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Magnesium in PDB 7ln4: Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)

Enzymatic activity of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, Class 3)

All present enzymatic activity of Cryo-Em Structure of Human P97 in Complex with NPL4/UFD1 and Polyubiquitinated Ub-Eos (Fom, 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 Polyubiquitinated Ub-Eos (Fom, Class 3) (pdb code 7ln4). 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 Polyubiquitinated Ub-Eos (Fom, Class 3), PDB code: 7ln4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7ln4

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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 Polyubiquitinated Ub-Eos (Fom, 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 Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:34.8
occ:1.00
 O3G B:ATP901 2.1 31.7 1.0
CG2 B:THR525 3.0 44.7 1.0
O1B B:ATP901 3.0 31.7 1.0
PG B:ATP901 3.1 31.7 1.0
O1G B:ATP901 3.2 31.7 1.0
CB B:THR525 3.2 44.7 1.0
OD2 A:ASP609 3.3 48.9 1.0
O3B B:ATP901 3.6 31.7 1.0
PB B:ATP901 3.8 31.7 1.0
O1A B:ATP901 3.9 31.7 1.0
NH2 A:ARG638 4.0 24.9 1.0
OD1 B:ASP577 4.1 28.2 1.0
OG1 B:THR525 4.2 44.7 1.0
OD2 B:ASP577 4.2 28.2 1.0
N B:THR525 4.2 44.7 1.0
CG A:ASP609 4.4 48.9 1.0
CA B:THR525 4.4 44.7 1.0
O2G B:ATP901 4.4 31.7 1.0
O3A B:ATP901 4.4 31.7 1.0
NE2 B:GLN578 4.5 22.1 1.0
CG B:ASP577 4.6 28.2 1.0
PA B:ATP901 4.6 31.7 1.0
OD1 A:ASP609 4.9 48.9 1.0

Magnesium binding site 2 out of 8 in 7ln4

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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 Polyubiquitinated Ub-Eos (Fom, 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 Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg903

b:20.8
occ:1.00
 OG1 C:THR525 2.1 31.7 1.0
O1G C:ATP902 2.1 31.7 1.0
O1B C:ATP902 2.2 31.7 1.0
CB C:THR525 3.3 31.7 1.0
PB C:ATP902 3.3 31.7 1.0
PG C:ATP902 3.3 31.7 1.0
O3B C:ATP902 3.4 31.7 1.0
NH2 B:ARG638 4.0 31.7 1.0
OD1 C:ASP577 4.1 41.5 1.0
O1A C:ATP902 4.1 31.7 1.0
CG2 C:THR525 4.1 31.7 1.0
O3A C:ATP902 4.1 31.7 1.0
N C:THR525 4.2 31.7 1.0
O2G C:ATP902 4.2 31.7 1.0
CA C:THR525 4.3 31.7 1.0
OD2 C:ASP577 4.3 41.5 1.0
NE2 C:GLN578 4.4 31.7 1.0
O3G C:ATP902 4.4 31.7 1.0
O2B C:ATP902 4.5 31.7 1.0
O B:ASP609 4.5 27.4 1.0
CG C:ASP577 4.6 41.5 1.0
PA C:ATP902 4.7 31.7 1.0
NH1 B:ARG635 4.8 31.7 1.0

Magnesium binding site 3 out of 8 in 7ln4

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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 Polyubiquitinated Ub-Eos (Fom, 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 Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg904

b:29.7
occ:1.00
 OG1 C:THR252 2.3 13.3 1.0
O3G C:ATP901 2.4 31.7 1.0
O2B C:ATP901 2.7 31.7 1.0
O3B C:ATP901 2.8 31.7 1.0
PG C:ATP901 3.2 31.7 1.0
PB C:ATP901 3.3 31.7 1.0
CB C:THR252 3.5 13.3 1.0
O1A C:ATP901 3.5 31.7 1.0
OD2 C:ASP304 3.9 33.6 1.0
OD1 C:ASP304 4.0 33.6 1.0
O3A C:ATP901 4.1 31.7 1.0
O2G C:ATP901 4.1 31.7 1.0
N C:THR252 4.3 13.3 1.0
PA C:ATP901 4.3 31.7 1.0
OE2 C:GLU305 4.4 39.5 1.0
CG C:ASP304 4.4 33.6 1.0
O1G C:ATP901 4.4 31.7 1.0
CG2 C:THR252 4.4 13.3 1.0
CA C:THR252 4.5 13.3 1.0
OD2 B:ASP333 4.5 36.9 1.0
NH2 B:ARG362 4.6 31.7 1.0
O1B C:ATP901 4.6 31.7 1.0
NH1 B:ARG359 4.8 31.7 1.0
O2A C:ATP901 5.0 31.7 1.0

Magnesium binding site 4 out of 8 in 7ln4

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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 Polyubiquitinated Ub-Eos (Fom, 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 Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg903

b:25.0
occ:1.00
 OG1 D:THR525 2.0 31.7 1.0
O2G D:ATP902 2.1 31.7 1.0
O1B D:ATP902 2.6 31.7 1.0
CB D:THR525 3.2 31.7 1.0
PG D:ATP902 3.5 31.7 1.0
PB D:ATP902 3.7 31.7 1.0
O3B D:ATP902 3.7 31.7 1.0
O1A D:ATP902 3.8 31.7 1.0
OD1 D:ASP577 3.9 31.7 1.0
CG2 D:THR525 3.9 31.7 1.0
OD2 D:ASP577 4.1 31.7 1.0
O C:ASP609 4.1 3.7 1.0
NH2 C:ARG638 4.2 31.7 1.0
O3A D:ATP902 4.2 31.7 1.0
NE2 D:GLN578 4.3 31.7 1.0
O1G D:ATP902 4.3 31.7 1.0
CA D:THR525 4.4 31.7 1.0
CG D:ASP577 4.4 31.7 1.0
N D:THR525 4.4 31.7 1.0
O3G D:ATP902 4.5 31.7 1.0
PA D:ATP902 4.6 31.7 1.0
NH1 C:ARG635 4.7 31.7 1.0

Magnesium binding site 5 out of 8 in 7ln4

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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 Polyubiquitinated Ub-Eos (Fom, 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 Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:29.1
occ:1.00
 OG1 D:THR252 2.0 31.7 1.0
O3G D:ATP901 2.1 31.7 1.0
O2B D:ATP901 2.3 31.7 1.0
CB D:THR252 3.3 31.7 1.0
PG D:ATP901 3.4 31.7 1.0
PB D:ATP901 3.5 31.7 1.0
O3B D:ATP901 3.5 31.7 1.0
O1A D:ATP901 3.6 31.7 1.0
NH2 C:ARG362 3.9 31.7 1.0
OD2 D:ASP304 4.1 34.1 1.0
OD1 D:ASP304 4.1 34.1 1.0
CG2 D:THR252 4.1 31.7 1.0
O2G D:ATP901 4.1 31.7 1.0
N D:THR252 4.2 31.7 1.0
O3A D:ATP901 4.2 31.7 1.0
OE2 D:GLU305 4.2 30.0 1.0
CA D:THR252 4.3 31.7 1.0
O1G D:ATP901 4.5 31.7 1.0
PA D:ATP901 4.5 31.7 1.0
CG D:ASP304 4.5 34.1 1.0
O C:ASP333 4.6 39.7 1.0
O1B D:ATP901 4.7 31.7 1.0

Magnesium binding site 6 out of 8 in 7ln4

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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 Polyubiquitinated Ub-Eos (Fom, 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 Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg903

b:24.8
occ:1.00
 OG1 E:THR525 2.1 31.7 1.0
O1G E:ATP902 2.3 31.7 1.0
O1B E:ATP902 2.8 31.7 1.0
CB E:THR525 3.4 31.7 1.0
OD1 E:ASP577 3.6 7.0 1.0
PG E:ATP902 3.6 31.7 1.0
PB E:ATP902 3.9 31.7 1.0
O3B E:ATP902 3.9 31.7 1.0
NE2 E:GLN578 3.9 31.7 1.0
O1A E:ATP902 4.0 31.7 1.0
CG2 E:THR525 4.0 31.7 1.0
OD2 E:ASP577 4.0 7.0 1.0
NH2 D:ARG638 4.2 31.7 1.0
CG E:ASP577 4.2 7.0 1.0
O D:ASP609 4.3 3.4 1.0
O3G E:ATP902 4.5 31.7 1.0
CA E:THR525 4.5 31.7 1.0
O3A E:ATP902 4.5 31.7 1.0
N E:THR525 4.5 31.7 1.0
O2G E:ATP902 4.7 31.7 1.0
PA E:ATP902 4.8 31.7 1.0

Magnesium binding site 7 out of 8 in 7ln4

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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 Polyubiquitinated Ub-Eos (Fom, 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 Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg904

b:19.4
occ:1.00
 OG1 E:THR252 2.1 31.7 1.0
O3G E:ATP901 2.3 31.7 1.0
O2B E:ATP901 2.4 31.7 1.0
CB E:THR252 3.2 31.7 1.0
PG E:ATP901 3.6 31.7 1.0
PB E:ATP901 3.6 31.7 1.0
O1A E:ATP901 3.6 31.7 1.0
O3B E:ATP901 3.7 31.7 1.0
CG2 E:THR252 4.0 31.7 1.0
NH2 D:ARG362 4.0 31.7 1.0
OD2 E:ASP304 4.0 31.5 1.0
OD1 E:ASP304 4.1 31.5 1.0
O3A E:ATP901 4.3 31.7 1.0
CA E:THR252 4.3 31.7 1.0
N E:THR252 4.3 31.7 1.0
CG E:ASP304 4.5 31.5 1.0
O D:ASP333 4.5 45.1 1.0
NH2 D:ARG359 4.5 31.7 1.0
O2G E:ATP901 4.5 31.7 1.0
O1G E:ATP901 4.5 31.7 1.0
PA E:ATP901 4.6 31.7 1.0
OE2 E:GLU305 4.7 12.6 1.0
O1B E:ATP901 4.8 31.7 1.0

Magnesium binding site 8 out of 8 in 7ln4

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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 Polyubiquitinated Ub-Eos (Fom, Class 3)


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 Polyubiquitinated Ub-Eos (Fom, Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg903

b:31.1
occ:1.00
 OG1 F:THR252 2.3 56.5 1.0
O2G F:ATP901 2.4 59.6 1.0
O3B F:ATP901 2.7 59.6 1.0
O2B F:ATP901 2.8 59.6 1.0
PG F:ATP901 3.0 59.6 1.0
O1A F:ATP901 3.2 59.6 1.0
O3G F:ATP901 3.3 59.6 1.0
PB F:ATP901 3.4 59.6 1.0
CB F:THR252 3.5 56.5 1.0
OD2 F:ASP304 3.5 51.4 1.0
OD1 F:ASP304 3.6 51.4 1.0
O3A F:ATP901 3.9 59.6 1.0
CG F:ASP304 4.0 51.4 1.0
PA F:ATP901 4.0 59.6 1.0
N F:THR252 4.2 56.5 1.0
O2A F:ATP901 4.4 59.6 1.0
O1G F:ATP901 4.4 59.6 1.0
CG2 F:THR252 4.4 56.5 1.0
CA F:THR252 4.4 56.5 1.0
O1B F:ATP901 4.7 59.6 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: Wed Oct 2 23:28:13 2024

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