Sodium in PDB 5jgl: Crystal Structure of Gtma in Complex with S-Adenosylmethionine

The structure of Crystal Structure of Gtma in Complex with S-Adenosylmethionine, PDB code: 5jgl was solved by S.K.Dolan, T.Bock, V.Hering, G.W.Jones, W.Blankenfeldt, S.Doyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.28 / 2.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.989, 114.142, 56.438, 90.00, 104.55, 90.00
R / Rfree (%)	19.2 / 23.4

The binding sites of Sodium atom in the Crystal Structure of Gtma in Complex with S-Adenosylmethionine (pdb code 5jgl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Gtma in Complex with S-Adenosylmethionine, PDB code: 5jgl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Gtma in Complex with S-Adenosylmethionine


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 Gtma in Complex with S-Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:22.1 occ:1.00 H A:PHE160 2.3 36.1 1.0 H A:PHE16 2.7 51.8 1.0 H A:VAL17 2.7 45.7 1.0 HG22 A:VAL17 2.9 42.4 1.0 HB2 A:PHE16 2.9 46.2 1.0 O A:HOH425 3.0 37.5 1.0 HG13 A:VAL17 3.0 44.0 1.0 N A:PHE160 3.2 30.1 1.0 HB2 A:PHE160 3.2 37.0 1.0 HA A:ASN159 3.2 33.6 1.0 CB A:SER15 3.3 55.6 1.0 N A:PHE16 3.3 43.2 1.0 HD1 A:TRP162 3.3 41.4 1.0 HD2 A:PHE16 3.3 43.9 1.0 N A:VAL17 3.5 38.1 1.0 HB2 A:ASN159 3.6 35.9 1.0 HE1 A:TRP162 3.8 41.4 1.0 CB A:PHE16 3.8 38.5 1.0 CG2 A:VAL17 3.8 35.4 1.0 CD1 A:TRP162 3.9 34.5 1.0 CG1 A:VAL17 3.9 36.7 1.0 CA A:ASN159 3.9 28.0 1.0 CA A:PHE16 3.9 42.0 1.0 CB A:PHE160 4.0 30.8 1.0 O A:PHE160 4.0 30.9 1.0 C A:ASN159 4.0 27.1 1.0 CA A:PHE160 4.1 26.9 1.0 NE1 A:TRP162 4.1 34.5 1.0 HG21 A:VAL17 4.1 42.4 1.0 C A:SER15 4.1 47.0 1.0 CD2 A:PHE16 4.2 36.5 1.0 HG11 A:VAL17 4.2 44.0 1.0 C A:PHE16 4.2 40.0 1.0 CB A:ASN159 4.2 29.9 1.0 CA A:SER15 4.3 52.4 1.0 CB A:VAL17 4.3 36.9 1.0 HB3 A:PHE16 4.5 46.2 1.0 CG A:PHE16 4.5 32.6 1.0 CA A:VAL17 4.5 41.0 1.0 HG23 A:VAL17 4.5 42.4 1.0 C A:PHE160 4.5 26.4 1.0 HD1 A:PHE160 4.5 39.4 1.0 HA A:SER15 4.6 62.8 1.0 CG A:PHE160 4.6 30.8 1.0 HG12 A:VAL17 4.6 44.0 1.0 HB3 A:ASN159 4.7 35.9 1.0 HB3 A:PHE160 4.8 37.0 1.0 CD1 A:PHE160 4.8 32.9 1.0 HA A:PHE16 4.9 50.4 1.0 HA A:PHE160 4.9 32.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Gtma in Complex with S-Adenosylmethionine


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 Gtma in Complex with S-Adenosylmethionine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:36.6 occ:1.00 H B:PHE160 2.4 44.5 1.0 H B:VAL17 2.6 82.2 1.0 HG23 B:VAL17 2.7 57.9 1.0 HA B:ASN159 2.7 43.4 1.0 HB2 B:PHE16 2.8 68.5 1.0 O B:HOH422 2.9 43.0 1.0 HB2 B:ASN159 3.0 40.7 1.0 HB3 B:PHE16 3.1 68.5 1.0 N B:PHE160 3.2 37.1 1.0 CB B:PHE16 3.4 57.1 1.0 N B:VAL17 3.4 68.5 1.0 CA B:ASN159 3.4 36.2 1.0 HD1 B:TRP162 3.6 44.1 1.0 CG2 B:VAL17 3.6 48.2 1.0 CB B:ASN159 3.6 33.9 1.0 HE1 B:TRP162 3.7 49.0 1.0 N B:PHE16 3.7 52.6 1.0 HB2 B:PHE160 3.8 42.2 1.0 HB B:VAL17 3.8 84.3 1.0 HD1 B:PHE160 3.8 49.7 1.0 C B:ASN159 3.8 37.0 1.0 O B:PHE160 3.9 37.4 1.0 CA B:PHE16 3.9 60.9 1.0 HG21 B:VAL17 3.9 57.9 1.0 HB3 B:ASN159 4.0 40.7 1.0 CD1 B:TRP162 4.1 36.7 1.0 C B:PHE16 4.1 65.3 1.0 CB B:VAL17 4.1 70.3 1.0 NE1 B:TRP162 4.1 40.8 1.0 CA B:PHE160 4.2 30.5 1.0 HE2 B:PHE185 4.3 46.3 1.0 HG22 B:VAL17 4.3 57.9 1.0 CA B:VAL17 4.3 71.8 1.0 HD22 B:ASN159 4.4 42.2 1.0 CB B:PHE160 4.5 35.1 1.0 C B:PHE160 4.5 32.9 1.0 HA B:VAL17 4.6 86.1 1.0 CD1 B:PHE160 4.6 41.4 1.0 CG B:PHE16 4.7 52.2 1.0 O B:GLN158 4.7 33.8 1.0 N B:ASN159 4.7 36.3 1.0 HA B:PHE16 4.9 73.0 1.0 CG B:ASN159 4.9 38.0 1.0 HE22 B:GLN182 5.0 45.7 1.0 HD2 B:PHE16 5.0 59.8 1.0

S.K.Dolan, T.Bock, V.Hering, R.A.Owens, G.W.Jones, W.Blankenfeldt, S.Doyle. Structural, Mechanistic and Functional Insight Into Gliotoxinbis-Thiomethylation Inaspergillus Fumigatus. Open Biol V. 7 2017.
ISSN: ESSN 2046-2441
PubMed: 28179499
DOI: 10.1098/RSOB.160292