Cadmium in PDB 8pxj: Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A

The structure of Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A, PDB code: 8pxj was solved by K.El Omari, R.Duman, V.Mykhaylyk, C.Orr, T.A.Bowden, A.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.30 / 2.75
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	106.83, 106.83, 74.86, 90, 90, 120
R / Rfree (%)	24.9 / 27.6

The binding sites of Cadmium atom in the Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A (pdb code 8pxj). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A, PDB code: 8pxj:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:97.6 occ:1.00 OD1 A:ASP154 2.4 82.4 1.0 CD2 A:HIS156 2.9 113.6 1.0 CG A:ASP154 3.1 78.3 1.0 CG A:HIS156 3.2 104.6 1.0 OD2 A:ASP154 3.3 81.3 1.0 NE2 A:HIS156 3.4 139.0 1.0 CB A:HIS156 3.7 94.7 1.0 ND1 A:HIS156 3.8 117.9 1.0 N A:HIS156 3.9 93.9 1.0 CE1 A:HIS156 4.0 132.9 1.0 CB A:ASP154 4.2 84.2 1.0 N A:HIS155 4.3 96.2 1.0 CA A:ASP154 4.4 91.0 1.0 CA A:HIS156 4.4 87.8 1.0 C A:ASP154 4.7 89.4 1.0 C A:HIS155 4.9 98.5 1.0

Cadmium binding site 2 out of 6 in the Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:105.5 occ:1.00 NE2 A:HIS155 2.3 118.2 1.0 CE1 A:HIS155 2.9 117.7 1.0 CD2 A:HIS155 3.4 119.0 1.0 ND1 A:HIS155 4.1 113.5 1.0 CG A:HIS155 4.4 116.8 1.0 O A:HIS153 4.6 109.3 1.0 O1 A:SO4311 4.7 196.5 0.5

Cadmium binding site 3 out of 6 in the Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd306 b:117.6 occ:1.00 OD2 A:ASP181 2.4 124.4 1.0 O A:HIS156 2.4 107.8 1.0 NE2 A:HIS182 2.5 105.8 1.0 CD2 A:HIS182 3.2 97.6 1.0 CE1 A:HIS182 3.4 108.5 1.0 C A:HIS156 3.4 88.6 1.0 CG A:ASP181 3.6 116.0 1.0 OD1 A:ASP181 4.0 132.9 1.0 OG1 A:THR158 4.0 94.9 1.0 N A:THR158 4.2 97.1 1.0 CG A:HIS182 4.2 99.0 1.0 CA A:HIS156 4.3 87.8 1.0 N A:PHE157 4.3 87.1 1.0 ND1 A:HIS182 4.3 111.0 1.0 CA A:PHE157 4.3 85.8 1.0 CB A:HIS156 4.6 94.7 1.0 O2 A:SO4310 4.7 177.4 1.0 NE2 A:GLN185 4.8 105.3 1.0 C A:PHE157 4.8 94.2 1.0 CB A:ASP181 4.9 116.4 1.0

Cadmium binding site 4 out of 6 in the Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd307 b:144.5 occ:1.00 NE2 A:HIS91 2.1 144.7 1.0 CD2 A:HIS91 2.5 133.9 1.0 CE1 A:HIS91 3.3 148.4 1.0 OE1 A:GLU107 3.4 145.2 1.0 CG A:HIS91 3.7 142.9 1.0 ND1 A:HIS91 4.1 139.4 1.0 CB A:GLU107 4.5 119.3 1.0 CD A:GLU107 4.5 154.7 1.0 C5 A:NAG301 4.5 136.2 1.0 CE A:LYS105 4.6 160.8 1.0 NZ A:LYS105 4.6 169.8 1.0 O4 A:NAG301 4.7 157.7 1.0 C6 A:NAG301 4.9 127.6 1.0 CB A:HIS91 5.0 139.1 1.0

Cadmium binding site 5 out of 6 in the Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd308 b:101.8 occ:0.33 OE1 A:GLU99 2.2 118.3 1.0 CD A:GLU99 2.9 124.7 1.0 OE2 A:GLU99 3.0 146.8 1.0 CG A:GLU99 4.3 110.9 1.0

Cadmium binding site 6 out of 6 in the Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Whitewater Arroyo Virus GP1 Glycoprotein, Solved at Wavelength 2.75 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd309 b:236.7 occ:0.50 O A:THR202 3.6 145.4 1.0 O A:CYS201 3.9 160.2 1.0 OE2 A:GLU180 3.9 198.8 1.0 CD A:GLU180 4.0 206.8 1.0 OE1 A:GLU180 4.1 220.3 1.0 C A:THR202 4.5 148.6 1.0 CG A:GLU180 4.8 193.3 1.0 CA A:THR202 4.8 148.4 1.0

K.El Omari, R.Duman, V.Mykhaylyk, C.M.Orr, M.Latimer-Smith, G.Winter, V.Grama, F.Qu, K.Bountra, H.S.Kwong, M.Romano, R.I.Reis, L.Vogeley, L.Vecchia, C.D.Owen, S.Wittmann, M.Renner, M.Senda, N.Matsugaki, Y.Kawano, T.A.Bowden, I.Moraes, J.M.Grimes, E.J.Mancini, M.A.Walsh, C.R.Guzzo, R.J.Owens, E.Y.Jones, D.G.Brown, D.I.Stuart, K.Beis, A.Wagner. Experimental Phasing Opportunities For Macromolecular Crystallography at Very Long Wavelengths. Commun Chem V. 6 219 2023.
ISSN: ESSN 2399-3669
PubMed: 37828292
DOI: 10.1038/S42004-023-01014-0