Magnesium in PDB 8cix: Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.

The structure of Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin., PDB code: 8cix was solved by C.Fu, Y.Liu, C.Walt, C.Bader, S.Rasheed, P.Lukat, M.Neuber, W.Blankenfeldt, O.Kalinina, R.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.88 / 1.76
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	83.936, 150.561, 71.594, 90, 90, 90
R / Rfree (%)	17.9 / 20.5

The structure of Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin. also contains other interesting chemical elements:

Sodium	(Na)	5 atoms
Calcium	(Ca)	7 atoms

The binding sites of Magnesium atom in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin. (pdb code 8cix). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin., PDB code: 8cix:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg412 b:30.5 occ:1.00 H A:MET1 2.5 29.9 1.0 H A:ALA67 2.6 30.0 1.0 HA3 A:GLY66 2.7 32.5 1.0 O A:HOH606 3.1 42.8 1.0 HB2 A:MET1 3.1 29.0 1.0 HB3 A:ARG0 3.1 39.8 1.0 HD12 A:LEU92 3.2 34.0 1.0 O A:HOH564 3.2 39.9 1.0 N A:MET1 3.3 24.9 1.0 N A:ALA67 3.3 25.0 1.0 HA A:ARG0 3.4 40.0 1.0 HA2 A:GLY66 3.4 32.5 1.0 CA A:GLY66 3.4 27.1 1.0 HE A:ARG0 3.6 40.9 1.0 O A:ALA67 3.6 26.2 1.0 HD11 A:LEU92 3.7 34.0 1.0 CD1 A:LEU92 3.8 28.3 1.0 CB A:MET1 3.9 24.1 1.0 C A:GLY66 3.9 25.9 1.0 CB A:ARG0 3.9 33.1 1.0 CA A:ARG0 3.9 33.3 1.0 HB3 A:MET1 4.0 29.0 1.0 HG2 A:ARG0 4.1 47.2 1.0 C A:ARG0 4.2 28.5 1.0 HD13 A:LEU92 4.2 34.0 1.0 CA A:MET1 4.2 25.2 1.0 HH21 A:ARG0 4.3 44.8 1.0 C A:ALA67 4.4 26.1 1.0 NE A:ARG0 4.4 34.1 1.0 CA A:ALA67 4.5 24.5 1.0 HA A:MET1 4.5 30.3 1.0 CG A:ARG0 4.5 39.4 1.0 O A:PRO65 4.5 27.6 1.0 HB2 A:ARG0 4.7 39.8 1.0 N A:GLY66 4.7 26.8 1.0 NH2 A:ARG0 5.0 37.3 1.0

Magnesium binding site 2 out of 4 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg413 b:28.8 occ:1.00 HG A:SER107 2.8 29.5 0.5 OG A:SER107 2.9 23.8 0.5 O A:HOH679 3.0 35.2 1.0 OG A:SER107 3.0 24.6 0.5 HH21 A:ARG96 3.0 38.5 0.6 HB2 A:LEU98 3.2 26.2 1.0 HB2 A:SER107 3.2 28.7 0.5 HD13 A:LEU98 3.3 25.5 1.0 HB3 A:SER107 3.4 28.7 0.5 HB2 A:GLU93 3.4 27.6 1.0 HE A:ARG96 3.4 33.0 0.6 HG A:SER107 3.5 28.6 0.5 NH2 A:ARG96 3.6 32.1 0.6 HB2 A:ARG96 3.6 30.7 0.4 CB A:SER107 3.7 23.9 0.5 CB A:SER107 3.7 23.9 0.5 HG3 A:GLU93 3.7 28.0 1.0 HB2 A:ARG96 3.8 31.2 0.6 NE A:ARG96 3.9 27.5 0.6 HD22 A:LEU98 3.9 27.0 1.0 HB3 A:ARG96 4.0 30.7 0.4 HG3 A:ARG96 4.0 31.2 0.4 HB3 A:GLU93 4.0 27.6 1.0 CB A:GLU93 4.1 23.0 1.0 CZ A:ARG96 4.1 27.9 0.6 CB A:LEU98 4.1 21.8 1.0 HH22 A:ARG96 4.1 38.5 0.6 CB A:ARG96 4.2 25.6 0.4 CD1 A:LEU98 4.2 21.2 1.0 HB3 A:ARG96 4.2 31.2 0.6 HA A:SER107 4.3 27.1 0.5 HA A:SER107 4.3 27.1 0.5 HB2 A:SER107 4.3 28.7 0.5 HB3 A:SER107 4.4 28.7 0.5 CG A:GLU93 4.4 23.3 1.0 CB A:ARG96 4.5 26.0 0.6 HA A:LEU98 4.5 23.0 1.0 HH21 A:ARG105 4.6 31.9 1.0 CG A:LEU98 4.6 19.8 1.0 CA A:SER107 4.6 22.6 0.5 CA A:SER107 4.6 22.5 0.5 CG A:ARG96 4.6 25.9 0.4 HD12 A:LEU98 4.6 25.5 1.0 HB3 A:LEU98 4.7 26.2 1.0 CD2 A:LEU98 4.7 22.5 1.0 HH22 A:ARG105 4.8 31.9 1.0 CA A:LEU98 4.8 19.1 1.0 HD11 A:LEU98 4.8 25.5 1.0 HG2 A:GLU93 4.9 28.0 1.0 NH2 A:ARG105 4.9 26.5 1.0 CD A:ARG96 5.0 28.6 0.6 HD2 A:ARG96 5.0 34.3 0.6 O A:GLU93 5.0 23.8 1.0 OXT A:ACT410 5.0 27.6 1.0

