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Magnesium in PDB 3hu2: Structure of P97 N-D1 R86A Mutant in Complex with Atpgs

Protein crystallography data

The structure of Structure of P97 N-D1 R86A Mutant in Complex with Atpgs, PDB code: 3hu2 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) 40.00 / 2.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 90.892, 102.645, 107.182, 97.52, 90.63, 91.45
R / Rfree (%) 25.8 / 29

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of P97 N-D1 R86A Mutant in Complex with Atpgs (pdb code 3hu2). 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 R86A Mutant in Complex with Atpgs, PDB code: 3hu2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3hu2

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Magnesium binding site 1 out of 6 in the Structure of P97 N-D1 R86A 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 R86A Mutant in Complex with Atpgs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:61.7
occ:1.00
 O2G A:AGS800 1.8 64.2 1.0
O1B A:AGS800 1.9 65.9 1.0
O A:HOH804 1.9 55.9 1.0
O A:HOH802 1.9 34.3 1.0
O A:HOH803 2.2 71.8 1.0
OG1 A:THR252 2.2 69.5 1.0
PG A:AGS800 3.0 61.5 1.0
PB A:AGS800 3.1 61.0 1.0
O3B A:AGS800 3.3 64.3 1.0
CB A:THR252 3.4 68.5 1.0
O3A A:AGS800 3.8 64.4 1.0
O3G A:AGS800 3.9 64.9 1.0
O1A A:AGS800 4.0 65.1 1.0
N A:THR252 4.0 68.3 1.0
OD1 A:ASP304 4.3 69.2 1.0
OD2 A:ASP304 4.3 70.3 1.0
O2B A:AGS800 4.3 64.8 1.0
PA A:AGS800 4.3 60.6 1.0
CA A:THR252 4.3 68.7 1.0
CG2 A:THR252 4.4 68.1 1.0
S1G A:AGS800 4.5 62.5 1.0
O2A A:AGS800 4.6 65.5 1.0
CG A:ASP304 4.7 70.4 1.0
CB A:LYS251 4.9 68.8 1.0

Magnesium binding site 2 out of 6 in 3hu2

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Magnesium binding site 2 out of 6 in the Structure of P97 N-D1 R86A 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 R86A Mutant in Complex with Atpgs within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:61.3
occ:1.00
 O2G B:AGS800 1.8 64.2 1.0
O B:HOH802 2.0 51.8 1.0
O1B B:AGS800 2.0 65.7 1.0
O B:HOH804 2.0 38.8 1.0
O B:HOH803 2.1 50.6 1.0
OG1 B:THR252 2.3 70.0 1.0
PG B:AGS800 2.9 60.7 1.0
PB B:AGS800 3.2 61.3 1.0
O3B B:AGS800 3.3 64.1 1.0
CB B:THR252 3.4 68.7 1.0
O3G B:AGS800 3.7 64.8 1.0
O1A B:AGS800 3.9 66.2 1.0
O3A B:AGS800 3.9 64.4 1.0
N B:THR252 4.2 68.4 1.0
CA B:THR252 4.3 69.0 1.0
OD1 B:ASP304 4.4 69.9 1.0
PA B:AGS800 4.4 61.1 1.0
CG2 B:THR252 4.4 68.0 1.0
OD2 B:ASP304 4.4 70.2 1.0
O2B B:AGS800 4.5 64.9 1.0
S1G B:AGS800 4.5 62.5 1.0
O2A B:AGS800 4.7 65.7 1.0
CG B:ASP304 4.8 70.3 1.0
CG B:GLU305 4.9 70.9 1.0

Magnesium binding site 3 out of 6 in 3hu2

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Magnesium binding site 3 out of 6 in the Structure of P97 N-D1 R86A 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 R86A Mutant in Complex with Atpgs within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg801

b:61.6
occ:1.00
 O2G C:AGS800 1.6 64.4 1.0
O C:HOH804 2.1 40.7 1.0
O C:HOH802 2.1 53.4 1.0
OG1 C:THR252 2.1 70.1 1.0
O1B C:AGS800 2.2 65.8 1.0
O C:HOH803 2.6 61.2 1.0
PG C:AGS800 2.9 61.3 1.0
PB C:AGS800 3.3 60.9 1.0
CB C:THR252 3.4 68.6 1.0
O3B C:AGS800 3.5 64.4 1.0
O3G C:AGS800 3.7 65.0 1.0
O2A C:AGS800 4.0 65.7 1.0
OD2 C:ASP304 4.0 70.0 1.0
O3A C:AGS800 4.1 64.3 1.0
OD1 C:ASP304 4.2 68.8 1.0
N C:THR252 4.2 68.3 1.0
CG2 C:THR252 4.3 68.2 1.0
CA C:THR252 4.4 68.8 1.0
S1G C:AGS800 4.4 62.3 1.0
CG C:ASP304 4.5 70.4 1.0
PA C:AGS800 4.6 61.0 1.0
O2B C:AGS800 4.6 65.2 1.0
CG C:GLU305 4.8 70.8 1.0

Magnesium binding site 4 out of 6 in 3hu2

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Magnesium binding site 4 out of 6 in the Structure of P97 N-D1 R86A 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 R86A Mutant in Complex with Atpgs within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg801

b:61.8
occ:1.00
 O2G D:AGS800 1.7 64.7 1.0
O1B D:AGS800 1.9 65.7 1.0
O D:HOH804 2.0 50.2 1.0
O D:HOH803 2.1 38.3 1.0
OG1 D:THR252 2.2 70.2 1.0
PG D:AGS800 2.8 61.9 1.0
PB D:AGS800 3.0 62.0 1.0
O3B D:AGS800 3.2 64.7 1.0
CB D:THR252 3.4 68.6 1.0
O D:HOH802 3.4 51.9 1.0
O3G D:AGS800 3.7 64.4 1.0
O2A D:AGS800 3.8 65.8 1.0
O3A D:AGS800 3.8 64.0 1.0
N D:THR252 4.1 68.9 1.0
PA D:AGS800 4.3 61.7 1.0
CA D:THR252 4.3 68.9 1.0
O2B D:AGS800 4.3 65.2 1.0
OD2 D:ASP304 4.4 70.1 1.0
OD1 D:ASP304 4.4 70.0 1.0
S1G D:AGS800 4.4 63.9 1.0
CG2 D:THR252 4.4 68.1 1.0
O1A D:AGS800 4.7 65.6 1.0
CG D:ASP304 4.8 70.5 1.0
CB D:LYS251 5.0 68.3 1.0
CG D:GLU305 5.0 70.6 1.0

Magnesium binding site 5 out of 6 in 3hu2

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Magnesium binding site 5 out of 6 in the Structure of P97 N-D1 R86A 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 R86A Mutant in Complex with Atpgs within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg801

b:60.6
occ:1.00
 O2G E:AGS800 1.8 64.1 1.0
O1B E:AGS800 1.9 65.5 1.0
O E:HOH804 2.0 39.3 1.0
O E:HOH803 2.1 40.4 1.0
O E:HOH802 2.1 50.8 1.0
OG1 E:THR252 2.2 70.8 1.0
PG E:AGS800 2.9 60.6 1.0
PB E:AGS800 3.1 60.0 1.0
O3B E:AGS800 3.3 64.6 1.0
CB E:THR252 3.4 68.7 1.0
O1A E:AGS800 3.8 65.3 1.0
O3A E:AGS800 3.8 64.4 1.0
O3G E:AGS800 3.8 63.9 1.0
N E:THR252 4.2 68.4 1.0
PA E:AGS800 4.2 61.4 1.0
CA E:THR252 4.4 68.8 1.0
O2B E:AGS800 4.4 64.5 1.0
CG2 E:THR252 4.4 68.3 1.0
OD1 E:ASP304 4.4 69.8 1.0
S1G E:AGS800 4.5 63.8 1.0
OD2 E:ASP304 4.5 70.3 1.0
O2A E:AGS800 4.6 65.5 1.0
CG E:ASP304 4.8 70.8 1.0
CB E:LYS251 5.0 68.2 1.0

Magnesium binding site 6 out of 6 in 3hu2

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Magnesium binding site 6 out of 6 in the Structure of P97 N-D1 R86A 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 R86A Mutant in Complex with Atpgs within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg801

b:61.4
occ:1.00
 O2G F:AGS800 1.7 64.2 1.0
O1B F:AGS800 1.9 65.6 1.0
O F:HOH804 2.0 35.6 1.0
OG1 F:THR252 2.2 70.5 1.0
O F:HOH803 2.3 35.9 1.0
O F:HOH802 2.5 40.6 1.0
PG F:AGS800 2.8 60.8 1.0
PB F:AGS800 3.1 61.4 1.0
O3B F:AGS800 3.3 64.5 1.0
CB F:THR252 3.4 68.8 1.0
O3G F:AGS800 3.7 64.2 1.0
O3A F:AGS800 4.0 63.8 1.0
O1A F:AGS800 4.0 65.5 1.0
N F:THR252 4.1 68.8 1.0
CA F:THR252 4.3 68.8 1.0
O2B F:AGS800 4.3 65.0 1.0
OD1 F:ASP304 4.3 69.4 1.0
CG2 F:THR252 4.4 68.5 1.0
OD2 F:ASP304 4.4 70.0 1.0
PA F:AGS800 4.4 61.5 1.0
S1G F:AGS800 4.4 62.3 1.0
CG F:ASP304 4.7 70.1 1.0
O2A F:AGS800 4.7 65.3 1.0
CG F:GLU305 4.9 70.5 1.0
CB F:LYS251 4.9 68.7 1.0

Reference:

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
Page generated: Wed Aug 14 15:21:26 2024

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