Calcium 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
Magnesium	(Mg)	4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 7 binding sites of Calcium where determined in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin., PDB code: 8cix:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca402 b:23.5 occ:1.00 O A:HOH751 2.3 24.4 1.0 O A:GLY85 2.4 23.1 1.0 O A:HOH727 2.4 28.1 1.0 OE2 A:GLU6 2.5 23.6 1.0 OE1 A:GLU6 2.5 22.6 1.0 CD A:GLU6 2.8 23.1 1.0 C A:GLY85 3.4 24.7 1.0 HA2 A:GLY85 3.6 29.4 1.0 CA A:GLY85 3.9 24.5 1.0 HA3 A:GLY85 3.9 29.4 1.0 HB2 A:GLU87 4.3 34.3 1.0 CG A:GLU6 4.3 23.0 1.0 O A:HOH833 4.4 48.5 1.0 O A:HOH591 4.5 21.2 1.0 C A:ALA86 4.5 23.5 1.0 N A:ALA86 4.6 21.6 1.0 O A:HOH815 4.6 44.2 1.0 HG3 A:GLU6 4.7 27.7 1.0 N A:GLU87 4.7 21.3 1.0 O A:ALA86 4.7 21.9 1.0 HG2 A:GLU6 4.8 27.7 1.0 HA A:ALA86 4.8 27.7 1.0 H A:GLU87 4.8 25.6 1.0 CA A:ALA86 4.9 23.0 1.0 HB3 A:GLU6 4.9 26.8 1.0

Calcium binding site 2 out of 7 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca403 b:70.0 occ:1.00 O A:HOH786 2.6 47.4 1.0 O A:HOH508 3.0 38.6 1.0 OG1 A:THR47 3.2 28.4 1.0 HB2 A:PRO117 3.3 42.6 1.0 HG1 A:THR47 3.3 34.1 1.0 HB2 A:GLU52 3.5 31.6 1.0 O A:HOH846 3.7 39.8 1.0 HA A:LEU49 3.8 34.8 1.0 HA A:ASN118 4.0 44.7 1.0 HB A:THR47 4.0 30.4 1.0 HG21 A:THR47 4.1 33.3 1.0 CB A:THR47 4.1 25.3 1.0 OE2 A:GLU52 4.2 35.3 1.0 H A:LEU119 4.2 46.2 1.0 HB2 A:LEU119 4.2 50.8 1.0 CB A:PRO117 4.2 35.5 1.0 H A:LEU49 4.3 33.5 1.0 N A:LEU119 4.3 38.5 1.0 CB A:GLU52 4.4 26.3 1.0 C A:ASN118 4.4 43.4 1.0 C A:PRO117 4.5 35.7 1.0 N A:ASN118 4.5 34.6 1.0 HB3 A:PRO117 4.5 42.6 1.0 O A:PRO117 4.5 32.0 1.0 CA A:ASN118 4.5 37.2 1.0 CA A:LEU49 4.5 29.0 1.0 HD12 A:LEU49 4.5 36.2 1.0 O A:LEU49 4.5 38.5 1.0 CG2 A:THR47 4.5 27.7 1.0 C A:LEU49 4.5 31.3 1.0 HG3 A:GLU52 4.5 37.1 1.0 HG2 A:PRO117 4.7 43.1 1.0 CD A:GLU52 4.7 35.1 1.0 HG23 A:THR47 4.7 33.3 1.0 O A:MET51 4.7 25.3 1.0 HB3 A:GLU52 4.8 31.6 1.0 H A:ASN118 4.8 41.5 1.0 CG A:GLU52 4.8 30.9 1.0 O A:HOH652 4.8 35.5 1.0 N A:LEU49 4.9 27.9 1.0 HA A:LEU119 5.0 47.4 1.0 O A:ASN118 5.0 39.5 1.0

