Cadmium in PDB 9hle: Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator

The structure of Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator, PDB code: 9hle was solved by G.Carloni, A.M.Wehenkel, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.56 / 2.04
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	64.418, 162.346, 148.765, 90, 90, 90
R / Rfree (%)	22 / 24.7

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 33;

Binding sites:

The binding sites of Cadmium atom in the Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator (pdb code 9hle). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 33 binding sites of Cadmium where determined in the Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator, PDB code: 9hle:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 33 in the Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd401 b:32.2 occ:0.76 O A:HOH604 2.1 28.0 1.0 OD2 A:ASP265 2.2 46.8 1.0 NE2 C:HIS290 2.2 33.0 1.0 OD2 A:ASP263 2.3 34.2 1.0 OD1 A:ASP263 2.5 32.8 1.0 CG A:ASP263 2.8 32.5 1.0 O A:HOH578 2.8 44.1 1.0 CG A:ASP265 3.1 43.1 1.0 CE1 C:HIS290 3.2 33.2 1.0 CD2 C:HIS290 3.2 32.1 1.0 CB A:ASP265 3.4 36.3 1.0 O A:HOH579 3.7 49.8 1.0 O A:HOH536 4.1 25.4 1.0 CB A:ASP263 4.3 29.2 1.0 OD1 A:ASP265 4.3 44.4 1.0 N A:ASP265 4.3 33.6 1.0 ND1 C:HIS290 4.3 33.3 1.0 CG C:HIS290 4.3 32.0 1.0 CA A:ASP265 4.4 33.7 1.0 CB C:ASN294 4.6 39.2 1.0 N A:MET266 4.8 30.9 1.0 OD1 C:ASP291 4.8 35.9 1.0 CD A:CD402 4.9 36.5 0.7 O A:HOH581 4.9 48.1 1.0

Cadmium binding site 2 out of 33 in the Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:36.5 occ:0.67 O A:HOH501 2.2 40.3 1.0 OD1 C:ASP291 2.2 35.9 1.0 OD1 A:ASP265 2.2 44.4 1.0 OD2 A:ASP265 2.8 46.8 1.0 CG A:ASP265 2.9 43.1 1.0 CG C:ASP291 2.9 36.7 1.0 OD2 C:ASP291 2.9 39.7 1.0 CD2 C:HIS290 4.3 32.1 1.0 CB A:ASP265 4.3 36.3 1.0 CB C:ASP291 4.4 30.5 1.0 CG2 C:VAL312 4.4 36.6 1.0 O C:HOH600 4.5 48.9 1.0 O A:HOH578 4.7 44.1 1.0 CB C:VAL312 4.8 35.8 1.0 CD A:CD401 4.9 32.2 0.8 O C:LEU287 4.9 25.6 1.0 O C:SER313 4.9 50.4 1.0 NE2 C:HIS290 4.9 33.0 1.0 CA C:ASP291 4.9 29.3 1.0 N A:ASP265 5.0 33.6 1.0 CA A:ASP265 5.0 33.7 1.0

Cadmium binding site 3 out of 33 in the Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:37.5 occ:0.65 OD2 A:ASP79 2.2 61.8 1.0 CG A:ASP79 3.3 57.5 1.0 NE2 A:HIS78 3.3 58.7 1.0 CD2 A:HIS78 3.7 56.3 1.0 OD1 A:ASP79 3.7 58.2 1.0 O A:HOH538 4.1 45.7 1.0 CE1 A:HIS78 4.5 59.0 1.0 CB A:ASP79 4.6 51.0 1.0 CG A:HIS78 5.0 55.0 1.0

Cadmium binding site 4 out of 33 in the Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:36.0 occ:0.71 O A:HOH573 2.1 35.9 1.0 O A:HOH505 2.2 34.8 1.0 ND1 A:HIS95 2.4 36.7 1.0 OD1 A:ASP97 2.5 47.1 1.0 O A:HOH609 2.5 33.5 1.0 OD2 A:ASP97 2.7 48.7 1.0 CG A:ASP97 2.9 46.3 1.0 CG A:HIS95 3.4 35.0 1.0 CE1 A:HIS95 3.4 37.5 1.0 NH1 A:ARG247 3.4 47.7 1.0 CB A:HIS95 3.6 33.6 1.0 O A:HOH598 4.1 45.5 1.0 CZ A:ARG247 4.1 44.6 1.0 NH2 A:ARG247 4.2 43.0 1.0 OD1 A:ASP98 4.3 34.9 1.0 CB A:ASP97 4.4 40.4 1.0 CD2 A:HIS95 4.6 35.8 1.0 O A:HOH509 4.6 52.2 1.0 NE2 A:HIS95 4.6 37.4 1.0 CG A:ASP98 4.7 34.4 1.0 OD2 A:ASP98 4.8 33.4 1.0

