Magnesium in PDB 5kwb: Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement)

The structure of Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement), PDB code: 5kwb was solved by H.Guan, J.A.Wojdyla, M.Wang, S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.25 / 1.91
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	86.556, 183.800, 63.342, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.1

The binding sites of Magnesium atom in the Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement) (pdb code 5kwb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement), PDB code: 5kwb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement)


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 Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg706 b:26.3 occ:1.00 HB2 A:ARG531 2.8 34.8 1.0 HH11 A:ARG531 2.9 50.8 1.0 HD3 A:ARG531 2.9 50.1 1.0 CB A:ARG531 3.7 29.0 1.0 NH1 A:ARG531 3.7 42.3 1.0 CD A:ARG531 3.8 41.7 1.0 HG2 A:ARG531 3.8 38.4 1.0 CG A:ARG531 4.0 32.0 1.0 HH12 A:ARG531 4.1 50.8 1.0 HB3 A:ARG531 4.3 34.8 1.0 HD2 A:ARG531 4.3 50.1 1.0 HA A:ARG531 4.4 28.2 1.0 H A:ARG531 4.5 27.6 1.0 CA A:ARG531 4.6 23.5 1.0 CZ A:ARG531 4.7 39.7 1.0 NE A:ARG531 4.7 44.6 1.0 N A:ARG531 4.9 23.0 1.0 HG3 A:ARG531 5.0 38.4 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement)


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 Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg707 b:16.4 occ:1.00 HE A:ARG464 2.4 23.4 1.0 HH21 A:ARG464 2.5 31.6 1.0 HE2 A:PHE408 2.8 26.2 1.0 HE2 A:TYR462 3.1 24.1 1.0 OH A:TYR462 3.1 23.6 1.0 NE A:ARG464 3.2 19.5 1.0 NH2 A:ARG464 3.3 26.3 1.0 CE2 A:PHE408 3.5 21.9 1.0 HD2 A:PHE408 3.5 28.2 1.0 CZ A:ARG464 3.7 19.8 1.0 CE2 A:TYR462 3.8 20.1 1.0 HH A:TYR462 3.8 28.3 1.0 HG2 A:ARG464 3.8 25.1 1.0 CD2 A:PHE408 3.8 23.5 1.0 NH1 A:ARG397 3.8 24.6 1.0 CZ A:TYR462 3.9 20.9 1.0 HH22 A:ARG464 4.0 31.6 1.0 HB3 A:SER578 4.0 23.4 1.0 CD A:ARG464 4.3 27.0 1.0 CG A:ARG464 4.4 20.9 1.0 CZ A:ARG397 4.4 26.4 1.0 O A:HOH927 4.5 29.0 1.0 HB2 A:SER578 4.5 23.4 1.0 HG3 A:ARG464 4.5 25.1 1.0 HD3 A:ARG464 4.6 32.5 1.0 CZ A:PHE408 4.6 18.3 1.0 NH2 A:ARG397 4.6 23.9 1.0 CB A:SER578 4.6 19.5 1.0 HZ A:PHE408 4.7 22.0 1.0 O A:HOH861 4.9 21.8 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement)


