Sodium in PDB 4ejy: Structure of MBOGG1 in Complex with High Affinity Dna Ligand

The structure of Structure of MBOGG1 in Complex with High Affinity Dna Ligand, PDB code: 4ejy was solved by T.Jiang, H.J.Yu, L.J.Bi, X.E.Zhang, M.Z.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.613, 102.884, 67.284, 90.00, 90.18, 90.00
R / Rfree (%)	22.2 / 25.8

The binding sites of Sodium atom in the Structure of MBOGG1 in Complex with High Affinity Dna Ligand (pdb code 4ejy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of MBOGG1 in Complex with High Affinity Dna Ligand, PDB code: 4ejy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of MBOGG1 in Complex with High Affinity Dna Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of MBOGG1 in Complex with High Affinity Dna Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:24.1 occ:1.00 O A:HOH478 2.3 26.7 1.0 OP1 C:DC22 2.3 23.4 1.0 O A:MET213 2.4 24.7 1.0 O A:ILE215 2.5 22.5 1.0 O C:HOH104 2.5 27.5 1.0 O A:VAL218 2.6 20.9 1.0 C A:MET213 3.4 24.4 1.0 O A:HOH451 3.4 34.4 1.0 P C:DC22 3.4 24.7 1.0 C A:ILE215 3.5 22.5 1.0 C A:VAL218 3.6 21.0 1.0 OP2 C:DC22 3.6 24.0 1.0 N A:VAL218 3.7 20.8 1.0 CA A:MET213 4.0 24.6 1.0 N A:GLY217 4.0 21.8 1.0 CA A:VAL218 4.1 20.8 1.0 CA A:ASN216 4.2 22.4 1.0 N A:ASN216 4.2 22.3 1.0 O A:HOH456 4.2 41.3 1.0 N A:ILE215 4.2 23.3 1.0 C A:THR214 4.3 24.0 1.0 O3' C:DT21 4.4 23.3 1.0 N A:THR214 4.4 24.5 1.0 CB A:MET213 4.4 24.9 1.0 CB A:VAL218 4.5 20.9 1.0 C A:ASN216 4.5 21.9 1.0 CA A:ILE215 4.5 22.7 1.0 O A:THR214 4.5 23.9 1.0 O5' C:DC22 4.6 25.3 1.0 CA A:THR214 4.7 24.4 1.0 N A:GLY219 4.7 21.2 1.0 C A:GLY217 4.7 21.1 1.0 O A:HOH535 4.9 45.8 1.0 CA A:GLY217 4.9 21.2 1.0 CG A:MET213 5.0 26.0 1.0

Sodium binding site 2 out of 2 in the Structure of MBOGG1 in Complex with High Affinity Dna Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of MBOGG1 in Complex with High Affinity Dna Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:34.7 occ:1.00 OP1 E:DC22 2.3 34.5 1.0 O B:HOH445 2.4 53.6 1.0 O E:HOH102 2.5 34.1 1.0 O B:ILE215 2.6 25.2 1.0 O B:MET213 2.6 27.2 1.0 O B:VAL218 2.7 26.5 1.0 P E:DC22 3.3 35.1 1.0 OP2 E:DC22 3.5 35.0 1.0 C B:MET213 3.6 27.2 1.0 C B:ILE215 3.6 25.4 1.0 C B:VAL218 3.7 26.5 1.0 O B:HOH482 3.7 34.3 1.0 N B:VAL218 3.8 26.0 1.0 N B:GLY217 4.0 25.6 1.0 CA B:ASN216 4.2 25.7 1.0 CA B:MET213 4.2 27.7 1.0 CA B:VAL218 4.3 26.2 1.0 N B:ASN216 4.3 25.5 1.0 O3' E:DT21 4.3 34.6 1.0 N B:ILE215 4.4 25.7 1.0 C B:THR214 4.4 26.2 1.0 C B:ASN216 4.5 25.6 1.0 O5' E:DC22 4.5 35.7 1.0 N B:THR214 4.6 26.8 1.0 CB B:MET213 4.6 27.9 1.0 CA B:ILE215 4.6 25.3 1.0 CB B:VAL218 4.7 26.0 1.0 N B:GLY219 4.7 26.8 1.0 O B:THR214 4.7 26.2 1.0 C B:GLY217 4.8 26.0 1.0 CA B:THR214 4.8 26.5 1.0 CA B:GLY217 4.9 25.7 1.0

H.J.Yu, M.Z.Yang, X.E.Zhang, L.J.Bi, T.Jiang. Crystal Structures of MBOGG1 in Complex with Two Abasic Dna Ligands J.Struct.Biol. V. 181 252 2013.
ISSN: ISSN 1047-8477
PubMed: 23246782
DOI: 10.1016/J.JSB.2012.12.003