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Magnesium in PDB 4kln: Structure of P97 N-D1 A232E Mutant in Complex with Atpgs

Enzymatic activity of Structure of P97 N-D1 A232E Mutant in Complex with Atpgs

All present enzymatic activity of Structure of P97 N-D1 A232E Mutant in Complex with Atpgs:
3.6.4.6;

Protein crystallography data

The structure of Structure of P97 N-D1 A232E Mutant in Complex with Atpgs, PDB code: 4kln was solved by D.Xia, W.K.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.29 / 2.62
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 91.147, 104.514, 109.528, 98.11, 90.55, 92.72
R / Rfree (%) 27.4 / 28.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of P97 N-D1 A232E Mutant in Complex with Atpgs (pdb code 4kln). 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 A232E Mutant in Complex with Atpgs, PDB code: 4kln:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4kln

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Magnesium binding site 1 out of 6 in the Structure of P97 N-D1 A232E 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 A232E Mutant in Complex with Atpgs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:12.5
occ:1.00
 O A:HOH902 1.9 37.5 1.0
O A:HOH903 2.0 12.2 1.0
O2G A:AGS800 2.0 28.6 1.0
OG1 A:THR252 2.1 53.6 1.0
O A:HOH901 2.2 23.8 1.0
O1B A:AGS800 2.3 29.7 1.0
CB A:THR252 3.2 53.6 1.0
PG A:AGS800 3.3 27.2 1.0
PB A:AGS800 3.4 28.1 1.0
O3B A:AGS800 3.6 27.6 1.0
OD2 A:ASP304 3.6 49.1 1.0
O2A A:AGS800 4.0 29.3 1.0
OD1 A:ASP304 4.0 48.8 1.0
N A:THR252 4.0 53.8 1.0
O3G A:AGS800 4.1 27.9 1.0
CA A:THR252 4.2 53.7 1.0
CG A:ASP304 4.2 50.1 1.0
CG2 A:THR252 4.2 53.6 1.0
O3A A:AGS800 4.4 28.8 1.0
PA A:AGS800 4.6 29.4 1.0
O2B A:AGS800 4.6 29.3 1.0
CG A:GLU305 4.6 55.5 1.0
S1G A:AGS800 4.8 28.1 1.0
O1A A:AGS800 4.9 29.9 1.0
OE2 A:GLU305 5.0 57.0 1.0

Magnesium binding site 2 out of 6 in 4kln

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Magnesium binding site 2 out of 6 in the Structure of P97 N-D1 A232E 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 A232E Mutant in Complex with Atpgs within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:15.0
occ:1.00
 O B:HOH902 1.9 41.1 1.0
O2G B:AGS800 1.9 29.3 1.0
O B:HOH903 2.0 20.5 1.0
OG1 B:THR252 2.1 53.9 1.0
O B:HOH901 2.1 22.4 1.0
O1B B:AGS800 2.2 30.2 1.0
PG B:AGS800 3.2 28.6 1.0
CB B:THR252 3.3 54.4 1.0
PB B:AGS800 3.4 29.7 1.0
O3B B:AGS800 3.5 28.8 1.0
OD2 B:ASP304 3.7 61.6 1.0
O2A B:AGS800 4.0 29.3 1.0
O3G B:AGS800 4.1 29.0 1.0
N B:THR252 4.1 54.0 1.0
OD1 B:ASP304 4.1 64.0 1.0
CA B:THR252 4.2 55.2 1.0
CG2 B:THR252 4.3 55.2 1.0
CG B:ASP304 4.3 62.9 1.0
O3A B:AGS800 4.3 29.5 1.0
PA B:AGS800 4.6 29.4 1.0
O2B B:AGS800 4.6 30.2 1.0
CG B:GLU305 4.7 64.4 1.0
S1G B:AGS800 4.7 28.4 1.0
O1A B:AGS800 4.8 29.8 1.0

Magnesium binding site 3 out of 6 in 4kln

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Magnesium binding site 3 out of 6 in the Structure of P97 N-D1 A232E 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 A232E Mutant in Complex with Atpgs within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg801

b:13.2
occ:1.00
 O C:HOH902 1.9 41.6 1.0
O2G C:AGS800 2.0 26.8 1.0
O C:HOH903 2.0 20.5 1.0
OG1 C:THR252 2.0 44.9 1.0
O C:HOH901 2.1 13.7 1.0
O1B C:AGS800 2.2 25.9 1.0
CB C:THR252 3.2 44.5 1.0
PG C:AGS800 3.3 25.8 1.0
PB C:AGS800 3.4 25.3 1.0
O3B C:AGS800 3.6 25.0 1.0
OD2 C:ASP304 3.6 57.4 1.0
O2A C:AGS800 4.0 27.4 1.0
N C:THR252 4.1 43.6 1.0
O3G C:AGS800 4.1 26.4 1.0
OD1 C:ASP304 4.1 59.0 1.0
CA C:THR252 4.2 44.3 1.0
CG2 C:THR252 4.2 44.9 1.0
CG C:ASP304 4.3 58.4 1.0
O3A C:AGS800 4.3 25.3 1.0
PA C:AGS800 4.6 26.4 1.0
CG C:GLU305 4.7 62.5 1.0
O2B C:AGS800 4.7 27.0 1.0
S1G C:AGS800 4.8 26.9 1.0
O1A C:AGS800 4.8 25.3 1.0

