Magnesium in PDB 8ip3: Cryo-Em Structure of HMRS2-Mg

The structure of Cryo-Em Structure of HMRS2-Mg also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of HMRS2-Mg (pdb code 8ip3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Cryo-Em Structure of HMRS2-Mg, PDB code: 8ip3:
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 Cryo-Em Structure of HMRS2-Mg


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 HMRS2-Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:68.9 occ:1.00 OD1 A:ASP247 4.2 63.8 1.0 OE2 B:GLU312 4.3 62.8 1.0 OE1 B:GLU312 4.4 62.8 1.0 OE2 A:GLU138 4.5 73.2 1.0 CB A:GLU243 4.5 64.3 1.0 CG A:GLU243 4.6 64.3 1.0 OD2 A:ASP247 4.8 63.8 1.0 CD B:GLU312 4.8 62.8 1.0 CD A:GLU243 4.8 64.3 1.0 OE1 A:GLU243 4.9 64.3 1.0 CG A:ASP247 4.9 63.8 1.0

Magnesium binding site 2 out of 12 in the Cryo-Em Structure of HMRS2-Mg


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 HMRS2-Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:96.9 occ:1.00 OE2 A:GLU297 2.9 79.2 1.0 OE2 A:GLU293 3.4 87.3 1.0 CD A:GLU297 4.1 79.2 1.0 OE2 E:GLU261 4.1 89.2 1.0 CD A:GLU293 4.5 87.3 1.0 CG A:GLU297 4.7 79.2 1.0 CG A:GLU293 4.9 87.3 1.0 O A:LEU259 5.0 77.1 1.0

Magnesium binding site 3 out of 12 in the Cryo-Em Structure of HMRS2-Mg


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 HMRS2-Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:103.0 occ:1.00 OD1 A:ASN362 3.9 120.8 1.0 OD1 B:ASN362 3.9 121.8 1.0 OD1 E:ASN362 4.0 120.8 1.0 OD1 C:ASN362 4.1 122.1 1.0 OD1 D:ASN362 4.1 121.4 1.0 O A:GLY360 4.3 115.1 1.0 ND2 B:ASN362 4.4 121.8 1.0 O E:GLY360 4.4 114.4 1.0 ND2 A:ASN362 4.4 120.8 1.0 O B:GLY360 4.4 115.6 1.0 ND2 C:ASN362 4.5 122.1 1.0 CG B:ASN362 4.5 121.8 1.0 CG A:ASN362 4.5 120.8 1.0 O D:GLY360 4.5 114.7 1.0 ND2 E:ASN362 4.6 120.8 1.0 O C:GLY360 4.6 115.2 1.0 ND2 D:ASN362 4.6 121.4 1.0 CG C:ASN362 4.6 122.1 1.0 CG E:ASN362 4.7 120.8 1.0 CG D:ASN362 4.7 121.4 1.0

Magnesium binding site 4 out of 12 in the Cryo-Em Structure of HMRS2-Mg


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 HMRS2-Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:66.1 occ:1.00 OD2 B:ASP329 4.4 60.2 1.0 OD2 C:ASP329 4.5 60.3 1.0 OD1 B:ASP329 4.5 60.2 1.0 OD2 A:ASP329 4.6 59.6 1.0 OD1 A:ASP329 4.6 59.6 1.0 NH1 B:ARG332 4.7 55.7 1.0 NH1 C:ARG332 4.7 55.8 1.0 OD1 C:ASP329 4.7 60.3 1.0 OD2 D:ASP329 4.7 59.4 1.0 OD2 E:ASP329 4.8 59.6 1.0 NH1 A:ARG332 4.8 55.3 1.0 NH1 D:ARG332 4.8 55.6 1.0 CG B:ASP329 4.9 60.2 1.0 OD1 E:ASP329 4.9 59.6 1.0 OD1 D:ASP329 4.9 59.4 1.0 NH1 E:ARG332 4.9 55.2 1.0 CG C:ASP329 5.0 60.3 1.0

