Magnesium in PDB 8d9r: Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Magnesium atom in the Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1 (pdb code 8d9r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 18 binding sites of Magnesium where determined in the Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1, PDB code: 8d9r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 18 in 8d9r

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Magnesium binding site 1 out of 18 in the Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:57.5
occ:1.00
 O1G C:GTP1001 2.1 83.0 1.0
CA C:THR31 3.0 69.2 1.0
N C:THR31 3.3 69.2 1.0
O1B C:GTP1001 3.4 83.0 1.0
PG C:GTP1001 3.5 83.0 1.0
O3A C:GTP1001 3.5 83.0 1.0
O3G C:GTP1001 3.9 83.0 1.0
PB C:GTP1001 3.9 83.0 1.0
O2A C:GTP1001 4.1 83.0 1.0
O3B C:GTP1001 4.2 83.0 1.0
PA C:GTP1001 4.3 83.0 1.0
C C:LYS30 4.3 68.9 1.0
C C:THR31 4.5 69.2 1.0
O2G C:GTP1001 4.6 83.0 1.0
O1A C:GTP1001 4.7 83.0 1.0
N C:THR48 4.8 55.9 1.0
CA C:THR48 4.8 55.9 1.0
O C:LYS30 5.0 68.9 1.0

Magnesium binding site 2 out of 18 in 8d9r

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Magnesium binding site 2 out of 18 in the Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1002

b:57.5
occ:1.00
 O1G H:GTP1001 2.1 83.0 1.0
CA H:THR31 3.0 69.2 1.0
N H:THR31 3.3 69.2 1.0
O1B H:GTP1001 3.4 83.0 1.0
PG H:GTP1001 3.5 83.0 1.0
O3A H:GTP1001 3.5 83.0 1.0
O3G H:GTP1001 3.9 83.0 1.0
PB H:GTP1001 3.9 83.0 1.0
O2A H:GTP1001 4.1 83.0 1.0
O3B H:GTP1001 4.2 83.0 1.0
PA H:GTP1001 4.3 83.0 1.0
C H:LYS30 4.3 68.9 1.0
C H:THR31 4.5 69.2 1.0
O2G H:GTP1001 4.6 83.0 1.0
O1A H:GTP1001 4.7 83.0 1.0
N H:THR48 4.8 55.9 1.0
CA H:THR48 4.8 55.9 1.0
O H:LYS30 5.0 68.9 1.0

Magnesium binding site 3 out of 18 in 8d9r

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Magnesium binding site 3 out of 18 in the Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg1002

b:57.5
occ:1.00
 O1G Z:GTP1001 2.1 83.0 1.0
CA Z:THR31 3.0 69.2 1.0
N Z:THR31 3.3 69.2 1.0
O1B Z:GTP1001 3.4 83.0 1.0
PG Z:GTP1001 3.5 83.0 1.0
O3A Z:GTP1001 3.5 83.0 1.0
O3G Z:GTP1001 3.9 83.0 1.0
PB Z:GTP1001 3.9 83.0 1.0
O2A Z:GTP1001 4.1 83.0 1.0
O3B Z:GTP1001 4.2 83.0 1.0
PA Z:GTP1001 4.3 83.0 1.0
C Z:LYS30 4.3 68.9 1.0
C Z:THR31 4.5 69.2 1.0
O2G Z:GTP1001 4.6 83.0 1.0
O1A Z:GTP1001 4.7 83.0 1.0
N Z:THR48 4.8 55.9 1.0
CA Z:THR48 4.8 55.9 1.0
O Z:LYS30 5.0 68.9 1.0

Magnesium binding site 4 out of 18 in 8d9r

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Magnesium binding site 4 out of 18 in the Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg1002

b:57.5
occ:1.00
 O1G J:GTP1001 2.1 83.0 1.0
CA J:THR31 3.0 69.2 1.0
N J:THR31 3.3 69.2 1.0
O1B J:GTP1001 3.4 83.0 1.0
PG J:GTP1001 3.5 83.0 1.0
O3A J:GTP1001 3.5 83.0 1.0
O3G J:GTP1001 3.9 83.0 1.0
PB J:GTP1001 3.9 83.0 1.0
O2A J:GTP1001 4.1 83.0 1.0
O3B J:GTP1001 4.2 83.0 1.0
PA J:GTP1001 4.3 83.0 1.0
C J:LYS30 4.3 68.9 1.0
C J:THR31 4.5 69.2 1.0
O2G J:GTP1001 4.6 83.0 1.0
O1A J:GTP1001 4.7 83.0 1.0
N J:THR48 4.8 55.9 1.0
CA J:THR48 4.8 55.9 1.0
O J:LYS30 5.0 68.9 1.0

Magnesium binding site 5 out of 18 in 8d9r

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Magnesium binding site 5 out of 18 in the Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg1002

b:57.5
occ:1.00
 O1G X:GTP1001 2.1 83.0 1.0
CA X:THR31 3.0 69.2 1.0
N X:THR31 3.3 69.2 1.0
O1B X:GTP1001 3.4 83.0 1.0
PG X:GTP1001 3.5 83.0 1.0
O3A X:GTP1001 3.5 83.0 1.0
O3G X:GTP1001 3.9 83.0 1.0
PB X:GTP1001 3.9 83.0 1.0
O2A X:GTP1001 4.1 83.0 1.0
O3B X:GTP1001 4.2 83.0 1.0
PA X:GTP1001 4.3 83.0 1.0
C X:LYS30 4.3 68.9 1.0
C X:THR31 4.5 69.2 1.0
O2G X:GTP1001 4.6 83.0 1.0
O1A X:GTP1001 4.7 83.0 1.0
N X:THR48 4.8 55.9 1.0
CA X:THR48 4.8 55.9 1.0
O X:LYS30 5.0 68.9 1.0

Magnesium binding site 6 out of 18 in 8d9r

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Magnesium binding site 6 out of 18 in the Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg1002

b:57.5
occ:1.00
 O1G 3:GTP1001 2.1 83.0 1.0
CA 3:THR31 3.0 69.2 1.0
N 3:THR31 3.3 69.2 1.0
O1B 3:GTP1001 3.4 83.0 1.0
PG 3:GTP1001 3.5 83.0 1.0
O3A 3:GTP1001 3.5 83.0 1.0
O3G 3:GTP1001 3.9 83.0 1.0
PB 3:GTP1001 3.9 83.0 1.0
O2A 3:GTP1001 4.1 83.0 1.0
O3B 3:GTP1001 4.2 83.0 1.0
PA 3:GTP1001 4.3 83.0 1.0
C 3:LYS30 4.3 68.9 1.0
C 3:THR31 4.5 69.2 1.0
O2G 3:GTP1001 4.6 83.0 1.0
O1A 3:GTP1001 4.7 83.0 1.0
N 3:THR48 4.8 55.9 1.0
CA 3:THR48 4.8 55.9 1.0
O 3:LYS30 5.0 68.9 1.0

Magnesium binding site 7 out of 18 in 8d9r

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Magnesium binding site 7 out of 18 in the Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1002

b:57.5
occ:1.00
 O1G K:GTP1001 2.1 83.0 1.0
CA K:THR31 3.0 69.2 1.0
N K:THR31 3.3 69.2 1.0
O1B K:GTP1001 3.4 83.0 1.0
PG K:GTP1001 3.5 83.0 1.0
O3A K:GTP1001 3.5 83.0 1.0
O3G K:GTP1001 3.9 83.0 1.0
PB K:GTP1001 3.9 83.0 1.0
O2A K:GTP1001 4.1 83.0 1.0
O3B K:GTP1001 4.2 83.0 1.0
PA K:GTP1001 4.3 83.0 1.0
C K:LYS30 4.3 68.9 1.0
C K:THR31 4.5 69.2 1.0
O2G K:GTP1001 4.6 83.0 1.0
O1A K:GTP1001 4.7 83.0 1.0
N K:THR48 4.8 55.9 1.0
CA K:THR48 4.8 55.9 1.0
O K:LYS30 5.0 68.9 1.0