Calcium binding site 3 out of 7 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca404 b:23.6 occ:1.00 OXT A:ACT409 2.3 30.4 1.0 OE1 A:GLU93 2.4 23.6 1.0 OXT A:ACT410 2.4 27.6 1.0 O A:ACT409 2.4 36.0 1.0 O A:HOH760 2.4 25.6 1.0 C A:ACT409 2.5 46.0 1.0 O A:ACT410 2.5 30.5 1.0 C A:ACT410 2.7 39.9 1.0 HB3 A:GLU93 3.4 27.6 1.0 CD A:GLU93 3.6 24.9 1.0 CH3 A:ACT409 3.9 41.3 1.0 HA A:GLU93 3.9 28.1 1.0 H3 A:ACT409 4.1 49.6 1.0 CH3 A:ACT410 4.1 40.0 1.0 CB A:GLU93 4.2 23.0 1.0 H2 A:ACT409 4.3 49.6 1.0 OE2 A:GLU93 4.4 23.4 1.0 H1 A:ACT410 4.4 48.0 1.0 CG A:GLU93 4.5 23.3 1.0 CA A:GLU93 4.5 23.4 1.0 H2 A:ACT410 4.5 48.0 1.0 H1 A:ACT409 4.5 49.6 1.0 O A:HOH677 4.6 32.1 1.0 O A:HOH819 4.6 43.7 1.0 H3 A:ACT410 4.7 48.0 1.0 O A:HOH639 4.7 28.9 1.0 HG3 A:GLU93 4.9 28.0 1.0 C A:GLU93 4.9 24.6 1.0 H A:GLY94 4.9 31.8 1.0

Calcium binding site 4 out of 7 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca405 b:35.8 occ:1.00 HD22 A:ASN335 2.4 28.2 1.0 HB2 A:ASN335 2.9 27.7 1.0 HB2 A:ALA353 2.9 44.3 1.0 O A:HOH628 2.9 29.2 1.0 ND2 A:ASN335 3.3 23.5 1.0 HB3 A:ALA352 3.5 35.9 1.0 HB2 A:GLU334 3.5 28.7 1.0 H A:ASN335 3.7 26.5 1.0 CB A:ASN335 3.8 23.1 1.0 CB A:ALA353 3.8 36.9 1.0 HD21 A:ASN335 3.8 28.2 1.0 HB3 A:ALA353 3.9 44.3 1.0 CG A:ASN335 4.0 23.5 1.0 N A:ASN335 4.2 22.1 1.0 H A:ALA353 4.4 34.6 1.0 CB A:ALA352 4.4 29.9 1.0 HB1 A:ALA353 4.4 44.3 1.0 N A:ALA353 4.4 28.8 1.0 HB3 A:ASN335 4.4 27.7 1.0 CB A:GLU334 4.4 23.9 1.0 HB1 A:ALA352 4.5 35.9 1.0 CA A:ASN335 4.5 21.1 1.0 H A:GLU334 4.6 32.3 1.0 CA A:ALA353 4.7 31.1 1.0 HB3 A:GLU334 4.7 28.7 1.0 C A:ALA352 4.8 33.7 1.0 O A:ASN335 4.8 24.5 1.0 HA A:ALA353 4.9 37.4 1.0 C A:GLU334 4.9 25.9 1.0 HB2 A:ALA352 5.0 35.9 1.0 OD1 A:ASP351 5.0 30.7 1.0

