Chlorine in PDB 7w64: Crystal Structure of Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf

Protein crystallography data

The structure of Crystal Structure of Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf, PDB code: 7w64 was solved by H.Oki, K.Kawahara, M.Iimori, Y.Imoto, T.Maruno, S.Uchiyama, Y.Muroga, A.Yoshida, T.Yoshida, T.Ohkubo, S.Matsuda, T.Iida, S.Nakamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.20 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.883, 128.555, 327.242, 90, 90, 90
R / Rfree (%) 22.2 / 26.4

Other elements in 7w64:

The structure of Crystal Structure of Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf also contains other interesting chemical elements:

Calcium (Ca) 11 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf (pdb code 7w64). 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 Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf, PDB code: 7w64:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 7w64

Go back to Chlorine Binding Sites List in 7w64
Chlorine binding site 1 out of 6 in the Crystal Structure of Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf


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 Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:55.0
occ:1.00
 N B:LYS351 3.2 43.9 1.0
N H:PHE1 3.3 44.0 1.0
ND2 A:ASN375 3.3 46.1 1.0
CA H:PHE1 3.6 46.6 1.0
O B:LYS351 3.6 52.4 1.0
C H:PHE1 3.9 47.5 1.0
O H:HOH101 4.0 56.0 1.0
CA B:ALA350 4.0 46.0 1.0
O H:HOH104 4.0 55.8 1.0
CA B:LYS351 4.0 50.4 1.0
N H:ASN2 4.1 52.6 1.0
CB B:LYS351 4.1 45.8 1.0
C B:ALA350 4.1 48.4 1.0
C B:LYS351 4.2 51.4 1.0
CG A:ASN375 4.3 44.2 1.0
CB B:ALA350 4.3 42.8 1.0
O A:HOH646 4.6 45.6 1.0
O H:PHE1 4.6 51.5 1.0
OD1 A:ASN375 4.6 45.2 1.0
CG B:LYS351 4.7 45.2 1.0

Chlorine binding site 2 out of 6 in 7w64

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Chlorine binding site 2 out of 6 in the Crystal Structure of Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf


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 Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl502

b:86.5
occ:1.00
 N J:PHE1 3.1 75.0 1.0
N D:LYS351 3.3 79.2 1.0
O D:LYS351 3.5 89.6 1.0
CA J:PHE1 3.5 70.1 1.0
C J:PHE1 3.7 74.2 1.0
ND2 F:ASN375 3.8 78.8 1.0
N J:ASN2 4.0 73.9 1.0
CA D:ALA350 4.1 81.6 1.0
CA D:LYS351 4.1 80.7 1.0
O J:PHE1 4.1 70.5 1.0
C D:ALA350 4.2 82.8 1.0
CB D:LYS351 4.2 74.4 1.0
C D:LYS351 4.2 86.2 1.0
CB D:ALA350 4.3 73.2 1.0
CG F:ASN375 4.5 74.4 1.0
OD1 F:ASN375 4.7 75.0 1.0
CG D:LYS351 4.8 77.6 1.0
CA J:ASN2 4.9 80.7 1.0

Chlorine binding site 3 out of 6 in 7w64

Go back to Chlorine Binding Sites List in 7w64
Chlorine binding site 3 out of 6 in the Crystal Structure of Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf


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 Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl504

b:95.2
occ:1.00
 N E:LYS351 2.7 91.3 1.0
O E:LYS351 2.9 83.9 1.0
CA E:LYS351 3.5 90.0 1.0
N K:PHE1 3.5 94.8 1.0
C E:LYS351 3.6 85.6 1.0
C E:ALA350 3.7 88.0 1.0
CA E:ALA350 3.7 86.2 1.0
CA K:PHE1 3.7 97.1 1.0
CB E:ALA350 3.8 85.0 1.0
CB E:LYS351 4.0 85.2 1.0
ND2 D:ASN375 4.1 87.3 1.0
OD1 D:ASN375 4.1 88.8 1.0
C K:PHE1 4.2 99.0 1.0
N K:ASN2 4.3 99.5 1.0
CG D:ASN375 4.5 90.5 1.0
CD E:LYS351 4.8 82.5 1.0
O E:ALA350 4.9 87.3 1.0
N E:ASP352 4.9 88.2 1.0
CD1 K:PHE1 4.9 87.1 1.0
CG E:LYS351 4.9 87.0 1.0

Chlorine binding site 4 out of 6 in 7w64

Go back to Chlorine Binding Sites List in 7w64
Chlorine binding site 4 out of 6 in the Crystal Structure of Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf


