Sodium in PDB 8a1h: Bacterial 6-4 Photolyase From Vibrio Cholerase

The structure of Bacterial 6-4 Photolyase From Vibrio Cholerase, PDB code: 8a1h was solved by L.-O.Essen, H.J.Emmerich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.59 / 1.65
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	199.687, 199.687, 76.996, 90, 90, 120
R / Rfree (%)	11.9 / 13.6

The structure of Bacterial 6-4 Photolyase From Vibrio Cholerase also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Iron	(Fe)	4 atoms

The binding sites of Sodium atom in the Bacterial 6-4 Photolyase From Vibrio Cholerase (pdb code 8a1h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Bacterial 6-4 Photolyase From Vibrio Cholerase, PDB code: 8a1h:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Bacterial 6-4 Photolyase From Vibrio Cholerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bacterial 6-4 Photolyase From Vibrio Cholerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na623 b:27.2 occ:0.30 O A:HOH1103 1.8 25.8 1.0 O A:HOH914 1.9 40.1 1.0 OE1 A:GLN333 2.7 20.7 1.0 H61A A:FAD601 2.9 22.2 1.0 NE2 A:HIS393 3.1 17.5 1.0 N7A A:FAD601 3.1 15.2 1.0 HE2 A:HIS393 3.2 21.0 1.0 O A:HOH1206 3.2 55.2 1.0 CD2 A:HIS393 3.3 19.3 1.0 CE1 A:HIS393 3.3 16.2 1.0 O A:HOH1092 3.4 20.8 0.5 N6A A:FAD601 3.6 18.5 1.0 O A:HOH1044 3.6 39.6 1.0 ND1 A:HIS393 3.6 16.6 1.0 CG A:HIS393 3.6 15.4 1.0 HD2 A:HIS393 3.7 23.1 1.0 HE1 A:HIS393 3.7 19.5 1.0 CD A:GLN333 3.7 22.7 1.0 C5A A:FAD601 3.9 13.8 1.0 HD1 A:TRP337 4.1 22.9 1.0 C8A A:FAD601 4.1 16.8 1.0 H62A A:FAD601 4.2 22.2 1.0 C6A A:FAD601 4.2 14.8 1.0 H8A A:FAD601 4.2 20.2 1.0 CD1 A:TRP337 4.2 19.1 1.0 HG3 A:GLN333 4.3 24.0 1.0 HB3 A:GLN333 4.4 19.8 1.0 CG A:GLN333 4.5 19.9 1.0 HB2 A:HIS393 4.5 20.5 1.0 H2' A:FAD601 4.6 17.0 1.0 O A:HOH937 4.6 37.5 1.0 CG A:TRP337 4.6 17.1 1.0 HE22 A:GLN333 4.6 30.7 1.0 HB2 A:TRP337 4.6 19.2 1.0 NE2 A:GLN333 4.6 25.5 1.0 CB A:HIS393 4.6 17.1 1.0 HE1 A:MET437 4.6 27.0 1.0 HB3 A:HIS393 4.7 20.5 1.0 O A:HOH916 4.7 24.4 1.0 NE1 A:TRP337 4.8 21.3 1.0 HA A:GLN333 4.8 17.5 1.0 HB3 A:TRP337 4.8 19.2 1.0 CB A:TRP337 4.9 16.0 1.0 CB A:GLN333 4.9 16.5 1.0 H1'2 A:FAD601 4.9 16.9 1.0 HE1 A:TRP337 5.0 25.6 1.0

Sodium binding site 2 out of 6 in the Bacterial 6-4 Photolyase From Vibrio Cholerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bacterial 6-4 Photolyase From Vibrio Cholerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na624 b:65.8 occ:0.97 O A:HOH989 2.1 45.9 1.0 O A:HOH727 2.1 47.3 1.0 O A:HOH754 2.2 62.3 1.0 O A:HOH1023 3.3 40.0 1.0 HZ2 A:TRP337 3.4 28.4 1.0 HH2 A:TRP337 3.6 25.8 1.0 HA A:ALA447 3.8 36.4 1.0 O A:ALA447 3.9 34.1 1.0 CZ2 A:TRP337 4.1 23.6 1.0 CH2 A:TRP337 4.2 21.5 1.0 HB3 A:MET171 4.2 28.2 0.7 OH A:TYR451 4.2 45.4 1.0 HB1 A:ALA447 4.2 39.4 1.0 O2 A:SO4616 4.2 47.2 0.5 HB A:THR448 4.3 48.2 1.0 O A:HOH924 4.3 26.0 1.0 HB3 A:MET171 4.4 27.8 0.3 OG1 A:THR448 4.4 35.6 1.0 C A:ALA447 4.4 30.4 1.0 HH A:TYR451 4.4 54.5 1.0 CA A:ALA447 4.5 30.3 1.0 O A:HOH725 4.7 51.4 1.0 CB A:ALA447 4.8 32.8 1.0 CB A:THR448 4.9 40.1 1.0 HB2 A:MET171 4.9 27.8 0.3

