Chlorine in PDB 6tqd: D00-D0 Domain of Intimin

The structure of D00-D0 Domain of Intimin, PDB code: 6tqd was solved by J.Weikum, J.C.Leo, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.83 / 1.48
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.039, 65.473, 79.378, 77.78, 76.55, 84.76
R / Rfree (%)	17.9 / 21.6

The structure of D00-D0 Domain of Intimin also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Bromine	(Br)	9 atoms

The binding sites of Chlorine atom in the D00-D0 Domain of Intimin (pdb code 6tqd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the D00-D0 Domain of Intimin, PDB code: 6tqd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of D00-D0 Domain of Intimin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl704 b:23.7 occ:1.00 H A:GLU640 2.1 9.9 1.0 HB A:THR638 2.6 13.4 1.0 HG3 A:GLU640 2.7 11.8 1.0 HB2 A:GLU640 2.8 11.2 1.0 O A:VAL558 2.8 11.5 1.0 O E:HOH1027 2.9 26.9 1.0 N A:GLU640 2.9 8.2 1.0 HB A:VAL558 2.9 10.4 1.0 HG1 A:THR638 3.1 15.7 1.0 H A:ALA639 3.1 11.4 1.0 HG12 A:VAL558 3.2 9.2 1.0 OG1 A:THR638 3.2 13.0 1.0 CB A:THR638 3.3 11.1 1.0 CB A:GLU640 3.3 9.3 1.0 CG A:GLU640 3.4 9.8 1.0 N A:ALA639 3.4 9.5 1.0 HB3 A:ALA639 3.5 17.6 1.0 CA A:GLU640 3.7 8.0 1.0 CB A:VAL558 3.7 8.7 1.0 CG1 A:VAL558 3.8 7.7 1.0 C A:VAL558 3.8 10.2 1.0 C A:THR638 3.9 6.6 1.0 C A:ALA639 3.9 7.3 1.0 CD A:GLU640 3.9 13.7 1.0 CA A:ALA639 4.0 8.7 1.0 O A:HOH883 4.1 16.1 1.0 HG11 A:VAL558 4.1 9.2 1.0 CB A:ALA639 4.2 14.6 1.0 O E:HOH1051 4.2 26.9 1.0 HG11 A:VAL594 4.2 13.1 1.0 H A:MET641 4.2 8.6 1.0 HG2 A:GLU640 4.2 11.8 1.0 CA A:THR638 4.2 6.7 1.0 HB3 A:GLU640 4.2 11.2 1.0 CA A:VAL558 4.3 8.7 1.0 HG13 A:VAL594 4.3 13.1 1.0 HG21 A:THR638 4.4 15.9 1.0 OE1 A:GLU640 4.4 14.8 1.0 HA A:GLU640 4.4 9.6 1.0 OE2 A:GLU640 4.4 18.7 1.0 CG2 A:THR638 4.4 13.2 1.0 H A:VAL558 4.5 10.9 1.0 O A:THR638 4.5 8.3 1.0 HB2 A:ALA639 4.6 17.6 1.0 HA A:THR638 4.6 7.9 1.0 HA2 A:GLY559 4.7 9.5 1.0 CG1 A:VAL594 4.7 10.9 1.0 HG13 A:VAL558 4.7 9.2 1.0 C A:GLU640 4.7 8.4 1.0 N A:MET641 4.7 7.2 1.0 HG3 A:MET641 4.7 10.6 1.0 HG22 A:THR638 4.8 15.9 1.0 N A:VAL558 4.8 9.1 1.0 HG12 A:VAL594 4.9 13.1 1.0 HG21 A:VAL558 4.9 12.6 1.0 HA A:ALA639 4.9 10.5 1.0 HB1 A:ALA639 4.9 17.6 1.0 CG2 A:VAL558 4.9 10.5 1.0 N A:GLY559 5.0 7.7 1.0

