Sodium in PDB 3gxw: Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A

The structure of Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A, PDB code: 3gxw was solved by S.Dengl, A.Mayer, M.Sun, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	54.499, 54.499, 253.434, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 24.1

The binding sites of Sodium atom in the Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A (pdb code 3gxw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A, PDB code: 3gxw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:28.4 occ:1.00 O A:SER38 2.5 13.9 1.0 O A:HOH1027 2.6 29.3 1.0 O A:HOH105 2.6 18.0 1.0 O A:HOH115 2.6 22.1 1.0 O A:GLY41 2.7 15.4 1.0 C A:GLY41 3.4 18.0 1.0 C A:SER38 3.5 17.1 1.0 CA A:ASP42 4.0 21.4 1.0 N A:ASP42 4.0 19.6 1.0 N A:SER38 4.0 15.4 1.0 OE1 A:GLN37 4.2 24.1 1.0 N A:GLY41 4.3 19.3 1.0 CA A:SER38 4.3 17.8 1.0 N A:SER39 4.3 16.9 1.0 CA A:GLY41 4.4 18.8 1.0 O A:HIS44 4.4 16.0 1.0 OD1 A:ASP42 4.4 31.5 1.0 CA A:SER39 4.5 17.3 1.0 C A:ASP42 4.6 20.4 1.0 O A:ASP42 4.8 20.6 1.0 C A:SER39 4.9 18.2 1.0

Sodium binding site 2 out of 4 in the Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:25.3 occ:1.00 O B:SER38 2.6 19.7 1.0 O B:HOH112 2.7 21.3 1.0 O B:HOH1286 2.7 27.7 1.0 O B:GLY41 2.7 19.6 1.0 C B:GLY41 3.4 22.5 1.0 C B:SER38 3.6 18.1 1.0 N B:ASP42 4.1 24.6 1.0 N B:SER38 4.2 15.8 1.0 CA B:ASP42 4.2 27.9 1.0 N B:GLY41 4.2 17.4 1.0 CA B:GLY41 4.3 20.0 1.0 N B:SER39 4.4 16.1 1.0 CA B:SER39 4.4 18.4 1.0 OE1 B:GLN37 4.5 20.0 1.0 O B:HIS44 4.5 15.8 1.0 CA B:SER38 4.5 16.7 1.0 OD1 B:ASP42 4.5 34.4 1.0 C B:ASP42 4.9 28.0 1.0 C B:SER39 4.9 17.4 1.0

Sodium binding site 3 out of 4 in the Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na104 b:30.0 occ:1.00 O C:SER38 2.6 19.7 1.0 O C:HOH1112 2.7 20.4 1.0 O C:HOH1018 2.7 29.7 1.0 O C:HOH1031 2.7 35.2 1.0 O C:GLY41 2.7 18.7 1.0 C C:GLY41 3.4 19.4 1.0 C C:SER38 3.6 19.3 1.0 N C:ASP42 4.0 20.5 1.0 N C:SER38 4.0 18.6 1.0 CA C:ASP42 4.1 25.1 1.0 N C:GLY41 4.1 18.2 1.0 OD1 C:ASP42 4.2 29.6 1.0 CA C:GLY41 4.2 18.8 1.0 O C:HOH1449 4.2 40.4 1.0 CA C:SER38 4.4 19.8 1.0 O C:HIS44 4.5 18.4 1.0 OE1 C:GLN37 4.5 32.5 1.0 N C:SER39 4.6 18.4 1.0 CA C:SER39 4.7 18.7 1.0 C C:ASP42 4.9 25.3 1.0 CB C:GLN37 4.9 24.1 1.0 C C:SER39 5.0 18.1 1.0

Sodium binding site 4 out of 4 in the Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na104 b:31.3 occ:1.00 O D:SER38 2.5 14.5 1.0 O D:HOH105 2.6 15.7 1.0 O D:HOH117 2.7 24.0 1.0 O D:GLY41 2.7 16.6 1.0 O D:HOH1022 2.7 32.4 1.0 O D:HOH136 2.7 30.1 1.0 C D:GLY41 3.4 17.1 1.0 C D:SER38 3.6 17.0 1.0 N D:SER38 4.0 18.0 1.0 N D:ASP42 4.0 16.8 1.0 CA D:ASP42 4.1 20.1 1.0 CE D:MSE4 4.2 70.7 1.0 N D:GLY41 4.2 16.7 1.0 CA D:GLY41 4.3 16.2 1.0 O D:HOH1376 4.3 35.3 1.0 CA D:SER38 4.4 17.2 1.0 O D:HIS44 4.4 19.1 1.0 OD1 D:ASP42 4.5 26.0 1.0 N D:SER39 4.5 17.2 1.0 OE1 D:GLN37 4.5 29.5 1.0 CA D:SER39 4.6 17.3 1.0 C D:ASP42 4.7 20.2 1.0 C D:SER39 5.0 17.4 1.0

S.Dengl, A.Mayer, M.Sun, P.Cramer. Structure and in Vivo Requirement of the Yeast SPT6 SH2 Domain J.Mol.Biol. V. 389 211 2009.
ISSN: ISSN 0022-2836
PubMed: 19371747
DOI: 10.1016/J.JMB.2009.04.016