Sodium in PDB 4ni7: Crystal Structure of Human Interleukin 6 in Complex with A Modified Nucleotide Aptamer (Somamer SL1025)

The structure of Crystal Structure of Human Interleukin 6 in Complex with A Modified Nucleotide Aptamer (Somamer SL1025), PDB code: 4ni7 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)	43.50 / 2.40
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	50.230, 50.230, 103.630, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 26

The binding sites of Sodium atom in the Crystal Structure of Human Interleukin 6 in Complex with A Modified Nucleotide Aptamer (Somamer SL1025) (pdb code 4ni7). 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), PDB code: 4ni7:
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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:43.9 occ:1.00 O6 B:OMG6 2.4 45.3 1.0 O6 B:DG1 2.5 56.4 1.0 O6 B:DG10 2.5 45.7 1.0 O6 B:DG32 2.5 62.6 1.0 O22 B:UPE9 2.6 61.7 1.0 C6 B:OMG6 3.4 45.2 1.0 C6 B:DG32 3.4 63.6 1.0 NA B:NA102 3.4 40.5 1.0 C6 B:DG1 3.4 55.8 1.0 C6 B:DG10 3.5 48.0 1.0 N1 B:DG1 3.6 54.9 1.0 N1 B:DG32 3.7 63.5 1.0 C21 B:UPE9 3.7 63.9 1.0 N1 B:OMG6 3.7 44.4 1.0 N1 B:DG10 3.9 48.6 1.0 O6 B:DG2 4.2 56.1 1.0 C6 B:UPE9 4.4 63.4 1.0 O6 B:DG5 4.4 41.4 1.0 N23 B:UPE9 4.5 65.5 1.0 C5 B:UPE9 4.5 63.7 1.0 C5 B:DG32 4.6 64.8 1.0 C5 B:OMG6 4.6 44.9 1.0 C24 B:UPE9 4.7 66.8 1.0 C5 B:DG1 4.7 56.4 1.0 C5 B:DG10 4.7 47.7 1.0 O6 B:DG31 4.8 50.4 1.0 OP2 B:UPE9 4.8 53.2 1.0 O4' B:UPE9 4.9 59.7 1.0 C6 B:DG5 4.9 42.9 1.0 C6 B:DG2 4.9 57.0 1.0 C2 B:DG1 5.0 54.9 1.0 C2 B:DG32 5.0 64.0 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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:40.5 occ:1.00 O6 B:DG2 2.2 56.1 1.0 O6 B:DG31 2.3 50.4 1.0 O6 B:DG11 2.4 41.4 1.0 O6 B:DG5 2.4 41.4 1.0 O6 B:DG10 2.6 45.7 1.0 O6 B:DG32 3.1 62.6 1.0 C6 B:DG2 3.2 57.0 1.0 C6 B:DG31 3.2 50.8 1.0 C6 B:DG5 3.4 42.9 1.0 NA B:NA101 3.4 43.9 1.0 C6 B:DG10 3.4 48.0 1.0 N1 B:DG2 3.5 56.6 1.0 N1 B:DA4 3.5 56.3 1.0 C6 B:DG11 3.5 42.9 1.0 N1 B:DG31 3.6 48.5 1.0 N1 B:DG5 3.6 41.7 1.0 O6 B:DG1 3.6 56.4 1.0 O6 B:OMG6 3.7 45.3 1.0 N1 B:DG11 3.9 40.7 1.0 N1 B:DG10 3.9 48.6 1.0 C6 B:DA4 3.9 57.4 1.0 N6 B:DA4 4.0 58.2 1.0 C6 B:DG32 4.1 63.6 1.0 C2 B:DA4 4.1 55.4 1.0 C6 B:DG1 4.3 55.8 1.0 N1 B:DG32 4.4 63.5 1.0 C5 B:DG10 4.4 47.7 1.0 C6 B:OMG6 4.4 45.2 1.0 C5 B:DG31 4.5 52.7 1.0 N1 B:OMG6 4.5 44.4 1.0 C5 B:DG2 4.5 59.4 1.0 N1 B:DG1 4.6 54.9 1.0 O2 B:DUZ30 4.7 50.1 1.0 C5 B:DG5 4.7 41.0 1.0 N3 B:DUZ30 4.8 48.9 1.0 C5 B:DG11 4.8 41.8 1.0 C2 B:DG2 4.8 57.4 1.0 C2 B:DG31 4.9 49.4 1.0 N7 B:DG10 4.9 46.1 1.0 C5 B:DA4 4.9 58.5 1.0 C2 B:DG5 5.0 42.7 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