Sodium in PDB 3dl2: Hexagonal Structure of the Ldh Domain of Human Ubiquitin- Conjugating Enzyme E2-Like Isoform A

The structure of Hexagonal Structure of the Ldh Domain of Human Ubiquitin- Conjugating Enzyme E2-Like Isoform A, PDB code: 3dl2 was solved by J.R.Walker, G.V.Avvakumov, S.Xue, E.M.Newman, P.J.Finerty Jr., C.Butler-Cole, C.Bountra, M.Wolkstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.97 / 2.10
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	105.603, 105.603, 131.918, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 22.6

The binding sites of Sodium atom in the Hexagonal Structure of the Ldh Domain of Human Ubiquitin- Conjugating Enzyme E2-Like Isoform A (pdb code 3dl2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hexagonal Structure of the Ldh Domain of Human Ubiquitin- Conjugating Enzyme E2-Like Isoform A, PDB code: 3dl2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hexagonal Structure of the Ldh Domain of Human Ubiquitin- Conjugating Enzyme E2-Like Isoform A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hexagonal Structure of the Ldh Domain of Human Ubiquitin- Conjugating Enzyme E2-Like Isoform A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:55.3 occ:1.00 OD1 A:ASN230 2.8 56.8 1.0 O A:VAL234 2.8 51.8 1.0 O A:LEU231 2.8 57.1 1.0 O A:HOH557 3.0 53.4 1.0 C A:LEU231 3.9 57.9 1.0 C A:VAL234 4.0 52.6 1.0 CG A:ASN230 4.0 55.1 1.0 O A:PRO232 4.2 69.3 1.0 C A:ASN230 4.3 51.8 1.0 N A:LEU231 4.3 51.1 1.0 N A:VAL234 4.4 57.5 1.0 CA A:ASN230 4.5 49.2 1.0 C A:PRO232 4.5 67.3 1.0 O A:HOH540 4.6 44.1 1.0 CA A:VAL234 4.6 53.4 1.0 CA A:PRO232 4.7 66.7 1.0 O A:ASN230 4.7 55.0 1.0 N A:PRO232 4.7 62.3 1.0 CA A:LEU231 4.7 54.4 1.0 CB A:ASN230 4.9 50.9 1.0 ND2 A:ASN230 4.9 57.8 1.0 O A:HOH559 5.0 49.7 1.0

Sodium binding site 2 out of 2 in the Hexagonal Structure of the Ldh Domain of Human Ubiquitin- Conjugating Enzyme E2-Like Isoform A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hexagonal Structure of the Ldh Domain of Human Ubiquitin- Conjugating Enzyme E2-Like Isoform A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:49.5 occ:1.00 OD1 B:ASN230 2.7 58.6 1.0 O B:LEU231 2.8 58.4 1.0 O B:VAL234 2.9 53.0 1.0 C B:LEU231 3.9 58.8 1.0 CG B:ASN230 3.9 56.8 1.0 C B:VAL234 4.0 53.6 1.0 O B:PRO232 4.2 70.2 1.0 C B:ASN230 4.2 53.0 1.0 N B:LEU231 4.3 52.6 1.0 CA B:ASN230 4.4 50.6 1.0 N B:VAL234 4.4 58.3 1.0 C B:PRO232 4.4 68.0 1.0 O B:HOH549 4.5 41.5 1.0 O B:ASN230 4.6 55.6 1.0 CA B:PRO232 4.7 66.9 1.0 N B:PRO232 4.7 62.6 1.0 CA B:VAL234 4.7 54.3 1.0 CA B:LEU231 4.7 55.5 1.0 CB B:ASN230 4.8 51.9 1.0 ND2 B:ASN230 4.8 59.5 1.0

J.R.Walker, G.V.Avvakumov, S.Xue, E.M.Newman, P.J.Finerty Jr., C.Butler-Cole, C.Bountra, M.Wolkstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon. Structural Investigation Into the L-Lactate Dehydrogenase Domain of Human Ubiquitin-Conjugating Enzyme E2-Like Isoform A. To Be Published.