Atomistry » Magnesium » PDB 7lc2-7lpp » 7ln5
Atomistry »
  Magnesium »
    PDB 7lc2-7lpp »
      7ln5 »

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

Go back to Magnesium Binding Sites List in 7ln5
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

Go back to Magnesium Binding Sites List in 7ln5
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

Go back to Magnesium Binding Sites List in 7ln5
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

Go back to Magnesium Binding Sites List in 7ln5
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

Go back to Magnesium Binding Sites List in 7ln5
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy