Magnesium in PDB 5e84: Atp-Bound State of Bip

The structure of Atp-Bound State of Bip, PDB code: 5e84 was solved by Q.Liu, J.Yang, M.Nune, Y.Zong, L.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.76 / 2.99
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	222.468, 222.468, 209.460, 90.00, 90.00, 120.00
R / Rfree (%)	24.3 / 28.7

The structure of Atp-Bound State of Bip also contains other interesting chemical elements:

Zinc

(Zn)

18 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Atp-Bound State of Bip (pdb code 5e84). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Atp-Bound State of Bip, PDB code: 5e84:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Atp-Bound State of Bip within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:54.8 occ:1.00 OD1 A:ASP611 2.6 64.7 1.0 OD2 A:ASP608 2.6 63.3 1.0 OD2 A:ASP611 3.0 59.1 1.0 CG A:ASP611 3.1 56.7 1.0 CG A:ASP608 3.5 60.0 1.0 OD1 A:ASP608 3.7 63.0 1.0 CB A:ASP611 4.6 48.5 1.0 CB A:ASP608 4.8 57.3 1.0

Magnesium binding site 2 out of 12 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Atp-Bound State of Bip within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:41.8 occ:1.00 OE2 A:GLU316 1.7 71.9 1.0 CD A:GLU316 2.4 70.8 1.0 OE1 A:GLU316 2.4 90.9 1.0 CG A:GLU316 3.9 62.1 1.0 CB A:GLU316 4.9 56.0 1.0

Magnesium binding site 3 out of 12 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Atp-Bound State of Bip within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg805 b:38.9 occ:1.00 OE2 A:GLU310 1.4 63.7 1.0 OD2 A:ASP317 1.8 51.8 1.0 OD1 A:ASP317 2.3 56.0 1.0 CG A:ASP317 2.3 52.4 1.0 CD A:GLU310 2.5 64.6 1.0 OE1 A:GLU310 3.2 71.6 1.0 CG A:GLU310 3.6 53.5 1.0 CB A:ASP317 3.9 47.8 1.0 N A:SER311 4.7 46.0 1.0 CB A:GLU310 4.7 46.9 1.0 CA A:ASP317 4.9 45.0 1.0 N A:ASP317 4.9 42.9 1.0 CA A:GLU310 4.9 45.6 1.0

Magnesium binding site 4 out of 12 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Atp-Bound State of Bip within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg804 b:58.6 occ:1.00 OD2 B:ASP608 2.1 98.5 1.0 OD1 B:ASP611 2.8 0.2 1.0 CG B:ASP608 3.0 0.3 1.0 OD1 B:ASP608 3.2 0.7 1.0 OD2 B:ASP611 3.3 0.4 1.0 CG B:ASP611 3.4 0.7 1.0 CB B:ASP608 4.4 0.7 1.0 CB B:ASP611 4.9 0.4 1.0

Magnesium binding site 5 out of 12 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Atp-Bound State of Bip within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg805 b:96.2 occ:1.00 OD2 B:ASP317 1.9 81.0 1.0 OE2 B:GLU310 2.3 0.8 1.0 CG B:ASP317 2.9 81.4 1.0 OD1 B:ASP317 3.2 77.7 1.0 CD B:GLU310 3.2 0.3 1.0 OE1 B:GLU310 3.4 0.1 1.0 CB B:ASP317 4.2 80.6 1.0 CG B:GLU310 4.6 0.5 1.0

Magnesium binding site 6 out of 12 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Atp-Bound State of Bip within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg806 b:87.3 occ:1.00 OE1 B:GLU316 2.7 0.3 1.0 OE2 B:GLU316 3.0 0.4 1.0 CD B:GLU316 3.2 0.9 1.0 CG B:GLU316 4.6 96.0 1.0

Magnesium binding site 7 out of 12 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Atp-Bound State of Bip within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg803 b:23.3 occ:1.00 OD1 C:ASP611 2.0 71.1 1.0 OD2 C:ASP608 2.0 49.0 1.0 OD1 C:ASP608 2.6 54.9 1.0 CG C:ASP608 2.6 50.8 1.0 CG C:ASP611 2.7 72.9 1.0 OD2 C:ASP611 2.8 73.4 1.0 CB C:ASP608 4.1 52.1 1.0 CB C:ASP611 4.2 66.3 1.0 N C:ASP611 4.3 65.5 1.0 CA C:ASP611 4.7 66.6 1.0 N C:ASP608 4.9 59.8 1.0

Magnesium binding site 8 out of 12 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Atp-Bound State of Bip within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg803 b:56.3 occ:1.00 OD1 D:ASP611 1.8 0.6 1.0 CG D:ASP611 2.8 0.3 1.0 OD2 D:ASP611 3.2 0.6 1.0 OD1 D:ASP608 3.7 0.3 1.0 OD2 D:ASP608 3.7 0.4 1.0 CG D:ASP608 4.1 0.6 1.0 CB D:ASP611 4.2 0.7 1.0 N D:ASP611 4.5 93.3 1.0 CA D:ASP611 4.5 91.8 1.0

Magnesium binding site 9 out of 12 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Atp-Bound State of Bip within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg804 b:36.9 occ:1.00 OE2 D:GLU316 2.0 69.0 1.0 OE1 D:GLU316 2.1 86.6 1.0 CD D:GLU316 2.4 77.9 1.0 CG D:GLU316 3.9 76.0 1.0 CB D:GLU316 4.8 76.4 1.0

Magnesium binding site 10 out of 12 in the Atp-Bound State of Bip


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Atp-Bound State of Bip within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg805 b:43.1 occ:1.00 OD2 D:ASP317 1.8 68.5 1.0 OE1 D:GLU310 2.4 82.2 1.0 CG D:ASP317 2.5 68.6 1.0 OD1 D:ASP317 2.6 75.2 1.0 CD D:GLU310 3.6 89.1 1.0 CB D:ASP317 4.0 65.2 1.0 OE2 D:GLU310 4.4 99.8 1.0 CG D:GLU310 4.5 85.0 1.0 CB D:GLU310 4.5 73.4 1.0 N D:SER311 4.5 73.1 1.0 CA D:GLU310 4.7 68.0 1.0

J.Yang, M.Nune, Y.Zong, L.Zhou, Q.Liu. Close and Allosteric Opening of the Polypeptide-Binding Site in A Human HSP70 Chaperone Bip. Structure V. 23 2191 2015.
ISSN: ISSN 0969-2126
PubMed: 26655470
DOI: 10.1016/J.STR.2015.10.012