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Magnesium in PDB 7ln1: Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3)

Enzymatic activity of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3)

All present enzymatic activity of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3):
3.6.4.6;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3) (pdb code 7ln1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3), PDB code: 7ln1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7ln1

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Magnesium binding site 1 out of 7 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:18.5
occ:1.00
 O1G B:ATP901 1.9 15.3 1.0
O1B B:ATP901 1.9 15.3 1.0
PG B:ATP901 2.2 15.3 1.0
O3B B:ATP901 2.3 15.3 1.0
PB B:ATP901 2.4 15.3 1.0
O2G B:ATP901 2.5 15.3 1.0
OG1 B:THR525 2.5 13.0 1.0
O3A B:ATP901 3.0 15.3 1.0
O1A B:ATP901 3.1 15.3 1.0
PA B:ATP901 3.6 15.3 1.0
CB B:THR525 3.6 13.0 1.0
O3G B:ATP901 3.7 15.3 1.0
N B:THR525 3.8 13.0 1.0
O2B B:ATP901 3.8 15.3 1.0
OD2 A:ASP609 4.2 19.8 1.0
NH2 A:ARG638 4.3 11.7 1.0
O2A B:ATP901 4.3 15.3 1.0
CA B:THR525 4.3 13.0 1.0
CB B:LYS524 4.7 14.7 1.0
N B:LYS524 4.7 14.7 1.0
CG2 B:THR525 4.8 13.0 1.0
NH2 A:ARG635 4.8 12.1 1.0
C B:LYS524 4.9 14.7 1.0
OD1 B:ASP577 4.9 10.9 1.0
O5' B:ATP901 4.9 15.3 1.0
NE2 B:GLN578 5.0 13.4 1.0
CE B:LYS524 5.0 14.7 1.0
CA B:LYS524 5.0 14.7 1.0

Magnesium binding site 2 out of 7 in 7ln1

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Magnesium binding site 2 out of 7 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg903

b:11.8
occ:1.00
 O1G C:ATP901 2.0 25.5 1.0
OG1 C:THR525 2.0 25.5 1.0
O1B C:ATP901 2.0 25.5 1.0
PG C:ATP901 3.1 25.5 1.0
PB C:ATP901 3.2 25.5 1.0
CB C:THR525 3.3 25.5 1.0
O3B C:ATP901 3.4 25.5 1.0
OD1 C:ASP577 3.8 18.3 1.0
NE2 C:GLN578 3.8 25.5 1.0
O2G C:ATP901 3.8 25.5 1.0
NH2 B:ARG638 4.0 25.5 1.0
N C:THR525 4.0 25.5 1.0
O3A C:ATP901 4.1 25.5 1.0
CA C:THR525 4.2 25.5 1.0
O1A C:ATP901 4.2 25.5 1.0
CG2 C:THR525 4.3 25.5 1.0
OD2 C:ASP577 4.3 18.3 1.0
O3G C:ATP901 4.4 25.5 1.0
O2B C:ATP901 4.4 25.5 1.0
O B:ASP609 4.5 14.0 1.0
CG C:ASP577 4.5 18.3 1.0
PA C:ATP901 4.8 25.5 1.0
NH2 B:ARG635 4.9 25.5 1.0
CD C:GLN578 5.0 25.5 1.0

Magnesium binding site 3 out of 7 in 7ln1

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Magnesium binding site 3 out of 7 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg903

b:12.3
occ:1.00
 O1G D:ATP902 2.0 25.5 1.0
OG1 D:THR525 2.1 25.5 1.0
O1B D:ATP902 2.5 25.5 1.0
CB D:THR525 3.2 25.5 1.0
PG D:ATP902 3.3 25.5 1.0
OD1 D:ASP577 3.6 16.7 1.0
PB D:ATP902 3.6 25.5 1.0
O3B D:ATP902 3.6 25.5 1.0
NH2 C:ARG638 3.9 25.5 1.0
NE2 D:GLN578 4.0 25.5 1.0
O C:ASP609 4.0 15.9 1.0
CG2 D:THR525 4.0 25.5 1.0
O3G D:ATP902 4.2 25.5 1.0
O1A D:ATP902 4.2 25.5 1.0
N D:THR525 4.3 25.5 1.0
CA D:THR525 4.3 25.5 1.0
CG D:ASP577 4.4 16.7 1.0
O3A D:ATP902 4.4 25.5 1.0
O2G D:ATP902 4.4 25.5 1.0
OD2 D:ASP577 4.5 16.7 1.0
O2B D:ATP902 4.8 25.5 1.0
O D:ASP577 4.9 16.7 1.0
PA D:ATP902 4.9 25.5 1.0