Chlorine binding site 2 out of 6 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of D00-D0 Domain of Intimin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl705 b:35.4 occ:1.00 HG A:SER569 2.7 34.9 1.0 OG A:SER569 3.3 29.0 1.0 O A:HOH1109 3.4 32.7 1.0 OE1 A:GLN655 3.4 52.0 1.0 HB A:VAL653 3.5 33.3 1.0 HB2 A:SER569 3.5 30.4 1.0 HA A:ALA570 3.8 25.3 1.0 HG21 A:VAL653 3.8 36.2 1.0 O A:HOH809 3.9 36.4 1.0 HG23 A:VAL653 3.9 36.2 1.0 CB A:SER569 3.9 25.3 1.0 N A:ALA570 4.0 20.8 1.0 C A:ALA570 4.1 21.9 1.0 H A:ALA570 4.2 24.8 1.0 CG2 A:VAL653 4.2 30.2 1.0 CA A:ALA570 4.2 21.0 1.0 C A:SER569 4.2 21.7 1.0 CB A:VAL653 4.3 27.7 1.0 O A:ALA570 4.3 22.1 1.0 N A:LYS571 4.5 22.4 1.0 O A:SER569 4.5 20.2 1.0 CD A:GLN655 4.5 49.6 1.0 HE22 A:GLN655 4.6 61.9 1.0 HA A:LYS571 4.6 27.9 1.0 O A:HOH1123 4.7 39.3 1.0 HG11 A:VAL653 4.7 38.3 1.0 H A:LYS571 4.7 26.7 1.0 HB3 A:SER569 4.7 30.4 1.0 CA A:SER569 4.7 23.9 1.0 O A:HOH961 4.8 35.7 1.0 O A:HOH810 4.9 30.6 1.0 H A:VAL653 4.9 27.0 1.0 NE2 A:GLN655 5.0 51.6 1.0 CG1 A:VAL653 5.0 31.9 1.0

Chlorine binding site 3 out of 6 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of D00-D0 Domain of Intimin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl706 b:23.8 occ:1.00 H A:ASN540 2.3 8.8 1.0 H A:LEU456 2.4 8.4 1.0 O A:HOH886 2.4 33.5 1.0 O A:HOH975 2.6 16.2 1.0 HB2 A:SER539 2.6 11.2 1.0 HA A:SER455 2.7 11.3 1.0 HB2 A:ASN540 2.9 8.9 1.0 HD22 A:ASN540 3.1 18.3 1.0 N A:ASN540 3.1 7.3 1.0 N A:LEU456 3.2 7.1 1.0 ND2 A:ASN540 3.3 15.2 1.0 CB A:ASN540 3.5 7.4 1.0 CG A:ASN540 3.5 11.8 1.0 CA A:SER455 3.5 9.4 1.0 CB A:SER539 3.6 9.3 1.0 O A:HOH926 3.6 25.5 1.0 HB2 A:SER455 3.6 15.6 1.0 HD21 A:ASN540 3.7 18.3 1.0 O A:LEU456 3.7 9.0 1.0 HB3 A:LEU456 3.8 9.1 1.0 HA A:SER539 3.8 7.7 1.0 C A:SER455 3.9 8.7 1.0 CA A:ASN540 3.9 7.2 1.0 CA A:SER539 4.0 6.4 1.0 C A:SER539 4.0 6.8 1.0 CB A:SER455 4.1 12.9 1.0 HB3 A:SER539 4.1 11.2 1.0 O A:LEU454 4.2 12.6 1.0 CA A:LEU456 4.2 6.9 1.0 HG A:SER539 4.2 8.7 1.0 OD1 A:ASN540 4.3 13.8 1.0 HB3 A:SER455 4.4 15.6 1.0 HB3 A:ASN540 4.4 8.9 1.0 C A:LEU456 4.4 7.1 1.0 OG A:SER539 4.4 7.2 1.0 CB A:LEU456 4.4 7.5 1.0 O A:HOH1120 4.5 17.5 1.0 HG21 A:VAL542 4.6 12.5 1.0 HA A:ASN540 4.6 8.7 1.0 N A:SER455 4.6 9.8 1.0 O A:ASN540 4.7 8.7 1.0 HG22 A:VAL542 4.7 12.5 1.0 HG23 A:VAL542 4.7 12.5 1.0 HB2 A:LEU456 4.8 9.1 1.0 C A:ASN540 4.8 8.3 1.0 C A:LEU454 4.8 11.8 1.0 CG2 A:VAL542 4.9 10.4 1.0 O B:HOH886 4.9 21.3 1.0 O B:HOH888 4.9 20.8 1.0

