Sodium in PDB 7vuk: Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp.

The structure of Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp., PDB code: 7vuk was solved by K.Fukui, T.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.37 / 3.38
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	133.654, 133.654, 197.461, 90, 90, 90
R / Rfree (%)	26.7 / 27.2

The structure of Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp. also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Magnesium	(Mg)	5 atoms

The binding sites of Sodium atom in the Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp. (pdb code 7vuk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp., PDB code: 7vuk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp.


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 the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:38.4 occ:1.00 O A:ALA51 3.5 65.3 1.0 CB A:ALA267 4.0 64.0 1.0 CB A:PRO55 4.0 76.7 1.0 O A:GLN264 4.2 61.8 1.0 CA A:PRO55 4.5 75.8 1.0 CG A:PRO55 4.5 80.8 1.0 CG A:GLN264 4.6 63.0 1.0 C A:ALA51 4.6 66.0 1.0 N A:ALA268 4.7 59.4 1.0 CD2 A:LEU52 4.8 54.4 1.0 C A:ALA267 4.9 62.5 1.0 CA A:LEU52 5.0 57.0 1.0 CA A:GLN264 5.0 62.1 1.0

Sodium binding site 2 out of 8 in the Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp.


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 the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:37.2 occ:1.00 OD1 A:ASP272 3.7 64.4 1.0 OD2 A:ASP272 4.0 70.8 1.0 CB A:ALA268 4.0 61.6 1.0 CG A:ASP272 4.2 67.9 1.0 CA A:ALA268 4.7 58.2 1.0 O A:ALA268 5.0 55.8 1.0

Sodium binding site 3 out of 8 in the Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp.


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 the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:26.1 occ:1.00 OE1 A:GLN410 3.5 76.9 1.0 CB A:ALA406 4.2 46.3 1.0 N A:ALA407 4.3 58.2 1.0 CA A:ALA407 4.3 58.7 1.0 CB A:PRO431 4.4 40.6 1.0 CB A:ALA407 4.5 65.5 1.0 CD A:GLN410 4.6 72.3 1.0 C A:ALA406 4.7 49.9 1.0

Sodium binding site 4 out of 8 in the Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp.


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 the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:31.3 occ:1.00 ND1 A:HIS428 3.9 55.9 1.0 NZ A:LYS433 4.2 47.1 1.0 OH A:TYR469 4.2 70.4 1.0 C A:GLY315 4.3 67.5 1.0 O A:GLY315 4.3 72.0 1.0 CE1 A:HIS428 4.6 61.0 1.0 CA A:GLY315 4.6 62.9 1.0 N A:PRO316 4.6 70.9 1.0 N A:GLY315 4.6 58.8 1.0 CA A:PRO316 4.7 71.0 1.0

Sodium binding site 5 out of 8 in the Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:32.3 occ:1.00 NZ A:LYS326 3.4 64.2 1.0 OE1 A:GLU9 3.5 70.6 1.0 NE2 A:HIS291 3.9 62.0 1.0 CG1 A:ILE294 4.1 48.4 1.0 CE1 A:HIS291 4.2 63.8 1.0 CD1 A:ILE294 4.3 48.5 1.0 CD2 A:HIS291 4.3 59.1 1.0 CD A:GLU9 4.4 66.3 1.0 OE2 A:GLU9 4.5 63.2 1.0 CB A:ALA323 4.6 60.8 1.0 CE A:LYS326 4.6 63.6 1.0 CD A:LYS326 4.7 58.2 1.0 ND1 A:HIS291 4.7 62.0 1.0 CG A:HIS291 4.8 56.8 1.0

Sodium binding site 6 out of 8 in the Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:33.6 occ:1.00 OE1 B:GLN336 3.3 59.2 1.0 N B:VAL354 3.9 64.8 1.0 CD B:GLN336 4.1 54.4 1.0 NE2 B:GLN336 4.1 52.4 1.0 O B:ASP352 4.2 91.9 1.0 O B:PRO351 4.3 88.6 1.0 CA B:ARG353 4.3 62.5 1.0 CG2 B:VAL354 4.3 79.9 1.0 CD2 B:LEU333 4.5 40.5 1.0 C B:ARG353 4.5 66.5 1.0 CB B:VAL354 4.6 62.9 1.0 C B:ASP352 4.7 73.7 1.0 N B:ARG353 4.9 59.0 1.0 CA B:VAL354 4.9 62.1 1.0

Sodium binding site 7 out of 8 in the Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:57.5 occ:1.00 O B:GLY315 3.6 122.6 1.0 NZ B:LYS433 3.6 68.2 1.0 O B:GLY466 3.7 99.2 1.0 C B:GLY315 4.0 101.3 1.0 CE2 B:TYR469 4.2 77.9 1.0 N B:GLY315 4.3 86.4 1.0 N B:PRO316 4.4 60.2 1.0 CD2 B:TYR469 4.4 73.2 1.0 CE B:LYS433 4.6 64.9 1.0 C B:GLY466 4.6 88.0 1.0 CA B:GLY315 4.8 89.0 1.0 ND1 B:HIS428 4.8 63.8 1.0 CA B:GLY466 4.9 81.1 1.0 CD B:PRO316 4.9 68.4 1.0 CA B:PRO316 4.9 69.0 1.0 O B:HIS428 5.0 46.9 1.0

Sodium binding site 8 out of 8 in the Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Core Region of Thermus Thermophilus MUTS2 Complexed with Adp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:26.0 occ:1.00 O B:HOH609 2.5 44.9 1.0 NZ B:LYS326 3.1 54.0 1.0 OE1 B:GLU9 3.1 47.0 1.0 OE2 B:GLU9 3.5 80.7 1.0 CD B:GLU9 3.7 59.1 1.0 CD1 B:ILE294 3.9 84.5 1.0 CE1 B:HIS291 4.2 40.9 1.0 NE2 B:HIS291 4.2 49.0 1.0 O B:HOH615 4.3 16.1 1.0 CE B:LYS326 4.3 56.2 1.0 CG1 B:ILE294 4.6 69.0 1.0 ND1 B:HIS291 4.7 42.4 1.0 CD2 B:HIS291 4.8 51.6 1.0 CB B:LEU293 4.9 40.2 1.0 CD B:LYS326 5.0 55.0 1.0

K.Fukui, M.Inoue, T.Murakawa, S.Baba, T.Kumasaka, T.Yano. Structural and Functional Insights Into the Mechanism By Which MUTS2 Recognizes A Dna Junction. Structure V. 30 973 2022.
ISSN: ISSN 0969-2126
PubMed: 35439431
DOI: 10.1016/J.STR.2022.03.014