Magnesium binding site 4 out of 7 in 7ln1

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Magnesium binding site 4 out of 7 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:15.8
occ:1.00
 O3G D:ATP901 1.9 25.5 1.0
O2G D:ATP901 2.0 25.5 1.0
OG1 D:THR252 2.0 25.5 1.0
PG D:ATP901 2.3 25.5 1.0
OD1 D:ASP304 2.9 13.6 1.0
O1G D:ATP901 3.1 25.5 1.0
OD2 D:ASP304 3.1 13.6 1.0
CG D:ASP304 3.4 13.6 1.0
OE2 D:GLU305 3.4 17.8 1.0
CB D:THR252 3.4 25.5 1.0
O3B D:ATP901 3.6 25.5 1.0
O2B D:ATP901 4.1 25.5 1.0
CG2 D:THR252 4.2 25.5 1.0
N D:THR252 4.2 25.5 1.0
CA D:THR252 4.3 25.5 1.0
CD D:GLU305 4.4 17.8 1.0
PB D:ATP901 4.6 25.5 1.0
NH2 C:ARG362 4.6 16.2 1.0
CB D:ASP304 4.9 13.6 1.0
CB D:ALA346 5.0 11.9 1.0

Magnesium binding site 5 out of 7 in 7ln1

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Magnesium binding site 5 out of 7 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg903

b:17.4
occ:1.00
 OG1 E:THR525 2.0 16.7 1.0
O1B E:ATP902 2.4 25.5 1.0
O1G E:ATP902 2.5 25.5 1.0
CB E:THR525 3.1 16.7 1.0
OD1 E:ASP577 3.4 25.5 1.0
OD2 E:ASP577 3.5 25.5 1.0
PB E:ATP902 3.6 25.5 1.0
PG E:ATP902 3.7 25.5 1.0
NE2 E:GLN578 3.7 22.2 1.0
O1A E:ATP902 3.7 25.5 1.0
O3B E:ATP902 3.8 25.5 1.0
NH2 D:ARG638 3.9 25.5 1.0
CG E:ASP577 3.9 25.5 1.0
CG2 E:THR525 3.9 16.7 1.0
O D:ASP609 4.0 13.5 1.0
CA E:THR525 4.3 16.7 1.0
O3A E:ATP902 4.3 25.5 1.0
N E:THR525 4.3 16.7 1.0
O2G E:ATP902 4.4 25.5 1.0
PA E:ATP902 4.6 25.5 1.0
CD E:GLN578 4.9 22.2 1.0
O3G E:ATP902 4.9 25.5 1.0
O2B E:ATP902 4.9 25.5 1.0
OD2 D:ASP609 4.9 13.5 1.0
CZ D:ARG638 5.0 25.5 1.0

Magnesium binding site 6 out of 7 in 7ln1

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Magnesium binding site 6 out of 7 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg904

b:17.9
occ:1.00
 O2B E:ATP901 1.9 25.5 1.0
OG1 E:THR252 2.0 14.1 1.0
O3G E:ATP901 2.0 25.5 1.0
CB E:THR252 3.1 14.1 1.0
PB E:ATP901 3.2 25.5 1.0
PG E:ATP901 3.3 25.5 1.0
O3B E:ATP901 3.4 25.5 1.0
O1A E:ATP901 3.5 25.5 1.0
NH2 D:ARG362 3.8 25.5 1.0
O3A E:ATP901 3.9 25.5 1.0
CG2 E:THR252 4.0 14.1 1.0
O1G E:ATP901 4.1 25.5 1.0
OD1 E:ASP304 4.2 13.2 1.0
N E:THR252 4.2 14.1 1.0
O D:ASP333 4.2 13.2 1.0
CA E:THR252 4.2 14.1 1.0
PA E:ATP901 4.3 25.5 1.0
O1B E:ATP901 4.3 25.5 1.0
O2G E:ATP901 4.4 25.5 1.0
OD2 E:ASP304 4.4 13.2 1.0
CG E:ASP304 4.7 13.2 1.0
OE2 E:GLU305 4.8 7.7 1.0

Magnesium binding site 7 out of 7 in 7ln1

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Magnesium binding site 7 out of 7 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg903

b:18.6
occ:1.00
 O2B F:ATP901 2.6 24.9 1.0
O2G F:ATP901 2.9 24.9 1.0
CB F:THR252 3.2 22.1 1.0
OD1 F:ASP304 3.3 24.4 1.0
CG2 F:THR252 3.4 22.1 1.0
OD2 F:ASP304 3.4 24.4 1.0
CG F:ASP304 3.7 24.4 1.0
PB F:ATP901 3.8 24.9 1.0
O3B F:ATP901 3.9 24.9 1.0
PG F:ATP901 3.9 24.9 1.0
OG1 F:THR252 4.0 22.1 1.0
O1A F:ATP901 4.1 24.9 1.0
O3G F:ATP901 4.2 24.9 1.0
N F:THR252 4.3 22.1 1.0
CA F:THR252 4.3 22.1 1.0
OE2 F:GLU305 4.4 21.6 1.0
CG F:GLU305 4.7 21.6 1.0
O3A F:ATP901 4.7 24.9 1.0
O1B F:ATP901 4.9 24.9 1.0
PA F:ATP901 5.0 24.9 1.0
CD F:GLU305 5.0 21.6 1.0

Reference:

M.Pan, Y.Yu, H.Ai, Q.Zheng, Y.Xie, L.Liu, M.Zhao. Mechanistic Insight Into Substrate Processing and Allosteric Inhibition of Human P97. Nat.Struct.Mol.Biol. V. 28 614 2021.
ISSN: ESSN 1545-9985
PubMed: 34262183
DOI: 10.1038/S41594-021-00617-2
Page generated: Thu Aug 14 09:05:59 2025

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