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Magnesium in PDB 4u0z: Eukaryotic Fic Domain Containing Protein with Bound Apcpp

Protein crystallography data

The structure of Eukaryotic Fic Domain Containing Protein with Bound Apcpp, PDB code: 4u0z was solved by A.R.Cole, T.D.Bunney, M.Katan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.34 / 2.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 77.100, 83.754, 130.023, 89.92, 89.57, 89.43
R / Rfree (%) 20.6 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Eukaryotic Fic Domain Containing Protein with Bound Apcpp (pdb code 4u0z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Eukaryotic Fic Domain Containing Protein with Bound Apcpp, PDB code: 4u0z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4u0z

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Magnesium binding site 1 out of 8 in the Eukaryotic Fic Domain Containing Protein with Bound Apcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Eukaryotic Fic Domain Containing Protein with Bound Apcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:71.6
occ:1.00
 O A:HOH696 2.7 44.4 1.0
O3G A:APC501 3.1 45.3 1.0
O A:HOH669 3.2 35.2 1.0
O1B A:APC501 3.6 52.4 1.0
O A:GLU234 3.6 55.0 1.0
C3A A:APC501 3.9 57.3 1.0
OD2 A:ASP367 3.9 69.6 1.0
PB A:APC501 4.3 50.9 1.0
O3B A:APC501 4.4 49.2 1.0
PG A:APC501 4.5 47.1 1.0
C A:GLU234 4.5 55.0 1.0
O A:HOH635 4.5 48.8 1.0
CA A:GLU234 4.5 50.1 1.0
NH2 A:ARG371 4.8 8.0 1.0
CG A:ASP367 4.9 64.8 1.0

Magnesium binding site 2 out of 8 in 4u0z

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Magnesium binding site 2 out of 8 in the Eukaryotic Fic Domain Containing Protein with Bound Apcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Eukaryotic Fic Domain Containing Protein with Bound Apcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:52.2
occ:1.00
 O B:HOH700 2.0 62.5 1.0
O B:HOH701 2.6 38.9 1.0
O1B B:APC501 3.0 82.2 1.0
OD2 B:ASP367 3.1 79.8 1.0
O3G B:APC501 3.2 66.5 1.0
C3A B:APC501 3.7 88.0 1.0
PB B:APC501 4.0 81.0 1.0
NH2 B:ARG371 4.1 46.6 1.0
CG B:ASP367 4.2 75.1 1.0
O B:GLU234 4.2 66.9 1.0
O3B B:APC501 4.5 75.5 1.0
OD1 B:ASP367 4.6 77.0 1.0
PG B:APC501 4.6 67.5 1.0
O B:HOH671 4.9 62.5 1.0

Magnesium binding site 3 out of 8 in 4u0z

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Magnesium binding site 3 out of 8 in the Eukaryotic Fic Domain Containing Protein with Bound Apcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Eukaryotic Fic Domain Containing Protein with Bound Apcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:32.5
occ:1.00
 O C:HOH713 2.4 30.8 1.0
OD2 C:ASP367 2.8 66.4 1.0
O C:HOH714 2.9 29.5 1.0
O3G C:APC501 3.3 41.6 1.0
O2B C:APC501 3.3 54.5 1.0
NH2 C:ARG371 3.6 11.2 1.0
CG C:ASP367 4.0 61.7 1.0
OE1 C:GLU263 4.3 43.4 1.0
C3A C:APC501 4.4 58.1 1.0
PB C:APC501 4.5 53.2 1.0
O C:GLU234 4.5 51.0 1.0
CZ C:ARG371 4.6 30.4 1.0
OD1 C:ASP367 4.6 65.3 1.0
PG C:APC501 4.7 39.1 1.0
O3B C:APC501 4.8 46.1 1.0

Magnesium binding site 4 out of 8 in 4u0z

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Magnesium binding site 4 out of 8 in the Eukaryotic Fic Domain Containing Protein with Bound Apcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Eukaryotic Fic Domain Containing Protein with Bound Apcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:86.1
occ:1.00
 O D:HOH686 1.9 78.6 1.0
O D:HOH685 3.0 67.5 1.0
OD2 D:ASP367 3.3 80.9 1.0
O3G D:APC501 3.4 80.6 1.0
O2B D:APC501 3.6 85.9 1.0
O D:GLU234 4.0 70.7 1.0
C3A D:APC501 4.1 91.7 1.0
NH2 D:ARG371 4.4 16.5 1.0
CG D:ASP367 4.4 73.7 1.0
PB D:APC501 4.5 86.2 1.0
OD1 D:ASP367 4.8 76.4 1.0
O3B D:APC501 4.8 84.3 1.0
PG D:APC501 4.9 81.1 1.0
OE1 D:GLU263 4.9 84.2 1.0
C D:GLU234 4.9 70.6 1.0