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 Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg708 b:65.1 occ:1.00 HO2 A:SUC705 1.7 66.2 1.0 HD21 A:ASN670 1.9 51.8 1.0 HO3' A:SUC705 2.0 68.9 1.0 O2 A:SUC705 2.0 55.2 1.0 HD22 A:ASN670 2.4 51.8 1.0 H1'1 A:SUC705 2.4 56.6 1.0 ND2 A:ASN670 2.4 43.1 1.0 O1 A:SUC705 2.8 53.8 1.0 O3' A:SUC705 2.8 57.4 1.0 C2 A:SUC705 3.1 45.5 1.0 H3 A:SUC705 3.1 62.5 1.0 C1' A:SUC705 3.2 47.2 1.0 O A:HOH1041 3.2 49.9 1.0 C2' A:SUC705 3.3 57.0 1.0 C1 A:SUC705 3.4 49.3 1.0 C3 A:SUC705 3.5 52.1 1.0 HG11 A:VAL638 3.5 38.4 1.0 C3' A:SUC705 3.6 63.0 1.0 H1'2 A:SUC705 3.6 56.6 1.0 HZ A:PHE672 3.7 51.7 1.0 CG A:ASN670 3.7 41.7 1.0 H1 A:SUC705 3.7 59.2 1.0 HO3 A:SUC705 3.8 56.0 1.0 O3 A:SUC705 3.9 46.6 1.0 H2 A:SUC705 4.0 54.5 1.0 H3' A:SUC705 4.0 75.6 1.0 HG12 A:VAL638 4.1 38.4 1.0 CG1 A:VAL638 4.3 32.0 1.0 HB3 A:TYR642 4.3 29.8 1.0 OD1 A:ASN670 4.3 44.3 1.0 O1' A:SUC705 4.4 51.6 1.0 CZ A:PHE672 4.6 43.1 1.0 HB2 A:ASN670 4.7 43.7 1.0 O2' A:SUC705 4.7 51.4 1.0 O5 A:SUC705 4.7 39.4 1.0 CB A:ASN670 4.8 36.4 1.0 HG13 A:VAL638 4.8 38.4 1.0 C4' A:SUC705 4.9 52.5 1.0 C4 A:SUC705 4.9 56.1 1.0 H4' A:SUC705 4.9 63.0 1.0 HB3 A:ASN670 4.9 43.7 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement)


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 Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg709 b:46.7 occ:1.00 O A:HOH911 2.4 30.2 1.0 HG A:SER534 2.4 38.0 1.0 O A:HOH872 2.5 25.5 1.0 O A:HOH910 2.8 30.1 1.0 O A:HOH936 2.9 33.6 1.0 OG A:SER534 3.1 31.7 1.0 HB2 A:SER534 3.2 28.6 1.0 HA A:ARG502 3.2 26.1 1.0 HD1 A:PHE473 3.5 26.6 1.0 CB A:SER534 3.6 23.8 1.0 O A:HOH854 3.6 26.5 1.0 H A:SER503 3.8 25.9 1.0 O A:CYS474 3.8 16.9 1.0 HB3 A:SER534 3.8 28.6 1.0 HE1 A:PHE473 3.9 29.0 1.0 H A:CYS474 3.9 19.8 1.0 CD1 A:PHE473 4.1 22.2 1.0 O A:HOH1018 4.1 41.8 1.0 CA A:ARG502 4.1 21.7 1.0 O A:TYR501 4.2 23.9 1.0 CE1 A:PHE473 4.2 24.2 1.0 HA A:PHE473 4.3 28.0 1.0 N A:SER503 4.4 21.6 1.0 O A:ASN500 4.5 21.5 1.0 N A:ARG502 4.6 23.4 1.0 HG3 A:ARG502 4.6 28.6 1.0 HB2 A:ASN500 4.6 25.2 1.0 H A:SER534 4.6 27.4 1.0 C A:TYR501 4.7 21.4 1.0 N A:CYS474 4.7 16.5 1.0 C A:ARG502 4.8 25.9 1.0 HB2 A:SER503 4.8 37.6 1.0 C A:CYS474 4.9 23.7 1.0 OE2 A:GLU553 4.9 28.3 1.0 CA A:SER534 5.0 22.3 1.0 HB2 A:ARG502 5.0 26.4 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement)


