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Magnesium in PDB 7ln6: Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State)

Enzymatic activity of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State)

All present enzymatic activity of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State):
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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State) (pdb code 7ln6). 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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State), PDB code: 7ln6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7ln6

Go back to Magnesium Binding Sites List in 7ln6
Magnesium binding site 1 out of 7 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State)


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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg904

b:2.3
occ:1.00
 O1G B:ATP901 2.1 4.8 1.0
OG1 B:THR525 2.1 7.7 1.0
O1B B:ATP901 3.3 4.8 1.0
CB B:THR525 3.5 7.7 1.0
PG B:ATP901 3.5 4.8 1.0
OD2 B:ASP577 3.7 4.2 1.0
OD1 B:ASP577 3.7 4.2 1.0
O3B B:ATP901 4.0 4.8 1.0
CG2 B:THR525 4.0 7.7 1.0
NE2 B:GLN578 4.0 5.5 1.0
NH2 A:ARG638 4.1 4.6 1.0
CG B:ASP577 4.1 4.2 1.0
PB B:ATP901 4.2 4.8 1.0
O A:ASP609 4.3 7.4 1.0
O2G B:ATP901 4.4 4.8 1.0
O1A B:ATP901 4.4 4.8 1.0
CA B:THR525 4.5 7.7 1.0
O3G B:ATP901 4.5 4.8 1.0
N B:THR525 4.5 7.7 1.0
O3A B:ATP901 4.9 4.8 1.0

Magnesium binding site 2 out of 7 in 7ln6

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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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State)


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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:3.4
occ:1.00
 OG1 C:THR525 2.1 14.3 1.0
O1G B:ATP903 2.8 5.0 1.0
O3B B:ATP903 3.0 5.0 1.0
O1B B:ATP903 3.2 5.0 1.0
CB C:THR525 3.4 14.3 1.0
PG B:ATP903 3.5 5.0 1.0
OD1 C:ASP577 3.5 14.3 1.0
PB B:ATP903 3.7 5.0 1.0
NE2 C:GLN578 3.9 9.0 1.0
NH2 B:ARG638 4.0 14.3 1.0
OD2 C:ASP577 4.1 14.3 1.0
CG2 C:THR525 4.2 14.3 1.0
CG C:ASP577 4.2 14.3 1.0
O B:ASP609 4.2 9.4 1.0
CA C:THR525 4.4 14.3 1.0
N C:THR525 4.4 14.3 1.0
O1A B:ATP903 4.5 5.0 1.0
O3G B:ATP903 4.5 5.0 1.0
O2G B:ATP903 4.6 5.0 1.0
CD C:GLN578 4.7 9.0 1.0
O3A B:ATP903 4.8 5.0 1.0
O2B B:ATP903 4.8 5.0 1.0

Magnesium binding site 3 out of 7 in 7ln6

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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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State)


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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg903

b:6.0
occ:1.00
 O1G D:ATP902 2.0 14.3 1.0
OG1 D:THR525 2.1 8.6 1.0
PG D:ATP902 3.2 14.3 1.0
CB D:THR525 3.3 8.6 1.0
OD1 D:ASP577 3.5 4.4 1.0
O1B D:ATP902 3.6 14.3 1.0
NH2 C:ARG638 3.7 14.3 1.0
O3B D:ATP902 3.7 14.3 1.0
O2G D:ATP902 3.7 14.3 1.0
O C:ASP609 3.8 7.3 1.0
CG2 D:THR525 4.0 8.6 1.0
NE2 D:GLN578 4.0 3.9 1.0
PB D:ATP902 4.2 14.3 1.0
O1A D:ATP902 4.4 14.3 1.0
CG D:ASP577 4.4 4.4 1.0
CA D:THR525 4.5 8.6 1.0
O3G D:ATP902 4.5 14.3 1.0
OD2 D:ASP577 4.6 4.4 1.0
N D:THR525 4.6 8.6 1.0
O3A D:ATP902 4.9 14.3 1.0
O D:ASP577 4.9 4.4 1.0
C C:ASP609 4.9 7.3 1.0
CZ C:ARG638 5.0 14.3 1.0

Magnesium binding site 4 out of 7 in 7ln6

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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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State)


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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:6.6
occ:1.00
 O3G D:ATP901 2.0 10.8 1.0
OG1 D:THR252 2.3 9.9 1.0
O2B D:ATP901 2.5 10.8 1.0
CB D:THR252 3.0 9.9 1.0
O1A D:ATP901 3.0 10.8 1.0
PG D:ATP901 3.2 10.8 1.0
O3B D:ATP901 3.2 10.8 1.0
PB D:ATP901 3.4 10.8 1.0
NH2 C:ARG362 3.6 15.9 1.0
O3A D:ATP901 3.9 10.8 1.0
PA D:ATP901 4.0 10.8 1.0
CG2 D:THR252 4.0 9.9 1.0
O2G D:ATP901 4.0 10.8 1.0
O C:ASP333 4.1 3.3 1.0
N D:THR252 4.1 9.9 1.0
CA D:THR252 4.2 9.9 1.0
O1G D:ATP901 4.3 10.8 1.0
OD2 D:ASP304 4.4 4.7 1.0
OD1 D:ASP304 4.4 4.7 1.0
OE1 D:GLU305 4.5 5.2 1.0
O2A D:ATP901 4.6 10.8 1.0
NH1 C:ARG359 4.7 14.3 1.0
O1B D:ATP901 4.7 10.8 1.0
CG D:ASP304 4.8 4.7 1.0
OD2 C:ASP333 4.9 3.3 1.0
CZ C:ARG362 4.9 15.9 1.0

