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Magnesium in PDB 7lmz: Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1)

Enzymatic activity of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1)

All present enzymatic activity of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1):
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 1) (pdb code 7lmz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1), PDB code: 7lmz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7lmz

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Magnesium binding site 1 out of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:15.2
occ:1.00
 OG1 B:THR525 2.0 21.2 1.0
O1G B:ATP901 2.1 29.8 1.0
O1B B:ATP901 2.5 29.8 1.0
OD2 A:ASP609 2.7 27.5 1.0
CB B:THR525 3.0 21.2 1.0
O1A B:ATP901 3.3 29.8 1.0
PG B:ATP901 3.3 29.8 1.0
PB B:ATP901 3.4 29.8 1.0
O3B B:ATP901 3.5 29.8 1.0
NH2 A:ARG638 3.6 14.9 1.0
CG A:ASP609 3.8 27.5 1.0
O3A B:ATP901 3.9 29.8 1.0
CG2 B:THR525 3.9 21.2 1.0
OD2 B:ASP577 4.1 13.1 1.0
N B:THR525 4.1 21.2 1.0
OD1 B:ASP577 4.1 13.1 1.0
PA B:ATP901 4.1 29.8 1.0
CA B:THR525 4.2 21.2 1.0
O2G B:ATP901 4.3 29.8 1.0
O3G B:ATP901 4.4 29.8 1.0
OD1 A:ASP609 4.4 27.5 1.0
NE2 B:GLN578 4.4 9.5 1.0
CG B:ASP577 4.5 13.1 1.0
CZ A:ARG638 4.8 14.9 1.0
O2B B:ATP901 4.8 29.8 1.0
O2A B:ATP901 4.8 29.8 1.0
CB A:ASP609 5.0 27.5 1.0

Magnesium binding site 2 out of 8 in 7lmz

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Magnesium binding site 2 out of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg903

b:22.5
occ:1.00
 OG1 C:THR252 2.0 19.8 1.0
O1G C:ATP901 2.1 29.8 1.0
O2B C:ATP901 2.9 29.8 1.0
CB C:THR252 3.0 19.8 1.0
PG C:ATP901 3.2 29.8 1.0
O3B C:ATP901 3.6 29.8 1.0
O2G C:ATP901 3.7 29.8 1.0
O1A C:ATP901 3.7 29.8 1.0
CG2 C:THR252 3.7 19.8 1.0
PB C:ATP901 3.8 29.8 1.0
OD2 C:ASP304 4.0 19.0 1.0
O B:ASP333 4.1 19.2 1.0
OD2 B:ASP333 4.1 19.2 1.0
NH2 B:ARG362 4.2 22.9 1.0
NH2 B:ARG359 4.2 25.0 1.0
CA C:THR252 4.2 19.8 1.0
O3A C:ATP901 4.3 29.8 1.0
OD1 C:ASP304 4.4 19.0 1.0
N C:THR252 4.4 19.8 1.0
PA C:ATP901 4.4 29.8 1.0
O3G C:ATP901 4.6 29.8 1.0
CG C:ASP304 4.6 19.0 1.0
CA B:GLY334 4.7 19.1 1.0
C B:ASP333 4.7 19.2 1.0
O2A C:ATP901 4.9 29.8 1.0
CG B:ASP333 4.9 19.2 1.0
OE2 C:GLU305 4.9 12.8 1.0
N B:GLY334 5.0 19.1 1.0

Magnesium binding site 3 out of 8 in 7lmz

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Magnesium binding site 3 out of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg904

b:23.4
occ:1.00
 O1G C:ATP902 2.0 29.8 1.0
OG1 C:THR525 2.3 29.8 1.0
O1B C:ATP902 2.6 29.8 1.0
PG C:ATP902 3.2 29.8 1.0
NH2 B:ARG638 3.3 29.8 1.0
CB C:THR525 3.4 29.8 1.0
O3B C:ATP902 3.6 29.8 1.0
PB C:ATP902 3.6 29.8 1.0
O B:ASP609 3.6 22.1 1.0
OD1 C:ASP577 3.9 10.3 1.0
O1A C:ATP902 4.0 29.8 1.0
NE2 C:GLN578 4.0 14.9 1.0
O3G C:ATP902 4.0 29.8 1.0
CG2 C:THR525 4.2 29.8 1.0
O3A C:ATP902 4.2 29.8 1.0
OD2 C:ASP577 4.3 10.3 1.0
CZ B:ARG638 4.3 29.8 1.0
NH2 B:ARG635 4.3 29.8 1.0
O2G C:ATP902 4.4 29.8 1.0
CG C:ASP577 4.5 10.3 1.0
N C:THR525 4.6 29.8 1.0
CA C:THR525 4.6 29.8 1.0
NH1 B:ARG638 4.7 29.8 1.0
PA C:ATP902 4.7 29.8 1.0
C B:ASP609 4.8 22.1 1.0
O2B C:ATP902 4.9 29.8 1.0

Magnesium binding site 4 out of 8 in 7lmz

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Magnesium binding site 4 out of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg903

b:16.0
occ:1.00
 OG1 D:THR252 2.0 27.6 1.0
O3G D:ATP901 2.1 29.8 1.0
O2B D:ATP901 2.2 29.8 1.0
CB D:THR252 3.3 27.6 1.0
PG D:ATP901 3.5 29.8 1.0
PB D:ATP901 3.5 29.8 1.0
O3B D:ATP901 3.7 29.8 1.0
OD1 D:ASP304 3.7 10.5 1.0
OE1 D:GLU305 3.8 8.7 1.0
O1A D:ATP901 4.0 29.8 1.0
N D:THR252 4.1 27.6 1.0
NH2 C:ARG362 4.1 29.8 1.0
OD2 D:ASP304 4.2 10.5 1.0
CG2 D:THR252 4.2 27.6 1.0
O2G D:ATP901 4.3 29.8 1.0
CA D:THR252 4.3 27.6 1.0
CG D:ASP304 4.4 10.5 1.0
O3A D:ATP901 4.4 29.8 1.0
O C:ASP333 4.5 18.0 1.0
O1G D:ATP901 4.5 29.8 1.0
O1B D:ATP901 4.5 29.8 1.0
NH2 C:ARG359 4.7 29.8 1.0
PA D:ATP901 4.9 29.8 1.0

Magnesium binding site 5 out of 8 in 7lmz

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Magnesium binding site 5 out of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:12.9
occ:1.00
 OG1 D:THR525 2.0 25.0 1.0
O1G D:ATP902 2.0 29.8 1.0
O1B D:ATP902 2.9 29.8 1.0
OD1 D:ASP577 3.2 16.4 1.0
CB D:THR525 3.3 25.0 1.0
PG D:ATP902 3.4 29.8 1.0
OD2 D:ASP577 3.8 16.4 1.0
NH2 C:ARG638 3.8 29.8 1.0
O3B D:ATP902 3.8 29.8 1.0
NE2 D:GLN578 3.9 29.8 1.0
CG D:ASP577 3.9 16.4 1.0
O C:ASP609 3.9 22.1 1.0
PB D:ATP902 3.9 29.8 1.0
CG2 D:THR525 4.0 25.0 1.0
O2G D:ATP902 4.2 29.8 1.0
O1A D:ATP902 4.2 29.8 1.0
N D:THR525 4.4 25.0 1.0
CA D:THR525 4.4 25.0 1.0
O3G D:ATP902 4.5 29.8 1.0
O3A D:ATP902 4.6 29.8 1.0
O D:ASP577 4.7 16.4 1.0
C C:ASP609 5.0 22.1 1.0

