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Magnesium in PDB 5ftm: Cryo-Em Structure of Human P97 Bound to Atpgs (Conformation II)

Enzymatic activity of Cryo-Em Structure of Human P97 Bound to Atpgs (Conformation II)

All present enzymatic activity of Cryo-Em Structure of Human P97 Bound to Atpgs (Conformation II):
3.6.4.6;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Human P97 Bound to Atpgs (Conformation II) (pdb code 5ftm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of Human P97 Bound to Atpgs (Conformation II), PDB code: 5ftm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5ftm

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Magnesium binding site 1 out of 6 in the Cryo-Em Structure of Human P97 Bound to Atpgs (Conformation II)


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 Bound to Atpgs (Conformation II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:30.0
occ:1.00
 OG1 A:THR525 2.3 25.0 1.0
O3B A:AGS901 2.5 46.3 1.0
O1A A:AGS901 2.6 46.1 1.0
O1B A:AGS901 3.4 39.1 1.0
O3G A:AGS901 3.4 47.6 1.0
CB A:THR525 3.4 29.6 1.0
PG A:AGS901 3.5 60.5 1.0
PB A:AGS901 3.5 41.9 1.0
PA A:AGS901 3.9 44.6 1.0
OD1 A:ASP577 4.1 63.1 1.0
OD2 A:ASP577 4.1 54.7 1.0
CG2 A:THR525 4.2 29.8 1.0
NH1 F:ARG635 4.2 64.6 1.0
O3A A:AGS901 4.2 41.4 1.0
CG A:ASP577 4.5 55.5 1.0
S1G A:AGS901 4.6 49.9 1.0
CA A:THR525 4.6 23.7 1.0
CD F:ARG635 4.6 59.3 1.0
N A:THR525 4.7 23.7 1.0
O5' A:AGS901 4.7 47.1 1.0
O2B A:AGS901 4.7 43.0 1.0
O2G A:AGS901 4.8 60.4 1.0
CZ F:ARG635 5.0 64.3 1.0

Magnesium binding site 2 out of 6 in 5ftm

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Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Human P97 Bound to Atpgs (Conformation II)


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 Bound to Atpgs (Conformation II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:30.0
occ:1.00
 OG1 B:THR525 2.3 25.0 1.0
O3B B:AGS901 2.5 46.3 1.0
O1A B:AGS901 2.6 46.1 1.0
O1B B:AGS901 3.4 39.1 1.0
O3G B:AGS901 3.4 47.6 1.0
CB B:THR525 3.4 29.6 1.0
PG B:AGS901 3.5 60.5 1.0
PB B:AGS901 3.5 41.9 1.0
PA B:AGS901 3.9 44.6 1.0
OD1 B:ASP577 4.1 63.1 1.0
OD2 B:ASP577 4.1 54.7 1.0
CG2 B:THR525 4.2 29.8 1.0
NH1 A:ARG635 4.2 64.6 1.0
O3A B:AGS901 4.2 41.4 1.0
CG B:ASP577 4.5 55.5 1.0
S1G B:AGS901 4.6 49.9 1.0
CA B:THR525 4.6 23.7 1.0
CD A:ARG635 4.6 59.3 1.0
N B:THR525 4.7 23.7 1.0
O5' B:AGS901 4.7 47.1 1.0
O2B B:AGS901 4.7 43.0 1.0
O2G B:AGS901 4.8 60.4 1.0
CZ A:ARG635 5.0 64.3 1.0

Magnesium binding site 3 out of 6 in 5ftm

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Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Human P97 Bound to Atpgs (Conformation II)


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 Bound to Atpgs (Conformation II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg903

b:30.0
occ:1.00
 OG1 C:THR525 2.3 25.0 1.0
O3B C:AGS901 2.5 46.3 1.0
O1A C:AGS901 2.6 46.1 1.0
O1B C:AGS901 3.4 39.1 1.0
O3G C:AGS901 3.4 47.6 1.0
CB C:THR525 3.4 29.6 1.0
PG C:AGS901 3.5 60.5 1.0
PB C:AGS901 3.5 41.9 1.0
PA C:AGS901 3.9 44.6 1.0
OD1 C:ASP577 4.1 63.1 1.0
OD2 C:ASP577 4.1 54.7 1.0
CG2 C:THR525 4.2 29.8 1.0
NH1 B:ARG635 4.2 64.6 1.0
O3A C:AGS901 4.2 41.4 1.0
CG C:ASP577 4.5 55.5 1.0
S1G C:AGS901 4.6 49.9 1.0
CA C:THR525 4.6 23.7 1.0
CD B:ARG635 4.6 59.3 1.0
N C:THR525 4.7 23.7 1.0
O5' C:AGS901 4.7 47.1 1.0
O2B C:AGS901 4.7 43.0 1.0
O2G C:AGS901 4.8 60.4 1.0
CZ B:ARG635 5.0 64.3 1.0

Magnesium binding site 4 out of 6 in 5ftm

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Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Human P97 Bound to Atpgs (Conformation II)


