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Magnesium in PDB 7vcu: Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound

Enzymatic activity of Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound

All present enzymatic activity of Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound:
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 Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound (pdb code 7vcu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound, PDB code: 7vcu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 7vcu

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Magnesium binding site 1 out of 12 in the Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg902

b:30.0
occ:1.00
 OD2 K:ASP304 2.1 76.4 1.0
O2G K:AGS901 2.3 103.2 1.0
OD1 K:ASP304 2.5 76.4 1.0
CG K:ASP304 2.6 76.4 1.0
OG1 K:THR252 2.9 92.3 1.0
O2B K:AGS901 3.4 103.2 1.0
PG K:AGS901 3.7 103.2 1.0
CB K:ASP304 4.1 76.4 1.0
O3G K:AGS901 4.2 103.2 1.0
CB K:THR252 4.3 92.3 1.0
O1A K:AGS901 4.6 103.2 1.0
O3B K:AGS901 4.7 103.2 1.0
PB K:AGS901 4.7 103.2 1.0
S1G K:AGS901 4.8 103.2 1.0
CG K:GLU305 4.9 75.4 1.0
CG2 K:THR252 5.0 92.3 1.0

Magnesium binding site 2 out of 12 in 7vcu

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Magnesium binding site 2 out of 12 in the Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:30.0
occ:1.00
 OD1 B:ASP304 2.2 77.4 1.0
OD2 B:ASP304 2.2 77.4 1.0
O2G B:AGS901 2.3 97.9 1.0
CG B:ASP304 2.5 77.4 1.0
OG1 B:THR252 3.3 86.8 1.0
O2B B:AGS901 3.6 97.9 1.0
PG B:AGS901 3.7 97.9 1.0
O3G B:AGS901 4.0 97.9 1.0
CB B:ASP304 4.1 77.4 1.0
CG B:GLU305 4.5 74.2 1.0
CB B:THR252 4.7 86.8 1.0
S1G B:AGS901 4.7 97.9 1.0
O3B B:AGS901 4.7 97.9 1.0
N B:GLU305 4.7 74.2 1.0
PB B:AGS901 4.8 97.9 1.0
CA B:ASP304 4.9 77.4 1.0
OE2 B:GLU305 4.9 74.2 1.0
O1A B:AGS901 4.9 97.9 1.0

Magnesium binding site 3 out of 12 in 7vcu

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Magnesium binding site 3 out of 12 in the Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:30.0
occ:1.00
 O2G C:AGS901 2.1 97.2 1.0
OD1 C:ASP304 2.4 75.6 1.0
OD2 C:ASP304 2.4 75.6 1.0
CG C:ASP304 2.7 75.6 1.0
OG1 C:THR252 3.2 87.8 1.0
O2B C:AGS901 3.4 97.2 1.0
PG C:AGS901 3.5 97.2 1.0
O3G C:AGS901 3.9 97.2 1.0
CB C:ASP304 4.2 75.6 1.0
O3B C:AGS901 4.5 97.2 1.0
CB C:THR252 4.6 87.8 1.0
PB C:AGS901 4.6 97.2 1.0
S1G C:AGS901 4.6 97.2 1.0
CG C:GLU305 4.7 75.9 1.0
O1A C:AGS901 4.7 97.2 1.0
N C:GLU305 4.9 75.9 1.0

Magnesium binding site 4 out of 12 in 7vcu

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Magnesium binding site 4 out of 12 in the Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg902

b:30.0
occ:1.00
 O2G D:AGS901 2.2 103.0 1.0
OD1 D:ASP304 2.3 74.2 1.0
OD2 D:ASP304 2.4 74.2 1.0
CG D:ASP304 2.7 74.2 1.0
OG1 D:THR252 3.0 89.2 1.0
O2B D:AGS901 3.3 103.0 1.0
PG D:AGS901 3.6 103.0 1.0
O3G D:AGS901 4.0 103.0 1.0
CB D:ASP304 4.2 74.2 1.0
CB D:THR252 4.4 89.2 1.0
PB D:AGS901 4.6 103.0 1.0
O3B D:AGS901 4.6 103.0 1.0
O1A D:AGS901 4.7 103.0 1.0
S1G D:AGS901 4.8 103.0 1.0
CG D:GLU305 4.8 73.7 1.0
N D:THR252 4.9 89.2 1.0
N D:GLU305 5.0 73.7 1.0
CA D:ASP304 5.0 74.2 1.0

Magnesium binding site 5 out of 12 in 7vcu

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Magnesium binding site 5 out of 12 in the Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg902

b:30.0
occ:1.00
 O2G E:AGS901 2.1 107.5 1.0
OD2 E:ASP304 2.2 80.8 1.0
OD1 E:ASP304 2.5 80.8 1.0
CG E:ASP304 2.7 80.8 1.0
OG1 E:THR252 3.1 98.2 1.0
O2B E:AGS901 3.5 107.5 1.0
PG E:AGS901 3.6 107.5 1.0
O3G E:AGS901 4.1 107.5 1.0
CB E:ASP304 4.2 80.8 1.0
CB E:THR252 4.5 98.2 1.0
O1A E:AGS901 4.6 107.5 1.0
O3B E:AGS901 4.6 107.5 1.0
S1G E:AGS901 4.7 107.5 1.0
PB E:AGS901 4.7 107.5 1.0
CG E:GLU305 4.7 81.3 1.0