Magnesium binding site 5 out of 7 in 7ln6

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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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State)


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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg903

b:5.5
occ:1.00
 OG1 E:THR525 2.1 6.0 1.0
O1G E:ATP902 2.7 8.4 1.0
CB E:THR525 3.3 6.0 1.0
O1B E:ATP902 3.5 8.4 1.0
O1A E:ATP902 3.6 8.4 1.0
OD2 E:ASP577 3.7 4.7 1.0
CG2 E:THR525 3.7 6.0 1.0
OD1 E:ASP577 3.8 4.7 1.0
NH2 D:ARG638 4.0 14.3 1.0
PG E:ATP902 4.0 8.4 1.0
NE2 E:GLN578 4.1 7.7 1.0
CG E:ASP577 4.2 4.7 1.0
O D:ASP609 4.3 7.4 1.0
PB E:ATP902 4.4 8.4 1.0
CA E:THR525 4.5 6.0 1.0
O3B E:ATP902 4.5 8.4 1.0
OD2 D:ASP609 4.5 7.4 1.0
O3G E:ATP902 4.6 8.4 1.0
PA E:ATP902 4.7 8.4 1.0
N E:THR525 4.7 6.0 1.0
O3A E:ATP902 4.8 8.4 1.0

Magnesium binding site 6 out of 7 in 7ln6

Go back to Magnesium Binding Sites List in 7ln6
Magnesium binding site 6 out of 7 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State)


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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg904

b:14.3
occ:1.00
 CG2 E:THR252 2.5 8.4 1.0
CB E:THR252 2.5 8.4 1.0
O3G E:ATP901 2.7 5.0 1.0
OG1 E:THR252 3.4 8.4 1.0
O3B E:ATP901 3.5 5.0 1.0
O2B E:ATP901 3.6 5.0 1.0
PG E:ATP901 3.7 5.0 1.0
CA E:THR252 3.7 8.4 1.0
O1A E:ATP901 3.8 5.0 1.0
N E:THR252 3.8 8.4 1.0
OD2 E:ASP304 3.8 6.3 1.0
OD1 E:ASP304 3.9 6.3 1.0
PB E:ATP901 4.2 5.0 1.0
CG E:ASP304 4.3 6.3 1.0
O1G E:ATP901 4.3 5.0 1.0
O D:ASP333 4.6 5.5 1.0
PA E:ATP901 4.7 5.0 1.0
O3A E:ATP901 4.8 5.0 1.0
NH2 D:ARG362 4.8 13.5 1.0
C E:THR252 4.9 8.4 1.0
OD1 D:ASP333 4.9 5.5 1.0
O2G E:ATP901 5.0 5.0 1.0

Magnesium binding site 7 out of 7 in 7ln6

Go back to Magnesium Binding Sites List in 7ln6
Magnesium binding site 7 out of 7 in the Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State)


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 Polyubiquitinated Ub-Eos (Chapso, Class 2, Open State) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg903

b:9.4
occ:1.00
 O3B F:ATP901 2.1 14.5 1.0
OG1 F:THR252 2.1 14.7 1.0
O2G F:ATP901 2.4 14.5 1.0
PG F:ATP901 2.4 14.5 1.0
O3G F:ATP901 2.5 14.5 1.0
O2B F:ATP901 2.7 14.5 1.0
PB F:ATP901 2.9 14.5 1.0
CB F:THR252 3.2 14.7 1.0
O1A F:ATP901 3.2 14.5 1.0
O3A F:ATP901 3.6 14.5 1.0
NH1 E:ARG359 3.6 7.9 1.0
N F:THR252 3.8 14.7 1.0
PA F:ATP901 3.8 14.5 1.0
O1G F:ATP901 3.9 14.5 1.0
CA F:THR252 4.0 14.7 1.0
O1B F:ATP901 4.2 14.5 1.0
O2A F:ATP901 4.2 14.5 1.0
CG2 F:THR252 4.3 14.7 1.0
OD2 F:ASP304 4.4 15.9 1.0
NZ F:LYS251 4.6 12.6 1.0
OD1 F:ASP304 4.6 15.9 1.0
OE2 F:GLU305 4.7 15.1 1.0
CE F:LYS251 4.9 12.6 1.0
C F:LYS251 4.9 12.6 1.0
CG F:ASP304 4.9 15.9 1.0
CZ E:ARG359 4.9 7.9 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 23:29:52 2024

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