Magnesium in PDB 3x0e: Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel)

The structure of Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel), PDB code: 3x0e was solved by M.Zhang, S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.61 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.124, 77.408, 38.497, 90.00, 107.94, 90.00
R / Rfree (%)	19.5 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel) (pdb code 3x0e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel), PDB code: 3x0e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:38.1 occ:1.00 H A:ALA143 2.3 27.0 1.0 O A:HOH452 2.5 38.5 1.0 HB3 A:ASN142 2.7 36.9 1.0 HA A:ALA140 2.8 38.1 1.0 O A:HOH444 2.8 33.1 1.0 H A:ASN142 3.0 29.1 1.0 HB1 A:ALA140 3.0 39.7 1.0 N A:ALA143 3.1 22.5 1.0 O A:HOH462 3.3 38.2 1.0 HB2 A:ALA143 3.3 22.6 1.0 CA A:ALA140 3.4 31.8 1.0 HE22 A:GLN133 3.4 27.3 1.0 N A:ASN142 3.5 24.2 1.0 CB A:ASN142 3.5 30.8 1.0 C A:ALA140 3.5 27.3 1.0 CB A:ALA140 3.6 33.1 1.0 NE2 A:GLN133 3.7 22.8 1.0 HB2 A:ASN142 3.7 36.9 1.0 HB3 A:ALA143 3.7 22.6 1.0 CA A:ASN142 3.8 29.1 1.0 CB A:ALA143 3.9 18.8 1.0 C A:ASN142 3.9 23.6 1.0 N A:ASN141 3.9 28.8 1.0 O A:ALA140 3.9 28.5 1.0 HB2 A:ALA140 3.9 39.7 1.0 HE21 A:GLN133 4.0 27.3 1.0 H A:ASN141 4.0 34.5 1.0 CA A:ALA143 4.0 22.2 1.0 CD A:GLN133 4.1 24.2 1.0 HD22 A:ASN142 4.2 48.7 1.0 OE1 A:GLN133 4.3 18.3 1.0 HB3 A:ALA140 4.4 39.7 1.0 C A:ASN141 4.4 26.3 1.0 HA A:ALA143 4.5 26.6 1.0 CG A:ASN142 4.7 37.5 1.0 MG A:MG303 4.7 41.6 1.0 N A:ALA140 4.7 24.8 1.0 HA A:ASN142 4.7 34.9 1.0 HG2 A:GLN133 4.8 28.5 1.0 HB1 A:ALA143 4.8 22.6 1.0 O A:ASP139 4.8 38.5 1.0 H A:LYS144 4.8 22.3 1.0 CA A:ASN141 4.8 36.6 1.0 ND2 A:ASN142 4.8 40.6 1.0 O A:HOH466 5.0 48.2 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:49.1 occ:1.00 O A:HOH410 2.5 23.4 1.0 HA A:THR153 3.3 23.3 1.0 O A:HOH424 3.4 30.2 1.0 O A:HOH454 3.5 36.1 1.0 O A:GLU152 3.8 20.5 1.0 O B:HOH423 4.1 33.0 1.0 HG2 A:GLU152 4.2 44.6 1.0 O A:THR153 4.2 17.9 1.0 CA A:THR153 4.3 19.4 1.0 O B:THR153 4.4 17.8 1.0 C A:GLU152 4.5 26.6 1.0 C A:THR153 4.6 18.8 1.0 HG3 A:GLU152 4.8 44.6 1.0 HG23 A:THR153 4.8 27.9 1.0 N A:THR153 4.8 17.3 1.0 CG A:GLU152 4.9 37.2 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:41.6 