Calcium 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:

Magnesium	(Mg)	5 atoms
Sodium	(Na)	1 atom

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

Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca401 b:16.8 occ:1.00 O A:GLY85 2.3 19.2 1.0 OE2 A:GLU87 2.4 13.4 0.6 O A:HOH718 2.4 23.3 1.0 OE2 A:GLU6 2.5 18.1 1.0 OE1 A:GLU6 2.5 17.7 1.0 CD A:GLU6 2.9 17.1 1.0 HG3 A:GLU87 3.4 30.4 0.6 C A:GLY85 3.4 18.0 1.0 CD A:GLU87 3.5 27.8 0.6 HA2 A:GLY85 3.7 23.5 1.0 CG A:GLU87 3.9 25.3 0.6 CA A:GLY85 4.0 19.6 1.0 HA3 A:GLY85 4.0 23.5 1.0 HB2 A:GLU87 4.3 21.8 0.4 CG A:GLU6 4.4 17.1 1.0 HG2 A:GLU87 4.4 30.4 0.6 OE1 A:GLU87 4.5 28.0 0.6 C A:ALA86 4.5 17.8 1.0 N A:ALA86 4.6 16.0 1.0 O A:HOH645 4.6 18.0 1.0 O A:HOH841 4.6 43.5 1.0 O A:ALA86 4.7 18.8 1.0 N A:GLU87 4.7 16.9 1.0 HG3 A:GLU6 4.7 20.5 1.0 O A:HOH823 4.7 51.0 1.0 HA A:ALA86 4.7 18.4 1.0 H A:GLU87 4.8 20.3 0.6 H A:GLU87 4.8 20.3 0.4 HG2 A:GLU6 4.8 20.5 1.0 HB3 A:GLU6 4.9 21.3 1.0 CA A:ALA86 4.9 15.3 1.0 HA A:GLU6 5.0 19.7 1.0

Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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:Ca402 b:25.1 occ:1.00 HD22 A:ASN335 2.4 21.6 1.0 HB2 A:ALA353 2.9 27.5 1.0 HB2 A:ASN335 3.0 20.8 1.0 O A:HOH595 3.1 19.0 1.0 ND2 A:ASN335 3.2 18.0 1.0 HB2 A:GLU334 3.5 22.7 1.0 HB3 A:ALA352 3.5 24.6 1.0 H A:ASN335 3.8 21.0 1.0 HD21 A:ASN335 3.8 21.6 1.0 CB A:ALA353 3.8 22.9 1.0 CB A:ASN335 3.8 17.3 1.0 HB3 A:ALA353 4.0 27.5 1.0 CG A:ASN335 4.0 16.2 1.0 N A:ASN335 4.2 17.5 1.0 HB1 A:ALA353 4.3 27.5 1.0 CB A:GLU334 4.3 18.9 1.0 H A:ALA353 4.4 27.1 1.0 CB A:ALA352 4.4 20.5 1.0 HB3 A:GLU334 4.4 22.7 1.0 N A:ALA353 4.4 22.6 1.0 HB3 A:ASN335 4.5 20.8 1.0 HB1 A:ALA352 4.6 24.6 1.0 CA A:ASN335 4.6 16.5 1.0 CA A:ALA353 4.6 25.2 1.0 HA A:ALA353 4.8 30.3 1.0 C A:ALA352 4.8 27.2 1.0 H A:GLU334 4.8 26.2 1.0 O A:ASN335 4.8 16.8 1.0 OD1 A:ASP351 5.0 20.9 1.0 C A:GLU334 5.0 21.6 1.0 O A:HOH514 5.0 32.4 1.0

Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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:Ca403 b:20.9 occ:1.00 OE1 A:GLU93 2.3 18.6 1.0 O3 A:GOL414 2.3 25.6 1.0 O1 A:GOL414 2.4 28.5 1.0 O A:HOH783 2.4 23.8 1.0 HB3 A:GLU93 3.4 19.8 1.0 CD A:GLU93 3.5 19.4 1.0 C3 A:GOL414 3.5 49.6 1.0 HO2 A:GOL414 3.6 72.8 1.0 C1 A:GOL414 3.7 48.8 1.0 H32 A:GOL414 3.9 59.5 1.0 HA A:GLU93 3.9 21.4 1.0 C2 A:GOL414 4.0 47.8 1.0 H12 A:GOL414 4.1 58.6 1.0 O2 A:GOL414 4.1 60.6 1.0 CB A:GLU93 4.2 16.5 1.0 H31 A:GOL414 4.3 59.5 1.0 OE2 A:GLU93 4.3 19.8 1.0 H11 A:GOL414 4.3 58.6 1.0 CG A:GLU93 4.4 18.7 1.0 CA A:GLU93 4.5 17.8 1.0 O A:HOH844 4.6 37.2 1.0 O A:HOH685 4.6 31.2 1.0 HG3 A:GLU93 4.8 22.4 1.0 H A:GLY94 4.8 26.7 1.0 C A:GLU93 4.9 19.7 1.0 H2 A:GOL414 4.9 57.4 1.0 HB2 A:GLU93 5.0 19.8 1.0

Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca 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:Ca404 b:60.2 occ:1.00 OE2 A:GLU300 2.8 23.8 1.0 CD A:GLU300 3.5 21.4 1.0 OE1 A:GLU300 3.7 21.8 1.0 HG2 A:GLU298 3.7 54.9 1.0 OE2 A:GLU298 3.8 58.2 1.0 HB3 A:GLU298 4.1 36.6 1.0 HB2 A:GLU298 4.4 36.6 1.0 CG A:GLU298 4.4 45.7 1.0 CD A:GLU298 4.5 64.3 1.0 CB A:GLU298 4.5 30.5 1.0 HG3 A:GLU300 4.6 21.8 1.0 CG A:GLU300 4.7 18.2 1.0 HG2 A:GLU300 5.0 21.8 1.0

Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca 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:Ca405 b:83.7 occ:1.00 OE1 A:GLN355 2.1 39.2 0.5 HB2 A:GLN355 3.0 39.5 0.5 H A:GLN355 3.0 37.7 0.5 H A:GLN355 3.0 37.7 0.5 HB2 A:GLN355 3.1 39.2 0.5 CD A:GLN355 3.2 35.1 0.5 N A:GLN355 3.7 31.4 1.0 HA A:SER354 3.8 37.3 1.0 NE2 A:GLN355 3.8 41.9 0.5 CB A:GLN355 3.9 32.6 0.5 HG3 A:GLN355 3.9 46.8 0.5 CB A:GLN355 3.9 32.9 0.5 CG A:GLN355 4.1 39.8 0.5 HE22 A:GLN355 4.1 44.6 0.5 NE2 A:GLN355 4.1 37.2 0.5 CG A:GLN355 4.3 39.0 0.5 HG2 A:GLN355 4.4 47.8 0.5 CA A:GLN355 4.4 31.0 0.5 CA A:GLN355 4.4 31.0 0.5 C A:SER354 4.6 25.1 1.0 CA A:SER354 4.6 31.1 1.0 HB3 A:GLN355 4.6 39.5 0.5 CD A:GLN355 4.6 40.7 0.5 HB3 A:GLN355 4.7 39.2 0.5 HE21 A:GLN355 4.9 44.6 0.5 HG3 A:GLN355 4.9 47.8 0.5

Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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:Ca406 b:29.1 occ:1.00 OE1 A:GLU8 2.1 26.4 1.0 O A:HOH547 2.4 36.2 1.0 CD A:GLU8 3.3 29.5 1.0 HG2 A:GLU8 3.6 39.0 1.0 HG2 A:GLU84 3.7 34.0 1.0 HB2 A:GLU8 3.7 28.4 1.0 HA2 A:GLY85 3.8 23.5 1.0 CG A:GLU8 3.9 32.5 1.0 HG3 A:GLU84 4.1 34.0 1.0 CB A:GLU8 4.2 23.6 1.0 H A:GLY85 4.2 21.5 1.0 OE2 A:GLU8 4.2 22.0 1.0 OE2 A:GLU84 4.3 85.6 1.0 O A:HOH645 4.3 18.0 1.0 CG A:GLU84 4.3 28.3 1.0 HB3 A:GLU8 4.4 28.4 1.0 N A:GLY85 4.5 17.9 1.0 CA A:GLY85 4.5 19.6 1.0 HA3 A:GLY85 4.7 23.5 1.0 HG3 A:GLU8 4.8 39.0 1.0 CD A:GLU84 4.8 67.1 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