Chlorine in PDB 6a07: Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution

Protein crystallography data

The structure of Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution, PDB code: 6a07 was solved by B.Ku, H.S.Lee, S.J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.56 / 1.50
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 88.798, 92.207, 95.364, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.5

Other elements in 6a07:

The structure of Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution (pdb code 6a07). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution, PDB code: 6a07:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6a07

Go back to Chlorine Binding Sites List in 6a07
Chlorine binding site 1 out of 4 in the Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:20.2
occ:1.00
N A:ILE94 3.2 12.0 1.0
CA A:SER93 3.6 12.2 1.0
CB A:SER93 3.7 12.5 1.0
C A:SER93 3.9 10.4 1.0
CB A:ILE94 4.0 12.8 1.0
CA A:ILE94 4.1 11.6 1.0
O A:ILE94 4.2 13.3 1.0
CG1 A:ILE94 4.2 14.8 1.0
C A:ILE94 4.7 10.8 1.0
OG A:SER93 4.8 13.9 1.0
O A:SER92 4.9 13.4 1.0
N A:SER93 4.9 10.3 1.0

Chlorine binding site 2 out of 4 in 6a07

Go back to Chlorine Binding Sites List in 6a07
Chlorine binding site 2 out of 4 in the Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:22.6
occ:1.00
NH2 A:ARG41 3.1 14.8 1.0
CE A:LYS172 3.8 23.7 1.0
O A:HOH491 3.9 26.2 1.0
CZ A:ARG41 4.1 13.7 1.0
CD A:LYS172 4.3 20.9 1.0
O A:HOH378 4.3 31.9 1.0
NH1 A:ARG41 4.4 15.1 1.0
NZ A:LYS172 4.4 33.4 1.0
CG A:LYS172 4.4 15.2 1.0
O A:HOH384 4.8 16.1 1.0

Chlorine binding site 3 out of 4 in 6a07

Go back to Chlorine Binding Sites List in 6a07
Chlorine binding site 3 out of 4 in the Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:33.3
occ:1.00
O A:HOH445 2.8 27.5 1.0
O A:HOH487 2.8 35.1 1.0
N A:LYS51 3.2 14.8 1.0
CB A:ARG48 3.6 18.8 1.0
CA A:ARG48 3.6 13.5 1.0
C A:ARG48 3.8 15.4 1.0
N A:GLN50 3.8 16.0 1.0
CB A:GLN50 3.8 20.3 1.0
CB A:LYS51 3.8 14.1 1.0
O A:ARG48 4.0 13.5 1.0
CG A:ARG48 4.0 21.1 1.0
C A:GLN50 4.0 14.0 1.0
CA A:GLN50 4.0 16.1 1.0
CA A:LYS51 4.1 15.0 1.0
N A:THR49 4.3 16.2 1.0
C A:THR49 4.8 15.8 1.0
CG A:GLN50 4.8 24.7 1.0
CD A:ARG48 4.9 23.4 1.0
N A:ARG48 5.0 12.8 1.0
OE1 A:GLN50 5.0 37.3 1.0

Chlorine binding site 4 out of 4 in 6a07

Go back to Chlorine Binding Sites List in 6a07
Chlorine binding site 4 out of 4 in the Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:40.4
occ:1.00
N A:GLU83 3.4 29.3 1.0
CG A:GLU83 3.5 31.6 0.5
CB A:GLU83 3.9 31.5 1.0
CA A:VAL82 3.9 20.6 1.0
O A:HOH361 4.1 32.3 1.0
O A:PRO81 4.2 26.7 1.0
C A:VAL82 4.2 26.6 1.0
CG1 A:VAL82 4.3 28.2 1.0
CA A:GLU83 4.3 28.4 1.0
CB A:VAL82 4.6 22.4 1.0
CD A:GLU83 4.7 31.6 0.5
OE2 A:GLU83 4.9 33.0 0.5
N A:VAL82 5.0 20.3 1.0

Reference:

H.S.Lee, S.Lee, J.S.Kim, H.R.Lee, H.C.Shin, M.S.Lee, K.S.Jin, C.H.Kim, B.Ku, C.M.Ryu, S.J.Kim. Structural and Physiological Exploration Ofsalmonellatyphi Yfdx Uncovers Its Dual Function in Bacterial Antibiotic Stress and Virulence. Front Microbiol V. 9 3329 2018.
ISSN: ESSN 1664-302X
PubMed: 30692978
DOI: 10.3389/FMICB.2018.03329
Page generated: Sat Dec 12 12:42:50 2020

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