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: Tue Dec 15 14:30:42 2020

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