Magnesium in PDB 8c0w: Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State (pdb code 8c0w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State, PDB code: 8c0w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 8c0w

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Magnesium binding site 1 out of 10 in the Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:62.9
occ:1.00
 O1B A:ATP1101 1.8 44.0 1.0
O2G A:ATP1101 2.0 44.0 1.0
PG A:ATP1101 2.1 44.0 1.0
O3B A:ATP1101 2.2 44.0 1.0
O1G A:ATP1101 2.3 44.0 1.0
PB A:ATP1101 2.3 44.0 1.0
NE2 A:HIS549 2.9 58.0 1.0
O3A A:ATP1101 3.5 44.0 1.0
O2B A:ATP1101 3.5 44.0 1.0
O3G A:ATP1101 3.6 44.0 1.0
CE1 A:HIS549 3.8 58.0 1.0
CD2 A:HIS549 3.9 58.0 1.0
O1A A:ATP1101 4.6 44.0 1.0
PA A:ATP1101 4.7 44.0 1.0
NZ A:LYS489 5.0 51.7 1.0
ND1 A:HIS549 5.0 58.0 1.0

Magnesium binding site 2 out of 10 in 8c0w

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Magnesium binding site 2 out of 10 in the Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:172.3
occ:1.00
 OG1 A:THR779 1.9 147.5 1.0
O1G A:ATP1102 2.0 142.5 1.0
OD2 A:ASP831 2.1 155.5 1.0
OD1 A:ASP831 2.1 155.5 1.0
O2G A:ATP1102 2.2 142.5 1.0
CG A:ASP831 2.4 155.5 1.0
PG A:ATP1102 2.4 142.5 1.0
CB A:THR779 3.2 147.5 1.0
O3B A:ATP1102 3.3 142.5 1.0
O1B A:ATP1102 3.4 142.5 1.0
CG2 A:THR779 3.6 147.5 1.0
NE2 A:GLN832 3.6 144.6 1.0
O3G A:ATP1102 3.8 142.5 1.0
PB A:ATP1102 3.9 142.5 1.0
CB A:ASP831 3.9 155.5 1.0
CZ A:PHE829 4.2 134.1 1.0
CA A:THR779 4.2 147.5 1.0
N A:THR779 4.5 147.5 1.0
O2B A:ATP1102 4.6 142.5 1.0
CD A:GLN832 4.6 144.6 1.0
CE2 A:PHE829 4.6 134.1 1.0
CA A:ASP831 4.7 155.5 1.0
N A:GLN832 4.9 144.6 1.0

Magnesium binding site 3 out of 10 in 8c0w

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Magnesium binding site 3 out of 10 in the Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1103

b:45.0
occ:1.00
 O1B B:ATP1101 1.7 41.9 1.0
O3G B:ATP1101 1.8 41.9 1.0
PB B:ATP1101 2.2 41.9 1.0
O3B B:ATP1101 2.5 41.9 1.0
OG1 B:THR468 2.6 47.0 1.0
PG B:ATP1101 2.7 41.9 1.0
O2B B:ATP1101 2.7 41.9 1.0
O2G B:ATP1101 3.4 41.9 1.0
O3A B:ATP1101 3.7 41.9 1.0
CB B:THR468 3.9 47.0 1.0
O1G B:ATP1101 3.9 41.9 1.0
OD1 B:ASN526 4.3 54.7 1.0
N B:THR468 4.4 47.0 1.0
CA B:THR468 4.7 47.0 1.0
ND2 B:ASN526 4.7 54.7 1.0
CB B:LYS467 4.8 47.6 1.0
CG2 B:THR468 4.9 47.0 1.0
PA B:ATP1101 4.9 41.9 1.0

Magnesium binding site 4 out of 10 in 8c0w

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Magnesium binding site 4 out of 10 in the Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1104

b:96.9
occ:1.00
 O3B B:ATP1102 1.8 105.9 1.0
O1A B:ATP1102 1.8 105.9 1.0
O3G B:ATP1102 1.9 105.9 1.0
O B:CYS742 2.3 103.4 1.0
PG B:ATP1102 2.3 105.9 1.0
O3A B:ATP1102 2.4 105.9 1.0
PA B:ATP1102 2.6 105.9 1.0
PB B:ATP1102 2.6 105.9 1.0
OG1 B:THR745 2.8 105.3 1.0
O2B B:ATP1102 3.1 105.9 1.0
CB B:THR745 3.2 105.3 1.0
O2G B:ATP1102 3.2 105.9 1.0
C B:CYS742 3.3 103.4 1.0
O2A B:ATP1102 3.5 105.9 1.0
O1G B:ATP1102 3.6 105.9 1.0
O5' B:ATP1102 3.9 105.9 1.0
N B:CYS742 3.9 103.4 1.0
O1B B:ATP1102 3.9 105.9 1.0
CA B:CYS742 4.0 103.4 1.0
CG2 B:THR745 4.0 105.3 1.0
N B:GLY743 4.2 100.6 1.0
CB B:CYS742 4.3 103.4 1.0
CA B:THR745 4.4 105.3 1.0
N B:THR745 4.4 105.3 1.0
C B:GLY741 4.5 108.1 1.0
CA B:GLY743 4.6 100.6 1.0
O B:GLY741 4.9 108.1 1.0
C B:GLY743 5.0 100.6 1.0

