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Manganese in PDB 3i9v: Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu

Enzymatic activity of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu

All present enzymatic activity of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu:
1.6.99.5;

Protein crystallography data

The structure of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu, PDB code: 3i9v was solved by L.A.Sazanov, J.M.Berrisford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 108.963, 150.514, 216.726, 90.00, 92.19, 90.00
R / Rfree (%) 23.5 / 28.3

Other elements in 3i9v:

The structure of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu also contains other interesting chemical elements:

Iron (Fe) 64 atoms
Calcium (Ca) 2 atoms

Manganese Binding Sites:

Pages:

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

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu (pdb code 3i9v). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu, PDB code: 3i9v:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 3i9v

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Manganese binding site 1 out of 12 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mn788

b:32.5
occ:1.00
 O 3:LEU274 2.0 42.9 1.0
OD1 3:ASP302 2.4 42.1 1.0
OD2 3:ASP302 2.4 53.4 1.0
CG 3:ASP302 2.6 50.9 1.0
C 3:LEU274 3.1 46.1 1.0
CA 3:LEU274 3.7 46.6 1.0
N 3:LEU274 3.7 48.5 1.0
CB 3:ASP302 3.7 54.9 1.0
CB 3:LEU274 3.8 47.0 1.0
ND1 3:HIS298 4.2 46.6 1.0
N 3:LEU275 4.3 45.9 1.0
O 3:HIS298 4.5 53.4 1.0
NH1 3:ARG243 4.6 48.6 1.0
CE1 3:HIS298 4.6 40.6 1.0
CA 3:LEU275 4.7 45.0 1.0
C 3:GLU273 4.8 44.1 1.0
CG 3:LEU274 4.8 45.9 1.0
OE1 3:GLU299 4.9 53.2 1.0
CA 3:ASP302 5.0 56.3 1.0

Manganese binding site 2 out of 12 in 3i9v

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Manganese binding site 2 out of 12 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mn410

b:66.0
occ:1.00
 OE2 4:GLU210 2.0 92.0 1.0
CD 4:GLU210 2.5 97.8 1.0
OE1 4:GLU210 3.1 0.2 1.0
CG 4:GLU210 3.3 90.3 1.0
CB 4:GLU210 4.8 89.1 1.0

Manganese binding site 3 out of 12 in 3i9v

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Manganese binding site 3 out of 12 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Mn202

b:63.9
occ:1.00
 NE2 7:HIS76 2.3 58.5 1.0
OE2 4:GLU318 2.3 57.2 1.0
CE1 7:HIS76 3.2 54.7 1.0
CD2 7:HIS76 3.2 61.5 1.0
CD 4:GLU318 3.5 57.8 1.0
OE1 4:GLU318 4.0 52.3 1.0
ND1 7:HIS76 4.3 52.7 1.0
OD2 7:ASP39 4.4 64.2 1.0
CG 7:HIS76 4.4 53.4 1.0
CD 7:ARG46 4.6 52.2 1.0
CG 4:GLU318 4.7 52.0 1.0
NH1 7:ARG75 4.9 94.3 1.0
O 7:PRO47 5.0 75.7 1.0

Manganese binding site 4 out of 12 in 3i9v

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Manganese binding site 4 out of 12 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mn789

b:61.5
occ:1.00
 ND1 3:HIS167 2.4 46.5 1.0
O 3:HIS167 2.6 43.1 1.0
OE2 7:GLU32 2.8 80.0 1.0
CE1 3:HIS167 3.2 47.2 1.0
CG 3:HIS167 3.5 39.4 1.0
C 3:HIS167 3.7 46.2 1.0
CB 3:HIS167 3.8 46.7 1.0
CD 7:GLU32 4.0 78.5 1.0
O 3:LYS166 4.3 46.8 1.0
NE2 3:HIS167 4.4 40.0 1.0
CA 3:HIS167 4.4 49.1 1.0
CD2 3:HIS167 4.5 40.5 1.0
OE1 7:GLU32 4.7 71.6 1.0
N 3:HIS168 4.8 45.8 1.0
CD 3:PRO169 4.9 32.8 1.0
CA 3:HIS168 4.9 46.0 1.0

Manganese binding site 5 out of 12 in 3i9v

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Manganese binding site 5 out of 12 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mn411

b:61.4
occ:1.00
 CG2 4:VAL223 2.7 94.8 1.0
OE2 4:GLU388 2.9 98.0 1.0
O 4:LYS386 3.6 84.3 1.0
CG1 4:VAL223 3.7 95.6 1.0
CB 4:VAL223 3.8 94.7 1.0
CD 4:GLU388 3.9 0.9 1.0
CG 4:GLU388 4.1 0.1 1.0
O 4:ALA384 4.2 90.6 1.0
N 4:VAL223 4.3 98.8 1.0
O 4:TYR383 4.5 89.7 1.0
CA 4:VAL223 4.6 93.6 1.0
C 4:LYS386 4.7 93.2 1.0
N 4:LYS386 4.7 94.4 1.0