Magnesium binding site 8 out of 18 in 8d9r

Go back to Magnesium Binding Sites List in 8d9r
Magnesium binding site 8 out of 18 in the Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg1002

b:57.5
occ:1.00
 O1G a:GTP1001 2.1 83.0 1.0
CA a:THR31 3.0 69.2 1.0
N a:THR31 3.3 69.2 1.0
O1B a:GTP1001 3.4 83.0 1.0
PG a:GTP1001 3.5 83.0 1.0
O3A a:GTP1001 3.5 83.0 1.0
O3G a:GTP1001 3.9 83.0 1.0
PB a:GTP1001 3.9 83.0 1.0
O2A a:GTP1001 4.1 83.0 1.0
O3B a:GTP1001 4.2 83.0 1.0
PA a:GTP1001 4.3 83.0 1.0
C a:LYS30 4.3 68.9 1.0
C a:THR31 4.5 69.2 1.0
O2G a:GTP1001 4.6 83.0 1.0
O1A a:GTP1001 4.7 83.0 1.0
N a:THR48 4.8 55.9 1.0
CA a:THR48 4.8 55.9 1.0
O a:LYS30 5.0 68.9 1.0

Magnesium binding site 9 out of 18 in 8d9r

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Magnesium binding site 9 out of 18 in the Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mg1002

b:57.5
occ:1.00
 O1G 4:GTP1001 2.1 83.0 1.0
CA 4:THR31 3.0 69.2 1.0
N 4:THR31 3.3 69.2 1.0
O1B 4:GTP1001 3.4 83.0 1.0
PG 4:GTP1001 3.5 83.0 1.0
O3A 4:GTP1001 3.5 83.0 1.0
O3G 4:GTP1001 3.9 83.0 1.0
PB 4:GTP1001 3.9 83.0 1.0
O2A 4:GTP1001 4.1 83.0 1.0
O3B 4:GTP1001 4.2 83.0 1.0
PA 4:GTP1001 4.3 83.0 1.0
C 4:LYS30 4.3 68.9 1.0
C 4:THR31 4.5 69.2 1.0
O2G 4:GTP1001 4.6 83.0 1.0
O1A 4:GTP1001 4.7 83.0 1.0
N 4:THR48 4.8 55.9 1.0
CA 4:THR48 4.8 55.9 1.0
O 4:LYS30 5.0 68.9 1.0

Magnesium binding site 10 out of 18 in 8d9r

Go back to Magnesium Binding Sites List in 8d9r
Magnesium binding site 10 out of 18 in the Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Ap-1, ARF1, Nef Lattice on Mhc-I Lipopeptide Incorporated Wide Membrane Tubes, Centered on Gamma-ARF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mg1002

b:57.5
occ:1.00
 O1G O:GTP1001 2.1 83.0 1.0
CA O:THR31 3.0 69.2 1.0
N O:THR31 3.3 69.2 1.0
O1B O:GTP1001 3.4 83.0 1.0
PG O:GTP1001 3.5 83.0 1.0
O3A O:GTP1001 3.5 83.0 1.0
O3G O:GTP1001 3.9 83.0 1.0
PB O:GTP1001 3.9 83.0 1.0
O2A O:GTP1001 4.1 83.0 1.0
O3B O:GTP1001 4.2 83.0 1.0
PA O:GTP1001 4.3 83.0 1.0
C O:LYS30 4.3 68.9 1.0
C O:THR31 4.5 69.2 1.0
O2G O:GTP1001 4.6 83.0 1.0
O1A O:GTP1001 4.7 83.0 1.0
N O:THR48 4.8 55.9 1.0
CA O:THR48 4.8 55.9 1.0
O O:LYS30 5.0 68.9 1.0

Reference:

R.M.Hooy, Y.Iwamoto, D.A.Tudorica, X.Ren, J.H.Hurley. Self-Assembly and Structure of A Clathrin-Independent Ap-1:ARF1 Tubular Membrane Coat. Sci Adv V. 8 D3914 2022.
ISSN: ESSN 2375-2548
PubMed: 36269825
DOI: 10.1126/SCIADV.ADD3914
Page generated: Fri Oct 4 00:21:47 2024

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