Sodium in PDB 5e8b: Crystal Structure of the S. Cerevisiae RTF1 Histone Modification Domain Mutant R126A

The structure of Crystal Structure of the S. Cerevisiae RTF1 Histone Modification Domain Mutant R126A, PDB code: 5e8b was solved by A.D.Wier, A.Heroux, A.P.Vandemark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.45 / 1.62
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	93.868, 93.868, 75.344, 90.00, 90.00, 120.00
R / Rfree (%)	14.7 / 19.3

The binding sites of Sodium atom in the Crystal Structure of the S. Cerevisiae RTF1 Histone Modification Domain Mutant R126A (pdb code 5e8b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the S. Cerevisiae RTF1 Histone Modification Domain Mutant R126A, PDB code: 5e8b:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the S. Cerevisiae RTF1 Histone Modification Domain Mutant R126A


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 the S. Cerevisiae RTF1 Histone Modification Domain Mutant R126A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:62.4 occ:1.00 OE1 A:GLU89 2.2 46.5 1.0 HG3 A:GLU93 2.6 49.4 1.0 OE2 A:GLU93 2.8 52.3 1.0 HB3 A:GLU89 2.9 39.8 1.0 HD2 A:ARG92 3.0 53.0 1.0 HG2 A:GLU93 3.2 49.4 1.0 CG A:GLU93 3.2 41.2 1.0 HE A:ARG92 3.3 57.3 1.0 CD A:GLU89 3.3 49.0 1.0 CD A:GLU93 3.4 50.4 1.0 O A:GLU89 3.5 28.3 1.0 CB A:GLU89 3.7 33.1 1.0 HB3 A:ARG92 3.7 33.9 1.0 HA A:GLU89 3.7 34.2 1.0 NE A:ARG92 3.8 47.8 1.0 CD A:ARG92 3.8 44.1 1.0 CG A:GLU89 4.0 41.2 1.0 CA A:GLU89 4.1 28.5 1.0 C A:GLU89 4.1 25.5 1.0 H A:GLU93 4.2 30.7 1.0 HG3 A:GLU89 4.3 49.5 1.0 OE2 A:GLU89 4.3 55.3 1.0 HD3 A:ARG92 4.3 53.0 1.0 HB2 A:GLU89 4.5 39.8 1.0 CB A:GLU93 4.6 31.9 1.0 CB A:ARG92 4.6 28.2 1.0 N A:GLU93 4.7 25.6 1.0 OE1 A:GLU93 4.7 54.5 1.0 CG A:ARG92 4.8 32.4 1.0 HA A:GLU93 4.9 32.5 1.0 HB2 A:GLU93 4.9 38.3 1.0 CZ A:ARG92 4.9 58.1 1.0 HG2 A:GLU89 4.9 49.5 1.0 CA A:GLU93 5.0 27.1 1.0 HH21 A:ARG92 5.0 72.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the S. Cerevisiae RTF1 Histone Modification Domain Mutant R126A


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 the S. Cerevisiae RTF1 Histone Modification Domain Mutant R126A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:70.7 occ:1.00 HA B:SER97 2.4 42.3 1.0 CA B:SER97 3.3 35.2 1.0 O B:GLU96 3.5 42.1 1.0 HB2 B:SER97 3.6 45.4 1.0 O B:SER97 3.6 41.7 1.0 C B:SER97 3.8 34.8 1.0 CB B:SER97 4.0 37.9 1.0 N B:SER97 4.2 34.8 1.0 C B:GLU96 4.3 37.2 1.0 HB3 B:SER97 4.3 45.4 1.0 N B:LEU98 4.8 30.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the S. Cerevisiae RTF1 Histone Modification Domain Mutant R126A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the S. Cerevisiae RTF1 Histone Modification Domain Mutant R126A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:59.9 occ:1.00 OE1 B:GLN118 2.4 28.8 1.0 HB2 B:GLN118 2.8 31.0 1.0 HG2 B:GLN118 3.3 35.2 1.0 CD B:GLN118 3.3 29.7 1.0 HE2 B:TYR117 3.4 38.0 1.0 HE3 B:MET114 3.5 36.6 1.0 HD2 B:TYR117 3.6 35.0 1.0 CG B:GLN118 3.6 29.4 1.0 CB B:GLN118 3.6 25.9 1.0 O B:HOH304 3.8 46.5 1.0 HE1 B:MET114 3.9 36.6 1.0 CE2 B:TYR117 4.1 31.6 1.0 CE B:MET114 4.1 30.5 1.0 CD2 B:TYR117 4.2 29.2 1.0 HA B:GLN118 4.2 28.1 1.0 HB3 B:GLN118 4.2 31.0 1.0 HE2 B:MET114 4.4 36.6 1.0 CA B:GLN118 4.5 23.4 1.0 HG3 B:GLN118 4.5 35.2 1.0 O B:HOH320 4.6 48.5 1.0 NE2 B:GLN118 4.6 32.6 1.0 O B:MET114 4.8 23.5 1.0 HB3 B:MET114 4.9 31.3 1.0 H B:GLN118 4.9 28.3 1.0 HE22 B:GLN118 4.9 39.1 1.0 N B:GLN118 5.0 23.6 1.0

S.B.Van Oss, M.K.Shirra, A.R.Bataille, A.D.Wier, K.Yen, V.Vinayachandran, I.L.Byeon, C.E.Cucinotta, A.Heroux, J.Jeon, J.Kim, A.P.Vandemark, B.F.Pugh, K.M.Arndt. The Histone Modification Domain of PAF1 Complex Subunit RTF1 Directly Stimulates H2B Ubiquitylation Through An Interaction with RAD6. Mol. Cell V. 64 815 2016.
ISSN: ISSN 1097-4164
PubMed: 27840029
DOI: 10.1016/J.MOLCEL.2016.10.008