Sodium in PDB 3mp8: Crystal Structure of SGF29 Tudor Domain

The structure of Crystal Structure of SGF29 Tudor Domain, PDB code: 3mp8 was solved by J.Li, M.Wu, J.Ruan, J.Zang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.14 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.760, 95.100, 114.430, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 21.6

The binding sites of Sodium atom in the Crystal Structure of SGF29 Tudor Domain (pdb code 3mp8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of SGF29 Tudor Domain, PDB code: 3mp8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of SGF29 Tudor Domain


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 SGF29 Tudor Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1267 b:39.9 occ:1.00 O A:HOH348 2.4 37.5 1.0 O A:HOH266 2.6 33.6 1.0 O A:HOH261 2.8 23.9 1.0 NE1 A:TRP896 3.2 12.9 1.0 CE1 A:PHE996 3.8 18.2 1.0 CZ2 A:TRP896 3.9 16.7 1.0 CE2 A:TRP896 3.9 14.9 1.0 CZ A:PHE996 4.0 16.3 1.0 CB A:ALA900 4.0 18.8 1.0 CB A:GLU1066 4.1 30.7 1.0 CD1 A:PHE996 4.3 17.9 1.0 O A:GLY904 4.3 21.7 1.0 CA A:TYR905 4.4 18.9 1.0 OE1 A:GLU1066 4.4 45.8 0.8 CD1 A:TRP896 4.4 12.8 1.0 CB A:TYR905 4.6 19.7 1.0 CE2 A:PHE996 4.6 17.7 1.0 CG A:GLU1066 4.6 38.4 1.0 O A:LYS994 4.7 15.6 1.0 N A:ALA906 4.8 18.2 1.0 CG A:PHE996 4.9 17.5 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of SGF29 Tudor Domain


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 SGF29 Tudor Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1268 b:59.0 occ:1.00 O A:HOH120 2.5 26.3 1.0 O A:HOH337 2.6 35.7 1.0 CA A:GLY990 3.7 22.6 1.0 OG1 A:THR987 3.9 19.6 1.0 O A:GLY990 3.9 23.7 1.0 C A:GLY990 4.2 23.9 1.0 CG2 A:THR987 4.3 19.9 1.0 CB A:THR987 4.4 19.0 1.0 O A:HOH244 4.5 26.7 1.0 N A:GLY990 4.8 22.0 1.0 O A:HOH91 4.8 18.5 1.0 CG2 A:THR866 5.0 18.1 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of SGF29 Tudor Domain


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 SGF29 Tudor Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1269 b:45.3 occ:1.00 OE2 A:GLU782 2.4 34.0 1.0 O A:HOH102 2.6 20.4 1.0 O4 A:MAL1 3.3 15.2 1.0 OE1 A:GLU891 3.3 19.2 1.0 O A:HOH397 3.5 32.2 1.0 CD A:GLU782 3.6 32.0 1.0 C5 A:MAL1 3.7 12.2 1.0 CD A:GLU891 3.9 19.6 1.0 C4 A:MAL1 3.9 12.6 1.0 CZ2 A:TRP800 4.1 14.0 1.0 OE2 A:GLU891 4.2 20.6 1.0 CG A:GLU782 4.2 28.8 1.0 C3 A:MAL1 4.2 13.7 1.0 C6 A:MAL1 4.3 11.4 1.0 O1 A:MAL1 4.4 15.0 1.0 C6' A:MAL1 4.5 17.8 1.0 OE1 A:GLU782 4.5 30.4 1.0 O6 A:MAL1 4.6 11.8 1.0 CH2 A:TRP800 4.6 15.3 1.0 O6' A:MAL1 4.6 20.7 1.0 NH2 A:ARG804 4.7 28.8 1.0 CG A:GLU891 4.8 16.7 1.0 O5 A:MAL1 4.8 11.3 1.0 C5' A:MAL1 4.9 18.8 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of SGF29 Tudor Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of SGF29 Tudor Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1270 b:52.9 occ:1.00 O A:HOH183 3.3 31.1 1.0 OE1 A:GLU1016 3.4 20.2 0.8 O A:HOH172 3.6 32.4 1.0 OD1 A:ASN1020 3.9 22.7 1.0 ND2 A:ASN1020 3.9 22.6 1.0 CG A:ASN1020 4.2 21.1 1.0 CD A:GLU1016 4.4 22.9 0.8 OE2 A:GLU1016 4.6 21.0 0.8 O A:HOH150 4.7 27.0 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of SGF29 Tudor Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of SGF29 Tudor Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1271 b:51.1 occ:1.00 O A:HOH338 2.2 41.8 1.0 OD2 A:ASP1230 3.1 45.6 1.0 O A:ALA1214 3.3 31.3 1.0 CD1 A:ILE1215 3.6 38.3 1.0 C A:ALA1214 3.8 30.9 1.0 CG A:ASP1230 3.8 45.6 1.0 OD1 A:ASP1230 3.9 45.5 1.0 N A:ALA1214 3.9 29.0 1.0 CB A:LYS1200 3.9 33.0 1.0 CG A:LYS1200 4.0 36.0 1.0 CA A:LYS1200 4.2 30.6 1.0 CG1 A:ILE1215 4.2 36.5 1.0 CA A:ALA1214 4.2 29.7 1.0 N A:VAL1201 4.5 28.2 1.0 CB A:PRO1213 4.5 24.7 1.0 N A:ILE1215 4.5 32.6 1.0 C A:PRO1213 4.5 26.6 1.0 O A:VAL1201 4.6 24.2 1.0 C A:LYS1200 4.7 29.9 1.0 CA A:PRO1213 4.8 25.9 1.0 CE A:LYS1200 4.9 39.0 1.0 CA A:ILE1215 4.9 33.7 1.0

C.Bian, C.Xu, J.Ruan, K.K.Lee, T.L.Burke, W.Tempel, D.Barsyte, J.Li, M.Wu, B.O.Zhou, B.E.Fleharty, A.Paulson, A.Allali-Hassani, J.Q.Zhou, G.Mer, P.A.Grant, J.L.Workman, J.Zang, J.Min. SGF29 Binds Histone H3K4ME2/3 and Is Required For Saga Complex Recruitment and Histone H3 Acetylation Embo J. V. 30 2829 2011.
ISSN: ISSN 0261-4189
PubMed: 21685874
DOI: 10.1038/EMBOJ.2011.193