binding site 1 out of 3 in the Imidazole-Triggered Ras-Specific Subtilisin SUBT_BACAM Complexed with Ysam Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Imidazole-Triggered Ras-Specific Subtilisin SUBT_BACAM Complexed with Ysam Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Na301

b:9.1
occ:1.00
O S:TYR171 2.1 7.7 1.0
O S:HOH410 2.3 11.1 1.0
O S:VAL174 2.3 6.0 1.0
O S:ALA169 2.5 5.1 1.0
O S:HOH408 2.6 13.4 0.7
C S:TYR171 3.2 7.2 1.0
C S:VAL174 3.4 4.6 1.0
C S:ALA169 3.5 4.0 1.0
N S:TYR171 3.7 5.8 1.0
O S:HOH577 3.7 26.4 0.7
C S:LYS170 3.7 6.2 1.0
N S:VAL174 3.9 5.2 1.0
OD2 S:ASP197 4.0 11.7 1.0
N S:PRO172 4.0 6.6 1.0
O S:LYS170 4.0 10.1 1.0
CA S:VAL174 4.0 4.7 1.0
CA S:TYR171 4.0 6.8 1.0
CA S:PRO172 4.1 7.2 1.0
O S:HOH577 4.1 20.8 0.3
CB S:VAL174 4.1 5.2 1.0
O S:HOH408 4.1 11.3 0.3
CB S:ALA176 4.1 4.5 1.0
O S:GLU195 4.1 7.9 1.0
C S:PRO172 4.1 6.3 1.0
O S:PRO172 4.2 7.1 1.0
N S:ALA176 4.2 3.8 1.0
CA S:LYS170 4.3 5.3 1.0
N S:LYS170 4.3 4.5 1.0
NH2 S:ARG247 4.5 11.8 1.0
N S:ILE175 4.5 4.2 1.0
CA S:ALA169 4.5 4.0 1.0
C S:ILE175 4.7 4.2 1.0
CA S:ALA176 4.7 3.6 1.0
CG1 S:VAL174 4.8 5.4 1.0
N S:SER173 4.8 5.8 1.0
O S:PRO168 4.8 5.4 1.0
CA S:ILE175 4.8 4.6 1.0
CB S:TYR171 4.9 7.4 1.0
CB S:GLU195 4.9 6.8 1.0
CG S:ASP197 5.0 9.6 1.0

Sodium binding site 2 out of 3 in 6uai

Go back to Sodium Binding Sites List in 6uai
Sodium binding site 2 out of 3 in the Imidazole-Triggered Ras-Specific Subtilisin SUBT_BACAM Complexed with Ysam Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Imidazole-Triggered Ras-Specific Subtilisin SUBT_BACAM Complexed with Ysam Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Na302

b:16.3
occ:0.70
NA S:NA302 0.0 16.3 0.7
NA S:NA302 1.7 12.1 0.3
OG S:SER62 1.9 11.0 0.5
O S:HOH454 2.6 9.8 1.0
O S:HOH670 2.7 31.4 1.0
OG S:SER62 2.7 6.7 0.5
N S:GLY64 3.0 5.9 1.0
CB S:SER62 3.2 8.3 0.5
CA S:GLY64 3.3 6.2 1.0
CB S:SER62 3.4 6.0 0.5
C S:SER62 3.9 8.7 0.5
N S:SER63 4.1 8.0 1.0
CG2 S:THR33 4.1 4.2 1.0
C S:SER62 4.1 9.1 0.5
O S:HOH424 4.1 33.8 1.0
O S:SER62 4.1 14.2 0.5
C S:SER63 4.2 5.7 1.0
CA S:SER62 4.2 5.9 0.5
O S:HOH616 4.2 20.4 1.0
CA S:SER62 4.2 6.9 0.5
O S:SER62 4.3 17.1 0.5
OG1 S:THR33 4.4 4.3 1.0
CB B:ALA279 4.4 7.8 1.0
OG S:SER63 4.5 9.5 0.5
C S:GLY64 4.6 4.6 1.0
CA S:SER63 4.6 8.0 0.5
CA S:SER63 4.6 6.8 0.5
N S:GLY65 4.8 4.4 1.0
CB S:THR33 4.8 4.2 1.0
OD1 S:ASP32 4.8 5.8 1.0
CB S:SER63 4.9 10.9 0.5
CA S:GLY100 4.9 6.4 1.0

Sodium binding site 3 out of 3 in 6uai

Go back to Sodium Binding Sites List in 6uai
Sodium binding site 3 out of 3 in the Imidazole-Triggered Ras-Specific Subtilisin SUBT_BACAM Complexed with Ysam Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Imidazole-Triggered Ras-Specific Subtilisin SUBT_BACAM Complexed with Ysam Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Na302

b:12.1
occ:0.30
NA S:NA302 0.0 12.1 0.3
NA S:NA302 1.7 16.3 0.7
OG S:SER62 2.5 6.7 0.5
OG S:SER62 2.5 11.0 0.5
O S:HOH454 2.6 9.8 1.0
CA S:GLY100 3.3 6.4 1.0
CB B:ALA279 3.4 7.8 1.0
CB S:SER62 3.4 8.3 0.5
CG2 S:THR33 3.5 4.2 1.0
CB S:SER62 3.5 6.0 0.5
O S:HOH670 3.5 31.4 1.0
O S:HOH424 3.6 33.8 1.0
N S:GLY100 3.9 6.3 1.0
N S:GLY64 4.5 5.9 1.0
C S:GLY100 4.6 5.7 1.0
CB S:THR33 4.6 4.2 1.0
OG1 S:THR33 4.7 4.3 1.0
CA S:SER62 4.7 5.9 0.5
C S:ASP99 4.7 6.8 1.0
CA S:SER62 4.7 6.9 0.5
O B:HOH304 4.8 44.1 1.0
CA S:GLY64 4.8 6.2 1.0
O S:GLY100 4.8 8.2 1.0
O S:HOH616 4.8 20.4 1.0
O S:GLY97 4.8 6.2 1.0
O S:ALA98 4.9 9.3 1.0
CA B:ALA279 4.9 5.8 1.0
OD1 S:ASP32 4.9 5.8 1.0
C S:SER62 4.9 8.7 0.5

Reference:

E.A.Toth, P.N.Bryan. A Programmable Proteolytic Machine That Specifically Degrades Oncogenic Ras in Vitro, in Engineered Bacteria, and in Human Cell Culture To Be Published.
Page generated: Mon Aug 18 07:43:34 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy