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Magnesium in PDB 7lmy: Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6

Enzymatic activity of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6

All present enzymatic activity of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6:
3.6.4.6;

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 (pdb code 7lmy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6, PDB code: 7lmy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 7lmy

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Magnesium binding site 1 out of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6


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 Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg904

b:2.9
occ:1.00
 OG1 A:THR252 2.0 5.0 1.0
O3G A:ATP901 2.4 14.8 1.0
O2B A:ATP901 2.9 14.8 1.0
O3B A:ATP901 3.2 14.8 1.0
CB A:THR252 3.2 5.0 1.0
PG A:ATP901 3.5 14.8 1.0
O1A A:ATP901 3.7 14.8 1.0
PB A:ATP901 3.7 14.8 1.0
OD2 A:ASP304 3.8 4.1 1.0
OD1 A:ASP304 3.9 4.1 1.0
CG2 A:THR252 4.0 5.0 1.0
CG A:ASP304 4.2 4.1 1.0
N A:THR252 4.3 5.0 1.0
CA A:THR252 4.3 5.0 1.0
O2G A:ATP901 4.3 14.8 1.0
O3A A:ATP901 4.4 14.8 1.0
O1G A:ATP901 4.6 14.8 1.0
PA A:ATP901 4.6 14.8 1.0
CG A:GLU305 4.9 6.9 1.0
O1B A:ATP901 4.9 14.8 1.0

Magnesium binding site 2 out of 12 in 7lmy

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Magnesium binding site 2 out of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6


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 Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg905

b:17.8
occ:1.00
 O2G A:ATP902 2.2 14.8 1.0
O1A A:ATP902 2.3 14.8 1.0
OG1 A:THR525 3.2 7.0 1.0
O1B A:ATP902 3.4 14.8 1.0
PG A:ATP902 3.6 14.8 1.0
PA A:ATP902 3.7 14.8 1.0
OD2 A:ASP577 3.7 12.3 1.0
NH2 F:ARG635 3.8 6.5 1.0
CB A:THR525 3.9 7.0 1.0
O3A A:ATP902 4.0 14.8 1.0
PB A:ATP902 4.0 14.8 1.0
O3B A:ATP902 4.1 14.8 1.0
O1G A:ATP902 4.3 14.8 1.0
CG2 A:THR525 4.4 7.0 1.0
O2A A:ATP902 4.6 14.8 1.0
O3G A:ATP902 4.6 14.8 1.0
O5' A:ATP902 4.7 14.8 1.0
C5' A:ATP902 4.7 14.8 1.0
CG A:ASP577 4.7 12.3 1.0
CZ F:ARG635 4.9 6.5 1.0

Magnesium binding site 3 out of 12 in 7lmy

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Magnesium binding site 3 out of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6


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 Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg904

b:3.8
occ:1.00
 OG1 B:THR252 2.0 6.4 1.0
O3G B:ATP901 2.4 14.8 1.0
O2B B:ATP901 2.9 14.8 1.0
CB B:THR252 3.2 6.4 1.0
O3B B:ATP901 3.2 14.8 1.0
PG B:ATP901 3.5 14.8 1.0
O1A B:ATP901 3.7 14.8 1.0
PB B:ATP901 3.7 14.8 1.0
OD2 B:ASP304 3.8 5.2 1.0
OD1 B:ASP304 3.8 5.2 1.0
CG2 B:THR252 4.0 6.4 1.0
CG B:ASP304 4.2 5.2 1.0
N B:THR252 4.3 6.4 1.0
CA B:THR252 4.3 6.4 1.0
O2G B:ATP901 4.3 14.8 1.0
O3A B:ATP901 4.4 14.8 1.0
O1G B:ATP901 4.6 14.8 1.0
PA B:ATP901 4.6 14.8 1.0
CG B:GLU305 4.9 6.4 1.0
O1B B:ATP901 4.9 14.8 1.0

Magnesium binding site 4 out of 12 in 7lmy

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Magnesium binding site 4 out of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6


