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Magnesium in PDB 7jy5: Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97)

Enzymatic activity of Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97)

All present enzymatic activity of Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97):
3.6.4.6;

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97) (pdb code 7jy5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97), PDB code: 7jy5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 7jy5

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Magnesium binding site 1 out of 12 in the Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:19.1
occ:1.00
 OG1 A:THR252 1.9 21.3 1.0
O3G A:AGS903 2.0 33.8 1.0
O2B A:AGS903 2.3 33.8 1.0
CB A:THR252 3.1 21.3 1.0
PG A:AGS903 3.5 33.8 1.0
OE2 A:GLU305 3.5 15.8 1.0
OD2 A:ASP304 3.7 13.9 1.0
PB A:AGS903 3.7 33.8 1.0
OD1 A:ASP304 3.8 13.9 1.0
CG2 A:THR252 3.9 21.3 1.0
O3B A:AGS903 4.1 33.8 1.0
CG A:ASP304 4.1 13.9 1.0
O2A A:AGS903 4.2 33.8 1.0
CA A:THR252 4.3 21.3 1.0
N A:THR252 4.3 21.3 1.0
CD A:GLU305 4.3 15.8 1.0
S1G A:AGS903 4.4 33.8 1.0
O2G A:AGS903 4.5 33.8 1.0
O1B A:AGS903 4.5 33.8 1.0
O1A A:AGS903 4.7 33.8 1.0
O3A A:AGS903 4.8 33.8 1.0
PA A:AGS903 4.8 33.8 1.0
OE1 A:GLU305 4.8 15.8 1.0

Magnesium binding site 2 out of 12 in 7jy5

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Magnesium binding site 2 out of 12 in the Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:24.7
occ:1.00
 O3G A:AGS904 2.1 33.8 1.0
OG1 A:THR525 2.1 23.4 1.0
O3A A:AGS904 2.4 33.8 1.0
O2B A:AGS904 2.6 33.8 1.0
PB A:AGS904 3.1 33.8 1.0
CB A:THR525 3.1 23.4 1.0
PG A:AGS904 3.5 33.8 1.0
OD2 A:ASP577 3.6 21.1 1.0
PA A:AGS904 3.8 33.8 1.0
O3B A:AGS904 3.8 33.8 1.0
CG2 A:THR525 3.9 23.4 1.0
O5' A:AGS904 4.1 33.8 1.0
O2A A:AGS904 4.2 33.8 1.0
CA A:THR525 4.3 23.4 1.0
S1G A:AGS904 4.3 33.8 1.0
O1B A:AGS904 4.4 33.8 1.0
N A:THR525 4.4 23.4 1.0
CG A:ASP577 4.4 21.1 1.0
OD1 A:ASP577 4.4 21.1 1.0
NH1 F:ARG635 4.5 18.1 1.0
O2G A:AGS904 4.6 33.8 1.0
CD F:ARG635 4.7 18.1 1.0
O1A A:AGS904 4.8 33.8 1.0

Magnesium binding site 3 out of 12 in 7jy5

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Magnesium binding site 3 out of 12 in the Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:20.3
occ:1.00
 OG1 B:THR252 1.9 22.7 1.0
O3G B:AGS903 2.0 33.8 1.0
O2B B:AGS903 2.2 33.8 1.0
CB B:THR252 3.1 22.7 1.0
PG B:AGS903 3.5 33.8 1.0
OE2 B:GLU305 3.6 18.9 1.0
PB B:AGS903 3.7 33.8 1.0
OD2 B:ASP304 3.7 14.5 1.0
OD1 B:ASP304 3.8 14.5 1.0
CG2 B:THR252 3.9 22.7 1.0
O2A B:AGS903 4.0 33.8 1.0
O3B B:AGS903 4.1 33.8 1.0
CG B:ASP304 4.2 14.5 1.0
CA B:THR252 4.2 22.7 1.0
N B:THR252 4.3 22.7 1.0
S1G B:AGS903 4.3 33.8 1.0
CD B:GLU305 4.4 18.9 1.0
O1B B:AGS903 4.5 33.8 1.0
O2G B:AGS903 4.5 33.8 1.0
O3A B:AGS903 4.6 33.8 1.0
PA B:AGS903 4.7 33.8 1.0
O1A B:AGS903 4.9 33.8 1.0
OE1 B:GLU305 4.9 18.9 1.0