Cadmium binding site 5 out of 33 in the Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd405 b:29.8 occ:0.59 NE2 A:HIS290 2.7 43.5 1.0 CD2 A:HIS290 3.4 41.1 1.0 CE1 A:HIS290 3.8 43.5 1.0 OD1 A:ASP291 4.5 34.9 1.0 CG A:HIS290 4.7 39.5 1.0 O A:HOH596 4.7 21.5 1.0 CB A:ASN294 4.8 45.7 1.0 ND1 A:HIS290 4.9 42.2 1.0

Cadmium binding site 6 out of 33 in the Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd406 b:40.9 occ:0.35 OD1 A:ASP49 2.2 67.8 1.0 OD2 A:ASP53 2.3 54.6 1.0 OD1 A:ASP53 2.6 45.9 1.0 CG A:ASP53 2.8 48.8 1.0 CG A:ASP49 2.9 66.9 1.0 OD2 A:ASP49 2.9 71.1 1.0 O A:HOH503 3.7 25.9 0.5 O A:ASP49 4.2 55.5 1.0 CB A:ASP53 4.3 46.8 1.0 CB A:ASP49 4.3 59.1 1.0 C A:ASP49 4.7 55.2 1.0 CA A:ASP49 4.8 56.0 1.0

Cadmium binding site 7 out of 33 in the Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd407 b:34.0 occ:0.57 O C:HOH586 2.1 36.6 1.0 OE1 A:GLU130 2.2 54.2 1.0 OE2 A:GLU130 2.4 52.7 1.0 OD2 C:ASP171 2.5 56.1 1.0 O A:HOH563 2.5 28.1 1.0 OD1 C:ASP171 2.5 51.6 1.0 CD A:GLU130 2.6 53.4 1.0 CG C:ASP171 2.8 52.1 1.0 CB C:ALA173 4.0 53.2 1.0 NH1 A:ARG133 4.1 67.3 1.0 CG A:GLU130 4.1 51.4 1.0 CB C:ASP171 4.3 47.3 1.0 N C:ALA173 4.5 52.8 1.0 O A:HOH527 4.6 39.7 1.0 CD C:PRO172 4.8 51.0 1.0 O A:HOH564 4.8 55.4 1.0 CA C:ALA173 4.9 52.9 1.0 CB A:GLU130 5.0 48.8 1.0

Cadmium binding site 8 out of 33 in the Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd408 b:45.9 occ:0.36 O A:HOH600 4.6 56.1 1.0

Cadmium binding site 9 out of 33 in the Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd409 b:45.3 occ:0.33 OE1 A:GLU125 2.1 61.3 1.0 CD A:GLU125 2.6 60.6 1.0 OE1 A:GLN224 2.6 51.2 1.0 OE2 A:GLU125 2.9 63.5 1.0 CD A:GLN224 3.4 47.2 1.0 CG A:GLU125 3.7 53.7 1.0 CG A:GLN224 3.7 43.9 1.0 CB A:GLU125 4.3 49.0 1.0 NE2 A:GLN224 4.4 45.5 1.0 CA A:GLU125 4.8 48.0 1.0

Cadmium binding site 10 out of 33 in the Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of Mycobacterium Tuberculosis Steb (RV1698), A Cell Division Regulator within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd410 b:35.3 occ:0.26 O A:HOH558 2.4 44.4 1.0 O A:HOH605 2.4 46.9 1.0 O A:THR192 2.6 42.8 1.0 OE2 A:GLU122 2.6 62.2 1.0 NZ A:LYS131 2.7 67.5 1.0 C A:THR192 3.2 42.5 1.0 CD A:GLU122 3.5 61.0 1.0 CA A:GLY193 3.6 41.1 1.0 OE1 A:GLU122 3.6 65.5 1.0 N A:GLY193 3.6 41.7 1.0 CE A:LYS131 4.0 64.4 1.0 CA A:THR192 4.1 42.4 1.0 C A:GLY193 4.6 40.3 1.0 CG A:GLU122 4.9 51.1 1.0 O A:GLY193 5.0 40.4 1.0 O A:GLU191 5.0 43.4 1.0

G.Carloni, Q.Gaday, J.Petit, M.Martinez, D.Megrian, A.Sogues, M.Ben Assaya, M.Kakonyi, A.Haouz, P.M.Alzari, A.M.Wehenkel. Mechanistic Insights Into the Allosteric Regulation of Cell Wall Hydrolase Ripa in Mycobacterium Tuberculosis. Biorxiv 2025.
ISSN: ISSN 2692-8205
PubMed: 40667032
DOI: 10.1101/2025.06.28.662095