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Chlorine in PDB 6nw9: Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120

Protein crystallography data

The structure of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120, PDB code: 6nw9 was solved by J.Y.Greenfield, O.Herzberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.16 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 99.439, 66.770, 161.600, 90.00, 103.58, 90.00
R / Rfree (%) 15.1 / 18.4

Other elements in 6nw9:

The structure of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 (pdb code 6nw9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120, PDB code: 6nw9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6nw9

Go back to Chlorine Binding Sites List in 6nw9
Chlorine binding site 1 out of 6 in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:29.6
occ:1.00
 O A:HOH1014 3.1 17.6 1.0
N A:GLU248 3.3 14.8 1.0
NE A:ARG222 3.5 24.8 1.0
O A:HOH986 3.7 33.5 1.0
CA A:ILE247 3.8 13.0 1.0
NH2 A:ARG222 4.0 25.5 1.0
O A:ASP246 4.0 15.9 1.0
C A:ILE247 4.1 16.6 1.0
CZ A:ARG222 4.2 26.6 1.0
CB A:GLU248 4.2 15.1 1.0
CG A:ARG222 4.3 18.7 1.0
CD1 A:ILE247 4.3 13.1 1.0
CA A:GLU248 4.3 14.3 1.0
O A:HOH1416 4.3 34.2 1.0
CG2 A:ILE247 4.3 11.9 1.0
CD A:ARG222 4.4 22.8 1.0
CB A:ILE247 4.6 9.5 1.0
O A:HOH1453 4.6 47.0 1.0
O A:HOH1435 4.7 48.6 1.0
O A:GLU248 4.7 11.6 1.0
CB A:ARG222 4.8 13.6 1.0
N A:ILE247 4.8 13.9 1.0
C A:ASP246 4.8 18.3 1.0

Chlorine binding site 2 out of 6 in 6nw9

Go back to Chlorine Binding Sites List in 6nw9
Chlorine binding site 2 out of 6 in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl702

b:26.1
occ:1.00
 O B:HOH1034 3.0 15.8 1.0
O B:HOH1304 3.0 43.0 1.0
NE B:ARG222 3.4 21.9 1.0
N B:GLU248 3.4 13.2 1.0
O B:HOH1301 3.6 46.5 1.0
CA B:ILE247 3.8 10.6 1.0
O B:HOH987 3.9 34.8 1.0
NH2 B:ARG222 4.0 21.7 1.0
O B:ASP246 4.0 15.5 1.0
C B:ILE247 4.1 11.7 1.0
CZ B:ARG222 4.1 27.0 1.0
CG B:ARG222 4.2 20.3 1.0
CD B:ARG222 4.3 20.1 1.0
CB B:GLU248 4.3 15.6 1.0
CG2 B:ILE247 4.3 11.7 1.0
CD1 B:ILE247 4.3 14.1 1.0
CA B:GLU248 4.4 12.1 1.0
CB B:ILE247 4.6 12.6 1.0
O B:HOH1374 4.7 34.5 1.0
O B:GLU248 4.7 13.4 1.0
N B:ILE247 4.8 12.5 1.0
C B:ASP246 4.8 15.0 1.0
CB B:ARG222 4.9 14.6 1.0

Chlorine binding site 3 out of 6 in 6nw9

Go back to Chlorine Binding Sites List in 6nw9
Chlorine binding site 3 out of 6 in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl703

b:43.6
occ:1.00
 O B:LYS231 2.7 16.2 1.0
N B:VAL201 2.9 14.9 1.0
O B:HOH969 3.0 32.0 1.0
O B:VAL201 3.4 15.7 1.0
NE B:ARG233 3.6 21.0 1.0
CA B:PHE200 3.6 15.8 1.0
C B:PHE200 3.7 21.5 1.0
C B:LYS231 3.8 18.0 1.0
CA B:VAL201 3.8 14.2 1.0
C B:VAL201 4.0 17.0 1.0
CD B:ARG233 4.0 19.6 1.0
CB B:VAL201 4.1 19.7 1.0
CD1 B:PHE200 4.1 23.4 1.0
CB B:LYS231 4.1 13.8 1.0
C1 B:EDO730 4.1 36.9 1.0
CB B:PHE200 4.2 14.5 1.0
CG B:LYS231 4.2 18.9 1.0
C2 B:EDO730 4.2 31.5 1.0
CG B:ARG233 4.4 13.3 1.0
CA B:LYS231 4.6 15.6 1.0
O B:ASP199 4.6 17.5 1.0
CZ B:ARG233 4.6 19.7 1.0
N B:ILE232 4.6 12.3 1.0
CG2 B:VAL201 4.6 25.2 1.0
CG B:PHE200 4.6 18.6 1.0
NH2 B:ARG233 4.8 26.0 1.0
CD B:LYS231 4.8 22.9 1.0
CA B:ILE232 4.8 13.0 1.0
N B:PHE200 4.9 13.5 1.0
O B:PHE200 4.9 17.6 1.0
N B:ARG233 5.0 12.7 1.0