Magnesium binding site 4 out of 12 in 7jy5

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Magnesium binding site 4 out of 12 in the Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:24.7
occ:1.00
 O3G B:AGS904 2.1 33.8 1.0
OG1 B:THR525 2.2 22.8 1.0
O3A B:AGS904 2.4 33.8 1.0
O2B B:AGS904 2.7 33.8 1.0
CB B:THR525 3.1 22.8 1.0
PB B:AGS904 3.2 33.8 1.0
PG B:AGS904 3.5 33.8 1.0
OD2 B:ASP577 3.6 25.5 1.0
PA B:AGS904 3.8 33.8 1.0
O3B B:AGS904 3.8 33.8 1.0
CG2 B:THR525 3.8 22.8 1.0
O5' B:AGS904 4.0 33.8 1.0
O2A B:AGS904 4.2 33.8 1.0
S1G B:AGS904 4.3 33.8 1.0
CA B:THR525 4.4 22.8 1.0
NH1 A:ARG635 4.4 17.6 1.0
N B:THR525 4.4 22.8 1.0
O1B B:AGS904 4.5 33.8 1.0
CG B:ASP577 4.5 25.5 1.0
OD1 B:ASP577 4.5 25.5 1.0
O2G B:AGS904 4.6 33.8 1.0
CD A:ARG635 4.7 17.6 1.0
O1A B:AGS904 4.9 33.8 1.0

Magnesium binding site 5 out of 12 in 7jy5

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Magnesium binding site 5 out of 12 in the Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg901

b:21.0
occ:1.00
 OG1 C:THR252 1.9 22.6 1.0
O3G C:AGS903 2.0 33.8 1.0
O2B C:AGS903 2.3 33.8 1.0
CB C:THR252 3.2 22.6 1.0
PG C:AGS903 3.5 33.8 1.0
OE2 C:GLU305 3.5 16.0 1.0
OD2 C:ASP304 3.7 13.8 1.0
PB C:AGS903 3.7 33.8 1.0
OD1 C:ASP304 3.8 13.8 1.0
CG2 C:THR252 3.9 22.6 1.0
O2A C:AGS903 3.9 33.8 1.0
O3B C:AGS903 4.1 33.8 1.0
CG C:ASP304 4.1 13.8 1.0
CA C:THR252 4.3 22.6 1.0
N C:THR252 4.3 22.6 1.0
CD C:GLU305 4.3 16.0 1.0
S1G C:AGS903 4.4 33.8 1.0
O1B C:AGS903 4.4 33.8 1.0
O2G C:AGS903 4.5 33.8 1.0
O3A C:AGS903 4.7 33.8 1.0
PA C:AGS903 4.8 33.8 1.0
OE1 C:GLU305 4.8 16.0 1.0

Magnesium binding site 6 out of 12 in 7jy5

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Magnesium binding site 6 out of 12 in the Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:22.7
occ:1.00
 O3G C:AGS904 2.1 33.8 1.0
OG1 C:THR525 2.1 21.9 1.0
O3A C:AGS904 2.3 33.8 1.0
O2B C:AGS904 2.4 33.8 1.0
PB C:AGS904 2.9 33.8 1.0
CB C:THR525 3.1 21.9 1.0
PG C:AGS904 3.4 33.8 1.0
O3B C:AGS904 3.6 33.8 1.0
OD2 C:ASP577 3.7 25.3 1.0
PA C:AGS904 3.7 33.8 1.0
CG2 C:THR525 3.9 21.9 1.0
O5' C:AGS904 4.0 33.8 1.0
O1B C:AGS904 4.2 33.8 1.0
O2A C:AGS904 4.3 33.8 1.0
CA C:THR525 4.3 21.9 1.0
N C:THR525 4.3 21.9 1.0
S1G C:AGS904 4.4 33.8 1.0
OD1 C:ASP577 4.4 25.3 1.0
CG C:ASP577 4.5 25.3 1.0
O2G C:AGS904 4.5 33.8 1.0
NH1 B:ARG635 4.6 19.1 1.0
O1A C:AGS904 4.7 33.8 1.0
CD B:ARG635 4.8 19.1 1.0

Magnesium binding site 7 out of 12 in 7jy5

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Magnesium binding site 7 out of 12 in the Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg901

b:18.8
occ:1.00
 OG1 D:THR252 1.9 21.7 1.0
O3G D:AGS903 2.0 33.8 1.0
O2B D:AGS903 2.3 33.8 1.0
CB D:THR252 3.1 21.7 1.0
PG D:AGS903 3.5 33.8 1.0
OE2 D:GLU305 3.5 15.6 1.0
OD2 D:ASP304 3.7 13.6 1.0
PB D:AGS903 3.7 33.8 1.0
OD1 D:ASP304 3.8 13.6 1.0
CG2 D:THR252 3.9 21.7 1.0
O3B D:AGS903 4.1 33.8 1.0
CG D:ASP304 4.1 13.6 1.0
O2A D:AGS903 4.2 33.8 1.0
CA D:THR252 4.3 21.7 1.0
N D:THR252 4.3 21.7 1.0
CD D:GLU305 4.3 15.6 1.0
S1G D:AGS903 4.4 33.8 1.0
O2G D:AGS903 4.5 33.8 1.0
O1B D:AGS903 4.5 33.8 1.0
O1A D:AGS903 4.7 33.8 1.0
O3A D:AGS903 4.8 33.8 1.0
PA D:AGS903 4.8 33.8 1.0
OE1 D:GLU305 4.8 15.6 1.0

