Sodium in PDB 5voo: Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8

The structure of Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8, PDB code: 5voo 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)	163.21 / 2.40
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	188.463, 188.463, 247.137, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 23

The structure of Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8 (pdb code 5voo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8, PDB code: 5voo:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8


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 with Methyltetrahydrofolate From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3002 b:38.9 occ:1.00 OG1 A:THR378 2.2 36.6 1.0 O A:HOH3142 2.3 25.2 1.0 O A:HOH3120 2.3 30.3 1.0 OG A:SER413 2.4 34.8 1.0 OD1 A:ASN376 2.6 33.3 1.0 H A:THR378 3.2 32.3 1.0 HD21 A:ASN376 3.2 32.6 1.0 CG A:ASN376 3.4 32.3 1.0 CB A:THR378 3.5 34.9 1.0 HG23 A:THR378 3.6 35.9 1.0 CB A:SER413 3.6 35.0 1.0 ND2 A:ASN376 3.7 32.6 1.0 HB3 A:SER413 3.7 35.0 1.0 HG21 A:THR378 3.8 35.9 1.0 CG2 A:THR378 3.9 35.9 1.0 N A:THR378 4.0 32.3 1.0 HB2 A:SER413 4.0 35.0 1.0 H A:GLY379 4.1 33.7 1.0 HB A:THR378 4.2 34.9 1.0 O A:HOH3139 4.2 38.5 1.0 H A:ALA377 4.3 31.0 1.0 CA A:THR378 4.3 34.3 1.0 O A:ALA415 4.4 42.7 1.0 O A:SER413 4.5 35.0 1.0 HD22 A:ASN376 4.5 32.6 1.0 HB3 A:ALA415 4.5 37.2 1.0 N A:GLY379 4.6 33.7 1.0 N A:ALA377 4.6 31.0 1.0 HA A:ASN376 4.6 32.5 1.0 CB A:ASN376 4.8 32.1 1.0 C A:SER413 4.8 34.5 1.0 CA A:SER413 4.8 33.6 1.0 HG1 C:THR417 4.8 63.9 1.0 HG22 A:THR378 4.8 35.9 1.0 HB3 A:ALA377 4.9 32.2 1.0 C A:THR378 4.9 33.9 1.0 C A:ASN376 5.0 31.2 1.0 H72 A:C2F3001 5.0 22.8 0.8

Sodium binding site 2 out of 6 in the Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8


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 with Methyltetrahydrofolate From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3003 b:58.5 occ:1.00 CL C:CL701 2.3 66.7 1.0 CL A:CL3005 2.6 57.5 1.0 O C:HOH852 3.2 49.0 1.0 HB3 A:GLU473 3.2 44.6 1.0 HB2 A:GLU473 3.3 44.6 1.0 OE1 A:GLU473 3.6 48.2 1.0 CB A:GLU473 3.8 44.6 1.0 HB3 C:GLU473 4.0 41.6 1.0 OE1 C:GLU473 4.1 51.0 1.0 HB2 A:ARG474 4.2 35.4 1.0 CD A:GLU473 4.2 54.3 1.0 H A:ARG474 4.3 36.2 1.0 HB2 C:GLU473 4.4 41.6 1.0 HH11 C:ARG474 4.4 42.5 1.0 N A:ARG474 4.4 36.2 1.0 HA A:ARG474 4.5 36.4 1.0 HH11 C:ARG477 4.5 40.6 1.0 HE C:ARG474 4.6 39.3 1.0 C A:GLU473 4.6 38.1 1.0 CG A:GLU473 4.6 49.7 1.0 CB C:GLU473 4.7 41.6 1.0 HB2 C:ARG474 4.7 36.0 1.0 HE A:ARG474 4.7 37.8 1.0 CD C:GLU473 4.8 52.4 1.0 CA A:GLU473 4.9 40.0 1.0 CA A:ARG474 4.9 36.4 1.0 HH21 A:ARG474 4.9 43.8 1.0 CB A:ARG474 5.0 35.4 1.0

Sodium binding site 3 out of 6 in the Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3004 b:50.4 occ:1.00 O A:HOH3148 2.0 35.4 1.0 O E:HOH3105 2.5 38.6 1.0 OE2 A:GLU496 3.1 39.6 1.0 HD22 E:LEU511 3.2 40.0 1.0 HH22 A:ARG512 3.4 38.0 1.0 HH21 A:ARG512 3.7 38.0 1.0 HD13 E:LEU511 3.7 42.6 1.0 NH2 A:ARG512 3.8 38.0 1.0 OE1 E:GLU515 4.0 42.9 1.0 HB2 A:LEU472 4.0 36.6 1.0 H A:LEU472 4.1 34.4 1.0 CD2 E:LEU511 4.1 40.0 1.0 CD A:GLU496 4.2 39.4 1.0 HA2 A:GLY471 4.2 32.8 1.0 HD21 E:LEU511 4.3 40.0 1.0 HB3 E:LEU511 4.4 38.9 1.0 HG2 A:GLU496 4.4 40.1 1.0 CD1 E:LEU511 4.5 42.6 1.0 O E:HOH3141 4.5 34.6 1.0 HD11 E:LEU511 4.7 42.6 1.0 N A:LEU472 4.7 34.4 1.0 HD23 E:LEU511 4.8 40.0 1.0 HA3 A:GLY471 4.8 32.8 1.0 HB3 A:LEU472 4.8 36.6 1.0 CG E:LEU511 4.8 40.2 1.0 HD21 E:LEU562 4.8 40.5 1.0 CB A:LEU472 4.8 36.6 1.0 O E:HOH3140 4.9 44.1 1.0 CG A:GLU496 4.9 40.1 1.0 CA A:GLY471 4.9 32.8 1.0