Sodium binding site 3 out of 6 in the Bacterial 6-4 Photolyase From Vibrio Cholerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bacterial 6-4 Photolyase From Vibrio Cholerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na625 b:57.0 occ:0.78 O A:HOH825 1.9 52.3 1.0 OE1 A:GLN353 2.3 40.5 1.0 O A:HOH1113 2.7 39.3 1.0 OE2 A:GLU427 2.8 23.9 1.0 OE1 A:GLU427 3.5 18.1 1.0 CD A:GLN353 3.5 56.7 1.0 CD A:GLU427 3.5 20.7 1.0 HE1 A:MET349 3.6 25.6 1.0 O A:HOH1297 3.6 57.2 1.0 O A:HOH1016 3.6 32.2 1.0 O A:HOH791 3.6 23.9 1.0 HB2 A:GLN353 4.0 29.4 1.0 HB3 A:GLN353 4.2 29.4 1.0 HE22 A:GLN353 4.3 60.6 1.0 NE2 A:GLN353 4.4 50.5 1.0 CE A:MET349 4.4 21.4 1.0 CB A:GLN353 4.4 24.4 1.0 HE2 A:MET349 4.5 25.6 1.0 CG A:GLN353 4.5 36.9 1.0 HG3 A:GLN353 4.7 44.3 1.0 HD22 A:LEU431 4.8 23.1 1.0 O A:HOH870 4.8 24.1 1.0 O A:HOH957 4.8 32.8 1.0 O A:HOH1120 4.8 56.2 1.0 HE3 A:MET349 4.9 25.6 1.0 HB2 A:ARG129 4.9 27.1 1.0 CG A:GLU427 4.9 18.0 1.0 O A:HOH1018 4.9 24.5 1.0

Sodium binding site 4 out of 6 in the Bacterial 6-4 Photolyase From Vibrio Cholerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Bacterial 6-4 Photolyase From Vibrio Cholerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na626 b:64.2 occ:0.86 O A:HOH966 2.0 33.3 1.0 O A:HOH1058 2.5 38.9 1.0 OG A:SER84 2.7 21.0 0.7 HB3 A:SER84 2.9 24.1 0.3 HG A:SER84 3.0 25.2 0.7 HA A:SER84 3.5 21.0 1.0 O A:HOH745 3.6 23.6 1.0 CB A:SER84 3.7 20.1 0.3 O A:HIS88 3.7 24.7 1.0 CB A:SER84 3.7 20.0 0.7 HB2 A:SER84 3.7 24.0 0.7 HG A:SER84 3.9 25.2 0.3 OG A:SER84 3.9 21.0 0.3 CA A:SER84 4.0 17.5 0.3 CA A:SER84 4.0 17.4 0.7 O A:SER84 4.0 19.1 1.0 HA A:HIS89 4.1 24.6 1.0 O A:HOH1205 4.1 62.3 1.0 C A:SER84 4.4 17.8 1.0 HG12 A:VAL90 4.4 25.1 0.6 H A:VAL90 4.4 24.7 1.0 HB2 A:SER84 4.5 24.1 0.3 HB3 A:SER84 4.5 24.0 0.7 O A:HOH1157 4.6 55.6 1.0 C A:HIS88 4.7 24.0 1.0 CA A:HIS89 5.0 20.5 1.0

Sodium binding site 5 out of 6 in the Bacterial 6-4 Photolyase From Vibrio Cholerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Bacterial 6-4 Photolyase From Vibrio Cholerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na627 b:66.4 occ:0.72 O A:HOH1249 2.0 44.4 1.0 O A:HOH854 2.1 37.8 1.0 O A:HOH804 2.7 58.3 1.0 OE1 A:GLU60 2.7 37.6 1.0 O A:HOH710 2.9 41.6 1.0 HB3 A:GLN57 3.5 28.3 1.0 CD A:GLU60 3.7 38.9 1.0 HA A:GLN57 3.7 27.7 1.0 OE2 A:GLU60 3.9 41.0 1.0 O A:ASN102 4.0 31.6 1.0 HB3 A:ASP103 4.0 34.4 1.0 CB A:GLN57 4.3 23.5 1.0 O A:HOH1123 4.4 56.1 1.0 CA A:GLN57 4.4 23.1 1.0 HB2 A:GLN57 4.4 28.3 1.0 N A:GLN57 4.6 22.0 1.0 HB3 A:HIS56 4.6 29.7 1.0 O A:HOH985 4.7 25.5 1.0 HA A:ASP103 4.7 35.7 1.0 O A:HOH1257 4.7 56.5 1.0 H A:GLN57 4.7 26.4 1.0 CB A:ASP103 4.8 28.6 1.0 HB2 A:ASP103 4.8 34.4 1.0 HB2 A:HIS56 4.9 29.7 1.0 HB2 A:GLU60 4.9 30.8 1.0

Sodium binding site 6 out of 6 in the Bacterial 6-4 Photolyase From Vibrio Cholerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Bacterial 6-4 Photolyase From Vibrio Cholerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na628 b:67.5 occ:0.62 CL A:CL629 2.1 60.6 1.0 HO1 A:GOL609 2.1 59.5 0.8 O1 A:GOL609 2.7 49.5 0.8 HD2 A:LYS208 3.1 42.7 1.0 H11 A:GOL609 3.2 55.8 0.8 C1 A:GOL609 3.4 46.5 0.8 H12 A:GOL609 3.5 55.8 0.8 HB3 A:LYS208 3.8 27.4 1.0 CD A:LYS208 4.0 35.6 1.0 H A:SER209 4.1 25.1 1.0 HD3 A:LYS208 4.3 42.7 1.0 HZ3 A:LYS208 4.4 106.7 1.0 HA A:LYS208 4.5 26.9 1.0 CB A:LYS208 4.6 22.8 1.0 CG A:LYS208 4.8 26.2 1.0 HG3 A:LYS208 4.8 31.5 1.0 C2 A:GOL609 4.8 34.1 0.8 HE2 A:LYS208 4.9 80.0 1.0 CE A:LYS208 4.9 66.7 1.0 N A:SER209 4.9 20.9 1.0

H.J.Emmerich, L.Schneider, L.O.Essen. Structural and Functional Analysis of A Prokaryotic (6-4) Photolyase From the Aquatic Pathogen Vibrio Cholerae. Photochem.Photobiol. 2023.
ISSN: ISSN 0031-8655
PubMed: 36692077
DOI: 10.1111/PHP.13783