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

The structure of Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-Griselimycin., PDB code: 8ciy 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)	19.98 / 1.54
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	83.907, 150.723, 71.502, 90, 90, 90
R / Rfree (%)	17.1 / 20

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

Calcium	(Ca)	6 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-Griselimycin. (pdb code 8ciy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-Griselimycin., PDB code: 8ciy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-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 Cyclohexyl-Griselimycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:25.4 occ:1.00 OD1 A:ASN118 2.2 43.8 1.0 O A:HOH765 2.4 45.5 1.0 O A:HOH650 2.5 37.9 1.0 O A:HOH640 2.6 32.7 1.0 O A:HOH890 2.7 50.8 1.0 CG A:ASN118 3.3 40.1 1.0 HD21 A:ASN118 3.5 41.1 1.0 ND2 A:ASN118 3.8 34.2 1.0 H A:LEU119 4.0 37.8 1.0 OE2 A:GLU52 4.2 30.4 1.0 O A:HOH699 4.2 31.8 1.0 O A:HOH786 4.2 41.0 1.0 OE1 A:GLU52 4.4 30.6 1.0 HA A:ASN118 4.5 41.9 1.0 O A:HOH552 4.5 33.5 1.0 HB3 A:LEU119 4.5 47.0 1.0 CB A:ASN118 4.6 41.5 1.0 N A:LEU119 4.7 31.5 1.0 HD22 A:ASN118 4.7 41.1 1.0 CD A:GLU52 4.7 32.9 1.0 HB2 A:ASN118 4.8 49.7 1.0 O A:LEU119 4.8 39.1 1.0 O A:HOH813 4.9 37.5 1.0 O A:HOH895 4.9 48.7 1.0 HH22 A:ARG224 4.9 41.0 1.0 CA A:ASN118 5.0 34.9 1.0

Magnesium binding site 2 out of 5 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-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 Cyclohexyl-Griselimycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:39.5 occ:1.00 OD2 A:ASP208 2.0 41.7 1.0 O A:HOH501 2.2 47.6 1.0 O A:ARG205 2.4 34.2 1.0 CG A:ASP208 2.6 61.6 1.0 OD1 A:ASP208 2.7 60.2 1.0 C A:ARG205 3.5 35.3 1.0 HA A:ARG205 3.6 37.6 1.0 HB3 A:ARG205 4.0 40.4 1.0 CA A:ARG205 4.0 31.4 1.0 CB A:ASP208 4.1 60.9 1.0 HA A:MET206 4.4 38.3 0.1 HB2 A:ASP208 4.4 73.1 1.0 HE21 A:GLN16 4.4 50.3 1.0 HB3 A:ASP208 4.5 73.1 1.0 HA A:MET206 4.5 38.4 0.9 CB A:ARG205 4.5 33.6 1.0 HE22 A:GLN16 4.5 50.3 1.0 N A:MET206 4.6 31.8 0.1 N A:MET206 4.6 31.5 0.9 NE2 A:GLN16 4.6 41.9 1.0 HG2 A:ARG205 4.9 54.4 1.0 CA A:MET206 4.9 31.9 0.1 CA A:MET206 4.9 32.0 0.9 O A:MET204 4.9 31.3 1.0 H A:LEU207 5.0 36.1 0.1

Magnesium binding site 3 out of 5 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-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 Cyclohexyl-Griselimycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:25.6 occ:1.00 HH12 A:ARG240 2.4 71.2 1.0 HH22 A:ARG240 2.4 68.5 1.0 H A:ASP243 2.4 27.4 1.0 O A:HOH746 2.9 31.6 1.0 HN2 B:MVA8 3.0 31.6 1.0 O A:HOH850 3.0 46.9 1.0 HA A:PRO242 3.1 24.2 1.0 NH1 A:ARG240 3.1 59.3 1.0 NH2 A:ARG240 3.1 57.1 1.0 HN1 B:MVA8 3.2 31.6 1.0 N A:ASP243 3.3 22.8 1.0 HB3 A:ASP243 3.3 26.2 1.0 HD3 A:ARG246 3.4 56.9 1.0 CN B:MVA8 3.5 26.3 1.0 CZ A:ARG240 3.6 61.3 1.0 HB2 A:ASP243 3.7 26.2 1.0 HB B:MVA8 3.7 33.1 1.0 HH11 A:ARG240 3.8 71.2 1.0 HN3 B:MVA8 3.8 31.6 1.0 HH21 A:ARG240 3.9 68.5 1.0 CB A:ASP243 3.9 21.9 1.0 CA A:PRO242 3.9 20.2 1.0 HD2 A:ARG246 3.9 56.9 1.0 HB3 A:PRO242 4.0 31.8 1.0 C A:PRO242 4.1 21.9 1.0 CD A:ARG246 4.1 47.4 1.0 CA A:ASP243 4.2 21.3 1.0 O B:HOH102 4.3 40.0 1.0 HB2 A:ARG246 4.4 28.6 1.0 CB A:PRO242 4.5 26.5 1.0 CB B:MVA8 4.7 27.6 1.0 O A:ASP243 4.7 22.3 1.0 HG21 B:MVA8 4.7 34.6 1.0 N B:MVA8 4.8 24.3 1.0 O B:MVA8 4.8 25.5 1.0 O A:PHE241 4.9 23.6 1.0 O B:HOH105 4.9 28.1 1.0 NE A:ARG240 4.9 69.2 1.0 C A:ASP243 4.9 21.4 1.0 HG3 A:ARG246 4.9 35.1 1.0 HA A:ASP243 5.0 25.6 1.0