Magnesium binding site 6 out of 12 in 7vcu

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Magnesium binding site 6 out of 12 in the Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg902

b:30.0
occ:1.00
 OD2 F:ASP304 2.0 76.4 1.0
OD1 F:ASP304 2.3 76.4 1.0
O2G F:AGS901 2.4 102.8 1.0
CG F:ASP304 2.4 76.4 1.0
OG1 F:THR252 3.6 95.0 1.0
PG F:AGS901 3.8 102.8 1.0
CB F:ASP304 3.9 76.4 1.0
O2B F:AGS901 4.0 102.8 1.0
CG F:GLU305 4.2 72.0 1.0
O3G F:AGS901 4.3 102.8 1.0
OE2 F:GLU305 4.5 72.0 1.0
S1G F:AGS901 4.6 102.8 1.0
N F:GLU305 4.7 72.0 1.0
CD F:GLU305 4.7 72.0 1.0
CA F:ASP304 4.8 76.4 1.0
O3B F:AGS901 4.9 102.8 1.0
CB F:THR252 5.0 95.0 1.0

Magnesium binding site 7 out of 12 in 7vcu

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Magnesium binding site 7 out of 12 in the Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:30.0
occ:1.00
 OD2 A:ASP304 2.1 74.6 1.0
O2G A:AGS901 2.3 101.9 1.0
OD1 A:ASP304 2.4 74.6 1.0
CG A:ASP304 2.5 74.6 1.0
OG1 A:THR252 3.4 87.8 1.0
PG A:AGS901 3.7 101.9 1.0
O2B A:AGS901 3.9 101.9 1.0
CB A:ASP304 4.0 74.6 1.0
O3G A:AGS901 4.2 101.9 1.0
CG A:GLU305 4.3 71.2 1.0
OE2 A:GLU305 4.6 71.2 1.0
S1G A:AGS901 4.6 101.9 1.0
N A:GLU305 4.8 71.2 1.0
O3B A:AGS901 4.8 101.9 1.0
CB A:THR252 4.8 87.8 1.0
CD A:GLU305 4.9 71.2 1.0
O1A A:AGS901 4.9 101.9 1.0
CA A:ASP304 4.9 74.6 1.0

Magnesium binding site 8 out of 12 in 7vcu

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Magnesium binding site 8 out of 12 in the Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg902

b:30.0
occ:1.00
 O2G L:AGS901 2.1 105.0 1.0
OD2 L:ASP304 2.3 75.5 1.0
OD1 L:ASP304 2.5 75.5 1.0
CG L:ASP304 2.7 75.5 1.0
OG1 L:THR252 2.9 92.8 1.0
O2B L:AGS901 3.3 105.0 1.0
PG L:AGS901 3.6 105.0 1.0
O3G L:AGS901 4.1 105.0 1.0
CB L:ASP304 4.2 75.5 1.0
CB L:THR252 4.3 92.8 1.0
O1A L:AGS901 4.5 105.0 1.0
O3B L:AGS901 4.6 105.0 1.0
PB L:AGS901 4.6 105.0 1.0
S1G L:AGS901 4.7 105.0 1.0
CG L:GLU305 4.9 76.0 1.0
N L:THR252 5.0 92.8 1.0

Magnesium binding site 9 out of 12 in 7vcu

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Magnesium binding site 9 out of 12 in the Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg902

b:30.0
occ:1.00
 OD2 G:ASP304 1.8 78.8 1.0
CG G:ASP304 2.3 78.8 1.0
OD1 G:ASP304 2.3 78.8 1.0
OG1 G:THR252 2.6 88.0 1.0
O2G G:AGS901 2.7 97.8 1.0
O2B G:AGS901 3.6 97.8 1.0
CB G:ASP304 3.8 78.8 1.0
CB G:THR252 4.0 88.0 1.0
PG G:AGS901 4.2 97.8 1.0
O3G G:AGS901 4.6 97.8 1.0
CG2 G:THR252 4.6 88.0 1.0
O1A G:AGS901 4.7 97.8 1.0
CA G:ASP304 4.8 78.8 1.0
CE2 G:PHE302 4.8 68.3 1.0
N G:THR252 4.9 88.0 1.0
CA G:THR252 4.9 88.0 1.0
PB G:AGS901 5.0 97.8 1.0

Magnesium binding site 10 out of 12 in 7vcu

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Magnesium binding site 10 out of 12 in the Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Human P97 Double Hexamer Conformer I with D1-Atpgammas and D2-Adp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg902

b:30.0
occ:1.00
 OD2 H:ASP304 2.2 75.6 1.0
O2G H:AGS901 2.2 109.7 1.0
OD1 H:ASP304 2.4 75.6 1.0
CG H:ASP304 2.6 75.6 1.0
OG1 H:THR252 3.4 96.0 1.0
PG H:AGS901 3.6 109.7 1.0
O2B H:AGS901 3.7 109.7 1.0
O3G H:AGS901 4.0 109.7 1.0
CB H:ASP304 4.1 75.6 1.0
CG H:GLU305 4.4 71.6 1.0
S1G H:AGS901 4.5 109.7 1.0
OE2 H:GLU305 4.7 71.6 1.0
O3B H:AGS901 4.7 109.7 1.0
CB H:THR252 4.8 96.0 1.0
O1A H:AGS901 4.8 109.7 1.0
N H:GLU305 4.8 71.6 1.0
PB H:AGS901 4.9 109.7 1.0
CD H:GLU305 5.0 71.6 1.0
CA H:ASP304 5.0 75.6 1.0

Reference:

H.Gao, F.Li, Z.Ji, Z.Shi, Y.Li, H.Yu. Cryo-Em Structures of Human P97 Double Hexamer Capture Potentiated Atpase-Competent State. Cell Discov V. 8 19 2022.
ISSN: ESSN 2056-5968
PubMed: 35190543
DOI: 10.1038/S41421-022-00379-1
Page generated: Thu Oct 3 10:24:46 2024

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