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Magnesium in PDB 7ln5: Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Chapso, Class 1, Close State)

Enzymatic activity of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Chapso, Class 1, Close State)

All present enzymatic activity of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Chapso, Class 1, Close 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 1, Close State) (pdb code 7ln5). 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 1, Close State), PDB code: 7ln5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7ln5

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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 Polyubiquitinated Ub-Eos (Chapso, Class 1, Close 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 1, Close State) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:25.6
occ:1.00
 OG1 B:THR525 2.1 19.2 1.0
O1G B:ATP901 2.1 26.6 1.0
OD2 A:ASP609 3.0 28.6 1.0
CB B:THR525 3.4 19.2 1.0
OD2 B:ASP577 3.5 21.1 1.0
PG B:ATP901 3.5 26.6 1.0
O1B B:ATP901 3.5 26.6 1.0
OD1 B:ASP577 3.5 21.1 1.0
CG2 B:THR525 3.7 19.2 1.0
NH2 A:ARG638 3.9 7.4 1.0
CG B:ASP577 3.9 21.1 1.0
O3B B:ATP901 4.0 26.6 1.0
NE2 B:GLN578 4.1 8.0 1.0
O3G B:ATP901 4.2 26.6 1.0
CG A:ASP609 4.3 28.6 1.0
PB B:ATP901 4.3 26.6 1.0
CA B:THR525 4.4 19.2 1.0
O1A B:ATP901 4.4 26.6 1.0
O2G B:ATP901 4.6 26.6 1.0
N B:THR525 4.6 19.2 1.0
O3A B:ATP901 5.0 26.6 1.0

Magnesium binding site 2 out of 7 in 7ln5

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

b:16.7
occ:1.00
 OG1 C:THR525 2.1 26.6 1.0
O1G C:ATP901 2.2 26.6 1.0
O1B C:ATP901 2.9 26.6 1.0
OD1 C:ASP577 3.3 11.5 1.0
CB C:THR525 3.4 26.6 1.0
PG C:ATP901 3.5 26.6 1.0
NH2 B:ARG638 3.6 26.6 1.0
O3B C:ATP901 3.7 26.6 1.0
PB C:ATP901 3.8 26.6 1.0
O B:ASP609 4.0 14.7 1.0
CG2 C:THR525 4.1 26.6 1.0
CG C:ASP577 4.1 11.5 1.0
NE2 C:GLN578 4.1 28.5 1.0
OD2 C:ASP577 4.2 11.5 1.0
O1A C:ATP901 4.2 26.6 1.0
CA C:THR525 4.5 26.6 1.0
O3G C:ATP901 4.5 26.6 1.0
N C:THR525 4.5 26.6 1.0
O2G C:ATP901 4.5 26.6 1.0
O3A C:ATP901 4.6 26.6 1.0
CZ B:ARG638 4.9 26.6 1.0
O C:ASP577 4.9 11.5 1.0
PA C:ATP901 5.0 26.6 1.0
NH2 B:ARG635 5.0 26.6 1.0

Magnesium binding site 3 out of 7 in 7ln5

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

b:14.3
occ:1.00
 OG1 D:THR525 2.0 26.6 1.0
O1G D:ATP902 2.1 26.6 1.0
O1B D:ATP902 2.5 26.6 1.0
CB D:THR525 3.3 26.6 1.0
PG D:ATP902 3.4 26.6 1.0
PB D:ATP902 3.6 26.6 1.0
NH2 C:ARG638 3.6 26.6 1.0
O3B D:ATP902 3.7 26.6 1.0
OD1 D:ASP577 3.8 11.9 1.0
OD2 D:ASP577 4.0 11.9 1.0
NE2 D:GLN578 4.1 1.9 1.0
CG2 D:THR525 4.1 26.6 1.0
O C:ASP609 4.1 26.6 1.0
O1A D:ATP902 4.1 26.6 1.0
O2G D:ATP902 4.2 26.6 1.0
N D:THR525 4.3 26.6 1.0
CG D:ASP577 4.3 11.9 1.0
O3A D:ATP902 4.4 26.6 1.0
CA D:THR525 4.4 26.6 1.0
O3G D:ATP902 4.5 26.6 1.0
NH2 C:ARG635 4.8 26.6 1.0
PA D:ATP902 4.8 26.6 1.0
CZ C:ARG638 4.8 26.6 1.0
O2B D:ATP902 4.9 26.6 1.0

