Sodium in PDB 5mlo: Crystal Structure of Human Pcna in Complex with ZRANB3 Pip Box Peptide

The structure of Crystal Structure of Human Pcna in Complex with ZRANB3 Pip Box Peptide, PDB code: 5mlo was solved by A.Ariza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.34 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.136, 86.802, 156.679, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 25.9

The binding sites of Sodium atom in the Crystal Structure of Human Pcna in Complex with ZRANB3 Pip Box Peptide (pdb code 5mlo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Human Pcna in Complex with ZRANB3 Pip Box Peptide, PDB code: 5mlo:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Human Pcna in Complex with ZRANB3 Pip Box Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Pcna in Complex with ZRANB3 Pip Box Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:48.7 occ:1.00 O A:ALA105 2.2 55.3 1.0 O A:HOH510 2.3 40.2 1.0 O A:HOH435 2.3 50.8 1.0 O A:GLN108 2.4 44.2 1.0 O A:HOH464 2.5 41.5 1.0 C A:ALA105 3.4 52.2 1.0 C A:GLN108 3.6 49.1 1.0 O A:PRO106 4.0 60.6 1.0 O A:HOH469 4.0 55.8 1.0 CA A:PRO106 4.0 62.2 1.0 C A:PRO106 4.0 61.8 1.0 N A:GLN108 4.1 56.5 1.0 N A:PRO106 4.2 60.0 1.0 N A:ALA105 4.4 43.8 1.0 CA A:ALA105 4.4 47.5 1.0 N A:GLU109 4.5 48.1 1.0 CA A:GLU109 4.5 48.2 1.0 CA A:GLN108 4.5 52.2 1.0 O A:LYS110 4.7 37.1 1.0 N A:ASN107 4.7 60.8 1.0 N A:LYS110 4.7 40.0 1.0 CB A:ALA105 4.8 44.6 1.0 O A:HOH473 4.8 36.3 1.0 OE1 A:GLU109 4.9 65.4 1.0 C A:GLU104 5.0 41.9 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Human Pcna in Complex with ZRANB3 Pip Box Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Pcna in Complex with ZRANB3 Pip Box Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:32.5 occ:1.00 OE1 A:GLN184 2.3 31.0 1.0 O A:LYS164 2.4 42.2 1.0 CD A:GLN184 3.2 31.1 1.0 NE2 A:GLN184 3.5 30.9 1.0 C A:LYS164 3.6 42.6 1.0 CA A:ASP165 4.1 43.0 1.0 N A:ASP165 4.3 41.5 1.0 CG A:GLN184 4.6 32.3 1.0 CA A:LYS164 4.7 44.4 1.0 CG A:LYS164 4.8 50.2 1.0 C A:ASP165 4.9 42.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Human Pcna in Complex with ZRANB3 Pip Box Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human Pcna in Complex with ZRANB3 Pip Box Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:81.6 occ:1.00 O C:HOH515 2.4 69.2 1.0 O C:GLN108 2.9 65.9 1.0 C C:GLN108 3.6 68.4 1.0 O C:PRO106 3.7 82.5 1.0 O C:ALA105 3.7 52.0 1.0 O C:HOH530 4.0 52.4 1.0 N C:GLN108 4.1 77.7 1.0 O C:HOH431 4.1 37.4 1.0 N C:GLU109 4.2 65.2 1.0 CA C:GLU109 4.2 54.6 1.0 C C:PRO106 4.3 78.2 1.0 CA C:GLN108 4.5 71.9 1.0 CG C:GLU109 4.6 66.8 1.0 CA C:PRO106 4.8 75.9 1.0 C C:ALA105 4.9 51.3 1.0 N C:ASN107 4.9 74.5 1.0 C C:ASN107 5.0 87.9 1.0 CB C:GLU109 5.0 61.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Human Pcna in Complex with ZRANB3 Pip Box Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human Pcna in Complex with ZRANB3 Pip Box Peptide within 5.0Å range: probe atom residue distance (Å) B Occ E:Na301 b:63.6 occ:1.00 O E:ALA105 2.4 61.9 1.0 O E:GLN108 2.8 66.9 1.0 O E:LYS110 3.4 35.7 1.0 C E:ALA105 3.5 59.3 1.0 N E:ALA105 3.5 49.5 1.0 N E:LYS110 3.9 43.0 1.0 CB E:GLU104 4.0 46.2 1.0 C E:GLN108 4.0 62.8 1.0 CA E:ALA105 4.0 53.5 1.0 C E:GLU104 4.0 46.2 1.0 CA E:GLU104 4.1 45.2 1.0 CA E:GLU109 4.2 49.6 1.0 C E:LYS110 4.2 37.2 1.0 CG2 E:VAL111 4.3 37.5 1.0 CB E:ALA105 4.4 52.9 1.0 C E:GLU109 4.5 46.0 1.0 N E:PRO106 4.6 64.9 1.0 N E:GLU109 4.6 53.9 1.0 O E:HOH431 4.6 72.5 1.0 CA E:LYS110 4.7 38.8 1.0 CA E:PRO106 4.8 67.1 1.0 OE1 E:GLU109 4.8 60.7 1.0 CG E:GLU104 4.8 48.7 1.0 O E:GLU104 4.8 45.8 1.0

M.Sebesta, C.D.O.Cooper, A.Ariza, C.J.Carnie, D.Ahel. Structural Insights Into the Function of ZRANB3 in Replication Stress Response. Nat Commun V. 8 15847 2017.
ISSN: ESSN 2041-1723
PubMed: 28621305
DOI: 10.1038/NCOMMS15847