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 Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg905

b:19.2
occ:1.00
 O2G B:ATP902 2.1 14.8 1.0
O1A B:ATP902 2.3 14.8 1.0
OG1 B:THR525 3.2 14.8 1.0
O1B B:ATP902 3.4 14.8 1.0
PG B:ATP902 3.6 14.8 1.0
PA B:ATP902 3.6 14.8 1.0
OD2 B:ASP577 3.7 12.9 1.0
NH2 A:ARG635 3.8 9.3 1.0
CB B:THR525 3.9 14.8 1.0
O3A B:ATP902 4.0 14.8 1.0
PB B:ATP902 4.0 14.8 1.0
O3B B:ATP902 4.0 14.8 1.0
O1G B:ATP902 4.3 14.8 1.0
CG2 B:THR525 4.4 14.8 1.0
O2A B:ATP902 4.5 14.8 1.0
O3G B:ATP902 4.6 14.8 1.0
O5' B:ATP902 4.7 14.8 1.0
C5' B:ATP902 4.7 14.8 1.0
CG B:ASP577 4.8 12.9 1.0
CZ A:ARG635 4.9 9.3 1.0

Magnesium binding site 5 out of 12 in 7lmy

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Magnesium binding site 5 out of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6


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 Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg904

b:4.0
occ:1.00
 OG1 C:THR252 2.0 6.4 1.0
O3G C:ATP901 2.4 14.8 1.0
O2B C:ATP901 2.9 14.8 1.0
O3B C:ATP901 3.2 14.8 1.0
CB C:THR252 3.2 6.4 1.0
PG C:ATP901 3.4 14.8 1.0
O1A C:ATP901 3.7 14.8 1.0
PB C:ATP901 3.7 14.8 1.0
OD2 C:ASP304 3.8 4.7 1.0
OD1 C:ASP304 3.9 4.7 1.0
CG2 C:THR252 4.0 6.4 1.0
CG C:ASP304 4.2 4.7 1.0
O2G C:ATP901 4.3 14.8 1.0
N C:THR252 4.3 6.4 1.0
CA C:THR252 4.3 6.4 1.0
O3A C:ATP901 4.4 14.8 1.0
O1G C:ATP901 4.6 14.8 1.0
PA C:ATP901 4.6 14.8 1.0
CG C:GLU305 4.9 5.6 1.0
O1B C:ATP901 4.9 14.8 1.0

Magnesium binding site 6 out of 12 in 7lmy

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Magnesium binding site 6 out of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6


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 Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg905

b:17.2
occ:1.00
 O2G C:ATP902 2.1 28.4 1.0
O1A C:ATP902 2.3 28.4 1.0
OG1 C:THR525 3.1 14.8 1.0
O1B C:ATP902 3.4 28.4 1.0
PG C:ATP902 3.6 28.4 1.0
PA C:ATP902 3.6 28.4 1.0
OD2 C:ASP577 3.7 11.8 1.0
NH2 B:ARG635 3.8 7.5 1.0
CB C:THR525 3.8 14.8 1.0
O3A C:ATP902 4.0 28.4 1.0
PB C:ATP902 4.0 28.4 1.0
O3B C:ATP902 4.0 28.4 1.0
O1G C:ATP902 4.3 28.4 1.0
CG2 C:THR525 4.4 14.8 1.0
O2A C:ATP902 4.5 28.4 1.0
O3G C:ATP902 4.6 28.4 1.0
O5' C:ATP902 4.7 28.4 1.0
C5' C:ATP902 4.7 28.4 1.0
CG C:ASP577 4.7 11.8 1.0
CZ B:ARG635 4.9 7.5 1.0
NH1 B:ARG635 5.0 7.5 1.0

Magnesium binding site 7 out of 12 in 7lmy

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Magnesium binding site 7 out of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6


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 Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg904

b:3.4
occ:1.00
 OG1 D:THR252 2.0 3.4 1.0
O3G D:ATP901 2.4 14.8 1.0
O2B D:ATP901 2.9 14.8 1.0
O3B D:ATP901 3.2 14.8 1.0
CB D:THR252 3.2 3.4 1.0
PG D:ATP901 3.4 14.8 1.0
O1A D:ATP901 3.7 14.8 1.0
PB D:ATP901 3.7 14.8 1.0
OD2 D:ASP304 3.9 5.3 1.0
OD1 D:ASP304 3.9 5.3 1.0
CG2 D:THR252 4.0 3.4 1.0
CG D:ASP304 4.2 5.3 1.0
O2G D:ATP901 4.3 14.8 1.0
N D:THR252 4.3 3.4 1.0
CA D:THR252 4.3 3.4 1.0
O3A D:ATP901 4.4 14.8 1.0
O1G D:ATP901 4.5 14.8 1.0
PA D:ATP901 4.6 14.8 1.0
CG D:GLU305 4.9 5.9 1.0
O1B D:ATP901 4.9 14.8 1.0