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 Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl101

b:54.5
occ:1.00
 N G:PHE1 2.6 47.6 1.0
N A:LYS351 3.2 41.8 1.0
CA G:PHE1 3.3 55.6 1.0
ND2 C:ASN375 3.5 46.5 1.0
O A:LYS351 3.6 52.4 1.0
C G:PHE1 3.6 47.0 1.0
N G:ASN2 4.0 51.8 1.0
CA A:ALA350 4.0 40.3 1.0
CA A:LYS351 4.0 45.5 1.0
O G:PHE1 4.0 43.5 1.0
CB A:LYS351 4.1 41.6 1.0
C A:ALA350 4.1 41.2 1.0
C A:LYS351 4.3 50.3 1.0
CG C:ASN375 4.3 41.9 1.0
CB A:ALA350 4.3 44.5 1.0
OD1 C:ASN375 4.5 52.1 1.0
O C:HOH639 4.7 48.7 1.0
CG A:LYS351 4.7 41.9 1.0
CB G:PHE1 4.7 44.8 1.0
OG C:SER373 4.8 44.9 1.0
CD1 G:PHE1 4.8 46.2 1.0

Chlorine binding site 5 out of 6 in 7w64

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Chlorine binding site 5 out of 6 in the Crystal Structure of Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf


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 Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl101

b:53.4
occ:1.00
 N I:PHE1 2.8 52.0 1.0
N C:LYS351 3.3 38.4 1.0
CA I:PHE1 3.3 46.9 1.0
ND2 B:ASN375 3.4 38.9 1.0
O C:LYS351 3.5 43.8 1.0
C I:PHE1 3.7 47.5 1.0
CB C:LYS351 4.0 38.1 1.0
CA C:LYS351 4.0 40.9 1.0
N I:ASN2 4.1 56.9 1.0
CG B:ASN375 4.1 40.6 1.0
C C:LYS351 4.2 48.6 1.0
C C:ALA350 4.2 41.3 1.0
OD1 B:ASN375 4.2 39.2 1.0
O I:PHE1 4.3 51.1 1.0
CA C:ALA350 4.3 44.3 1.0
O B:HOH666 4.3 48.5 1.0
OG B:SER373 4.5 41.1 1.0
CG C:LYS351 4.6 38.4 1.0
CB C:ALA350 4.7 34.6 1.0
CB I:PHE1 4.7 45.8 1.0
CB B:SER373 4.9 40.1 1.0
CD1 I:PHE1 5.0 44.9 1.0

Chlorine binding site 6 out of 6 in 7w64

Go back to Chlorine Binding Sites List in 7w64
Chlorine binding site 6 out of 6 in the Crystal Structure of Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf


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 Minor Pilin Tcpb From Vibrio Cholerae Complexed with N-Terminal Peptide Fragment of Tcpf within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl101

b:66.4
occ:1.00
 N L:PHE1 3.0 67.1 1.0
N F:LYS351 3.2 59.6 1.0
CA L:PHE1 3.3 65.6 1.0
ND2 E:ASN375 3.4 59.2 1.0
O F:LYS351 3.5 62.2 1.0
C L:PHE1 3.9 69.0 1.0
CA F:LYS351 4.0 56.9 1.0
CB F:LYS351 4.1 55.0 1.0
CA F:ALA350 4.1 52.8 1.0
C F:ALA350 4.2 58.3 1.0
N L:ASN2 4.2 69.2 1.0
C F:LYS351 4.2 56.3 1.0
CG E:ASN375 4.4 59.9 1.0
CB F:ALA350 4.4 48.3 1.0
O L:PHE1 4.5 72.2 1.0
CG F:LYS351 4.6 54.8 1.0
OD1 E:ASN375 4.6 59.5 1.0
CD1 L:PHE1 4.7 59.6 1.0
CB L:PHE1 4.7 61.0 1.0
OG E:SER373 4.8 59.3 1.0

Reference:

H.Oki, K.Kawahara, M.Iimori, Y.Imoto, H.Nishiumi, T.Maruno, S.Uchiyama, Y.Muroga, A.Yoshida, T.Yoshida, T.Ohkubo, S.Matsuda, T.Iida, S.Nakamura. Structural Basis For the Toxin-Coregulated Pilus-Dependent Secretion of Vibrio Cholerae Colonization Factor. Sci Adv V. 8 O3013 2022.
ISSN: ESSN 2375-2548
PubMed: 36240278
DOI: 10.1126/SCIADV.ABO3013
Page generated: Tue Apr 4 22:10:35 2023

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