Magnesium binding site 5 out of 10 in 8c0w

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Magnesium binding site 5 out of 10 in the Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1103

b:78.8
occ:1.00
 O3A C:ATP1101 1.9 110.7 1.0
O1G C:ATP1101 2.0 110.7 1.0
O1A C:ATP1101 2.1 110.7 1.0
O1B C:ATP1101 2.1 110.7 1.0
PB C:ATP1101 2.1 110.7 1.0
O3B C:ATP1101 2.3 110.7 1.0
PA C:ATP1101 2.4 110.7 1.0
PG C:ATP1101 2.7 110.7 1.0
O2A C:ATP1101 3.5 110.7 1.0
O5' C:ATP1101 3.5 110.7 1.0
O3G C:ATP1101 3.6 110.7 1.0
O2B C:ATP1101 3.6 110.7 1.0
O2G C:ATP1101 3.9 110.7 1.0
NE2 C:HIS549 4.3 82.0 1.0
CE1 C:HIS549 4.4 82.0 1.0
C5' C:ATP1101 4.7 110.7 1.0
O C:VAL487 4.9 59.0 1.0
CB C:ALA490 5.0 56.8 1.0

Magnesium binding site 6 out of 10 in 8c0w

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Magnesium binding site 6 out of 10 in the Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1104

b:59.7
occ:1.00
 O2B C:ATP1102 1.9 75.8 1.0
O2G C:ATP1102 1.9 75.8 1.0
O1A C:ATP1102 2.0 75.8 1.0
OG1 C:THR779 2.2 77.1 1.0
PB C:ATP1102 2.2 75.8 1.0
O3B C:ATP1102 2.2 75.8 1.0
PG C:ATP1102 2.3 75.8 1.0
O3A C:ATP1102 2.4 75.8 1.0
PA C:ATP1102 2.6 75.8 1.0
O1G C:ATP1102 2.6 75.8 1.0
CB C:THR779 3.1 77.1 1.0
O2A C:ATP1102 3.4 75.8 1.0
N C:THR779 3.5 77.1 1.0
O1B C:ATP1102 3.7 75.8 1.0
O3G C:ATP1102 3.7 75.8 1.0
CA C:THR779 3.9 77.1 1.0
O5' C:ATP1102 3.9 75.8 1.0
CG C:LYS778 4.2 83.0 1.0
NZ C:LYS778 4.3 83.0 1.0
CG2 C:THR779 4.3 77.1 1.0
C5' C:ATP1102 4.4 75.8 1.0
C C:LYS778 4.5 83.0 1.0
N C:LYS778 4.7 83.0 1.0
N C:GLY775 4.8 89.2 1.0

Magnesium binding site 7 out of 10 in 8c0w

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Magnesium binding site 7 out of 10 in the Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1103

b:58.3
occ:1.00
 O2B D:ATP1101 1.8 59.1 1.0
O3B D:ATP1101 1.8 59.1 1.0
O1G D:ATP1101 1.9 59.1 1.0
OG1 D:THR468 2.1 63.2 1.0
PB D:ATP1101 2.3 59.1 1.0
PG D:ATP1101 2.3 59.1 1.0
O3A D:ATP1101 3.2 59.1 1.0
O2G D:ATP1101 3.3 59.1 1.0
O1B D:ATP1101 3.5 59.1 1.0
O3G D:ATP1101 3.5 59.1 1.0
CB D:THR468 3.5 63.2 1.0
OD2 D:ASP525 4.3 60.9 1.0
CG2 D:THR468 4.3 63.2 1.0
N D:THR468 4.3 63.2 1.0
PA D:ATP1101 4.3 59.1 1.0
O2A D:ATP1101 4.4 59.1 1.0
CA D:THR468 4.5 63.2 1.0
O1A D:ATP1101 4.7 59.1 1.0