occ:1.00 HD22 A:ASN142 2.4 48.7 1.0 HA A:ALA143 2.9 26.6 1.0 ND2 A:ASN142 3.0 40.6 1.0 O A:HOH452 3.1 38.5 1.0 HD21 A:ASN142 3.2 48.7 1.0 HG21 A:VAL146 3.2 27.7 1.0 HB2 A:ALA143 3.6 22.6 1.0 CA A:ALA143 3.7 22.2 1.0 HB3 A:ASN142 3.8 36.9 1.0 N A:ALA143 3.8 22.5 1.0 HG23 A:VAL146 3.9 27.7 1.0 CG2 A:VAL146 4.0 23.1 1.0 O A:HOH404 4.0 23.9 1.0 HB2 A:ALA130 4.1 15.8 1.0 CG A:ASN142 4.1 37.5 1.0 CB A:ALA143 4.1 18.8 1.0 H A:ALA143 4.1 27.0 1.0 C A:ASN142 4.1 23.6 1.0 HB A:VAL146 4.2 22.5 1.0 O A:ASN142 4.3 19.9 1.0 HA A:ALA130 4.3 15.2 1.0 HB1 A:ALA130 4.4 15.8 1.0 HB1 A:ALA143 4.4 22.6 1.0 CB A:ASN142 4.4 30.8 1.0 HZ A:PHE126 4.4 25.3 1.0 O A:HOH402 4.5 19.2 1.0 CB A:ALA130 4.6 13.2 1.0 CB A:VAL146 4.6 18.8 1.0 HG11 A:VAL146 4.6 20.0 1.0 MG A:MG301 4.7 38.1 1.0 HG22 A:VAL146 4.7 27.7 1.0 O A:HOH466 4.8 48.2 1.0 OE1 A:GLN133 4.8 18.3 1.0 CZ A:PHE126 4.8 21.1 1.0 HB3 A:ALA143 4.9 22.6 1.0 CA A:ASN142 5.0 29.1 1.0 C A:ALA143 5.0 18.0 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:47.3 occ:1.00 O B:LYS201 2.5 37.5 1.0 O B:HOH440 3.1 37.6 1.0 HG23 A:THR149 3.1 32.1 1.0 HB3 B:ASP196 3.4 28.1 1.0 HG21 A:THR149 3.6 32.1 1.0 C B:LYS201 3.6 37.3 1.0 O B:HOH410 3.6 31.8 1.0 CG2 A:THR149 3.8 26.8 1.0 O B:HOH424 3.9 32.9 1.0 HB2 B:ASP196 4.1 28.1 1.0 CB B:ASP196 4.2 23.4 1.0 HA B:LEU197 4.3 23.9 1.0 HG22 A:THR149 4.3 32.1 1.0 OG1 A:THR153 4.3 17.8 1.0 HG1 A:THR153 4.4 21.4 1.0 O A:HOH454 4.5 36.1 1.0 O B:ASP196 4.6 19.6 1.0 O B:HOH431 4.6 34.0 1.0 C B:ASP196 4.6 21.5 1.0 OG1 A:THR149 4.6 29.8 1.0 N B:LEU197 4.8 19.1 1.0 HD2 B:LYS193 4.8 25.3 1.0 CB A:THR149 4.9 23.6 1.0 H B:LYS201 4.9 36.6 1.0 CA B:LYS201 4.9 33.7 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Ectodomain of Human CD81 Large Extracellular Loop (HCD81-Lel) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:73.6 occ:1.00 O B:HOH452 2.4 47.8 1.0 O B:HOH446 2.7 42.1 1.0 HB1 B:ALA140 4.2 92.7 1.0 HB2 B:ASN142 4.5 69.9 1.0 H B:ASN142 4.6 88.0 1.0 H B:ASN141 4.6 0.5 1.0 HB2 B:ASN141 4.9 0.1 1.0

W.Yang, M.Zhang, X.Chi, X.Liu, B.Qin, S.Cui. An Intramolecular Bond at Cluster of Differentiation 81 Ectodomain Is Important For Hepatitis C Virus Entry Faseb J. 2015.
ISSN: ESSN 1530-6860
PubMed: 26116703
DOI: 10.1096/FJ.15-272880