Sodium binding site 4 out of 6 in the Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na703 b:40.9 occ:1.00 HG B:SER413 2.0 33.4 1.0 O B:HOH872 2.2 32.6 1.0 O B:HOH891 2.3 41.8 1.0 OG1 B:THR378 2.3 34.8 1.0 O B:HOH836 2.3 33.6 1.0 OG B:SER413 2.6 33.4 1.0 OD1 B:ASN376 2.7 36.0 1.0 H B:THR378 3.2 32.1 1.0 HD21 B:ASN376 3.2 31.4 1.0 CG B:ASN376 3.5 33.5 1.0 CB B:THR378 3.6 33.8 1.0 HG23 B:THR378 3.7 32.0 1.0 ND2 B:ASN376 3.7 31.4 1.0 CB B:SER413 3.8 32.4 1.0 HB3 B:SER413 3.9 32.4 1.0 CG2 B:THR378 4.0 32.0 1.0 HG21 B:THR378 4.0 32.0 1.0 N B:THR378 4.0 32.1 1.0 H B:GLY379 4.1 34.1 1.0 HB2 B:SER413 4.2 32.4 1.0 HB B:THR378 4.3 33.8 1.0 CA B:THR378 4.3 33.6 1.0 O B:HOH844 4.4 34.0 1.0 O B:ALA415 4.4 34.2 1.0 HB3 B:ALA415 4.4 34.0 1.0 H B:ALA377 4.4 30.9 1.0 O B:SER413 4.4 33.0 1.0 HD22 B:ASN376 4.5 31.4 1.0 N B:GLY379 4.6 34.1 1.0 O B:HOH887 4.6 47.4 1.0 N B:ALA377 4.8 30.9 1.0 HA B:ASN376 4.8 33.8 1.0 C B:SER413 4.9 31.8 1.0 C B:THR378 4.9 33.9 1.0 CB B:ASN376 4.9 34.2 1.0 HG22 B:THR378 4.9 32.0 1.0 CA B:SER413 5.0 32.4 1.0 HB3 B:ALA377 5.0 32.9 1.0

Sodium binding site 5 out of 6 in the Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na3002 b:54.8 occ:1.00 HG D:SER413 2.1 48.5 1.0 O D:HOH3125 2.2 37.6 1.0 OG1 D:THR378 2.4 47.6 1.0 O D:HOH3116 2.5 43.1 1.0 OG D:SER413 2.8 48.5 1.0 OD1 D:ASN376 3.0 45.1 1.0 HD21 D:ASN376 3.4 43.6 1.0 H D:THR378 3.6 41.7 1.0 HB3 D:SER413 3.7 45.0 1.0 CB D:THR378 3.7 45.7 1.0 HG23 D:THR378 3.7 46.0 1.0 CB D:SER413 3.8 45.0 1.0 HG21 D:THR378 3.8 46.0 1.0 CG D:ASN376 3.8 43.0 1.0 CG2 D:THR378 3.9 46.0 1.0 ND2 D:ASN376 3.9 43.6 1.0 HB2 D:SER413 4.1 45.0 1.0 HB D:THR378 4.3 45.7 1.0 N D:THR378 4.3 41.7 1.0 HB3 D:ALA415 4.4 41.5 1.0 H D:GLY379 4.5 43.8 1.0 CA D:THR378 4.6 43.9 1.0 O D:ALA415 4.7 46.4 1.0 O D:SER413 4.7 44.5 1.0 HD22 D:ASN376 4.8 43.6 1.0 H D:ALA377 4.8 42.3 1.0 H72 D:C2F3001 4.9 31.2 0.8 HG22 D:THR378 4.9 46.0 1.0

Sodium binding site 6 out of 6 in the Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na3002 b:64.6 occ:1.00 HG F:SER413 2.2 52.4 1.0 O F:HOH3115 2.3 53.6 1.0 O F:HOH3107 2.5 44.5 1.0 HG1 F:THR378 2.6 54.6 1.0 OG1 F:THR378 2.8 54.6 1.0 OG F:SER413 2.8 52.4 1.0 OD1 F:ASN376 3.1 46.2 1.0 HG23 F:THR378 3.5 50.5 1.0 H F:THR378 3.6 53.9 1.0 HG21 F:THR378 3.7 50.5 1.0 HD21 F:ASN376 3.8 47.1 1.0 HB3 F:SER413 3.9 51.1 1.0 CG2 F:THR378 3.9 50.5 1.0 CB F:THR378 3.9 52.6 1.0 CB F:SER413 3.9 51.1 1.0 HB3 F:ALA415 3.9 56.0 1.0 CG F:ASN376 4.0 47.4 1.0 HB2 F:SER413 4.2 51.1 1.0 ND2 F:ASN376 4.3 47.1 1.0 N F:THR378 4.4 53.9 1.0 O F:ALA415 4.4 52.8 1.0 HB F:THR378 4.6 52.6 1.0 H F:ALA377 4.7 52.2 1.0 H F:ALA415 4.7 53.0 1.0 CA F:THR378 4.7 53.6 1.0 H F:GLY379 4.7 52.3 1.0 HG22 F:THR378 4.8 50.5 1.0 CB F:ALA415 4.9 56.0 1.0 HB3 F:ALA377 4.9 56.2 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