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 Bound to Atpgs (Conformation II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg903

b:30.0
occ:1.00
 OG1 D:THR525 2.3 25.0 1.0
O3B D:AGS901 2.5 46.3 1.0
O1A D:AGS901 2.6 46.1 1.0
O1B D:AGS901 3.4 39.1 1.0
O3G D:AGS901 3.4 47.6 1.0
CB D:THR525 3.4 29.6 1.0
PG D:AGS901 3.5 60.5 1.0
PB D:AGS901 3.5 41.9 1.0
PA D:AGS901 3.9 44.6 1.0
OD1 D:ASP577 4.1 63.1 1.0
OD2 D:ASP577 4.1 54.7 1.0
CG2 D:THR525 4.2 29.8 1.0
NH1 C:ARG635 4.2 64.6 1.0
O3A D:AGS901 4.2 41.4 1.0
CG D:ASP577 4.5 55.5 1.0
S1G D:AGS901 4.6 49.9 1.0
CA D:THR525 4.6 23.7 1.0
CD C:ARG635 4.6 59.3 1.0
N D:THR525 4.7 23.7 1.0
O5' D:AGS901 4.7 47.1 1.0
O2B D:AGS901 4.7 43.0 1.0
O2G D:AGS901 4.8 60.4 1.0
CZ C:ARG635 5.0 64.3 1.0

Magnesium binding site 5 out of 6 in 5ftm

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Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Human P97 Bound to Atpgs (Conformation II)


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 Bound to Atpgs (Conformation II) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg903

b:30.0
occ:1.00
 OG1 E:THR525 2.3 25.0 1.0
O3B E:AGS901 2.5 46.3 1.0
O1A E:AGS901 2.6 46.1 1.0
O1B E:AGS901 3.4 39.1 1.0
O3G E:AGS901 3.4 47.6 1.0
CB E:THR525 3.4 29.6 1.0
PG E:AGS901 3.5 60.5 1.0
PB E:AGS901 3.5 41.9 1.0
PA E:AGS901 3.9 44.6 1.0
OD1 E:ASP577 4.1 63.1 1.0
OD2 E:ASP577 4.1 54.7 1.0
CG2 E:THR525 4.2 29.8 1.0
NH1 D:ARG635 4.2 64.6 1.0
O3A E:AGS901 4.2 41.4 1.0
CG E:ASP577 4.5 55.5 1.0
S1G E:AGS901 4.6 49.9 1.0
CA E:THR525 4.6 23.7 1.0
CD D:ARG635 4.6 59.3 1.0
N E:THR525 4.7 23.7 1.0
O5' E:AGS901 4.7 47.1 1.0
O2B E:AGS901 4.7 43.0 1.0
O2G E:AGS901 4.8 60.4 1.0
CZ D:ARG635 5.0 64.3 1.0

Magnesium binding site 6 out of 6 in 5ftm

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Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Human P97 Bound to Atpgs (Conformation II)


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 Bound to Atpgs (Conformation II) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg903

b:30.0
occ:1.00
 OG1 F:THR525 2.3 25.0 1.0
O3B F:AGS901 2.5 46.3 1.0
O1A F:AGS901 2.6 46.1 1.0
O1B F:AGS901 3.4 39.1 1.0
O3G F:AGS901 3.4 47.6 1.0
CB F:THR525 3.4 29.6 1.0
PG F:AGS901 3.5 60.5 1.0
PB F:AGS901 3.5 41.9 1.0
PA F:AGS901 3.9 44.6 1.0
OD1 F:ASP577 4.1 63.1 1.0
OD2 F:ASP577 4.1 54.7 1.0
CG2 F:THR525 4.2 29.8 1.0
NH1 E:ARG635 4.2 64.6 1.0
O3A F:AGS901 4.2 41.4 1.0
CG F:ASP577 4.5 55.5 1.0
S1G F:AGS901 4.6 49.9 1.0
CA F:THR525 4.6 23.7 1.0
CD E:ARG635 4.6 59.3 1.0
N F:THR525 4.7 23.7 1.0
O5' F:AGS901 4.7 47.1 1.0
O2B F:AGS901 4.7 43.0 1.0
O2G F:AGS901 4.8 60.4 1.0
CZ E:ARG635 5.0 64.3 1.0

Reference:

S.Banerjee, A.Bartesaghi, A.Merk, P.Rao, S.L.Bulfer, Y.Yan, N.Green, B.Mroczkowski, R.J.Neitz, P.Wipf, V.Falconieri, R.J.Deshaies, J.L.S.Milne, D.Huryn, M.Arkin, S.Subramaniam. 2.3 A Resolution Cryo-Em Structure of Human P97 and Mechanism of Allosteric Inhibition Science V. 351 871 2016.
ISSN: ISSN 0036-8075
PubMed: 26822609
DOI: 10.1126/SCIENCE.AAD7974
Page generated: Sun Sep 29 04:25:20 2024

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