Magnesium binding site 4 out of 7 in 7ln5

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

b:12.7
occ:1.00
 OG1 D:THR252 2.0 26.6 1.0
O3G D:ATP901 2.1 26.6 1.0
O2B D:ATP901 2.7 26.6 1.0
CB D:THR252 3.2 26.6 1.0
PG D:ATP901 3.3 26.6 1.0
O3B D:ATP901 3.4 26.6 1.0
O1A D:ATP901 3.5 26.6 1.0
PB D:ATP901 3.6 26.6 1.0
NH2 C:ARG362 3.8 26.6 1.0
OD2 D:ASP304 3.9 19.6 1.0
CG2 D:THR252 4.0 26.6 1.0
OD1 D:ASP304 4.1 19.6 1.0
O3A D:ATP901 4.2 26.6 1.0
N D:THR252 4.3 26.6 1.0
O1G D:ATP901 4.3 26.6 1.0
CA D:THR252 4.3 26.6 1.0
OE2 D:GLU305 4.3 19.0 1.0
O2G D:ATP901 4.3 26.6 1.0
PA D:ATP901 4.4 26.6 1.0
O C:ASP333 4.4 27.9 1.0
CG D:ASP304 4.4 19.6 1.0
O1B D:ATP901 4.9 26.6 1.0

Magnesium binding site 5 out of 7 in 7ln5

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

b:13.8
occ:1.00
 O1G E:ATP902 2.1 26.6 1.0
OG1 E:THR525 2.1 16.7 1.0
O1B E:ATP902 2.6 26.6 1.0
CB E:THR525 3.3 16.7 1.0
PG E:ATP902 3.3 26.6 1.0
O1A E:ATP902 3.5 26.6 1.0
PB E:ATP902 3.5 26.6 1.0
OD1 E:ASP577 3.6 10.9 1.0
NE2 E:GLN578 3.6 9.4 1.0
O3B E:ATP902 3.6 26.6 1.0
NH2 D:ARG638 3.9 26.6 1.0
O3A E:ATP902 4.0 26.6 1.0
OD2 E:ASP577 4.1 10.9 1.0
O2G E:ATP902 4.1 26.6 1.0
CG2 E:THR525 4.2 16.7 1.0
N E:THR525 4.2 16.7 1.0
CG E:ASP577 4.2 10.9 1.0
CA E:THR525 4.3 16.7 1.0
PA E:ATP902 4.3 26.6 1.0
NH2 D:ARG635 4.4 26.6 1.0
O D:ASP609 4.5 12.2 1.0
O3G E:ATP902 4.5 26.6 1.0
CD E:GLN578 4.9 9.4 1.0
O2B E:ATP902 4.9 26.6 1.0

Magnesium binding site 6 out of 7 in 7ln5

Go back to Magnesium Binding Sites List in 7ln5
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 1, Close 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 1, Close State) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg904

b:11.7
occ:1.00
 OG1 E:THR252 2.0 26.6 1.0
O2B E:ATP901 2.1 26.6 1.0
O3G E:ATP901 2.1 26.6 1.0
CB E:THR252 3.3 26.6 1.0
PB E:ATP901 3.4 26.6 1.0
PG E:ATP901 3.4 26.6 1.0
O1A E:ATP901 3.5 26.6 1.0
O3B E:ATP901 3.6 26.6 1.0
NH2 D:ARG362 3.7 26.6 1.0
OE2 E:GLU305 4.1 10.5 1.0
OD1 E:ASP304 4.1 7.8 1.0
O3A E:ATP901 4.1 26.6 1.0
O2G E:ATP901 4.1 26.6 1.0
CG2 E:THR252 4.2 26.6 1.0
N E:THR252 4.2 26.6 1.0
OD2 E:ASP304 4.3 7.8 1.0
CA E:THR252 4.3 26.6 1.0
PA E:ATP901 4.4 26.6 1.0
O D:ASP333 4.5 21.3 1.0
O1B E:ATP901 4.5 26.6 1.0
O1G E:ATP901 4.6 26.6 1.0
CG E:ASP304 4.6 7.8 1.0
NH2 D:ARG359 4.8 26.6 1.0
CZ D:ARG362 5.0 26.6 1.0

Magnesium binding site 7 out of 7 in 7ln5

Go back to Magnesium Binding Sites List in 7ln5
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 1, Close 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 1, Close State) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg903

b:34.2
occ:1.00
 O2G F:ATP901 2.1 30.2 1.0
O3B F:ATP901 2.4 30.2 1.0
PG F:ATP901 2.5 30.2 1.0
O3G F:ATP901 2.5 30.2 1.0
OG1 F:THR252 2.7 28.3 1.0
O2B F:ATP901 3.0 30.2 1.0
O1A F:ATP901 3.2 30.2 1.0
PB F:ATP901 3.3 30.2 1.0
CB F:THR252 3.6 28.3 1.0
O3A F:ATP901 3.9 30.2 1.0
O1G F:ATP901 3.9 30.2 1.0
OD2 F:ASP304 4.1 32.7 1.0
PA F:ATP901 4.1 30.2 1.0
OE2 F:GLU305 4.4 33.4 1.0
N F:THR252 4.4 28.3 1.0
CG2 F:THR252 4.6 28.3 1.0
O1B F:ATP901 4.6 30.2 1.0
OD1 F:ASP304 4.6 32.7 1.0
CA F:THR252 4.6 28.3 1.0
CG F:ASP304 4.8 32.7 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 23:29:26 2024

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