Magnesium binding site 8 out of 10 in 8c0w

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Magnesium binding site 8 out of 10 in the Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1103

b:63.5
occ:1.00
 O2G E:ATP1101 1.9 61.6 1.0
O3A E:ATP1101 1.9 61.6 1.0
O1A E:ATP1101 2.0 61.6 1.0
O3B E:ATP1101 2.0 61.6 1.0
PB E:ATP1101 2.2 61.6 1.0
PG E:ATP1101 2.3 61.6 1.0
O2B E:ATP1101 2.3 61.6 1.0
PA E:ATP1101 2.4 61.6 1.0
O1G E:ATP1101 2.8 61.6 1.0
O2A E:ATP1101 3.4 61.6 1.0
O5' E:ATP1101 3.5 61.6 1.0
O1B E:ATP1101 3.6 61.6 1.0
O3G E:ATP1101 3.6 61.6 1.0
CB E:ALA490 4.1 38.4 1.0
C5' E:ATP1101 4.5 61.6 1.0
N E:ALA490 4.6 38.4 1.0
NE2 E:HIS549 4.7 84.5 1.0
N E:LYS489 5.0 51.5 1.0

Magnesium binding site 9 out of 10 in 8c0w

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Magnesium binding site 9 out of 10 in the Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1104

b:136.1
occ:1.00
 O1B E:ATP1102 1.8 140.3 1.0
O3B E:ATP1102 2.0 140.3 1.0
OG1 E:THR779 2.0 137.1 1.0
PG E:ATP1102 2.2 140.3 1.0
O3G E:ATP1102 2.2 140.3 1.0
NH2 F:ARG855 2.2 157.0 1.0
O2G E:ATP1102 2.2 140.3 1.0
PB E:ATP1102 2.3 140.3 1.0
CB E:THR779 3.4 137.1 1.0
O3A E:ATP1102 3.4 140.3 1.0
CZ F:ARG855 3.4 157.0 1.0
O2B E:ATP1102 3.5 140.3 1.0
O1G E:ATP1102 3.7 140.3 1.0
NH1 F:ARG855 4.0 157.0 1.0
N E:THR779 4.2 137.1 1.0
CA E:THR779 4.2 137.1 1.0
CG2 E:THR779 4.2 137.1 1.0
NE F:ARG855 4.4 157.0 1.0
O2A E:ATP1102 4.4 140.3 1.0
PA E:ATP1102 4.6 140.3 1.0
CZ F:ARG852 4.6 166.6 1.0
NH1 F:ARG852 4.6 166.6 1.0
NE F:ARG852 4.7 166.6 1.0
CD F:ARG852 4.9 166.6 1.0

Magnesium binding site 10 out of 10 in 8c0w

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Magnesium binding site 10 out of 10 in the Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate in Twin Seam State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1103

b:60.8
occ:1.00
 O3B F:ATP1101 1.8 59.2 1.0
O1A F:ATP1101 1.9 59.2 1.0
OG1 F:THR468 2.0 56.9 1.0
PG F:ATP1101 2.2 59.2 1.0
O3G F:ATP1101 2.3 59.2 1.0
PA F:ATP1101 2.3 59.2 1.0
O2G F:ATP1101 2.4 59.2 1.0
O2A F:ATP1101 2.4 59.2 1.0
CB F:THR468 2.7 56.9 1.0
O3A F:ATP1101 2.8 59.2 1.0
PB F:ATP1101 3.0 59.2 1.0
N F:THR468 3.2 56.9 1.0
CA F:THR468 3.5 56.9 1.0
O1G F:ATP1101 3.7 59.2 1.0
O2B F:ATP1101 3.8 59.2 1.0
O5' F:ATP1101 3.9 59.2 1.0
CG2 F:THR468 3.9 56.9 1.0
O1B F:ATP1101 4.0 59.2 1.0
N F:LYS467 4.2 57.9 1.0
C F:LYS467 4.4 57.9 1.0
C F:GLY466 4.5 56.8 1.0
C F:THR468 4.6 56.9 1.0
N F:ARG469 4.6 57.4 1.0
CA F:LYS467 4.8 57.9 1.0
CA F:GLY466 4.8 56.8 1.0
O F:GLY466 4.9 56.8 1.0
C5' F:ATP1101 4.9 59.2 1.0

Reference:

M.Ruttermann, M.Koci, P.Lill, E.D.Geladas, F.Kaschani, B.U.Klink, R.Erdmann, C.Gatsogiannis. Structure of the Peroxisomal PEX1/PEX6 Atpase Complex Bound to A Substrate. Nat Commun V. 14 5942 2023.
ISSN: ESSN 2041-1723
PubMed: 37741838
DOI: 10.1038/S41467-023-41640-9
Page generated: Thu Oct 3 20:01:21 2024

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