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Calcium 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:

Manganese (Mn) 12 atoms
Iron (Fe) 64 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3i9v

Go back to Calcium Binding Sites List in 3i9v
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca790

b:30.7
occ:1.00
 O 7:GLY64 2.5 56.2 1.0
OE1 7:GLU32 3.0 71.6 1.0
OD1 3:ASP165 3.2 66.8 1.0
ND1 3:HIS168 3.4 44.3 1.0
C 7:GLY64 3.6 55.1 1.0
CB 3:HIS168 3.6 45.1 1.0
OG 7:SER60 3.9 54.2 1.0
CG 3:HIS168 3.9 41.4 1.0
CD 7:GLU32 4.0 78.5 1.0
CA 7:GLY64 4.2 60.7 1.0
OE2 7:GLU32 4.2 80.0 1.0
OE2 7:GLU34 4.3 47.8 1.0
CG 3:ASP165 4.3 59.6 1.0
O 3:LYS166 4.4 46.8 1.0
CA 3:HIS168 4.5 46.0 1.0
CG 7:PRO66 4.5 58.5 1.0
CE1 3:HIS168 4.5 51.8 1.0
N 7:GLU65 4.6 51.3 1.0
CB 7:SER60 4.6 50.1 1.0
CD 7:PRO66 4.6 56.2 1.0
OE1 7:GLU34 4.7 50.1 1.0
OD2 3:ASP165 4.8 59.5 1.0
CD 7:GLU34 4.9 46.8 1.0
CA 7:GLU65 4.9 52.3 1.0

Calcium binding site 2 out of 2 in 3i9v

Go back to Calcium Binding Sites List in 3i9v
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca 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
C:Ca790

b:39.4
occ:1.00
 OE1 H:GLU32 2.8 70.4 1.0
O H:GLY64 2.8 52.4 1.0
OD1 C:ASP165 3.0 71.6 1.0
ND1 C:HIS168 3.4 47.7 1.0
CB C:HIS168 3.5 46.1 1.0
CD H:GLU32 3.7 77.8 1.0
C H:GLY64 3.9 57.2 1.0
OE2 H:GLU32 3.9 83.1 1.0
CG C:HIS168 3.9 46.6 1.0
OG H:SER60 4.0 55.0 1.0
OE2 H:GLU34 4.1 44.2 1.0
O C:LYS166 4.1 50.5 1.0
CG C:ASP165 4.2 60.9 1.0
CA C:HIS168 4.4 45.7 1.0
CA H:GLY64 4.4 63.6 1.0
OE1 H:GLU34 4.5 51.9 1.0
CE1 C:HIS168 4.6 52.0 1.0
CG H:PRO66 4.6 59.2 1.0
CD H:GLU34 4.7 47.5 1.0
OD2 C:ASP165 4.7 56.9 1.0
CB H:SER60 4.8 54.9 1.0
CD H:PRO66 4.9 56.0 1.0
N H:GLU65 4.9 59.1 1.0
O C:HIS167 5.0 40.1 1.0
N C:HIS168 5.0 42.9 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: Tue Jul 8 13:16:18 2025

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