Magnesium in PDB 6lcd: Crystal Structure of Aatps with Ppi

The structure of Crystal Structure of Aatps with Ppi, PDB code: 6lcd was solved by H.He, T.Mori, I.Abe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.75 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.492, 113.688, 149.915, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 28.3

The binding sites of Magnesium atom in the Crystal Structure of Aatps with Ppi (pdb code 6lcd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Aatps with Ppi, PDB code: 6lcd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Aatps with Ppi


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 Aatps with Ppi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:79.9 occ:1.00 O3B A:FPP501 2.6 89.2 0.7 NZ A:LYS314 2.7 77.0 1.0 CD A:ARG401 2.8 74.9 1.0 NE A:ARG401 2.9 82.5 1.0 CG A:ARG401 3.2 74.0 1.0 O1A A:FPP501 3.4 66.6 0.7 PB A:FPP501 3.8 95.8 0.7 O2A A:FPP501 3.9 91.7 0.7 PA A:FPP501 3.9 80.8 0.7 CE A:LYS314 4.1 82.5 1.0 CZ A:ARG401 4.2 83.6 1.0 O3A A:FPP501 4.2 75.8 0.7 O1B A:FPP501 4.3 94.0 0.7 CD1 A:PHE146 4.6 83.1 1.0 CE1 A:PHE146 4.6 78.4 1.0 CB A:ARG401 4.7 66.6 1.0 O A:HOH601 4.7 74.5 1.0 NH2 A:ARG401 4.8 78.5 1.0 CE1 A:TYR402 4.8 62.4 1.0 CD A:LYS314 4.8 70.7 1.0 OH A:TYR402 4.9 64.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Aatps with Ppi


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 Aatps with Ppi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:72.9 occ:1.00 O1 A:FPP501 3.0 76.2 0.7 O2A A:FPP501 3.4 91.7 0.7 PA A:FPP501 3.6 80.8 0.7 NH2 A:ARG264 3.6 68.8 1.0 O3A A:FPP501 3.7 75.8 0.7 MG A:MG504 3.7 77.3 1.0 NH1 A:ARG264 3.8 63.9 1.0 OD2 A:ASP267 3.8 67.7 1.0 CZ A:ARG264 4.2 67.5 1.0 O A:HOH601 4.2 74.5 1.0 O1B A:FPP501 4.4 94.0 0.7 OD1 A:ASN307 4.5 47.8 1.0 PB A:FPP501 4.7 95.8 0.7 CG A:ASP267 4.9 74.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Aatps with Ppi


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 Aatps with Ppi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:77.3 occ:1.00 OE1 A:GLU315 2.3 71.4 1.0 OD1 A:ASN307 2.9 47.8 1.0 O3A A:FPP501 3.0 75.8 0.7 OG A:SER311 3.1 52.2 1.0 O1 A:FPP501 3.2 76.2 0.7 NH2 A:ARG264 3.2 68.8 1.0 CD A:GLU315 3.5 69.0 1.0 MG A:MG503 3.7 72.9 1.0 O2B A:FPP501 3.8 83.6 0.7 PA A:FPP501 3.8 80.8 0.7 CB A:SER311 3.9 58.1 1.0 OD1 A:ASP308 4.0 59.2 1.0 CG A:ASN307 4.0 45.6 1.0 PB A:FPP501 4.1 95.8 0.7 OE2 A:GLU315 4.1 72.3 1.0 CZ A:ARG264 4.2 67.5 1.0 O A:ASN307 4.5 49.2 1.0 CG A:GLU315 4.6 68.2 1.0 ND2 A:ASN307 4.6 52.4 1.0 O1A A:FPP501 4.7 66.6 0.7 O1B A:FPP501 4.8 94.0 0.7 O2A A:FPP501 4.9 91.7 0.7 NH1 A:ARG264 4.9 63.9 1.0 C A:ASN307 4.9 49.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Aatps with Ppi


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 Aatps with Ppi within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:63.1 occ:1.00 OE2 B:GLU315 2.4 59.6 1.0 OD1 B:ASN307 2.6 57.8 1.0 OG B:SER311 3.0 47.0 1.0 NH2 B:ARG264 3.2 73.5 1.0 CD B:GLU315 3.6 52.3 1.0 CG B:ASN307 3.6 47.2 1.0 O3A B:FPP501 3.7 93.3 0.8 O1A B:FPP501 3.9 77.2 0.8 O3B B:FPP501 3.9 93.5 0.8 CB B:SER311 3.9 48.6 1.0 OD1 B:ASP308 4.0 50.7 1.0 ND2 B:ASN307 4.1 52.5 1.0 CZ B:ARG264 4.2 65.6 1.0 OE1 B:GLU315 4.2 55.2 1.0 PA B:FPP501 4.3 88.3 0.8 O1 B:FPP501 4.3 88.6 0.8 NH1 B:ARG264 4.4 72.1 1.0 O B:ASN307 4.4 49.3 1.0 PB B:FPP501 4.5 0.8 0.8 CG B:GLU315 4.8 48.6 1.0 C B:ASN307 4.8 48.0 1.0 CB B:ASN307 4.9 39.0 1.0

H.He, T.Mori, I.Abe. Crystal Structure of Aatps Nat Commun 2020.
ISSN: ESSN 2041-1723