Chlorine binding site 4 out of 6 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of D00-D0 Domain of Intimin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl704 b:23.7 occ:1.00 HZ2 B:LYS637 2.9 25.5 1.0 O B:HOH1008 3.0 21.0 1.0 O B:HOH1033 3.0 27.4 1.0 HA B:ALA639 3.1 22.3 1.0 HG2 B:LYS637 3.2 19.4 1.0 HB2 B:SER597 3.2 15.5 0.6 HB3 B:SER597 3.2 15.5 0.4 HZ3 B:LYS637 3.3 25.5 1.0 HD3 B:LYS637 3.4 21.5 1.0 HB3 B:LYS637 3.4 15.2 1.0 C B:THR638 3.4 11.8 1.0 OG B:SER597 3.5 15.6 0.6 NZ B:LYS637 3.5 21.2 1.0 O E:HOH1042 3.5 33.1 1.0 O B:THR638 3.5 14.2 1.0 HB2 B:SER597 3.5 15.5 0.4 O B:LYS637 3.6 13.6 1.0 N B:ALA639 3.7 15.1 1.0 HA B:THR638 3.7 14.6 1.0 CB B:SER597 3.8 12.9 0.6 CG B:LYS637 3.8 16.1 1.0 CB B:SER597 3.8 12.9 0.4 CA B:ALA639 3.9 18.5 1.0 C B:LYS637 3.9 12.0 1.0 CA B:THR638 4.0 12.2 1.0 CD B:LYS637 4.0 17.9 1.0 CB B:LYS637 4.1 12.6 1.0 H B:SER597 4.1 13.5 0.4 N B:THR638 4.1 13.6 1.0 H B:SER597 4.1 13.3 0.6 H B:ALA639 4.1 18.1 1.0 HZ1 B:LYS637 4.2 25.5 1.0 HG B:SER597 4.3 18.7 0.6 CE B:LYS637 4.4 21.8 1.0 O B:HOH1125 4.4 37.2 1.0 HB3 B:SER597 4.4 15.5 0.6 O E:HOH1040 4.5 43.9 1.0 HB2 B:ALA639 4.5 21.6 1.0 O E:HOH1071 4.5 42.0 1.0 CA B:LYS637 4.6 11.1 1.0 H B:THR638 4.7 16.3 1.0 OG B:SER597 4.7 13.9 0.4 HG3 B:LYS637 4.7 19.4 1.0 N B:SER597 4.7 11.2 0.4 N B:SER597 4.7 11.1 0.6 CB B:ALA639 4.8 18.0 1.0 HD2 B:LYS637 4.8 21.5 1.0 HE3 B:LYS637 4.9 26.2 1.0 HB2 B:LYS637 4.9 15.2 1.0 C B:ALA639 4.9 18.0 1.0 CA B:SER597 4.9 11.5 0.6 CA B:SER597 4.9 11.6 0.4 O B:HOH812 5.0 26.4 1.0

