Sodium 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:

Calcium	(Ca)	7 atoms
Magnesium	(Mg)	4 atoms

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

Sodium binding site 1 out of 5 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na416 b:37.6 occ:1.00 O A:HOH548 2.6 37.3 1.0 O A:GLY228 2.7 34.0 1.0 O A:PHE230 2.8 26.2 1.0 O A:HOH808 2.8 40.4 1.0 HG13 A:ILE231 3.0 34.7 1.0 HG12 A:ILE231 3.1 34.7 1.0 HB3 A:HIS226 3.2 34.4 1.0 H A:PHE230 3.2 29.7 1.0 HA A:ASP229 3.4 36.4 1.0 N A:PHE230 3.5 24.7 1.0 C A:PHE230 3.5 24.5 1.0 CG1 A:ILE231 3.5 28.9 1.0 H A:VAL227 3.6 31.0 1.0 C A:GLY228 3.6 32.8 1.0 HD1 A:HIS226 3.7 41.9 1.0 HA A:HIS226 3.8 30.9 1.0 HD11 A:ILE231 3.8 42.4 1.0 O A:HOH795 3.8 48.4 1.0 C A:ASP229 3.8 27.2 1.0 CA A:ASP229 4.0 30.3 1.0 CB A:HIS226 4.0 28.6 1.0 CA A:PHE230 4.1 24.3 1.0 N A:VAL227 4.1 25.8 1.0 N A:ASP229 4.2 29.7 1.0 CD1 A:ILE231 4.2 35.3 1.0 CA A:HIS226 4.3 25.7 1.0 O A:VAL227 4.3 29.5 1.0 N A:ILE231 4.3 25.1 1.0 ND1 A:HIS226 4.3 34.9 1.0 C A:VAL227 4.4 32.0 1.0 O A:HOH624 4.5 43.5 1.0 HA A:ILE231 4.5 27.3 1.0 C A:HIS226 4.5 26.8 1.0 HA A:PHE230 4.6 29.2 1.0 N A:GLY228 4.6 31.0 1.0 O A:ASP229 4.6 26.5 1.0 CG A:HIS226 4.7 32.8 1.0 CA A:GLY228 4.7 34.7 1.0 HB2 A:HIS226 4.7 34.4 1.0 CA A:ILE231 4.7 22.8 1.0 HD13 A:ILE231 4.8 42.4 1.0 CB A:ILE231 4.8 29.3 1.0 O A:HOH824 4.8 46.5 1.0 HD12 A:ILE231 4.9 42.4 1.0 H A:ILE231 4.9 30.1 1.0 CA A:VAL227 4.9 29.9 1.0 H A:GLY228 4.9 37.2 1.0 HG3 A:ARG56 4.9 35.1 0.4

Sodium binding site 2 out of 5 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na417 b:45.3 occ:1.00 O A:HOH644 2.3 38.3 1.0 O A:HOH778 2.3 48.9 1.0 O A:HOH653 2.3 42.7 1.0 OG1 A:THR45 3.2 25.2 1.0 HG21 A:VAL54 3.4 31.5 1.0 HG21 A:THR45 3.4 29.3 1.0 O A:HOH701 3.6 38.9 1.0 HG1 A:THR45 3.6 30.3 1.0 O A:ACT411 3.7 45.8 1.0 HG22 A:VAL54 3.7 31.5 1.0 HD23 A:LEU34 3.8 31.5 1.0 HG11 A:VAL54 3.8 31.1 1.0 CA A:CA407 3.8 37.3 1.0 CG2 A:VAL54 4.0 26.2 1.0 OE1 A:GLN36 4.0 33.6 1.0 CB A:THR45 4.2 20.6 1.0 CG2 A:THR45 4.2 24.4 1.0 HG13 A:VAL54 4.2 31.1 1.0 OE2 A:GLU52 4.3 35.3 1.0 C A:ACT411 4.3 49.8 1.0 O A:HOH603 4.4 23.4 1.0 HB A:THR45 4.4 24.8 1.0 CG1 A:VAL54 4.4 25.9 1.0 HH22 A:ARG56 4.5 26.6 0.4 HG23 A:THR45 4.5 29.3 1.0 HD21 A:LEU34 4.6 31.5 1.0 CD2 A:LEU34 4.6 26.2 1.0 HE22 A:GLN36 4.6 42.0 1.0 OXT A:ACT411 4.6 47.7 1.0 HG23 A:VAL54 4.7 31.5 1.0 CD A:GLU52 4.7 35.1 1.0 OD1 A:ASN118 4.8 37.5 1.0 OE1 A:GLU52 4.9 33.1 1.0 CB A:VAL54 4.9 23.0 1.0 CD A:GLN36 4.9 31.7 1.0 HG22 A:THR45 5.0 29.3 1.0 HD22 A:LEU34 5.0 31.5 1.0