Magnesium binding site 5 out of 12 in the Cryo-Em Structure of HMRS2-Mg


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 HMRS2-Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:73.0 occ:1.00 OD1 B:ASP247 4.2 64.1 1.0 OE2 C:GLU312 4.3 62.3 1.0 OE1 C:GLU312 4.4 62.3 1.0 CB B:GLU243 4.5 64.2 1.0 OE2 B:GLU138 4.5 72.1 1.0 CG B:GLU243 4.6 64.2 1.0 CD C:GLU312 4.8 62.3 1.0 CD B:GLU243 4.8 64.2 1.0 OD2 B:ASP247 4.8 64.1 1.0 OE1 B:GLU243 4.9 64.2 1.0 CG B:ASP247 5.0 64.1 1.0

Magnesium binding site 6 out of 12 in the Cryo-Em Structure of HMRS2-Mg


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 HMRS2-Mg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:99.8 occ:1.00 OE2 B:GLU293 3.0 87.1 1.0 OE2 B:GLU297 3.1 78.7 1.0 OE2 A:GLU261 3.8 89.3 1.0 CD B:GLU293 4.2 87.1 1.0 CD B:GLU297 4.3 78.7 1.0 CD A:GLU261 4.7 89.3 1.0 CG B:GLU293 4.8 87.1 1.0 OE1 A:GLU261 4.8 89.3 1.0

Magnesium binding site 7 out of 12 in the Cryo-Em Structure of HMRS2-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of HMRS2-Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:71.0 occ:1.00 OD1 C:ASP247 3.9 63.6 1.0 OE2 D:GLU312 4.2 62.4 1.0 CB C:GLU243 4.2 64.1 1.0 CG C:GLU243 4.4 64.1 1.0 OE2 C:GLU138 4.5 71.5 1.0 OE1 D:GLU312 4.5 62.4 1.0 OD2 C:ASP247 4.6 63.6 1.0 CG C:ASP247 4.7 63.6 1.0 CD C:GLU243 4.7 64.1 1.0 OE1 C:GLU243 4.7 64.1 1.0 CD D:GLU312 4.8 62.4 1.0 O C:GLU243 4.9 64.1 1.0 CA C:GLU243 4.9 64.1 1.0

Magnesium binding site 8 out of 12 in the Cryo-Em Structure of HMRS2-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of HMRS2-Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:101.2 occ:1.00 OE2 C:GLU297 3.0 78.3 1.0 OE2 C:GLU293 3.3 86.1 1.0 OE2 B:GLU261 3.8 89.4 1.0 CD C:GLU297 4.2 78.3 1.0 CD C:GLU293 4.4 86.1 1.0 CD B:GLU261 4.7 89.4 1.0 CG C:GLU297 4.9 78.3 1.0 OE1 B:GLU261 4.9 89.4 1.0 CG C:GLU293 4.9 86.1 1.0

Magnesium binding site 9 out of 12 in the Cryo-Em Structure of HMRS2-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of HMRS2-Mg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:70.8 occ:1.00 OD1 D:ASP247 3.9 63.7 1.0 OE2 E:GLU312 4.2 63.2 1.0 OE2 D:GLU138 4.3 72.7 1.0 CB D:GLU243 4.4 64.2 1.0 OE1 E:GLU312 4.5 63.2 1.0 OD2 D:ASP247 4.5 63.7 1.0 CG D:GLU243 4.6 64.2 1.0 CG D:ASP247 4.6 63.7 1.0 CD E:GLU312 4.8 63.2 1.0 CD D:GLU243 4.9 64.2 1.0 O D:GLU243 4.9 64.2 1.0 CD D:GLU138 4.9 72.7 1.0 OE1 D:GLU243 4.9 64.2 1.0 OE1 D:GLU138 5.0 72.7 1.0

Magnesium binding site 10 out of 12 in the Cryo-Em Structure of HMRS2-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of HMRS2-Mg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:101.5 occ:1.00 OE2 D:GLU293 3.0 86.5 1.0 OE2 D:GLU297 3.3 77.3 1.0 OE2 C:GLU261 3.8 89.6 1.0 CD D:GLU293 4.2 86.5 1.0 CD D:GLU297 4.5 77.3 1.0 CD C:GLU261 4.7 89.6 1.0 CG D:GLU293 4.8 86.5 1.0 O D:LEU259 4.8 76.9 1.0 OE1 C:GLU261 4.9 89.6 1.0

M.Li, Y.Li, X.Yang, Y.Q.Shen. Molecular Basis of MG2+ Permeation Through the Mitochondrial Human MRS2 Channel To Be Published.