Chlorine binding site 5 out of 6 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of D00-D0 Domain of Intimin within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl703 b:32.0 occ:1.00 H C:ASP627 2.6 22.3 1.0 HG22 C:THR604 3.0 30.3 1.0 HA C:SER626 3.0 18.9 1.0 HG23 C:VAL606 3.1 22.1 1.0 HA C:ALA605 3.2 19.2 1.0 O C:HOH1007 3.4 40.6 1.0 N C:ASP627 3.4 18.6 1.0 OG C:SER626 3.5 17.1 1.0 HG2 C:LYS628 3.6 43.0 1.0 HB2 C:ASP627 3.6 28.9 1.0 CA C:SER626 3.8 15.7 1.0 CG2 C:THR604 3.8 25.2 1.0 CA C:ALA605 3.9 16.0 1.0 HG23 C:THR604 3.9 30.3 1.0 CG2 C:VAL606 4.0 18.4 1.0 O C:HOH1050 4.0 35.8 1.0 H C:LYS628 4.0 26.3 1.0 N C:ALA605 4.1 16.3 1.0 HG C:SER626 4.1 20.5 1.0 C C:SER626 4.2 17.2 1.0 CB C:SER626 4.2 18.0 1.0 HG21 C:THR604 4.2 30.3 1.0 C C:ALA605 4.2 14.2 1.0 HG21 C:VAL606 4.2 22.1 1.0 HG22 C:VAL606 4.3 22.1 1.0 C C:THR604 4.3 17.4 1.0 HB2 C:SER626 4.4 21.6 1.0 CA C:ASP627 4.4 21.2 1.0 CB C:ASP627 4.4 24.1 1.0 O C:THR604 4.4 19.1 1.0 H C:ALA605 4.4 19.6 1.0 CG C:LYS628 4.4 35.8 1.0 N C:LYS628 4.5 21.9 1.0 O C:ALA605 4.5 18.8 1.0 HG3 C:LYS628 4.5 43.0 1.0 HB2 C:LYS628 4.5 34.2 1.0 O C:LYS625 4.6 15.6 1.0 N C:VAL606 4.6 13.9 1.0 OD2 C:ASP627 4.6 32.6 1.0 H C:VAL606 4.7 16.6 1.0 C C:ASP627 4.9 21.5 1.0 O C:HOH924 4.9 33.4 1.0 N C:SER626 5.0 13.3 1.0 CB C:THR604 5.0 23.7 1.0 CB C:LYS628 5.0 28.5 1.0 CG C:ASP627 5.0 30.4 1.0

Chlorine binding site 6 out of 6 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of D00-D0 Domain of Intimin within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl703 b:23.7 occ:1.00 H D:ASP627 2.6 14.3 1.0 HA D:ALA605 3.0 8.5 1.0 HA D:SER626 3.0 8.2 1.0 O D:HOH830 3.0 35.1 1.0 HG23 D:VAL606 3.1 20.6 1.0 HG22 D:THR604 3.2 13.9 1.0 N D:ASP627 3.5 11.9 1.0 O D:HOH1014 3.6 19.0 1.0 OG D:SER626 3.6 14.4 1.0 HB2 D:ASP627 3.6 27.0 1.0 CA D:ALA605 3.7 7.1 1.0 CA D:SER626 3.8 6.9 1.0 CG2 D:VAL606 4.0 17.2 1.0 N D:ALA605 4.0 8.1 1.0 C D:ALA605 4.1 8.6 1.0 CG2 D:THR604 4.1 11.5 1.0 O D:THR604 4.1 12.7 1.0 C D:SER626 4.2 9.4 1.0 CB D:SER626 4.2 10.7 1.0 HG D:SER626 4.2 17.3 1.0 HG22 D:VAL606 4.2 20.6 1.0 HG21 D:VAL606 4.2 20.6 1.0 C D:THR604 4.2 8.5 1.0 HG2 D:LYS628 4.3 31.6 1.0 H D:LYS628 4.3 14.3 1.0 HG23 D:THR604 4.3 13.9 1.0 HB2 D:SER626 4.4 12.8 1.0 CB D:ASP627 4.4 22.5 1.0 H D:ALA605 4.4 9.7 1.0 OD2 D:ASP627 4.4 39.5 1.0 O D:ALA605 4.4 10.2 1.0 CA D:ASP627 4.4 15.4 1.0 O D:LYS625 4.5 9.1 1.0 N D:VAL606 4.5 7.2 1.0 HG21 D:THR604 4.6 13.9 1.0 H D:VAL606 4.6 8.7 1.0 HB2 D:LYS628 4.6 25.2 1.0 N D:LYS628 4.7 11.9 1.0 CG D:ASP627 4.8 34.9 1.0 N D:SER626 4.9 9.1 1.0 C D:ASP627 5.0 14.2 1.0

J.Weikum, A.Kulakova, G.Tesei, S.Yoshimoto, L.V.Jaegerum, M.Schutz, K.Hori, M.Skepo, P.Harris, J.C.Leo, J.P.Morth. The Extracellular Juncture Domains in the Intimin Passenger Adopt A Constitutively Extended Conformation Inducing Restraints to Its Sphere of Action. Sci Rep V. 10 21249 2020.
ISSN: ESSN 2045-2322
PubMed: 33277518
DOI: 10.1038/S41598-020-77706-7