Chlorine binding site 4 out of 6 in 6nw9

Go back to Chlorine Binding Sites List in 6nw9
Chlorine binding site 4 out of 6 in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl729

b:18.4
occ:0.87
 O B:HOH1282 3.0 27.4 1.0
NH2 C:ARG585 3.1 17.4 1.0
OG B:SER614 3.2 19.8 1.0
N B:SER614 3.3 16.8 1.0
OG B:SER598 3.3 17.5 1.0
N B:SER598 3.6 14.7 1.0
CB B:ALA597 3.8 13.1 1.0
CE1 C:TYR602 3.8 16.8 1.0
O B:TRP612 3.8 16.5 1.0
CB B:SER614 3.9 25.9 1.0
CA B:ASN613 3.9 16.3 1.0
CZ C:ARG585 4.1 19.4 1.0
C B:ASN613 4.1 13.2 1.0
CA B:ALA597 4.1 11.8 1.0
C B:ALA597 4.1 13.2 1.0
CA B:SER614 4.2 16.5 1.0
NE C:ARG585 4.2 14.0 1.0
CA B:SER598 4.2 12.5 1.0
O C:HOH1232 4.3 34.6 1.0
CG2 C:THR604 4.3 17.1 1.0
CD1 C:TYR602 4.3 17.9 1.0
CB B:SER598 4.4 15.2 1.0
CZ C:TYR602 4.4 17.2 1.0
ND2 B:ASN613 4.4 16.0 1.0
OH C:TYR602 4.5 17.9 1.0
CG B:ASN613 4.6 20.9 1.0
C B:TRP612 4.7 16.4 1.0
CB B:ASN613 4.8 16.1 1.0
N B:ASN613 4.8 14.7 1.0
N B:VAL615 4.9 17.6 1.0
OD1 B:ASN613 4.9 21.8 1.0

Chlorine binding site 5 out of 6 in 6nw9

Go back to Chlorine Binding Sites List in 6nw9
Chlorine binding site 5 out of 6 in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl701

b:18.9
occ:1.00
 O C:HOH1237 2.9 37.8 1.0
OG C:SER614 3.1 26.2 1.0
OG C:SER598 3.2 15.6 1.0
N C:SER614 3.2 19.5 1.0
NH2 A:ARG585 3.3 14.7 1.0
N C:SER598 3.6 14.6 1.0
CB C:SER614 3.8 19.2 1.0
CE2 A:TYR602 3.9 14.5 1.0
CB C:ALA597 3.9 13.8 1.0
O C:TRP612 3.9 14.9 1.0
CA C:ASN613 4.0 17.7 1.0
C C:ASN613 4.1 19.8 1.0
CA C:SER614 4.1 18.3 1.0
C C:ALA597 4.1 12.8 1.0
CG2 A:THR604 4.2 14.8 1.0
NE A:ARG585 4.2 15.7 1.0
CZ A:ARG585 4.2 15.9 1.0
CA C:ALA597 4.2 16.5 1.0
CA C:SER598 4.2 13.4 1.0
CB C:SER598 4.3 11.7 1.0
CD2 A:TYR602 4.3 15.6 1.0
CG C:ASN613 4.5 20.5 1.0
ND2 C:ASN613 4.6 20.0 1.0
CZ A:TYR602 4.7 18.6 1.0
OD1 C:ASN613 4.7 23.8 1.0
N C:VAL615 4.8 20.8 1.0
CB C:ASN613 4.8 14.6 1.0
C C:TRP612 4.8 20.0 1.0
OH A:TYR602 4.9 26.2 1.0
N C:ASN613 4.9 15.3 1.0
C C:SER614 5.0 24.2 1.0
CB A:THR604 5.0 17.4 1.0

Chlorine binding site 6 out of 6 in 6nw9

Go back to Chlorine Binding Sites List in 6nw9
Chlorine binding site 6 out of 6 in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl702

b:23.2
occ:1.00
 O C:HOH911 3.1 14.2 1.0
N C:GLU248 3.3 9.8 1.0
O C:HOH1291 3.4 41.9 1.0
NE C:ARG222 3.4 19.5 1.0
O C:HOH1051 3.5 26.7 1.0
CA C:ILE247 3.8 7.7 1.0
O C:ASP246 3.9 13.0 1.0
NH2 C:ARG222 3.9 22.2 1.0
C C:ILE247 4.1 10.0 1.0
CZ C:ARG222 4.1 24.2 1.0
CG C:ARG222 4.2 13.2 1.0
CB C:GLU248 4.3 10.8 1.0
CD1 C:ILE247 4.3 10.4 1.0
CD C:ARG222 4.3 15.8 1.0
CA C:GLU248 4.4 7.4 1.0
CG2 C:ILE247 4.4 10.2 1.0
CB C:ILE247 4.6 7.6 1.0
O C:HOH1265 4.7 41.4 1.0
C C:ASP246 4.8 13.9 1.0
N C:ILE247 4.8 9.5 1.0
CB C:ARG222 4.8 11.8 1.0
O C:GLU248 4.8 11.4 1.0
O C:HOH1351 4.8 33.4 1.0
O C:HOH1327 5.0 43.6 1.0
O C:HOH985 5.0 15.3 1.0

Reference:

J.Greenfield, X.Shang, H.Luo, Y.Zhou, R.D.Heselpoth, D.C.Nelson, O.Herzberg. Structure and Tailspike Glycosidase Machinery of ORF212 From E. Coli O157:H7 Phage CBA120 (TSP3). Sci Rep V. 9 7349 2019.
ISSN: ESSN 2045-2322
PubMed: 31089181
DOI: 10.1038/S41598-019-43748-9
Page generated: Mon Jul 29 12:16:32 2024

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