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Magnesium in PDB 2ybb: Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)

Enzymatic activity of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)

All present enzymatic activity of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876):
1.10.2.2; 1.6.5.3; 1.6.99.5; 1.9.3.1;

Other elements in 2ybb:

The structure of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) also contains other interesting chemical elements:

Copper (Cu) 3 atoms
Calcium (Ca) 1 atom
Iron (Fe) 45 atoms
Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) (pdb code 2ybb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876), PDB code: 2ybb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 2ybb

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Magnesium binding site 1 out of 7 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg442

b:41.0
occ:1.00
 NE2 1:HIS35 2.2 53.3 1.0
CE1 1:HIS35 2.4 57.1 1.0
CD2 1:HIS35 3.5 57.2 1.0
ND1 1:HIS35 3.7 55.9 1.0
CG 1:HIS35 4.3 52.2 1.0
CE2 1:TYR31 4.9 55.4 1.0
OH 1:TYR31 4.9 51.8 1.0

Magnesium binding site 2 out of 7 in 2ybb

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Magnesium binding site 2 out of 7 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg206

b:32.4
occ:1.00
 NE2 1:HIS350 3.1 49.6 1.0
CG 2:GLU123 3.4 40.4 1.0
N 2:GLU123 3.5 35.9 1.0
OG 2:SER68 3.7 48.7 1.0
CE1 1:HIS350 3.7 53.6 1.0
CD2 1:HIS350 3.7 47.4 1.0
CA 2:VAL122 3.9 36.7 1.0
CB 2:GLU123 4.0 37.9 1.0
CG1 2:VAL122 4.0 41.3 1.0
C 2:VAL122 4.0 35.5 1.0
OE2 1:GLU351 4.0 45.6 1.0
CB 2:SER68 4.1 39.0 1.0
CA 2:GLU123 4.3 38.7 1.0
CD 2:GLU123 4.4 43.7 1.0
OE2 2:GLU123 4.4 44.3 1.0
CB 2:VAL122 4.5 37.2 1.0
O 2:LYS121 4.5 42.2 1.0
ND1 1:HIS350 4.6 53.4 1.0
CG 1:HIS350 4.6 47.9 1.0
N 2:VAL122 5.0 37.0 1.0
NH2 3:ARG205 5.0 43.4 1.0

Magnesium binding site 3 out of 7 in 2ybb

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Magnesium binding site 3 out of 7 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg788

b:23.1
occ:1.00
 OD2 3:ASP302 2.1 35.9 1.0
CG 3:ASP302 2.3 42.3 1.0
O 3:LEU274 2.5 44.8 1.0
OD1 3:ASP302 2.6 43.3 1.0
CB 3:ASP302 3.3 50.0 1.0
C 3:LEU274 3.7 44.5 1.0
N 3:LEU274 4.3 44.6 1.0
CA 3:LEU274 4.4 41.7 1.0
NH1 3:ARG243 4.5 50.7 1.0
CA 3:ASP302 4.7 47.4 1.0
CB 3:LEU274 4.7 42.8 1.0
N 3:LEU275 4.7 45.0 1.0
CA 3:LEU275 4.9 45.6 1.0

Magnesium binding site 4 out of 7 in 2ybb

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Magnesium binding site 4 out of 7 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg789

b:42.1
occ:1.00
 ND1 3:HIS167 2.5 55.9 1.0
O 3:HIS167 2.8 43.8 1.0
CE1 3:HIS167 2.9 56.9 1.0
OE2 7:GLU32 3.3 67.1 1.0
CG 3:HIS167 3.8 53.2 1.0
C 3:HIS167 4.0 44.4 1.0
NE2 3:HIS167 4.1 53.6 1.0
CD 7:GLU32 4.3 66.7 1.0
CD 3:PRO169 4.3 37.6 1.0
CB 3:HIS167 4.5 51.5 1.0
CD2 3:HIS167 4.6 50.5 1.0
OE1 7:GLU32 4.7 66.7 1.0
CA 3:HIS168 4.9 41.7 1.0
CA 3:HIS167 4.9 48.4 1.0
N 3:HIS168 4.9 42.8 1.0
O 3:LYS166 5.0 47.6 1.0

Magnesium binding site 5 out of 7 in 2ybb

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Magnesium binding site 5 out of 7 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mg410

b:59.4
occ:1.00
 CG2 4:VAL223 2.5 93.8 1.0
OE2 4:GLU388 2.6 98.7 1.0
O 4:LYS386 3.4 96.5 1.0
CD 4:GLU388 3.5 0.6 1.0
O 4:ALA384 3.6 89.5 1.0
CG 4:GLU388 3.7 0.7 1.0
CB 4:VAL223 4.0 94.2 1.0
O 4:TYR383 4.3 85.9 1.0
C 4:LYS386 4.4 96.6 1.0
N 4:VAL223 4.5 95.7 1.0
C 4:ALA384 4.6 84.3 1.0
CB 4:LYS386 4.6 92.5 1.0
CG1 4:VAL223 4.6 91.1 1.0
N 4:LYS386 4.6 88.5 1.0
OE1 4:GLU388 4.7 0.8 1.0
O 4:VAL223 4.7 93.5 1.0
CA 4:LYS386 4.8 89.8 1.0
CA 4:VAL223 4.8 94.2 1.0

Magnesium binding site 6 out of 7 in 2ybb

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Magnesium binding site 6 out of 7 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
5:Mg208

b:26.7
occ:1.00
 NE2 5:HIS144 2.4 55.3 1.0
CE1 5:HIS144 3.0 57.5 1.0
CD2 5:HIS144 3.6 57.7 1.0
ND1 5:HIS144 4.2 56.7 1.0
CG 5:HIS144 4.6 57.8 1.0

Magnesium binding site 7 out of 7 in 2ybb

Go back to Magnesium Binding Sites List in 2ybb
Magnesium binding site 7 out of 7 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg518

b:12.0
occ:1.00
 OE1 M:GLU198 2.5 31.5 1.0
OD2 L:ASP369 2.5 16.9 1.0
NE2 L:HIS368 2.7 21.7 1.0
CE1 L:HIS368 2.7 14.5 1.0
OE2 M:GLU198 3.2 26.3 1.0
CD M:GLU198 3.2 28.6 1.0
CG L:ASP369 3.7 17.2 1.0
CD2 L:HIS368 4.0 23.7 1.0
ND1 L:HIS368 4.1 7.0 1.0
OD2 M:ASP173 4.1 31.5 1.0
OD1 L:ASP369 4.5 23.2 1.0
CB L:ASP369 4.6 7.0 1.0
CG M:GLU198 4.6 18.3 1.0
O M:SER197 4.7 18.9 1.0
CG L:HIS368 4.7 10.3 1.0
CE2 L:TYR129 4.8 7.0 1.0
OD1 M:ASP173 4.9 22.4 1.0
CG M:ASP173 4.9 23.3 1.0

Reference:

T.Althoff, D.J.Mills, J.-L.Popot, W.Kuehlbrandt. Arrangement of Electron Transport Chain Components in Bovine Mitochondrial Supercomplex I(1)III(2)IV(1). Embo J. V. 30 4652 2011.
ISSN: ISSN 0261-4189
PubMed: 21909073
DOI: 10.1038/EMBOJ.2011.324
Page generated: Wed Aug 14 07:29:39 2024

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