Sodium in PDB 7o1f: Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide

The structure of Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide, PDB code: 7o1f was solved by M.A.Alphey, S.Macneill, D.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.39 / 2.45
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	71.891, 84.711, 84.89, 60.94, 89.6, 81.22
R / Rfree (%)	22 / 26.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Sodium atom in the Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide (pdb code 7o1f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 18 binding sites of Sodium where determined in the Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide, PDB code: 7o1f:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 18 in the Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:39.3 occ:1.00 O A:LEU241 2.5 38.9 1.0 O A:GLY243 2.6 45.3 1.0 C A:LEU241 3.7 39.2 1.0 C A:GLY243 3.8 45.3 1.0 CB A:SER240 4.2 45.2 1.0 N A:LEU241 4.2 37.0 1.0 OG A:SER240 4.3 52.3 1.0 N A:GLY243 4.3 42.6 1.0 C A:GLY242 4.4 43.3 1.0 N A:GLY242 4.6 40.7 1.0 C A:SER240 4.6 37.0 1.0 CA A:GLY243 4.6 44.5 1.0 CA A:LEU241 4.6 40.1 1.0 CA A:GLY242 4.6 42.5 1.0 N A:SER244 4.9 45.0 1.0 O A:GLY242 4.9 47.8 1.0 CA A:SER240 4.9 40.9 1.0 O A:SER245 4.9 37.0 1.0

Sodium binding site 2 out of 18 in the Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:49.2 occ:1.00 OG A:SER240 2.4 52.3 1.0 O A:SER240 2.5 40.1 1.0 OG A:SER222 2.5 52.3 1.0 O A:HOH404 3.0 48.9 1.0 C A:SER240 3.5 37.0 1.0 OG1 A:THR224 3.6 41.1 1.0 CB A:SER240 3.7 45.2 1.0 CB A:SER222 3.8 45.6 1.0 CA A:SER240 4.0 40.9 1.0 N A:SER240 4.1 37.1 1.0 O A:THR224 4.2 40.2 1.0 O A:HOH421 4.5 47.7 1.0 N A:LEU241 4.5 37.0 1.0 N A:THR224 4.6 35.5 1.0 CA A:SER222 4.6 44.2 1.0 C A:THR224 4.8 36.5 1.0 CB A:THR224 4.8 38.4 1.0 N A:ASN223 4.9 42.1 1.0 CA A:THR224 5.0 37.4 1.0

Sodium binding site 3 out of 18 in the Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:66.4 occ:1.00 O A:GLN38 2.6 43.1 1.0 C A:GLN38 3.8 41.3 1.0 CB A:GLN123 4.0 72.3 1.0 CB A:ASN27 4.1 40.9 1.0 CA A:GLN123 4.1 72.5 1.0 N A:GLU124 4.3 71.6 1.0 O A:ASN27 4.3 49.3 1.0 N A:GLN38 4.3 39.9 1.0 OD2 A:ASP29 4.4 59.6 1.0 N A:ASN27 4.4 42.8 1.0 ND2 A:ASN27 4.4 43.0 1.0 CA A:GLN38 4.5 40.8 1.0 C A:GLN123 4.7 69.7 1.0 CA A:ASN27 4.7 41.8 1.0 CB A:GLN38 4.7 43.3 1.0 N A:ALA39 4.7 40.7 1.0 CG A:ASN27 4.8 45.3 1.0 N A:HIS125 4.9 73.7 1.0 O A:HOH407 4.9 53.1 1.0 CA A:ALA39 4.9 40.1 1.0 C A:ASN27 5.0 42.5 1.0

Sodium binding site 4 out of 18 in the Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:50.3 occ:1.00 O B:GLY243 2.5 46.6 1.0 O B:LEU241 2.8 36.3 1.0 C B:GLY243 3.8 43.7 1.0 C B:LEU241 4.0 38.1 1.0 CB B:SER240 4.2 37.0 1.0 N B:GLY243 4.4 43.6 1.0 N B:LEU241 4.5 35.5 1.0 C B:GLY242 4.6 41.6 1.0 CA B:GLY243 4.6 45.2 1.0 N B:SER244 4.7 41.2 1.0 C B:SER240 4.8 34.5 1.0 CA B:SER244 4.8 41.5 1.0 OG B:SER240 4.9 43.2 1.0 N B:GLY242 4.9 39.9 1.0 CA B:LEU241 4.9 36.3 1.0 CA B:GLY242 4.9 41.8 1.0 O B:SER245 5.0 30.8 1.0 CA B:SER240 5.0 35.2 1.0

Sodium binding site 5 out of 18 in the Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:45.1 occ:1.00 O B:CYS62 2.4 60.4 1.0 OD1 B:ASP32 2.5 49.4 1.0 OD2 B:ASP32 2.8 53.3 1.0 CG B:ASP32 2.9 49.2 1.0 C B:CYS62 3.7 57.9 1.0 CB B:ASP32 4.3 46.9 1.0 OD1 B:ASP63 4.5 66.7 1.0 N B:ASP63 4.6 56.3 1.0 N B:CYS62 4.6 61.0 1.0 CA B:CYS62 4.6 57.5 1.0 CA B:ASP63 4.7 59.3 1.0 CB B:CYS62 4.9 57.3 1.0

Sodium binding site 6 out of 18 in the Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:37.6 occ:1.00 O C:HOH417 2.1 45.8 1.0 O C:HOH422 2.1 38.7 1.0 O C:GLY243 2.3 42.8 1.0 O C:LEU241 2.4 46.3 1.0 O C:HOH423 2.7 47.0 1.0 C C:GLY243 3.5 41.1 1.0 C C:LEU241 3.6 45.6 1.0 N C:LEU241 4.1 53.4 1.0 CB C:SER240 4.1 58.6 1.0 N C:GLY243 4.2 41.5 1.0 OG C:SER240 4.3 78.3 1.0 C C:GLY242 4.3 42.1 1.0 N C:SER244 4.4 42.5 1.0 CA C:GLY243 4.4 41.8 1.0 O C:SER245 4.4 38.4 1.0 CA C:SER244 4.4 42.4 1.0 C C:SER240 4.5 54.3 1.0 CA C:LEU241 4.5 48.8 1.0 N C:GLY242 4.6 43.1 1.0 O C:GLY242 4.6 39.6 1.0 CA C:SER240 4.7 54.0 1.0 CA C:GLY242 4.7 43.9 1.0

Sodium binding site 7 out of 18 in the Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:59.2 occ:1.00 O C:SER240 2.7 49.5 1.0 OG C:SER222 3.1 46.7 1.0 O C:HOH423 3.4 47.0 1.0 OG C:SER240 3.5 78.3 1.0 C C:SER240 3.8 54.3 1.0 CB C:SER222 4.1 41.4 1.0 CG F:PRO191 4.3 48.6 1.0 CA C:SER222 4.4 42.3 1.0 N C:LEU241 4.5 53.4 1.0 CA C:LEU241 4.6 48.8 1.0 CB C:SER240 4.6 58.6 1.0 N C:ASN223 4.6 45.6 1.0 OG1 C:THR224 4.7 47.1 1.0 CA C:SER240 4.7 54.0 1.0 C C:LEU241 4.8 45.6 1.0 C C:SER222 5.0 43.5 1.0

Sodium binding site 8 out of 18 in the Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:41.6 occ:1.00 O C:CYS62 2.3 59.2 1.0 OD1 C:ASP32 2.6 55.7 1.0 OD2 C:ASP32 2.7 62.5 1.0 CG C:ASP32 3.0 56.2 1.0 C C:CYS62 3.5 55.7 1.0 OD1 C:ASP63 4.3 61.9 1.0 CA C:ASP63 4.3 60.5 1.0 N C:ASP63 4.4 57.6 1.0 CB C:ASP32 4.5 53.6 1.0 CA C:CYS62 4.6 54.4 1.0 N C:CYS62 4.7 51.3 1.0 CB C:CYS62 4.9 55.4 1.0 C C:ASP63 5.0 62.3 1.0

Sodium binding site 9 out of 18 in the Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:42.8 occ:1.00 O D:HOH434 2.3 46.4 1.0 O D:GLY243 2.3 45.1 1.0 O D:LEU241 2.6 42.8 1.0 C D:GLY243 3.6 45.0 1.0 C D:LEU241 3.8 42.6 1.0 CB D:SER240 4.2 44.9 1.0 N D:GLY243 4.3 45.1 1.0 OG D:SER240 4.3 58.4 1.0 N D:LEU241 4.3 42.5 1.0 C D:GLY242 4.4 43.2 1.0 CA D:GLY243 4.4 46.4 1.0 N D:SER244 4.5 43.4 1.0 CA D:SER244 4.6 42.3 1.0 C D:SER240 4.6 43.0 1.0 CA D:LEU241 4.7 44.0 1.0 O D:SER245 4.7 33.0 1.0 N D:GLY242 4.7 41.8 1.0 CA D:GLY242 4.8 44.6 1.0 O D:GLY242 4.8 42.0 1.0 CA D:SER240 4.9 43.7 1.0

Sodium binding site 10 out of 18 in the Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Pcna From Chaetomium Thermophilum in Complex with POLD4 Pip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:48.9 occ:1.00 OG D:SER222 2.6 32.9 1.0 O D:SER240 2.8 42.3 1.0 OG D:SER240 2.9 58.4 1.0 OG1 D:THR224 3.2 36.8 1.0 C D:SER240 3.8 43.0 1.0 CB D:SER222 4.0 30.1 1.0 O D:THR224 4.0 29.1 1.0 CB D:SER240 4.1 44.9 1.0 N D:THR224 4.2 30.9 1.0 CA D:SER240 4.3 43.7 1.0 N D:SER240 4.4 39.8 1.0 CB D:THR224 4.4 33.3 1.0 C D:THR224 4.5 29.4 1.0 CA D:THR224 4.6 31.2 1.0 CA D:SER222 4.7 30.3 1.0 N D:ASN223 4.7 32.4 1.0 CG2 D:THR224 4.9 35.0 1.0 N D:LEU241 4.9 42.5 1.0 C D:SER222 5.0 31.7 1.0

D.Yang, M.S.Alphey, S.A.Macneill. Non-Canonical Binding of the Chaetomium Thermophilum POLD4 N-Terminal Pip Motif to Pcna Involves Q-Pocket and Compact 2-Fork Plug Interactions But No 3 10 Helix. Febs J. 2022.
ISSN: ISSN 1742-464X
PubMed: 35942639
DOI: 10.1111/FEBS.16590