Magnesium binding site 4 out of 5 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-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 Cyclohexyl-Griselimycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg410 b:24.0 occ:1.00 HG A:SER107 2.6 26.4 0.5 HH21 A:ARG96 2.8 47.1 1.0 OG A:SER107 2.9 18.3 0.6 O A:HOH709 2.9 34.4 1.0 OG A:SER107 3.1 22.0 0.5 HB2 A:LEU98 3.2 20.0 1.0 HB3 A:SER107 3.2 21.8 0.6 HB2 A:SER107 3.2 21.9 0.5 HB2 A:GLU93 3.3 19.8 1.0 HD13 A:LEU98 3.3 23.4 1.0 HE A:ARG96 3.3 33.1 1.0 NH2 A:ARG96 3.4 39.2 1.0 HG A:SER107 3.6 21.9 0.6 CB A:SER107 3.6 18.2 0.6 HG3 A:GLU93 3.6 22.4 1.0 O A:HOH628 3.7 48.2 1.0 CB A:SER107 3.7 18.2 0.5 HB2 A:ARG96 3.7 27.8 1.0 NE A:ARG96 3.8 27.6 1.0 HH22 A:ARG96 3.9 47.1 1.0 HD22 A:LEU98 3.9 24.4 1.0 HB3 A:GLU93 4.0 19.8 1.0 CB A:GLU93 4.0 16.5 1.0 CZ A:ARG96 4.0 30.0 1.0 CB A:LEU98 4.1 16.6 1.0 CD1 A:LEU98 4.2 19.5 1.0 H31 A:GOL414 4.2 59.5 1.0 HB3 A:ARG96 4.2 27.8 1.0 HB2 A:SER107 4.2 21.8 0.6 CG A:GLU93 4.3 18.7 1.0 HA A:SER107 4.3 20.9 0.5 HA A:SER107 4.3 21.0 0.6 HB3 A:SER107 4.4 21.9 0.5 CB A:ARG96 4.4 23.2 1.0 HA A:LEU98 4.4 18.9 1.0 HD12 A:LEU98 4.5 23.4 1.0 CG A:LEU98 4.5 17.5 1.0 CA A:SER107 4.6 17.4 0.5 HH21 A:ARG105 4.6 23.3 1.0 CA A:SER107 4.6 17.5 0.6 CD2 A:LEU98 4.7 20.3 1.0 HB3 A:LEU98 4.7 20.0 1.0 CA A:LEU98 4.8 15.7 1.0 HG2 A:GLU93 4.8 22.4 1.0 H32 A:GOL414 4.8 59.5 1.0 HH22 A:ARG105 4.8 23.3 1.0 C3 A:GOL414 4.8 49.6 1.0 HD11 A:LEU98 4.9 23.4 1.0 O A:GLU93 4.9 19.0 1.0 NH2 A:ARG105 5.0 19.4 1.0 CD A:ARG96 5.0 33.8 1.0 O3 A:GOL414 5.0 25.6 1.0

Magnesium binding site 5 out of 5 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-Griselimycin.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Cyclohexyl-Griselimycin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg411 b:25.1 occ:1.00 H A:SER346 2.4 21.5 1.0 O B:HOH110 2.9 39.5 1.0 O A:HOH574 3.1 27.9 1.0 HE1 A:MET362 3.2 29.9 1.0 N A:SER346 3.3 17.9 1.0 HA A:SER345 3.3 24.9 1.0 HB3 A:SER346 3.4 25.2 1.0 O A:HOH704 3.4 30.9 1.0 HD B:MP86 3.5 23.4 1.0 HE B:MP86 3.5 29.7 1.0 OG A:SER346 3.6 21.7 1.0 HB3 A:SER345 3.7 27.4 1.0 HG A:SER346 3.8 26.1 1.0 SD A:MET362 3.8 21.0 1.0 CB A:SER346 3.9 21.0 1.0 CE A:MET362 3.9 24.9 1.0 CA A:SER345 4.0 20.7 1.0 HEA B:MP86 4.1 29.7 1.0 C A:SER345 4.2 17.6 1.0 CA A:SER346 4.2 15.9 1.0 CE B:MP86 4.2 24.8 1.0 CB A:SER345 4.3 22.8 1.0 CD B:MP86 4.4 19.5 1.0 HE3 A:MET362 4.5 29.9 1.0 HE2 A:MET362 4.5 29.9 1.0 HA B:LEU5 4.6 20.5 1.0 HD23 B:LEU5 4.7 24.9 1.0 HDA B:MP86 4.7 23.4 1.0 HA A:SER346 4.8 19.1 1.0 HB2 A:SER346 4.8 25.2 1.0 OG A:SER345 4.9 24.9 1.0 CG B:MP86 4.9 22.4 1.0 HEB B:MP86 5.0 29.7 1.0 O A:HOH827 5.0 36.7 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