Sodium in PDB 5vop: Methionine Synthase Folate-Binding Domain From Thermus Thermophilus HB8 Native

The structure of Methionine Synthase Folate-Binding Domain From Thermus Thermophilus HB8 Native, PDB code: 5vop was solved by M.Koutmos, K.Yamada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.44 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	111.482, 111.482, 242.679, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 22.2

The binding sites of Sodium atom in the Methionine Synthase Folate-Binding Domain From Thermus Thermophilus HB8 Native (pdb code 5vop). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Methionine Synthase Folate-Binding Domain From Thermus Thermophilus HB8 Native, PDB code: 5vop:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Methionine Synthase Folate-Binding Domain From Thermus Thermophilus HB8 Native


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Methionine Synthase Folate-Binding Domain From Thermus Thermophilus HB8 Native within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3005 b:68.5 occ:1.00 HG A:SER413 2.0 52.2 1.0 O A:HOH3163 2.2 48.4 1.0 OG1 A:THR378 2.4 56.0 1.0 O A:HOH3118 2.4 50.5 1.0 OG A:SER413 2.6 52.2 1.0 OD1 A:ASN376 2.7 48.2 1.0 H A:THR378 3.2 48.6 1.0 HD21 A:ASN376 3.2 50.3 1.0 CG A:ASN376 3.5 48.0 1.0 HG23 A:THR378 3.5 53.8 1.0 CB A:THR378 3.6 52.3 1.0 ND2 A:ASN376 3.7 50.3 1.0 HB3 A:SER413 3.7 49.0 1.0 CB A:SER413 3.8 49.0 1.0 HG21 A:THR378 3.9 53.8 1.0 CG2 A:THR378 3.9 53.8 1.0 H A:GLY379 4.0 51.9 1.0 N A:THR378 4.0 48.6 1.0 HB2 A:SER413 4.1 49.0 1.0 O A:HOH3150 4.2 56.9 1.0 HB A:THR378 4.3 52.3 1.0 CA A:THR378 4.3 51.8 1.0 H A:ALA377 4.5 46.5 1.0 O A:ALA415 4.5 52.5 1.0 HD22 A:ASN376 4.5 50.3 1.0 HB3 A:ALA415 4.5 51.5 1.0 N A:GLY379 4.6 51.9 1.0 O A:SER413 4.6 49.6 1.0 N A:ALA377 4.8 46.5 1.0 HA A:ASN376 4.8 47.1 1.0 HG22 A:THR378 4.8 53.8 1.0 C A:THR378 4.9 52.2 1.0 CB A:ASN376 4.9 48.0 1.0 C A:SER413 4.9 45.5 1.0 CA A:SER413 5.0 43.7 1.0 HB3 A:ALA377 5.0 47.2 1.0

Sodium binding site 2 out of 2 in the Methionine Synthase Folate-Binding Domain From Thermus Thermophilus HB8 Native


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Methionine Synthase Folate-Binding Domain From Thermus Thermophilus HB8 Native within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3002 b:82.4 occ:1.00 HG B:SER413 2.1 58.5 1.0 OG1 B:THR378 2.3 65.9 1.0 O B:HOH3127 2.3 53.6 1.0 OG B:SER413 2.8 58.5 1.0 OD1 B:ASN376 3.1 55.1 1.0 H B:THR378 3.2 62.0 1.0 CB B:THR378 3.5 69.2 1.0 HD21 B:ASN376 3.6 53.0 1.0 HG23 B:THR378 3.6 71.4 1.0 HB3 B:SER413 3.7 57.4 1.0 HG21 B:THR378 3.8 71.4 1.0 CB B:SER413 3.8 57.4 1.0 CG2 B:THR378 3.8 71.4 1.0 CG B:ASN376 3.9 53.7 1.0 N B:THR378 4.0 62.0 1.0 ND2 B:ASN376 4.0 53.0 1.0 HB2 B:SER413 4.1 57.4 1.0 HB B:THR378 4.2 69.2 1.0 HB3 B:ALA415 4.2 50.6 1.0 CA B:THR378 4.3 69.1 1.0 H B:ALA377 4.4 58.6 1.0 H B:GLY379 4.5 73.4 1.0 O B:ALA415 4.5 49.5 1.0 N B:ALA377 4.8 58.6 1.0 O B:SER413 4.8 50.5 1.0 HG22 B:THR378 4.8 71.4 1.0 HD22 B:ASN376 4.8 53.0 1.0 N B:GLY379 4.9 73.4 1.0 HB3 B:ALA377 4.9 64.5 1.0

K.Yamada, M.Koutmos. The Folate-Binding Module of Thermus Thermophilus Cobalamin-Dependent Methionine Synthase Displays A Distinct Variation of the Classical Tim Barrel: A Tim Barrel with A `Twist'. Acta Crystallogr D Struct V. 74 41 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 29372898
DOI: 10.1107/S2059798317018290