Chlorine 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:

Sodium

(Na)

6 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8, PDB code: 5voo:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Methionine Synthase Folate-Binding Domain with Methyltetrahydrofolate From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl3005 b:57.5 occ:1.00 NA A:NA3003 2.6 58.5 1.0 HH21 A:ARG474 2.6 43.8 1.0 HH11 A:ARG477 2.7 38.3 1.0 HE A:ARG474 2.8 37.8 1.0 CL C:CL701 3.3 66.7 1.0 NH2 A:ARG474 3.4 43.8 1.0 NH1 A:ARG477 3.4 38.3 1.0 HD2 A:ARG477 3.6 39.2 1.0 NE A:ARG474 3.6 37.8 1.0 HH12 A:ARG477 3.6 38.3 1.0 HB2 C:ARG474 3.7 36.0 1.0 CZ A:ARG474 3.9 40.5 1.0 HD3 A:ARG477 4.0 39.2 1.0 HA A:ARG474 4.0 36.4 1.0 HB2 A:ARG474 4.0 35.4 1.0 HH22 A:ARG474 4.0 43.8 1.0 HH11 C:ARG474 4.2 42.5 1.0 CD A:ARG477 4.2 39.2 1.0 HB3 C:ASP470 4.3 36.7 1.0 HB2 C:GLU473 4.4 41.6 1.0 HE C:ARG474 4.5 39.3 1.0 CZ A:ARG477 4.6 38.2 1.0 CB C:ARG474 4.6 36.0 1.0 H C:ARG474 4.7 34.7 1.0 O C:ASP470 4.7 34.8 1.0 CD A:ARG474 4.7 37.1 1.0 NH1 C:ARG474 4.7 42.5 1.0 CA A:ARG474 4.7 36.4 1.0 CB A:ARG474 4.8 35.4 1.0 HD3 A:ARG474 4.8 37.1 1.0 HB3 C:ARG474 4.8 36.0 1.0 HB3 A:GLU473 4.9 44.6 1.0 HB3 C:GLU473 4.9 41.6 1.0 NE A:ARG477 4.9 39.7 1.0 HB2 A:ARG477 4.9 39.3 1.0 NE C:ARG474 5.0 39.3 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 C:Cl701 b:66.7 occ:1.00 NA A:NA3003 2.3 58.5 1.0 HE C:ARG474 2.4 39.3 1.0 HH11 C:ARG474 2.5 42.5 1.0 HH11 C:ARG477 2.7 40.6 1.0 O C:HOH852 3.1 49.0 1.0 NE C:ARG474 3.2 39.3 1.0 CL A:CL3005 3.3 57.5 1.0 NH1 C:ARG474 3.3 42.5 1.0 NH1 C:ARG477 3.5 40.6 1.0 HD2 C:ARG477 3.5 36.4 1.0 HB2 C:ARG474 3.6 36.0 1.0 HD3 C:ARG477 3.6 36.4 1.0 HA C:ARG474 3.7 36.4 1.0 CZ C:ARG474 3.7 40.5 1.0 HH12 C:ARG477 3.7 40.6 1.0 HB2 A:ARG474 3.9 35.4 1.0 HH12 C:ARG474 4.0 42.5 1.0 CD C:ARG477 4.1 36.4 1.0 HD3 C:ARG474 4.3 38.4 1.0 CD C:ARG474 4.3 38.4 1.0 CB C:ARG474 4.3 36.0 1.0 CA C:ARG474 4.4 36.4 1.0 HB3 A:ASP470 4.5 35.7 1.0 HH21 A:ARG474 4.5 43.8 1.0 CZ C:ARG477 4.6 38.9 1.0 HB2 C:ARG477 4.6 36.5 1.0 HB3 C:GLU473 4.7 41.6 1.0 N C:ARG474 4.7 34.7 1.0 HB2 A:GLU473 4.8 44.6 1.0 NH2 A:ARG474 4.8 43.8 1.0 NE C:ARG477 4.8 36.4 1.0 CG C:ARG474 4.9 36.1 1.0 HE A:ARG474 4.9 37.8 1.0 HB3 C:ARG477 4.9 36.5 1.0 CB A:ARG474 4.9 35.4 1.0 HG2 C:PRO447 4.9 36.2 1.0 H C:ARG474 5.0 34.7 1.0 H A:ARG474 5.0 36.2 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