Sodium in PDB 6b9j: Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138

The structure of Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138, PDB code: 6b9j was solved by D.M.Zajonc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	117.14 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	234.282, 253.842, 73.760, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 26.9

The binding sites of Sodium atom in the Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138 (pdb code 6b9j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138, PDB code: 6b9j:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138 within 5.0Å range: probe atom residue distance (Å) B Occ X:Na302 b:73.2 occ:1.00 ND1 X:HIS110 3.8 48.8 1.0 CE1 X:HIS110 4.5 49.9 1.0 CG X:HIS110 4.9 49.0 1.0

Sodium binding site 2 out of 7 in the Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138 within 5.0Å range: probe atom residue distance (Å) B Occ X:Na303 b:78.7 occ:1.00 NA X:NA304 2.9 79.4 1.0 CD2 X:HIS176 3.9 61.1 1.0 NH2 X:ARG220 4.0 80.4 1.0 CG X:HIS176 4.8 59.8 1.0 NE2 X:HIS176 4.9 60.0 1.0 CB X:HIS176 4.9 57.6 1.0

Sodium binding site 3 out of 7 in the Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138 within 5.0Å range: probe atom residue distance (Å) B Occ X:Na304 b:79.4 occ:1.00 NA X:NA303 2.9 78.7 1.0 NH2 X:ARG220 4.0 80.4 1.0 NH1 X:ARG220 4.8 76.4 1.0 CZ X:ARG220 4.9 76.2 1.0

Sodium binding site 4 out of 7 in the Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138 within 5.0Å range:

Sodium binding site 5 out of 7 in the Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:76.6 occ:1.00 O L:PRO45 3.9 78.3 1.0 N H:TRP107 4.1 72.2 1.0 O H:TRP107 4.3 75.1 1.0 CD2 H:PHE106 4.3 0.5 1.0 CE2 H:PHE106 4.4 0.7 1.0 CG H:PHE106 4.6 0.6 1.0 CZ H:PHE106 4.6 0.2 1.0 CA H:PHE106 4.7 82.0 1.0 CB H:TRP107 4.7 71.8 1.0 CA L:ARG46 4.8 86.0 1.0 CA H:TRP107 4.8 72.8 1.0 C H:PHE106 4.9 75.6 1.0 CD1 H:PHE106 4.9 0.6 1.0 CE1 H:PHE106 4.9 0.7 1.0 C L:PRO45 5.0 77.2 1.0 C H:TRP107 5.0 75.2 1.0

Sodium binding site 6 out of 7 in the Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138 within 5.0Å range: probe atom residue distance (Å) B Occ Y:Na302 b:70.4 occ:1.00 ND1 Y:HIS110 3.8 51.1 1.0 O Y:LYS109 4.2 47.6 1.0 CE1 Y:HIS110 4.6 53.0 1.0 CA Y:HIS110 4.8 48.0 1.0 CG Y:HIS110 4.8 50.5 1.0 CB Y:HIS110 4.9 49.4 1.0

Sodium binding site 7 out of 7 in the Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Vaccinia Virus D8 Protein Bound to Human Fab VV138 within 5.0Å range: probe atom residue distance (Å) B Occ Y:Na303 b:70.5 occ:1.00 CD2 Y:LEU21 4.0 0.6 1.0 CG Y:TYR232 4.2 71.7 1.0 CB Y:PHE56 4.2 80.7 1.0 CD1 Y:TYR232 4.2 72.0 1.0 CD2 Y:TYR232 4.3 74.7 1.0 CE1 Y:TYR232 4.4 76.3 1.0 CE2 Y:TYR232 4.5 76.0 1.0 CG Y:PHE56 4.6 90.4 1.0 CZ Y:TYR232 4.6 76.5 1.0 CB Y:TYR232 4.7 70.4 1.0 CD2 Y:PHE56 4.9 93.6 1.0

M.H.Matho, A.Schlossman, I.M.Gilchuk, G.Miller, Z.Mikulski, M.Hupfer, J.Wang, A.Bitra, X.Meng, Y.Xiang, T.Kaever, T.Doukov, K.Ley, S.Crotty, B.Peters, L.C.Hsieh-Wilson, J.E.Crowe, D.M.Zajonc. Structure-Function Characterization of Three Human Antibodies Targeting the Vaccinia Virus Adhesion Molecule D8. J. Biol. Chem. V. 293 390 2018.
ISSN: ESSN 1083-351X
PubMed: 29123031
DOI: 10.1074/JBC.M117.814541