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Magnesium in PDB 3iam: Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh

Enzymatic activity of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh

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

Protein crystallography data

The structure of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh, PDB code: 3iam 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) 29.57 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 109.002, 151.015, 216.624, 90.00, 93.07, 90.00
R / Rfree (%) 23.1 / 26.2

Other elements in 3iam:

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

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

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 10 in 3iam

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Magnesium binding site 1 out of 10 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg788

b:23.1
occ:1.00
 OD1 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
OD2 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 2 out of 10 in 3iam

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Magnesium binding site 2 out of 10 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh 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 3 out of 10 in 3iam

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Magnesium binding site 3 out of 10 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh 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 4 out of 10 in 3iam

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Magnesium binding site 4 out of 10 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh 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
CE1 1:TYR31 4.9 55.4 1.0
OH 1:TYR31 4.9 51.8 1.0

Magnesium binding site 5 out of 10 in 3iam

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Magnesium binding site 5 out of 10 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh 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 10 in 3iam

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Magnesium binding site 6 out of 10 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh 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 7 out of 10 in 3iam

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Magnesium binding site 7 out of 10 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg788

b:35.8
occ:1.00
 OD1 C:ASP302 2.3 38.7 1.0
O C:LEU274 2.5 45.3 1.0
CG C:ASP302 2.6 43.1 1.0
OD2 C:ASP302 2.9 42.3 1.0
CB C:ASP302 3.6 51.1 1.0
C C:LEU274 3.7 45.4 1.0
NH1 C:ARG243 4.2 51.9 1.0
N C:LEU274 4.5 45.6 1.0
CA C:LEU274 4.5 42.9 1.0
N C:LEU275 4.7 45.4 1.0
CA C:LEU275 4.8 46.2 1.0
CB C:LEU274 4.9 43.9 1.0
CD1 C:LEU275 4.9 48.6 1.0
CA C:ASP302 5.0 48.8 1.0

Magnesium binding site 8 out of 10 in 3iam

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Magnesium binding site 8 out of 10 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg789

b:44.5
occ:1.00
 ND1 C:HIS167 2.8 56.8 1.0
O C:HIS167 3.0 43.9 1.0
CE1 C:HIS167 3.2 57.2 1.0
OE2 H:GLU32 3.6 66.1 1.0
CG C:HIS167 4.1 55.1 1.0
C C:HIS167 4.2 44.6 1.0
CD C:PRO169 4.3 40.0 1.0
NE2 C:HIS167 4.5 54.1 1.0
CD H:GLU32 4.6 66.3 1.0
CB C:HIS167 4.7 52.0 1.0
CD2 C:HIS167 4.9 52.1 1.0
OE2 G:GLU74 5.0 59.9 1.0

Magnesium binding site 9 out of 10 in 3iam

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Magnesium binding site 9 out of 10 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg208

b:44.3
occ:1.00
 NE2 E:HIS144 2.7 58.0 1.0
CE1 E:HIS144 3.4 59.6 1.0
CD2 E:HIS144 3.9 59.4 1.0
ND1 E:HIS144 4.6 59.9 1.0
CG E:HIS144 4.9 60.5 1.0

Magnesium binding site 10 out of 10 in 3iam

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Magnesium binding site 10 out of 10 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Reduced, 2 Mol/Asu, with Bound Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg442

b:54.1
occ:1.00
 NE2 A:HIS35 2.8 54.6 1.0
CE1 A:HIS35 3.0 58.3 1.0
CD2 A:HIS35 3.8 57.7 1.0
ND1 A:HIS35 4.1 56.4 1.0
CG A:HIS35 4.5 53.5 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: Wed Aug 14 16:01:00 2024

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