Magnesium binding site 6 out of 8 in 7lmz

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Magnesium binding site 6 out of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg903

b:21.3
occ:1.00
 OG1 E:THR252 2.0 18.3 1.0
O3G E:ATP901 2.1 29.8 1.0
O2B E:ATP901 2.2 29.8 1.0
CB E:THR252 3.3 18.3 1.0
PG E:ATP901 3.4 29.8 1.0
PB E:ATP901 3.5 29.8 1.0
O3B E:ATP901 3.7 29.8 1.0
OD1 E:ASP304 3.7 18.8 1.0
N E:THR252 4.0 18.3 1.0
CA E:THR252 4.2 18.3 1.0
NH2 D:ARG362 4.2 29.8 1.0
CG2 E:THR252 4.2 18.3 1.0
O1A E:ATP901 4.2 29.8 1.0
OD2 E:ASP304 4.3 18.8 1.0
O2G E:ATP901 4.3 29.8 1.0
O1G E:ATP901 4.4 29.8 1.0
CG E:ASP304 4.4 18.8 1.0
O3A E:ATP901 4.4 29.8 1.0
OE2 E:GLU305 4.5 18.0 1.0
O1B E:ATP901 4.5 29.8 1.0
O D:ASP333 4.6 19.9 1.0
CE E:LYS251 4.9 29.8 1.0
NH2 D:ARG359 5.0 29.8 1.0
PA E:ATP901 5.0 29.8 1.0
CB E:LYS251 5.0 29.8 1.0

Magnesium binding site 7 out of 8 in 7lmz

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Magnesium binding site 7 out of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1)


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 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg904

b:12.2
occ:1.00
 OG1 E:THR525 2.0 18.4 1.0
O1G E:ATP902 2.5 29.8 1.0
O1B E:ATP902 2.7 29.8 1.0
OD1 E:ASP577 3.2 8.8 1.0
CB E:THR525 3.2 18.4 1.0
OD2 E:ASP577 3.4 8.8 1.0
NE2 E:GLN578 3.5 13.8 1.0
PG E:ATP902 3.5 29.8 1.0
O1A E:ATP902 3.7 29.8 1.0
CG E:ASP577 3.7 8.8 1.0
PB E:ATP902 3.8 29.8 1.0
NH2 D:ARG638 3.8 29.8 1.0
O3B E:ATP902 3.8 29.8 1.0
O2G E:ATP902 3.9 29.8 1.0
CG2 E:THR525 3.9 18.4 1.0
O D:ASP609 4.0 16.1 1.0
CA E:THR525 4.3 18.4 1.0
N E:THR525 4.4 18.4 1.0
O3A E:ATP902 4.4 29.8 1.0
NH2 D:ARG635 4.4 29.8 1.0
PA E:ATP902 4.6 29.8 1.0
CD E:GLN578 4.7 13.8 1.0
CZ D:ARG638 4.8 29.8 1.0
O3G E:ATP902 4.9 29.8 1.0

Magnesium binding site 8 out of 8 in 7lmz

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Magnesium binding site 8 out of 8 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and UB6 (Class 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg903

b:24.9
occ:1.00
 O2G F:ATP901 2.0 46.0 1.0
O2B F:ATP901 3.1 46.0 1.0
OD1 F:ASP304 3.1 45.6 1.0
PG F:ATP901 3.2 46.0 1.0
O3B F:ATP901 3.3 46.0 1.0
CB F:THR252 3.6 40.6 1.0
CG2 F:THR252 3.6 40.6 1.0
PB F:ATP901 3.8 46.0 1.0
O1G F:ATP901 3.8 46.0 1.0
OD2 F:ASP304 3.9 45.6 1.0
CG F:ASP304 3.9 45.6 1.0
N F:THR252 4.1 40.6 1.0
O3G F:ATP901 4.4 46.0 1.0
CA F:THR252 4.5 40.6 1.0
OG1 F:THR252 4.6 40.6 1.0
OE1 F:GLU305 4.6 37.2 1.0
O1A F:ATP901 4.7 46.0 1.0
CG F:GLU305 4.7 37.2 1.0
O1B F:ATP901 4.8 46.0 1.0
O3A F:ATP901 4.9 46.0 1.0
CB F:ALA346 4.9 37.2 1.0
CB F:LYS251 4.9 38.0 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: Wed Oct 2 23:26:08 2024

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