Magnesium binding site 4 out of 6 in 4kln

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Magnesium binding site 4 out of 6 in the Structure of P97 N-D1 A232E 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 A232E Mutant in Complex with Atpgs within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg801

b:24.8
occ:1.00
 O D:HOH902 1.9 44.8 1.0
O2G D:AGS800 2.0 36.8 1.0
O D:HOH903 2.0 28.2 1.0
OG1 D:THR252 2.1 51.0 1.0
O D:HOH901 2.1 26.7 1.0
O1B D:AGS800 2.2 36.4 1.0
PG D:AGS800 3.3 34.8 1.0
CB D:THR252 3.3 50.2 1.0
PB D:AGS800 3.4 35.5 1.0
O3B D:AGS800 3.5 34.4 1.0
OD2 D:ASP304 3.6 65.5 1.0
O2A D:AGS800 4.0 38.3 1.0
N D:THR252 4.0 47.6 1.0
O3G D:AGS800 4.1 36.6 1.0
OD1 D:ASP304 4.1 67.0 1.0
CA D:THR252 4.2 49.5 1.0
CG D:ASP304 4.3 66.3 1.0
CG2 D:THR252 4.3 50.2 1.0
O3A D:AGS800 4.3 36.0 1.0
PA D:AGS800 4.6 39.0 1.0
O2B D:AGS800 4.6 36.3 1.0
CG D:GLU305 4.6 63.8 1.0
S1G D:AGS800 4.8 36.4 1.0
O1A D:AGS800 4.9 37.2 1.0

Magnesium binding site 5 out of 6 in 4kln

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Magnesium binding site 5 out of 6 in the Structure of P97 N-D1 A232E 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 A232E Mutant in Complex with Atpgs within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg801

b:19.6
occ:1.00
 O E:HOH902 2.0 44.9 1.0
O2G E:AGS800 2.0 42.4 1.0
O E:HOH903 2.0 28.1 1.0
OG1 E:THR252 2.1 66.9 1.0
O E:HOH901 2.1 37.1 1.0
O1B E:AGS800 2.2 40.0 1.0
PG E:AGS800 3.2 41.0 1.0
CB E:THR252 3.3 64.8 1.0
PB E:AGS800 3.4 41.0 1.0
O3B E:AGS800 3.5 40.5 1.0
OD2 E:ASP304 3.6 57.9 1.0
O2A E:AGS800 4.0 40.5 1.0
N E:THR252 4.1 63.1 1.0
O3G E:AGS800 4.1 41.6 1.0
OD1 E:ASP304 4.2 59.0 1.0
CA E:THR252 4.2 64.3 1.0
CG E:ASP304 4.3 58.6 1.0
CG2 E:THR252 4.3 65.6 1.0
O3A E:AGS800 4.3 39.9 1.0
PA E:AGS800 4.6 39.8 1.0
O2B E:AGS800 4.6 40.8 1.0
CG E:GLU305 4.7 61.2 1.0
S1G E:AGS800 4.8 42.0 1.0
O1A E:AGS800 4.9 39.5 1.0

Magnesium binding site 6 out of 6 in 4kln

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Magnesium binding site 6 out of 6 in the Structure of P97 N-D1 A232E 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 A232E Mutant in Complex with Atpgs within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg801

b:4.2
occ:1.00
 O F:HOH903 1.9 3.9 1.0
O F:HOH902 1.9 5.5 1.0
O2G F:AGS800 2.0 13.5 1.0
O F:HOH901 2.2 8.3 1.0
OG1 F:THR252 2.2 47.5 1.0
O1B F:AGS800 2.2 12.6 1.0
PG F:AGS800 3.2 12.8 1.0
CB F:THR252 3.3 47.5 1.0
PB F:AGS800 3.4 12.8 1.0
OD2 F:ASP304 3.5 37.1 1.0
O3B F:AGS800 3.5 12.7 1.0
N F:THR252 4.0 47.1 1.0
O2A F:AGS800 4.0 12.5 1.0
O3G F:AGS800 4.0 13.5 1.0
OD1 F:ASP304 4.1 36.6 1.0
CG F:ASP304 4.2 37.1 1.0
CA F:THR252 4.2 47.4 1.0
CG2 F:THR252 4.3 48.3 1.0
O3A F:AGS800 4.4 12.7 1.0
PA F:AGS800 4.6 12.9 1.0
O F:HOH913 4.6 69.6 1.0
O2B F:AGS800 4.6 12.3 1.0
CG F:GLU305 4.6 38.7 1.0
O1A F:AGS800 4.9 12.8 1.0
S1G F:AGS800 4.9 14.2 1.0

Reference:

W.K.Tang, D.Xia. Altered Intersubunit Communication Is the Molecular Basis For Functional Defects of Pathogenic P97 Mutants. J.Biol.Chem. V. 288 36624 2013.
ISSN: ISSN 0021-9258
PubMed: 24196964
DOI: 10.1074/JBC.M113.488924
Page generated: Mon Dec 14 19:03:22 2020

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