Sodium in PDB 4ihs: Crystal Structure of BENM_DBD/Catb Site 1 Dna Complex

The structure of Crystal Structure of BENM_DBD/Catb Site 1 Dna Complex, PDB code: 4ihs was solved by A.Alanazi, C.Momany, E.L.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.95 / 3.10
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	156.493, 156.493, 141.525, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.3

The binding sites of Sodium atom in the Crystal Structure of BENM_DBD/Catb Site 1 Dna Complex (pdb code 4ihs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of BENM_DBD/Catb Site 1 Dna Complex, PDB code: 4ihs:

Sodium binding site 1 out of 1 in the Crystal Structure of BENM_DBD/Catb Site 1 Dna Complex


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 BENM_DBD/Catb Site 1 Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:95.7 occ:1.00 O8 A:MLI101 2.6 0.7 1.0 O8 C:MLI101 2.7 0.5 1.0 OD1 C:ASP76 2.7 93.7 1.0 HA C:ASP76 3.0 76.6 1.0 HA A:ASP76 3.1 79.9 1.0 HG12 A:VAL75 3.2 74.7 1.0 O6 C:MLI101 3.3 0.1 1.0 C3 A:MLI101 3.5 0.5 1.0 HB2 C:ASP76 3.6 81.1 1.0 HG22 A:VAL79 3.6 76.4 1.0 CG C:ASP76 3.7 89.2 1.0 O9 A:MLI101 3.8 0.0 1.0 CA C:ASP76 3.8 75.8 1.0 C3 C:MLI101 3.9 0.5 1.0 CB C:ASP76 3.9 81.1 1.0 CA A:ASP76 3.9 79.7 1.0 N A:ASP76 4.0 76.0 1.0 HB A:VAL79 4.0 76.1 1.0 HB2 A:ASP76 4.1 84.4 1.0 CG1 A:VAL75 4.1 74.3 1.0 O A:VAL75 4.1 75.2 1.0 HH11 A:ARG7 4.2 91.4 1.0 C A:VAL75 4.2 74.9 1.0 HB A:VAL75 4.3 72.1 1.0 C2 C:MLI101 4.3 0.5 1.0 HB C:VAL79 4.3 72.7 1.0 OD1 A:ASP76 4.3 91.4 1.0 HG11 A:VAL75 4.4 74.7 1.0 H A:ASP76 4.4 75.9 1.0 CG2 A:VAL79 4.5 77.0 1.0 CB A:ASP76 4.5 85.1 1.0 C1 C:MLI101 4.5 0.9 1.0 H12 C:MLI101 4.6 0.3 1.0 O C:ASP76 4.6 78.2 1.0 CB A:VAL75 4.7 72.5 1.0 CB A:VAL79 4.7 76.6 1.0 N C:ASP76 4.7 74.0 1.0 HG13 A:VAL75 4.8 75.5 1.0 C C:ASP76 4.8 76.0 1.0 HG21 A:VAL79 4.8 76.9 1.0 HG11 A:VAL79 4.8 78.1 1.0 O9 C:MLI101 4.8 0.4 1.0 HB3 C:ASP76 4.8 81.1 1.0 OD2 C:ASP76 4.8 92.1 1.0 C1 A:MLI101 4.9 0.2 1.0 NH1 A:ARG7 4.9 92.3 1.0 HG12 C:VAL75 4.9 68.5 1.0 H12 A:MLI101 4.9 0.3 1.0 CG A:ASP76 4.9 91.1 1.0 HE2 B:MET1 4.9 0.3 1.0 HH12 A:ARG7 4.9 93.1 1.0 HG22 C:VAL79 4.9 74.0 1.0

A.M.Alanazi, E.L.Neidle, C.Momany. The Dna-Binding Domain of Benm Reveals the Structural Basis For the Recognition of A T-N11-A Sequence Motif By Lysr-Type Transcriptional Regulators. Acta Crystallogr.,Sect.D V. 69 1995 2013.
ISSN: ISSN 0907-4449
PubMed: 24100318
DOI: 10.1107/S0907444913017320