Magnesium binding site 8 out of 12 in 7lmy

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Magnesium binding site 8 out of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6


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 Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg905

b:18.6
occ:1.00
 O2G D:ATP902 2.2 14.8 1.0
O1A D:ATP902 2.3 14.8 1.0
OG1 D:THR525 3.1 6.6 1.0
O1B D:ATP902 3.4 14.8 1.0
PG D:ATP902 3.6 14.8 1.0
PA D:ATP902 3.6 14.8 1.0
OD2 D:ASP577 3.7 12.0 1.0
NH2 C:ARG635 3.8 6.9 1.0
CB D:THR525 3.8 6.6 1.0
O3A D:ATP902 4.0 14.8 1.0
PB D:ATP902 4.0 14.8 1.0
O3B D:ATP902 4.0 14.8 1.0
O1G D:ATP902 4.3 14.8 1.0
CG2 D:THR525 4.4 6.6 1.0
O2A D:ATP902 4.5 14.8 1.0
O3G D:ATP902 4.6 14.8 1.0
O5' D:ATP902 4.7 14.8 1.0
C5' D:ATP902 4.7 14.8 1.0
CG D:ASP577 4.7 12.0 1.0
CZ C:ARG635 4.9 6.9 1.0

Magnesium binding site 9 out of 12 in 7lmy

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Magnesium binding site 9 out of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg904

b:3.0
occ:1.00
 OG1 E:THR252 2.0 7.5 1.0
O3G E:ATP901 2.4 14.8 1.0
O2B E:ATP901 2.9 14.8 1.0
CB E:THR252 3.2 7.5 1.0
O3B E:ATP901 3.2 14.8 1.0
PG E:ATP901 3.5 14.8 1.0
O1A E:ATP901 3.7 14.8 1.0
PB E:ATP901 3.7 14.8 1.0
OD2 E:ASP304 3.8 4.6 1.0
OD1 E:ASP304 3.9 4.6 1.0
CG2 E:THR252 4.0 7.5 1.0
CG E:ASP304 4.2 4.6 1.0
N E:THR252 4.3 7.5 1.0
CA E:THR252 4.3 7.5 1.0
O2G E:ATP901 4.3 14.8 1.0
O3A E:ATP901 4.4 14.8 1.0
O1G E:ATP901 4.6 14.8 1.0
PA E:ATP901 4.6 14.8 1.0
CG E:GLU305 4.9 6.9 1.0
O1B E:ATP901 4.9 14.8 1.0

Magnesium binding site 10 out of 12 in 7lmy

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Magnesium binding site 10 out of 12 in the Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of Human P97 in Complex with Nms-873 in the Presence of Atp, NPL4/UFD1, and UB6 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg905

b:18.5
occ:1.00
 O2G E:ATP902 2.2 14.8 1.0
O1A E:ATP902 2.3 14.8 1.0
OG1 E:THR525 3.1 5.1 1.0
O1B E:ATP902 3.4 14.8 1.0
PG E:ATP902 3.6 14.8 1.0
PA E:ATP902 3.6 14.8 1.0
OD2 E:ASP577 3.7 12.5 1.0
NH2 D:ARG635 3.8 9.6 1.0
CB E:THR525 3.8 5.1 1.0
O3A E:ATP902 4.0 14.8 1.0
PB E:ATP902 4.0 14.8 1.0
O3B E:ATP902 4.0 14.8 1.0
O1G E:ATP902 4.3 14.8 1.0
CG2 E:THR525 4.4 5.1 1.0
O2A E:ATP902 4.5 14.8 1.0
O3G E:ATP902 4.6 14.8 1.0
O5' E:ATP902 4.7 14.8 1.0
C5' E:ATP902 4.7 14.8 1.0
CG E:ASP577 4.7 12.5 1.0
CZ D:ARG635 4.9 9.6 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 23:26:04 2024

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