Magnesium in PDB 3hu1: Structure of P97 N-D1 R95G Mutant in Complex with Atpgs

The structure of Structure of P97 N-D1 R95G Mutant in Complex with Atpgs, PDB code: 3hu1 was solved by W.-K.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.81
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	92.756, 103.279, 107.688, 97.66, 91.88, 89.75
R / Rfree (%)	24 / 27.1

The binding sites of Magnesium atom in the Structure of P97 N-D1 R95G Mutant in Complex with Atpgs (pdb code 3hu1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of P97 N-D1 R95G Mutant in Complex with Atpgs, PDB code: 3hu1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of P97 N-D1 R95G Mutant in Complex with Atpgs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of P97 N-D1 R95G Mutant in Complex with Atpgs within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:55.7 occ:1.00 O2G A:AGS800 1.7 56.7 1.0 O1B A:AGS800 1.8 58.5 1.0 O A:HOH803 2.1 39.3 1.0 O A:HOH802 2.1 36.1 1.0 OG1 A:THR252 2.2 63.7 1.0 O A:HOH804 2.5 39.9 1.0 PG A:AGS800 2.8 53.3 1.0 PB A:AGS800 3.0 55.0 1.0 O3B A:AGS800 3.1 57.1 1.0 CB A:THR252 3.3 63.5 1.0 O1A A:AGS800 3.7 59.6 1.0 O3G A:AGS800 3.7 56.4 1.0 N A:THR252 3.9 63.4 1.0 O3A A:AGS800 4.0 59.2 1.0 O2B A:AGS800 4.1 58.3 1.0 CA A:THR252 4.2 63.3 1.0 PA A:AGS800 4.3 55.9 1.0 CG2 A:THR252 4.4 62.5 1.0 OD1 A:ASP304 4.4 63.8 1.0 S1G A:AGS800 4.5 54.9 1.0 OD2 A:ASP304 4.5 67.4 1.0 O2A A:AGS800 4.7 60.5 1.0 CG A:ASP304 4.9 65.8 1.0 CB A:LYS251 4.9 63.0 1.0 OE1 A:GLU305 5.0 68.5 1.0

Magnesium binding site 2 out of 6 in the Structure of P97 N-D1 R95G Mutant in Complex with Atpgs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of P97 N-D1 R95G Mutant in Complex with Atpgs within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:55.6 occ:1.00 O2G B:AGS800 1.7 56.9 1.0 O B:HOH804 1.8 34.7 1.0 O B:HOH802 1.9 36.4 1.0 O B:HOH803 2.0 34.4 1.0 O1B B:AGS800 2.2 59.2 1.0 OG1 B:THR252 2.2 63.3 1.0 PG B:AGS800 3.0 51.9 1.0 PB B:AGS800 3.3 55.1 1.0 O3B B:AGS800 3.3 56.8 1.0 CB B:THR252 3.4 63.1 1.0 O2A B:AGS800 3.7 60.4 1.0 O3G B:AGS800 3.9 56.4 1.0 N B:THR252 4.1 63.3 1.0 OD2 B:ASP304 4.2 67.5 1.0 O3A B:AGS800 4.2 59.4 1.0 OD1 B:ASP304 4.2 63.0 1.0 CA B:THR252 4.3 62.9 1.0 PA B:AGS800 4.4 56.1 1.0 CG2 B:THR252 4.4 62.8 1.0 S1G B:AGS800 4.4 54.7 1.0 O2B B:AGS800 4.5 58.1 1.0 CG B:ASP304 4.7 65.8 1.0 OE1 B:GLU305 4.8 69.4 1.0 O1A B:AGS800 4.8 60.3 1.0 CG B:GLU305 4.8 65.2 1.0 CB B:LYS251 4.9 63.2 1.0

Magnesium binding site 3 out of 6 in the Structure of P97 N-D1 R95G Mutant in Complex with Atpgs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of P97 N-D1 R95G Mutant in Complex with Atpgs within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg801 b:54.7 occ:1.00 O C:HOH803 1.8 57.2 1.0 O2G C:AGS800 1.8 57.5 1.0 O C:HOH804 2.0 70.0 1.0 OG1 C:THR252 2.0 63.9 1.0 O1B C:AGS800 2.0 58.6 1.0 O C:HOH802 2.2 43.0 1.0 PG C:AGS800 3.1 53.3 1.0 PB C:AGS800 3.2 54.6 1.0 CB C:THR252 3.2 63.7 1.0 O3B C:AGS800 3.4 56.7 1.0 O2A C:AGS800 3.7 59.5 1.0 O3G C:AGS800 4.0 56.5 1.0 N C:THR252 4.0 62.9 1.0 O3A C:AGS800 4.2 59.8 1.0 OD2 C:ASP304 4.2 66.6 1.0 CA C:THR252 4.2 63.1 1.0 CG2 C:THR252 4.2 62.3 1.0 OD1 C:ASP304 4.3 63.3 1.0 PA C:AGS800 4.4 57.1 1.0 O2B C:AGS800 4.4 58.4 1.0 S1G C:AGS800 4.6 55.0 1.0 CG C:ASP304 4.7 65.7 1.0 O1A C:AGS800 4.8 60.2 1.0 CB C:LYS251 5.0 63.0 1.0 CG C:GLU305 5.0 65.0 1.0

