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

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

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:

Chlorine

(Cl)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium 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 Calcium atom.
In total 11 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 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 Calcium with other atoms in the Ca 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:Ca501 b:66.1 occ:1.00 O A:LEU325 2.5 44.9 1.0 OD1 A:ASN326 2.5 56.7 1.0 C A:LEU325 3.6 44.6 1.0 CG A:ASN326 3.7 53.4 1.0 CA A:ASN326 4.1 46.1 1.0 N A:ASN326 4.3 43.7 1.0 CB A:ASN326 4.4 50.0 1.0 N A:LEU325 4.5 47.0 1.0 O A:HOH659 4.5 45.3 1.0 CB A:CYS321 4.6 50.1 1.0 CA A:LEU325 4.7 42.9 1.0 O A:PRO322 4.7 50.4 1.0 ND2 A:ASN326 4.8 56.4 1.0 N A:GLY324 4.9 46.4 1.0

Calcium binding site 2 out of 11 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 Calcium with other atoms in the Ca 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 B:Ca501 b:67.5 occ:1.00 OE1 A:GLU232 4.0 66.4 1.0 O A:THR230 4.4 63.0 1.0 O A:HOH655 4.4 63.0 1.0 O B:LEU100 4.5 77.0 1.0 OD1 B:ASN58 4.5 61.4 1.0 OD1 B:ASN57 4.8 62.0 1.0 ND2 B:ASN58 5.0 60.9 1.0

Calcium binding site 3 out of 11 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 Calcium with other atoms in the Ca 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 B:Ca502 b:59.6 occ:1.00 OE2 B:GLU209 2.3 58.6 1.0 OE1 B:GLU209 2.5 52.9 1.0 CD B:GLU209 2.7 52.6 1.0 CG B:GLU209 4.2 50.3 1.0 O B:HOH670 4.4 48.6 1.0 O B:HOH604 4.6 53.6 1.0 CD1 B:LEU212 4.9 53.6 1.0

Calcium binding site 4 out of 11 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 Calcium with other atoms in the Ca 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 B:Ca503 b:88.1 occ:1.00 ND2 B:ASN317 4.4 50.5 1.0 OD2 A:ASP293 4.9 68.4 1.0 CB B:ASN317 4.9 39.6 1.0

Calcium binding site 5 out of 11 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 Calcium with other atoms in the Ca 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 C:Ca501 b:65.2 occ:1.00 OD1 B:ASP177 2.4 56.6 1.0 OD1 C:ASP108 2.6 65.8 1.0 OD2 C:ASP108 2.9 65.0 1.0 CG C:ASP108 3.1 68.5 1.0 CG B:ASP177 3.6 56.4 1.0 O C:HOH608 3.8 63.1 1.0 OE2 B:GLU199 4.3 55.7 1.0 OD2 B:ASP177 4.4 56.7 1.0 CA B:ASP177 4.4 58.8 1.0 OE1 B:GLU199 4.4 55.9 1.0 CB B:ASP177 4.5 59.1 1.0 N B:TYR178 4.5 58.6 1.0 CB C:ALA106 4.5 58.5 1.0 CB C:ASP108 4.6 60.0 1.0 O B:GLN176 4.6 57.0 1.0 CD B:GLU199 4.7 54.0 1.0 C C:ASP108 4.9 65.2 1.0 O B:TYR178 4.9 55.7 1.0 O C:ASP108 4.9 64.3 1.0

Calcium binding site 6 out of 11 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 Calcium with other atoms in the Ca 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 C:Ca502 b:85.1 occ:1.00 O C:ASN423 4.5 57.5 1.0 NZ C:LYS295 4.6 62.0 1.0 OXT C:ASN423 5.0 64.8 1.0

Calcium binding site 7 out of 11 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 Calcium with other atoms in the Ca binding site number 7 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:Ca501 b:85.4 occ:1.00 OD2 D:ASP238 2.6 70.3 1.0 OE2 F:GLU232 2.7 76.5 1.0 OG D:SER240 3.1 63.0 1.0 OE1 D:GLN236 3.6 64.4 1.0 CB D:SER240 3.6 54.0 1.0 CG D:ASP238 3.7 57.6 1.0 CD F:GLU232 3.8 71.1 1.0 NH2 D:ARG49 4.0 69.6 1.0 OD1 D:ASP238 4.0 64.1 1.0 OE1 F:GLU232 4.2 69.1 1.0 OD1 D:ASP102 4.3 77.4 1.0 CZ D:ARG49 4.3 73.2 1.0 NH1 D:ARG49 4.6 61.4 1.0 CD D:GLN236 4.7 62.7 1.0 O D:GLN103 4.8 77.8 1.0 CB D:ASP238 4.9 49.8 1.0 NE D:ARG49 5.0 70.0 1.0

Calcium binding site 8 out of 11 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 Calcium with other atoms in the Ca binding site number 8 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:Ca501 b:74.0 occ:1.00 OE1 D:GLU232 4.2 57.7 1.0 O D:THR230 4.3 60.6 1.0 OD1 E:ASN57 4.3 50.8 1.0 O E:LEU100 4.6 69.8 1.0 OD1 E:ASN58 4.7 62.9 1.0 CA E:ASN57 4.8 51.9 1.0 O E:HOH618 4.9 50.7 1.0 O E:HOH629 4.9 43.6 1.0 ND2 E:ASN58 5.0 56.4 1.0

Calcium binding site 9 out of 11 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 Calcium with other atoms in the Ca binding site number 9 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:Ca502 b:70.0 occ:1.00 OE2 E:GLU209 2.4 54.8 1.0 OE1 E:GLU209 2.6 64.8 1.0 CD E:GLU209 2.8 59.5 1.0 CG E:GLU209 4.3 56.9 1.0 O E:HOH603 4.5 62.5 1.0

Calcium binding site 10 out of 11 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 Calcium with other atoms in the Ca binding site number 10 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:Ca503 b:103.0 occ:1.00 OD2 E:ASP108 2.7 73.6 1.0 OE2 D:GLU203 3.6 89.2 1.0 OE1 D:GLU203 3.6 81.2 1.0 CG E:ASP108 3.8 69.3 1.0 O E:HOH621 3.9 75.7 1.0 CD D:GLU203 4.0 80.7 1.0 OD1 E:ASP108 4.1 71.9 1.0 O E:HOH654 4.3 73.4 1.0

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