Magnesium binding site 8 out of 12 in 7jy5

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Magnesium binding site 8 out of 12 in the Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg902

b:23.6
occ:1.00
 O3G D:AGS904 2.1 33.8 1.0
OG1 D:THR525 2.2 23.2 1.0
O3A D:AGS904 2.4 33.8 1.0
O2B D:AGS904 2.6 33.8 1.0
PB D:AGS904 3.1 33.8 1.0
CB D:THR525 3.1 23.2 1.0
PG D:AGS904 3.5 33.8 1.0
OD2 D:ASP577 3.6 21.8 1.0
PA D:AGS904 3.8 33.8 1.0
O3B D:AGS904 3.8 33.8 1.0
CG2 D:THR525 3.9 23.2 1.0
O5' D:AGS904 4.1 33.8 1.0
O2A D:AGS904 4.2 33.8 1.0
S1G D:AGS904 4.3 33.8 1.0
O1B D:AGS904 4.4 33.8 1.0
CA D:THR525 4.4 23.2 1.0
N D:THR525 4.4 23.2 1.0
CG D:ASP577 4.4 21.8 1.0
OD1 D:ASP577 4.4 21.8 1.0
NH1 C:ARG635 4.5 17.8 1.0
O2G D:AGS904 4.6 33.8 1.0
CD C:ARG635 4.7 17.8 1.0
O1A D:AGS904 4.8 33.8 1.0

Magnesium binding site 9 out of 12 in 7jy5

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Magnesium binding site 9 out of 12 in the Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg901

b:20.9
occ:1.00
 OG1 E:THR252 1.9 22.5 1.0
O3G E:AGS903 2.0 33.8 1.0
O2B E:AGS903 2.2 33.8 1.0
CB E:THR252 3.1 22.5 1.0
PG E:AGS903 3.5 33.8 1.0
OE2 E:GLU305 3.6 17.1 1.0
PB E:AGS903 3.7 33.8 1.0
OD2 E:ASP304 3.7 13.7 1.0
OD1 E:ASP304 3.8 13.7 1.0
CG2 E:THR252 3.9 22.5 1.0
O2A E:AGS903 4.0 33.8 1.0
O3B E:AGS903 4.1 33.8 1.0
CG E:ASP304 4.2 13.7 1.0
CA E:THR252 4.2 22.5 1.0
N E:THR252 4.3 22.5 1.0
S1G E:AGS903 4.3 33.8 1.0
CD E:GLU305 4.4 17.1 1.0
O1B E:AGS903 4.5 33.8 1.0
O2G E:AGS903 4.5 33.8 1.0
O3A E:AGS903 4.6 33.8 1.0
PA E:AGS903 4.7 33.8 1.0
O1A E:AGS903 4.9 33.8 1.0
OE1 E:GLU305 4.9 17.1 1.0

Magnesium binding site 10 out of 12 in 7jy5

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Magnesium binding site 10 out of 12 in the Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Human P97 in Complex with Atpgammas and NPL4/UFD1 (Masked Around P97) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg902

b:24.1
occ:1.00
 O3G E:AGS904 2.1 33.8 1.0
OG1 E:THR525 2.2 23.2 1.0
O3A E:AGS904 2.4 33.8 1.0
O2B E:AGS904 2.7 33.8 1.0
CB E:THR525 3.1 23.2 1.0
PB E:AGS904 3.2 33.8 1.0
PG E:AGS904 3.5 33.8 1.0
OD2 E:ASP577 3.6 21.1 1.0
PA E:AGS904 3.8 33.8 1.0
O3B E:AGS904 3.8 33.8 1.0
CG2 E:THR525 3.8 23.2 1.0
O5' E:AGS904 4.0 33.8 1.0
O2A E:AGS904 4.2 33.8 1.0
S1G E:AGS904 4.3 33.8 1.0
CA E:THR525 4.3 23.2 1.0
NH1 D:ARG635 4.4 17.5 1.0
N E:THR525 4.4 23.2 1.0
O1B E:AGS904 4.5 33.8 1.0
CG E:ASP577 4.5 21.1 1.0
OD1 E:ASP577 4.5 21.1 1.0
O2G E:AGS904 4.6 33.8 1.0
CD D:ARG635 4.7 17.5 1.0
O1A E:AGS904 4.9 33.8 1.0

Reference:

M.Pan, Q.Zheng, Y.Yu, H.Ai, Y.Xie, X.Zeng, C.Wang, L.Liu, M.Zhao. Seesaw Conformations of NPL4 in the Human P97 Complex and the Inhibitory Mechanism of A Disulfiram Derivative. Nat Commun V. 12 121 2021.
ISSN: ESSN 2041-1723
PubMed: 33402676
DOI: 10.1038/S41467-020-20359-X
Page generated: Wed Oct 2 22:01:36 2024

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