Sodium in PDB 4ni9: Crystal Structure of Human Interleukin 6 in Complex with A Modified Nucleotide Aptamer (Somamer SL1025), Form 2

The structure of Crystal Structure of Human Interleukin 6 in Complex with A Modified Nucleotide Aptamer (Somamer SL1025), Form 2, PDB code: 4ni9 was solved by D.Davies, T.Edwards, A.Gelinas, T.Jarvis, M.Clifton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.55
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	69.020, 69.020, 108.470, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 23.9

The binding sites of Sodium atom in the Crystal Structure of Human Interleukin 6 in Complex with A Modified Nucleotide Aptamer (Somamer SL1025), Form 2 (pdb code 4ni9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Interleukin 6 in Complex with A Modified Nucleotide Aptamer (Somamer SL1025), Form 2, PDB code: 4ni9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Interleukin 6 in Complex with A Modified Nucleotide Aptamer (Somamer SL1025), Form 2


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 Human Interleukin 6 in Complex with A Modified Nucleotide Aptamer (Somamer SL1025), Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:29.2 occ:1.00 O6 B:DG31 2.2 54.7 1.0 O6 B:DG2 2.2 53.0 1.0 O6 B:DG11 2.3 42.0 1.0 O6 B:DG5 2.5 45.9 1.0 O6 B:DG10 2.7 49.9 1.0 C6 B:DG2 3.1 56.0 1.0 C6 B:DG31 3.2 55.5 1.0 N1 B:DA4 3.2 51.5 1.0 C6 B:DG11 3.3 42.3 1.0 C6 B:DG10 3.3 50.1 1.0 N1 B:DG2 3.4 55.6 1.0 O6 B:DG32 3.4 59.4 1.0 C6 B:DG5 3.4 46.0 1.0 N1 B:DG31 3.5 54.6 1.0 N1 B:DG5 3.7 47.4 1.0 N1 B:DG11 3.7 41.8 1.0 N1 B:DG10 3.7 50.9 1.0 C6 B:DA4 3.7 53.1 1.0 C2 B:DA4 3.8 51.0 1.0 N6 B:DA4 3.9 52.6 1.0 NA B:NA102 3.9 30.9 1.0 O6 B:OMG6 4.1 48.5 1.0 O6 B:DG1 4.1 47.0 1.0 C6 B:DG32 4.3 61.4 1.0 C5 B:DG10 4.4 48.0 1.0 N3 B:DUZ30 4.4 45.2 1.0 C5 B:DG31 4.5 56.0 1.0 C5 B:DG2 4.5 56.8 1.0 O2 B:DUZ30 4.5 48.1 1.0 C5 B:DA4 4.6 54.2 1.0 C5 B:DG11 4.7 41.9 1.0 N1 B:DG32 4.7 62.9 1.0 N3 B:DA4 4.7 51.8 1.0 C6 B:DG1 4.7 48.5 1.0 C2 B:DG2 4.7 57.2 1.0 C5 B:DG5 4.8 46.5 1.0 C6 B:OMG6 4.8 45.8 1.0 C2 B:DG10 4.8 50.2 1.0 N1 B:OMG6 4.8 44.6 1.0 C2 B:DG31 4.8 54.9 1.0 C2 B:DUZ30 4.8 46.7 1.0 N1 B:DG1 4.9 47.3 1.0 N7 B:DG10 5.0 47.5 1.0 C4 B:DA4 5.0 53.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Interleukin 6 in Complex with A Modified Nucleotide Aptamer (Somamer SL1025), Form 2


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 Human Interleukin 6 in Complex with A Modified Nucleotide Aptamer (Somamer SL1025), Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:30.9 occ:1.00 O22 B:UPE9 2.3 54.5 1.0 O6 B:OMG6 2.4 48.5 1.0 O6 B:DG32 2.5 59.4 1.0 O6 B:DG1 2.6 47.0 1.0 O6 B:DG10 2.7 49.9 1.0 N1 B:DG1 3.3 47.3 1.0 C6 B:DG1 3.4 48.5 1.0 C6 B:DG32 3.4 61.4 1.0 C6 B:OMG6 3.4 45.8 1.0 C21 B:UPE9 3.4 54.5 1.0 C6 B:DG10 3.6 50.1 1.0 N1 B:DG32 3.6 62.9 1.0 N1 B:OMG6 3.8 44.6 1.0 N1 B:DG10 3.9 50.9 1.0 NA B:NA101 3.9 29.2 1.0 C24 B:UPE9 4.0 57.6 1.0 N23 B:UPE9 4.1 56.0 1.0 O6 B:DG2 4.2 53.0 1.0 OP2 B:UPE9 4.3 46.5 1.0 C5 B:UPE9 4.5 53.5 1.0 O6 B:DG5 4.5 45.9 1.0 C6 B:UPE9 4.5 52.3 1.0 C5 B:DG32 4.6 60.4 1.0 C5 B:OMG6 4.6 45.5 1.0 C2 B:DG1 4.6 49.1 1.0 O6 B:DG31 4.7 54.7 1.0 C5 B:DG1 4.7 49.5 1.0 C5 B:DG10 4.9 48.0 1.0 C6 B:DG2 4.9 56.0 1.0 C2 B:DG32 4.9 63.5 1.0 C6 B:DG5 4.9 46.0 1.0

A.D.Gelinas, D.R.Davies, T.E.Edwards, J.C.Rohloff, J.D.Carter, C.Zhang, S.Gupta, Y.Ishikawa, M.Hirota, Y.Nakaishi, T.C.Jarvis, N.Janjic. Crystal Structure of Interleukin-6 in Complex with A Modified Nucleic Acid Ligand. J.Biol.Chem. V. 289 8720 2014.
ISSN: ISSN 0021-9258
PubMed: 24415767
DOI: 10.1074/JBC.M113.532697