Manganese binding site 6 out of 12 in 3i9v

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Manganese binding site 6 out of 12 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mn206

b:65.0
occ:1.00
 NE2 1:HIS350 2.9 50.6 1.0
CG1 2:VAL122 3.1 55.4 1.0
OG 2:SER68 3.2 69.5 1.0
CE1 1:HIS350 3.6 52.8 1.0
CB 2:SER68 3.6 59.0 1.0
CA 2:VAL122 3.7 45.4 1.0
OE2 2:GLU123 3.7 52.0 1.0
CD2 1:HIS350 3.8 49.0 1.0
N 2:GLU123 3.8 41.9 1.0
CB 2:VAL122 4.0 46.5 1.0
CG 2:GLU123 4.0 48.9 1.0
O 2:LYS121 4.1 46.3 1.0
C 2:VAL122 4.2 43.2 1.0
CD 2:GLU123 4.3 51.2 1.0
ND1 1:HIS350 4.6 44.4 1.0
CG 1:HIS350 4.7 46.8 1.0
N 2:VAL122 4.8 44.1 1.0
CB 2:GLU123 4.8 53.9 1.0
OE2 1:GLU351 4.8 41.1 1.0
C 2:LYS121 4.9 46.2 1.0
CA 2:GLU123 4.9 47.2 1.0
CG2 2:VAL122 4.9 51.6 1.0

Manganese binding site 7 out of 12 in 3i9v

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Manganese binding site 7 out of 12 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu within 5.0Å range:
probe atom residue distance (Å) B Occ
5:Mn208

b:67.1
occ:1.00
 NE2 5:HIS144 2.3 78.1 1.0
CE1 5:HIS144 3.1 82.6 1.0
CD2 5:HIS144 3.4 73.6 1.0
ND1 5:HIS144 4.3 75.9 1.0
CG 5:HIS144 4.4 72.8 1.0
CA 5:GLY123 4.9 75.0 1.0

Manganese binding site 8 out of 12 in 3i9v

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Manganese binding site 8 out of 12 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn788

b:47.3
occ:1.00
 O C:LEU274 2.0 46.6 1.0
OD1 C:ASP302 2.5 45.0 1.0
OD2 C:ASP302 2.6 61.5 1.0
CG C:ASP302 2.7 56.5 1.0
C C:LEU274 3.1 47.8 1.0
CA C:LEU274 3.7 46.9 1.0
CB C:LEU274 3.8 48.2 1.0
N C:LEU274 3.8 51.4 1.0
CB C:ASP302 3.9 57.8 1.0
ND1 C:HIS298 4.1 50.0 1.0
N C:LEU275 4.2 47.7 1.0
NH1 C:ARG243 4.5 51.8 1.0
CE1 C:HIS298 4.5 44.1 1.0
O C:HIS298 4.6 55.3 1.0
CA C:LEU275 4.6 46.1 1.0
C C:GLU273 4.8 47.1 1.0
OE1 C:GLU299 4.9 60.6 1.0
CG C:LEU274 4.9 48.3 1.0
O C:LEU275 5.0 42.5 1.0

Manganese binding site 9 out of 12 in 3i9v

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Manganese binding site 9 out of 12 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn410

b:63.8
occ:1.00
 OE2 D:GLU210 2.8 96.6 1.0
CD D:GLU210 3.1 0.0 1.0
OE1 D:GLU210 3.4 0.5 1.0
CG D:GLU210 4.1 92.0 1.0
CB D:ALA206 4.5 92.7 1.0

Manganese binding site 10 out of 12 in 3i9v

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Manganese binding site 10 out of 12 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 2 Mol/Asu within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn202

b:68.0
occ:1.00
 NE2 H:HIS76 2.2 59.7 1.0
OE2 D:GLU318 2.3 57.6 1.0
CD2 H:HIS76 3.1 64.1 1.0
CE1 H:HIS76 3.2 58.1 1.0
CD D:GLU318 3.5 59.2 1.0
OD2 H:ASP39 3.8 70.1 1.0
OE1 D:GLU318 4.1 56.6 1.0
CG H:HIS76 4.2 56.6 1.0
ND1 H:HIS76 4.2 59.8 1.0
CB H:ASP39 4.6 57.8 1.0
CG H:ASP39 4.6 63.8 1.0
O H:ASP39 4.7 51.9 1.0
CG D:GLU318 4.7 50.6 1.0
NH1 H:ARG75 4.7 96.2 1.0
O H:PRO47 5.0 71.8 1.0

Reference:

J.M.Berrisford, L.A.Sazanov. Structural Basis For the Mechanism of Respiratory Complex I J.Biol.Chem. V. 284 29773 2009.
ISSN: ISSN 0021-9258
PubMed: 19635800
DOI: 10.1074/JBC.M109.032144
Page generated: Sat Oct 5 16:33:51 2024

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