Sodium binding site 3 out of 5 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na418 b:43.6 occ:1.00 O A:HOH816 2.3 37.6 1.0 O A:HOH569 2.5 46.6 1.0 O A:HOH684 2.9 29.1 1.0 HA A:SER101 2.9 23.8 1.0 O A:GLU87 3.2 21.6 1.0 HB2 A:ALA89 3.3 28.4 1.0 O A:ARG100 3.4 20.8 1.0 HB3 A:GLU87 3.5 34.3 1.0 H A:ALA89 3.6 25.1 1.0 HB3 A:ALA89 3.7 28.4 1.0 H A:GLY102 3.7 27.0 1.0 CA A:SER101 3.8 19.8 1.0 O A:HOH625 3.9 39.4 1.0 C A:GLU87 3.9 23.6 1.0 CB A:ALA89 3.9 23.7 1.0 N A:ALA89 4.0 20.9 1.0 HG2 A:GLU87 4.0 44.9 1.0 C A:ARG100 4.1 18.7 1.0 HA A:ILE88 4.1 24.1 1.0 HG A:SER101 4.2 28.0 1.0 N A:SER101 4.3 19.4 1.0 CB A:GLU87 4.3 28.6 1.0 OE1 A:GLU87 4.3 41.8 1.0 HG23 A:THR4 4.4 37.9 1.0 N A:ILE88 4.4 21.8 1.0 N A:GLY102 4.4 22.4 1.0 C A:ILE88 4.5 22.8 1.0 CG A:GLU87 4.5 37.4 1.0 CA A:ILE88 4.6 20.0 1.0 HB2 A:SER101 4.6 25.7 1.0 CA A:ALA89 4.6 20.4 1.0 HB2 A:ARG100 4.6 24.6 1.0 HB3 A:ARG100 4.6 24.6 1.0 C A:SER101 4.7 21.0 1.0 CB A:SER101 4.7 21.4 1.0 CA A:GLU87 4.7 22.9 1.0 HB1 A:ALA89 4.7 28.4 1.0 OG A:SER101 4.8 23.3 1.0 HG21 A:THR4 4.8 37.9 1.0 CD A:GLU87 5.0 46.4 1.0 H A:ILE88 5.0 26.2 1.0 CB A:ARG100 5.0 20.4 1.0 O A:HOH725 5.0 27.7 1.0

Sodium binding site 4 out of 5 in the Dna-Polymerase Sliding Clamp (Dnan) From Escherichia Coli in Complex with Griselimycin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na419 b:57.5 occ:1.00 O A:HOH784 2.2 44.4 1.0 O A:HOH592 2.4 21.6 1.0 O A:ASN295 2.6 21.6 1.0 O A:HOH696 2.7 25.6 1.0 OD1 A:ASN295 3.1 40.0 1.0 O A:HOH779 3.2 21.8 1.0 H A:ASN295 3.3 25.6 1.0 C A:ASN295 3.5 22.9 1.0 HB2 A:ASN275 3.7 24.7 1.0 H A:ASN275 3.8 25.3 1.0 O A:HOH747 3.9 25.9 1.0 CG A:ASN295 4.0 36.6 1.0 HA A:ASN296 4.0 28.4 1.0 N A:ASN295 4.0 21.3 1.0 O A:GLY280 4.2 21.7 1.0 CA A:ASN295 4.3 22.5 1.0 N A:ASN296 4.5 22.5 1.0 HA A:SER274 4.5 22.8 1.0 CB A:ASN275 4.5 20.6 1.0 N A:ASN275 4.5 21.1 1.0 CB A:ASN295 4.6 29.4 1.0 HB3 A:ASN275 4.6 24.7 1.0 CA A:ASN296 4.7 23.6 1.0 HD22 A:ASN275 4.8 32.1 1.0 H A:GLY280 4.8 28.3 1.0 HB2 A:ASN295 4.8 35.3 1.0 ND2 A:ASN295 4.9 39.7 1.0 HD21 A:ASN295 4.9 47.7 1.0 HA3 A:GLY280 4.9 27.6 1.0 HA A:ALA294 5.0 26.0 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na420 b:44.5 occ:1.00 H A:ARG0 2.1 45.0 1.0 O A:HOH565 2.7 27.4 1.0 O A:HOH844 2.9 33.5 1.0 N A:ARG0 3.0 37.5 1.0 O A:HOH623 3.0 36.9 1.0 HB2 A:ARG0 3.0 39.8 1.0 HA2 A:GLY-1 3.3 65.0 1.0 O A:HOH777 3.3 38.0 1.0 O A:ARG0 3.5 28.8 1.0 O A:HOH631 3.6 29.6 1.0 CA A:ARG0 3.7 33.3 1.0 CB A:ARG0 3.7 33.1 1.0 HG3 A:ARG0 3.7 47.2 1.0 C A:ARG0 3.9 28.5 1.0 C A:GLY-1 3.9 46.6 1.0 CA A:GLY-1 4.0 54.2 1.0 CG A:ARG0 4.2 39.4 1.0 HA3 A:GLY-1 4.3 65.0 1.0 O A:HOH639 4.4 28.9 1.0 HB2 A:LYS2 4.5 32.9 1.0 HD3 A:ARG0 4.5 40.1 1.0 HB3 A:ARG0 4.5 39.8 1.0 HA A:ARG0 4.6 40.0 1.0 H A:LEU92 4.6 26.2 1.0 HB2 A:GLN91 4.6 28.3 1.0 O A:LEU92 4.7 24.4 1.0 HD2 A:LYS2 4.7 50.0 1.0 CD A:ARG0 4.9 33.4 1.0 O A:MET1 5.0 25.0 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