Calcium binding site 5 out of 7 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 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:Ca406 b:45.8 occ:1.00 H A:ASP243 2.4 31.4 1.0 HA A:PRO242 3.1 30.9 1.0 HN2 B:MVA8 3.1 43.4 1.0 HN3 B:MVA8 3.2 43.4 1.0 HB3 A:ASP243 3.2 35.4 1.0 HD3 A:ARG246 3.2 68.7 1.0 N A:ASP243 3.3 26.1 1.0 CN B:MVA8 3.6 36.1 1.0 HB2 A:ASP243 3.7 35.4 1.0 CB A:ASP243 3.8 29.5 1.0 CA A:PRO242 3.8 25.8 1.0 HN1 B:MVA8 3.9 43.4 1.0 HB3 A:PRO242 3.9 35.5 1.0 HD2 A:ARG246 3.9 68.7 1.0 HB B:MVA8 4.0 44.4 1.0 CD A:ARG246 4.0 57.2 1.0 C A:PRO242 4.1 25.2 1.0 CA A:ASP243 4.1 28.5 1.0 HB2 A:ARG246 4.2 40.0 1.0 CB A:PRO242 4.2 29.6 1.0 HB2 A:PRO242 4.3 35.5 1.0 O B:HOH103 4.5 42.7 1.0 O A:ASP243 4.6 25.3 1.0 HG13 B:MVA8 4.8 44.6 1.0 C A:ASP243 4.8 27.5 1.0 N B:MVA8 4.9 37.5 1.0 CB B:MVA8 4.9 37.0 1.0 HE A:ARG246 4.9 93.3 1.0 HA A:ASP243 4.9 34.3 1.0 NE A:ARG246 4.9 77.8 1.0 O B:MVA8 5.0 45.5 1.0 CG A:ARG246 5.0 39.1 1.0 CB A:ARG246 5.0 33.3 1.0

Calcium binding site 6 out of 7 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 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:Ca407 b:37.3 occ:1.00 OD1 A:ASN118 2.3 37.5 1.0 O A:HOH644 2.5 38.3 1.0 O A:ACT411 2.5 45.8 1.0 O A:HOH652 2.5 35.5 1.0 O A:HOH778 2.6 48.9 1.0 O A:HOH538 2.6 45.9 1.0 OXT A:ACT411 2.7 47.7 1.0 C A:ACT411 2.9 49.8 1.0 CG A:ASN118 3.4 43.0 1.0 HD22 A:ASN118 3.7 53.8 1.0 NA A:NA417 3.8 45.3 1.0 H A:LEU119 3.9 46.2 1.0 ND2 A:ASN118 4.0 44.8 1.0 OE2 A:GLU52 4.2 35.3 1.0 O A:HOH701 4.3 38.9 1.0 CH3 A:ACT411 4.4 41.1 1.0 HA A:ASN118 4.4 44.7 1.0 OE1 A:GLU52 4.4 33.1 1.0 O A:HOH530 4.5 34.8 1.0 HB3 A:LEU119 4.6 50.8 1.0 O A:LEU119 4.6 46.0 1.0 N A:LEU119 4.6 38.5 1.0 CB A:ASN118 4.6 38.8 1.0 CD A:GLU52 4.7 35.1 1.0 H2 A:ACT411 4.8 49.3 1.0 H1 A:ACT411 4.8 49.3 1.0 HB2 A:ASN118 4.8 46.5 1.0 O A:HOH783 4.8 40.7 1.0 HH22 A:ARG224 4.8 43.8 1.0 HD21 A:ASN118 4.9 53.8 1.0 H3 A:ACT411 4.9 49.3 1.0 CA A:ASN118 5.0 37.2 1.0

Calcium binding site 7 out of 7 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 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:Ca408 b:54.1 occ:1.00 O A:HOH692 2.4 40.4 1.0 OE2 A:GLU334 2.4 36.3 1.0 O A:HOH702 2.5 42.5 1.0 O A:HOH772 2.5 39.3 1.0 OE1 A:GLU334 2.6 31.5 1.0 CD A:GLU334 2.8 31.7 1.0 O A:HOH633 4.1 52.7 1.0 HA A:GLU334 4.2 29.1 1.0 OD2 A:ASP261 4.2 55.5 1.0 CG A:GLU334 4.3 29.1 1.0 O A:HOH599 4.4 43.5 1.0 O A:HOH688 4.4 37.9 1.0 O A:HOH615 4.5 51.9 1.0 O A:HOH566 4.6 26.0 1.0 HG2 A:GLU334 4.7 34.9 1.0 HG3 A:GLU334 4.8 34.9 1.0 CG A:ASP261 5.0 49.0 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