Magnesium binding site 4 out of 6 in the Structure of P97 N-D1 R95G Mutant in Complex with Atpgs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of P97 N-D1 R95G Mutant in Complex with Atpgs within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg801 b:55.2 occ:1.00 O2G D:AGS800 1.7 57.0 1.0 O1B D:AGS800 1.9 58.2 1.0 O D:HOH804 1.9 45.8 1.0 O D:HOH802 2.2 38.2 1.0 OG1 D:THR252 2.3 63.8 1.0 O D:HOH803 2.6 48.0 1.0 PG D:AGS800 2.8 53.0 1.0 PB D:AGS800 3.0 54.7 1.0 O3B D:AGS800 3.1 57.3 1.0 CB D:THR252 3.4 63.5 1.0 O3G D:AGS800 3.6 56.1 1.0 O2A D:AGS800 3.8 59.8 1.0 N D:THR252 3.9 63.5 1.0 O3A D:AGS800 4.0 60.1 1.0 CA D:THR252 4.2 63.4 1.0 O2B D:AGS800 4.2 57.8 1.0 OD1 D:ASP304 4.3 63.5 1.0 PA D:AGS800 4.3 54.9 1.0 S1G D:AGS800 4.4 54.4 1.0 OD2 D:ASP304 4.4 66.7 1.0 CG2 D:THR252 4.5 62.7 1.0 O1A D:AGS800 4.7 59.6 1.0 CG D:ASP304 4.8 65.7 1.0 CB D:LYS251 4.8 62.7 1.0 C D:LYS251 5.0 63.5 1.0

Magnesium binding site 5 out of 6 in the Structure of P97 N-D1 R95G Mutant in Complex with Atpgs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of P97 N-D1 R95G Mutant in Complex with Atpgs within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg801 b:54.9 occ:1.00 O2G E:AGS800 1.7 56.7 1.0 O E:HOH804 1.9 30.7 1.0 O1B E:AGS800 2.0 58.4 1.0 O E:HOH803 2.0 37.5 1.0 O E:HOH802 2.2 38.4 1.0 OG1 E:THR252 2.4 64.2 1.0 PG E:AGS800 2.9 51.8 1.0 PB E:AGS800 3.1 53.9 1.0 O3B E:AGS800 3.3 56.6 1.0 CB E:THR252 3.5 63.3 1.0 O1A E:AGS800 3.7 59.8 1.0 O3G E:AGS800 3.9 56.0 1.0 O3A E:AGS800 4.1 59.4 1.0 N E:THR252 4.2 63.0 1.0 O2B E:AGS800 4.3 57.9 1.0 S1G E:AGS800 4.3 54.4 1.0 PA E:AGS800 4.4 56.3 1.0 CA E:THR252 4.4 63.1 1.0 OD2 E:ASP304 4.5 67.4 1.0 OD1 E:ASP304 4.5 63.2 1.0 CG2 E:THR252 4.5 62.7 1.0 O2A E:AGS800 4.8 59.7 1.0 CG E:ASP304 4.9 65.8 1.0 CG E:GLU305 4.9 65.0 1.0

Magnesium binding site 6 out of 6 in the Structure of P97 N-D1 R95G Mutant in Complex with Atpgs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of P97 N-D1 R95G Mutant in Complex with Atpgs within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg801 b:55.1 occ:1.00 O2G F:AGS800 1.7 56.8 1.0 O1B F:AGS800 1.8 58.3 1.0 O F:HOH803 2.0 38.1 1.0 O F:HOH802 2.1 34.7 1.0 O F:HOH804 2.1 33.5 1.0 OG1 F:THR252 2.3 64.3 1.0 PG F:AGS800 2.9 51.2 1.0 PB F:AGS800 3.0 54.0 1.0 O3B F:AGS800 3.2 56.1 1.0 CB F:THR252 3.4 63.6 1.0 O1A F:AGS800 3.7 59.5 1.0 O3G F:AGS800 3.8 55.5 1.0 N F:THR252 4.0 63.3 1.0 O3A F:AGS800 4.0 59.4 1.0 O2B F:AGS800 4.2 57.8 1.0 CA F:THR252 4.3 63.3 1.0 OD1 F:ASP304 4.3 63.8 1.0 OD2 F:ASP304 4.3 67.1 1.0 PA F:AGS800 4.4 56.0 1.0 S1G F:AGS800 4.4 54.2 1.0 CG2 F:THR252 4.5 62.9 1.0 CG F:ASP304 4.8 65.6 1.0 O2A F:AGS800 4.8 59.4 1.0 CB F:LYS251 4.9 62.9 1.0 OE1 F:GLU305 4.9 68.3 1.0 CG F:GLU305 4.9 65.1 1.0

W.K.Tang, D.Li, C.C.Li, L.Esser, R.Dai, L.Guo, D.Xia. A Novel Atp-Dependent Conformation in P97 N-D1 Fragment Revealed By Crystal Structures of Disease-Related Mutants. Embo J. V. 29 2217 2010.
ISSN: ISSN 0261-4189
PubMed: 20512113
DOI: 10.1038/EMBOJ.2010.104