Atomistry » Magnesium » PDB 2ybb-2yni » 2ybb
Atomistry »
  Magnesium »
    PDB 2ybb-2yni »
      2ybb »

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

Go back to Magnesium Binding Sites List in 2ybb
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

Go back to Magnesium Binding Sites List in 2ybb
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

Go back to Magnesium Binding Sites List in 2ybb
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

Go back to Magnesium Binding Sites List in 2ybb
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

Go back to Magnesium Binding Sites List in 2ybb
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

Go back to Magnesium Binding Sites List in 2ybb
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy