Chlorine in PDB 4d7m: Tetr(D) in Complex with Anhydrotetracycline and Magnesium

The structure of Tetr(D) in Complex with Anhydrotetracycline and Magnesium, PDB code: 4d7m was solved by S.Werten, D.Dalm, G.J.Palm, W.Hinrichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.60 / 1.55
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	65.628, 65.628, 178.598, 90.00, 90.00, 90.00
R / Rfree (%)	17.627 / 21.669

The structure of Tetr(D) in Complex with Anhydrotetracycline and Magnesium also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Chlorine atom in the Tetr(D) in Complex with Anhydrotetracycline and Magnesium (pdb code 4d7m). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Tetr(D) in Complex with Anhydrotetracycline and Magnesium, PDB code: 4d7m:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Tetr(D) in Complex with Anhydrotetracycline and Magnesium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Tetr(D) in Complex with Anhydrotetracycline and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:26.6 occ:1.00 O A:HOH2025 2.9 49.3 1.0 O A:HOH2077 3.0 51.7 1.0 OG A:SER74 3.1 21.6 1.0 N A:SER74 3.2 20.6 1.0 CB A:SER77 3.6 21.8 1.0 CB A:SER74 3.6 21.6 1.0 CA A:SER74 4.0 20.9 1.0 OG A:SER77 4.0 21.7 1.0 CA A:GLU73 4.1 23.9 1.0 C A:GLU73 4.1 22.8 1.0 CG A:GLU73 4.2 22.9 1.0 CB A:GLU73 4.7 24.4 1.0 O A:GLY72 4.8 29.0 1.0 O A:SER74 4.9 20.0 1.0 C A:SER74 5.0 20.1 1.0 CA A:SER77 5.0 20.5 1.0

Chlorine binding site 2 out of 4 in the Tetr(D) in Complex with Anhydrotetracycline and Magnesium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Tetr(D) in Complex with Anhydrotetracycline and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:25.1 occ:1.00 N A:LEU4 3.0 23.1 1.0 O A:HOH2006 3.2 36.5 1.0 CA A:LEU4 3.7 22.6 1.0 CB A:LEU4 3.7 21.4 1.0 C A:LEU4 3.8 26.9 1.0 C A:ARG3 4.0 26.0 1.0 CA A:ARG3 4.0 25.3 1.0 N A:ASN5 4.1 23.2 1.0 CD A:ARG3 4.2 31.9 1.0 NE A:ARG3 4.2 31.4 1.0 CG A:LEU4 4.3 20.4 1.0 O A:LEU4 4.4 29.5 1.0 CG A:ARG3 4.5 29.7 1.0 CB A:ARG3 4.8 29.7 1.0 O A:SER2 4.8 25.4 1.0 CD1 A:LEU4 5.0 19.1 1.0

Chlorine binding site 3 out of 4 in the Tetr(D) in Complex with Anhydrotetracycline and Magnesium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Tetr(D) in Complex with Anhydrotetracycline and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:46.6 occ:1.00 O A:HOH2009 2.9 47.0 1.0 N A:GLU7 3.1 25.1 1.0 N A:ARG6 3.5 26.5 1.0 CB A:GLU7 3.5 30.1 1.0 CB A:ARG6 3.8 30.7 1.0 CB A:ASN5 3.8 26.1 1.0 ND2 A:ASN5 3.8 29.9 1.0 CG A:ASN5 3.9 28.1 1.0 CA A:GLU7 3.9 27.3 1.0 CA A:ARG6 3.9 28.1 1.0 C A:ARG6 4.0 24.8 1.0 C A:ASN5 4.2 26.2 1.0 OD1 A:ASN5 4.5 30.4 1.0 CA A:ASN5 4.5 25.7 1.0 CG A:ARG6 4.7 38.7 1.0 OE1 A:GLU7 4.8 42.7 1.0 CG A:GLU7 5.0 34.3 1.0

Chlorine binding site 4 out of 4 in the Tetr(D) in Complex with Anhydrotetracycline and Magnesium


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Tetr(D) in Complex with Anhydrotetracycline and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl305 b:40.6 occ:1.00 O A:HOH2081 2.8 53.0 1.0 NE1 A:TRP75 3.1 20.0 1.0 NE2 A:GLN76 3.4 20.1 1.0 O A:HOH2080 3.5 29.6 1.0 CD2 A:LEU201 3.9 29.3 1.0 CE2 A:TRP75 4.0 18.5 1.0 CD1 A:TRP75 4.1 20.5 1.0 CZ2 A:TRP75 4.2 18.6 1.0 CD A:GLN76 4.3 18.0 1.0 OE1 A:GLN76 4.4 19.6 1.0 CG2 A:THR202 4.5 35.0 1.0 CG A:GLU198 4.5 22.9 1.0 CD A:GLU198 4.8 27.3 1.0

S.Werten, D.Dalm, G.J.Palm, C.C.Grimm, W.Hinrichs. Tetracycline Repressor Allostery Does Not Depend on Divalent Metal Recognition. Biochemistry 2014.
ISSN: ESSN 1520-4995
PubMed: 25432019
DOI: 10.1021/BI5012805