Magnesium binding site 5 out of 8 in 4u0z

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Magnesium binding site 5 out of 8 in the Eukaryotic Fic Domain Containing Protein with Bound Apcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Eukaryotic Fic Domain Containing Protein with Bound Apcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:59.2
occ:1.00
 OD2 E:ASP367 2.5 77.7 1.0
O E:HOH667 2.7 35.5 1.0
O1B E:APC501 2.8 61.9 1.0
O E:HOH676 2.8 65.7 1.0
O3G E:APC501 3.3 51.1 1.0
C3A E:APC501 3.5 66.4 1.0
CG E:ASP367 3.6 66.2 1.0
PB E:APC501 3.9 60.3 1.0
OD1 E:ASP367 4.0 70.9 1.0
NH2 E:ARG371 4.1 6.6 1.0
O3B E:APC501 4.4 57.1 1.0
PG E:APC501 4.6 49.8 1.0
O E:GLU234 4.8 51.4 1.0
CB E:ASP367 4.9 35.3 1.0

Magnesium binding site 6 out of 8 in 4u0z

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Magnesium binding site 6 out of 8 in the Eukaryotic Fic Domain Containing Protein with Bound Apcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Eukaryotic Fic Domain Containing Protein with Bound Apcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:53.0
occ:1.00
 O F:HOH696 3.0 40.9 1.0
C3A F:APC501 3.2 88.9 1.0
O2A F:APC501 3.5 94.9 1.0
PA F:APC501 3.8 94.1 1.0
O F:HOH695 4.1 23.1 1.0
OD2 F:ASP367 4.3 79.6 1.0
OD1 F:ASP367 4.3 71.7 1.0
O1B F:APC501 4.4 82.9 1.0
O1A F:APC501 4.4 95.8 1.0
O F:HOH632 4.4 78.6 1.0
PB F:APC501 4.6 83.3 1.0
CG F:ASP367 4.7 69.9 1.0
O F:HOH633 4.8 26.9 1.0

Magnesium binding site 7 out of 8 in 4u0z

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Magnesium binding site 7 out of 8 in the Eukaryotic Fic Domain Containing Protein with Bound Apcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Eukaryotic Fic Domain Containing Protein with Bound Apcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg502

b:48.6
occ:1.00
 O G:HOH727 2.3 25.6 1.0
OD2 G:ASP367 2.5 75.8 1.0
O2B G:APC501 2.9 58.7 1.0
O G:HOH728 2.9 39.4 1.0
O3G G:APC501 3.1 41.3 1.0
CG G:ASP367 3.6 64.4 1.0
C3A G:APC501 3.7 64.0 1.0
NH2 G:ARG371 3.8 7.9 1.0
PB G:APC501 3.9 54.5 1.0
OD1 G:ASP367 4.1 67.9 1.0
O3B G:APC501 4.4 49.0 1.0
PG G:APC501 4.5 42.6 1.0
O G:GLU234 4.8 54.4 1.0
CB G:ASP367 4.8 37.9 1.0
CZ G:ARG371 4.9 28.5 1.0

Magnesium binding site 8 out of 8 in 4u0z

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Magnesium binding site 8 out of 8 in the Eukaryotic Fic Domain Containing Protein with Bound Apcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Eukaryotic Fic Domain Containing Protein with Bound Apcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg502

b:64.4
occ:1.00
 O H:GLU234 2.6 67.8 1.0
O H:HOH699 2.6 75.2 1.0
O H:HOH698 2.9 57.1 1.0
C H:GLU234 3.4 66.4 1.0
O3G H:APC501 3.5 82.2 1.0
CA H:GLU234 3.5 62.0 1.0
C3A H:APC501 4.3 90.3 1.0
O2B H:APC501 4.4 85.0 1.0
N H:GLY235 4.7 60.7 1.0
O3B H:APC501 4.7 84.6 1.0
PG H:APC501 4.7 82.6 1.0
PB H:APC501 4.8 84.8 1.0
N H:GLU234 5.0 62.0 1.0
O1A H:APC501 5.0 95.4 1.0

Reference:

T.D.Bunney, A.R.Cole, M.Broncel, D.Esposito, E.W.Tate, M.Katan. Crystal Structure of the Human, Fic-Domain Containing Protein Hype and Implications For Its Functions. Structure 2014.
ISSN: ISSN 0969-2126
PubMed: 25435325
DOI: 10.1016/J.STR.2014.10.007
Page generated: Tue Aug 12 00:19:29 2025

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