Magnesium binding site 3 out of 4 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg414 b:32.8 occ:1.00 HD21 A:ASN32 2.3 28.7 1.0 HG A:LEU111 2.8 35.1 1.0 O A:HOH640 2.9 36.1 1.0 HD3 A:PRO71 3.0 33.5 1.0 O A:SER109 3.1 30.2 1.0 ND2 A:ASN32 3.1 23.9 1.0 HB3 A:SER109 3.2 34.7 0.5 OG A:SER109 3.3 30.5 0.5 HG A:SER109 3.3 36.6 0.5 HA A:THR110 3.4 29.8 1.0 C A:SER109 3.5 24.8 1.0 C A:THR110 3.6 24.4 1.0 HB2 A:SER109 3.7 34.7 0.5 HD22 A:ASN32 3.7 28.7 1.0 CG A:LEU111 3.7 29.3 1.0 HG3 A:PRO71 3.7 41.4 1.0 OD1 A:ASN32 3.8 22.8 1.0 CA A:THR110 3.8 24.8 1.0 N A:THR110 3.8 24.1 1.0 HD12 A:LEU111 3.8 33.4 1.0 O A:THR110 3.9 26.6 1.0 CG A:ASN32 3.9 23.9 1.0 N A:LEU111 3.9 23.6 1.0 CB A:SER109 3.9 28.9 0.5 CD A:PRO71 4.0 27.9 1.0 HD11 A:LEU111 4.0 33.4 1.0 O A:HOH721 4.0 46.0 1.0 H A:LEU111 4.0 28.4 1.0 CB A:SER109 4.0 28.9 0.5 CD1 A:LEU111 4.1 27.8 1.0 OG A:SER109 4.2 30.7 0.5 O A:HOH546 4.3 40.6 1.0 CA A:SER109 4.4 24.1 0.5 CG A:PRO71 4.4 34.5 1.0 HG A:SER109 4.4 36.9 0.5 CA A:SER109 4.4 24.2 0.5 HB2 A:LEU111 4.4 35.2 1.0 H A:THR110 4.4 29.0 1.0 HA A:VAL70 4.4 26.1 1.0 HD2 A:PRO71 4.5 33.5 1.0 CB A:LEU111 4.5 29.3 1.0 HD21 A:LEU111 4.6 37.0 1.0 CD2 A:LEU111 4.6 30.8 1.0 HD23 A:LEU111 4.6 37.0 1.0 CA A:LEU111 4.8 26.9 1.0 HB2 A:SER109 4.8 34.7 0.5 N A:PRO71 4.8 22.1 1.0 HB3 A:SER109 4.8 34.7 0.5 O A:THR69 4.9 25.7 1.0

Magnesium binding site 4 out of 4 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg415 b:47.0 occ:1.00 O A:HOH555 2.0 43.0 1.0 O A:HOH756 2.4 43.2 1.0 OG A:SER345 2.6 28.8 1.0 HG A:SER345 3.1 34.6 1.0 HB3 A:SER345 3.6 30.8 1.0 CB A:SER345 3.7 25.6 1.0 HA A:SER345 4.1 31.8 1.0 HG23 A:VAL344 4.4 39.2 1.0 HB2 A:SER345 4.4 30.8 1.0 CA A:SER345 4.4 26.5 1.0 O A:HOH812 4.5 41.6 1.0 OD2 A:ASP342 4.6 35.1 1.0 OD1 A:ASP342 4.7 30.5 1.0 O B:HOH110 4.8 39.6 1.0 O A:HOH787 4.8 23.9 1.0 O A:VAL344 4.9 28.2 1.0

C.Fu, Y.Liu, C.Walt, S.Rasheed, C.Bader, P.Lukat, M.Neuber, J.Haeckl, W.Blankenfeldt, O.Kalinina, R.Muller. Elucidation of Unusual Biosynthesis and Dnan-Targeting Mode of Action of Potent Anti-Tuberculosis Antibiotics Mycoplanecins Nat Commun 2023.
ISSN: ESSN 2041-1723