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 Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg710 b:51.8 occ:1.00 O A:HOH1000 2.6 42.7 1.0 O A:CYS327 2.7 32.0 1.0 HD2 A:PHE349 3.0 31.7 1.0 HA A:CYS327 3.1 39.2 1.0 O A:HOH1059 3.2 33.6 1.0 HE2 A:PHE349 3.3 34.6 1.0 C A:CYS327 3.6 28.7 1.0 CD2 A:PHE349 3.6 26.4 1.0 CA A:CYS327 3.8 32.7 1.0 CE2 A:PHE349 3.8 28.8 1.0 HE2 A:LYS347 4.0 54.3 1.0 O A:HOH1094 4.0 49.8 1.0 HZ1 A:LYS347 4.0 80.4 1.0 HB2 A:ASP328 4.2 41.3 1.0 HB3 A:CYS327 4.2 39.3 1.0 O A:ASP326 4.3 35.3 1.0 HZ3 A:LYS347 4.5 80.4 1.0 NZ A:LYS347 4.6 67.0 1.0 CB A:CYS327 4.6 32.8 1.0 SG A:CYS352 4.6 32.0 1.0 HB3 A:CYS352 4.7 43.3 1.0 O A:HOH928 4.7 34.2 1.0 O A:HOH884 4.7 51.4 1.0 HA A:PHE349 4.7 30.0 1.0 CE A:LYS347 4.7 45.2 1.0 N A:ASP328 4.8 27.2 1.0 HB2 A:CYS352 4.8 43.3 1.0 CG A:PHE349 4.8 25.1 1.0 N A:CYS327 4.9 33.2 1.0 HB3 A:PHE349 4.9 30.7 1.0 CB A:CYS352 5.0 36.1 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-Ctd, 1.9 Angstrom, Molecular Replacement) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg711 b:45.8 occ:1.00 HG12 A:ILE595 2.0 49.5 1.0 HD22 A:ASN593 2.4 43.4 1.0 OD2 A:ASP389 2.8 22.1 1.0 CG1 A:ILE595 2.8 41.3 1.0 HG13 A:ILE595 2.8 49.5 1.0 O A:VAL387 3.1 24.4 1.0 ND2 A:ASN593 3.1 36.2 1.0 O A:ASN593 3.2 21.3 1.0 HH A:TYR414 3.2 26.4 1.0 CG A:ASP389 3.3 23.2 1.0 HB3 A:ASN593 3.3 27.6 1.0 H A:ASP389 3.3 22.0 1.0 HG12 A:VAL387 3.3 26.9 1.0 HD11 A:ILE595 3.4 62.0 1.0 H A:ILE595 3.4 25.0 1.0 HD21 A:ASN593 3.5 43.4 1.0 HB2 A:ASP389 3.6 23.3 1.0 CD1 A:ILE595 3.6 51.7 1.0 OH A:TYR414 3.6 22.0 1.0 C A:ASN593 3.7 21.2 1.0 N A:ILE595 3.7 20.9 1.0 N A:ASP389 3.8 18.3 1.0 HH21 A:ARG346 3.8 30.6 1.0 OD1 A:ASP389 3.8 21.0 1.0 C A:VAL387 3.9 28.6 1.0 HB A:ILE595 3.9 29.2 1.0 CB A:ILE595 3.9 24.3 1.0 HA A:LEU388 3.9 27.9 1.0 CB A:ASP389 3.9 19.4 1.0 CG A:ASN593 4.0 25.5 1.0 HD13 A:ILE595 4.0 62.0 1.0 CB A:ASN593 4.0 23.0 1.0 HB A:VAL387 4.0 33.1 1.0 CG1 A:VAL387 4.2 22.4 1.0 HA A:PHE594 4.2 25.3 1.0 C A:PHE594 4.2 22.6 1.0 HG11 A:VAL387 4.3 26.9 1.0 N A:PHE594 4.3 22.3 1.0 C A:LEU388 4.3 18.9 1.0 NH2 A:ARG346 4.4 25.5 1.0 CA A:ILE595 4.4 20.7 1.0 CA A:LEU388 4.4 23.3 1.0 HD12 A:ILE595 4.4 62.0 1.0 CA A:PHE594 4.4 21.1 1.0 N A:LEU388 4.5 22.8 1.0 CA A:ASN593 4.5 20.2 1.0 CB A:VAL387 4.5 27.6 1.0 O A:HOH974 4.5 26.2 1.0 CA A:ASP389 4.5 18.3 1.0 HE A:ARG346 4.6 28.9 1.0 HH22 A:ARG346 4.7 30.6 1.0 HB3 A:ASP389 4.8 23.3 1.0 HA A:ILE595 4.8 24.9 1.0 HB2 A:ASN593 4.8 27.6 1.0 O A:HOH1066 4.8 36.2 1.0 CA A:VAL387 4.9 20.7 1.0 O A:PHE594 4.9 27.6 1.0 HG13 A:VAL387 4.9 26.9 1.0 H A:ASN593 4.9 27.3 1.0 CZ A:TYR414 5.0 20.9 1.0 H A:PHE594 5.0 26.7 1.0

X.Ou, H.Guan, B.Qin, Z.Mu, J.A.Wojdyla, M.Wang, S.R.Dominguez, Z.Qian, S.Cui. Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 Nat Commun V. 8 15216 2017.
ISSN: ESSN 2041-1723
PubMed: 28534504
DOI: 10.1038/NCOMMS15216