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Calcium in PDB 3ias: Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution

Enzymatic activity of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution

All present enzymatic activity of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution:
1.6.99.5;

Protein crystallography data

The structure of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution, PDB code: 3ias 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) 29.98 / 3.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.080, 266.112, 201.731, 90.00, 104.71, 90.00
R / Rfree (%) 23.7 / 27

Other elements in 3ias:

The structure of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution also contains other interesting chemical elements:

Iron (Fe) 128 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution (pdb code 3ias). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution, PDB code: 3ias:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 3ias

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Calcium binding site 1 out of 16 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


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, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca788

b:43.9
occ:1.00
 OD2 3:ASP302 2.3 53.6 1.0
OD1 3:ASP302 2.4 54.7 1.0
CG 3:ASP302 2.7 58.1 1.0
O 3:LEU274 2.9 54.2 1.0
C 3:LEU274 4.1 54.3 1.0
O 3:GLU299 4.2 60.6 1.0
OE1 3:GLU299 4.3 60.1 1.0
CB 3:ASP302 4.3 64.7 1.0
NH1 3:ARG243 4.3 62.0 1.0
O 3:HIS298 4.4 57.2 1.0
ND1 3:HIS298 4.7 57.4 1.0
N 3:LEU274 4.8 55.8 1.0
CA 3:LEU274 4.9 51.5 1.0
CA 3:GLU299 4.9 59.1 1.0
C 3:GLU299 5.0 58.6 1.0
CE1 3:HIS298 5.0 56.7 1.0

Calcium binding site 2 out of 16 in 3ias

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Calcium binding site 2 out of 16 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


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, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
9:Ca201

b:37.4
occ:1.00
 OE2 9:GLU71 3.8 54.8 1.0
NH1 5:ARG163 4.3 53.0 1.0
OE1 3:GLU273 4.4 65.1 1.0
OE1 9:GLU71 4.5 56.5 1.0
CD 9:GLU71 4.6 55.4 1.0

Calcium binding site 3 out of 16 in 3ias

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Calcium binding site 3 out of 16 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Ca202

b:58.0
occ:1.00
 OD1 2:ASP9 2.3 86.4 1.0
CG 2:ASP9 3.0 83.8 1.0
OD2 2:ASP9 3.0 80.7 1.0
OE2 2:GLU12 4.0 94.5 1.0
CB 2:ASP9 4.5 81.7 1.0
CD 2:GLU12 4.7 97.4 1.0
OE1 2:GLU12 4.8 0.5 1.0

Calcium binding site 4 out of 16 in 3ias

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Calcium binding site 4 out of 16 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca789

b:50.5
occ:1.00
 O 7:GLY64 2.9 62.9 1.0
OE1 7:GLU32 3.2 80.2 1.0
CB 3:HIS168 3.3 56.6 1.0
OD1 3:ASP165 3.3 72.8 1.0
ND1 3:HIS168 3.5 59.8 1.0
CG 3:HIS168 3.6 56.9 1.0
OG 7:SER60 3.7 64.2 1.0
C 7:GLY64 3.8 62.7 1.0
OE2 7:GLU34 3.8 63.8 1.0
CA 7:GLY64 4.2 63.4 1.0
CA 3:HIS168 4.2 57.5 1.0
CG 3:ASP165 4.3 66.6 1.0
CD 7:GLU32 4.4 79.0 1.0
CB 7:SER60 4.4 63.2 1.0
OD2 3:ASP165 4.5 65.8 1.0
CE1 3:HIS168 4.5 64.9 1.0
CG 7:PRO66 4.6 58.0 1.0
CD2 3:HIS168 4.6 58.8 1.0
O 3:LYS166 4.7 61.7 1.0
CD 7:PRO66 4.8 58.7 1.0
N 7:GLU65 4.9 59.5 1.0
CD 7:GLU34 4.9 62.9 1.0
OE2 7:GLU32 5.0 85.8 1.0
N 3:HIS168 5.0 54.5 1.0

Calcium binding site 5 out of 16 in 3ias

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Calcium binding site 5 out of 16 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca788

b:46.4
occ:1.00
 OD2 C:ASP302 2.3 53.2 1.0
O C:LEU274 2.6 55.6 1.0
OD1 C:ASP302 2.6 53.5 1.0
CG C:ASP302 2.8 57.7 1.0
C C:LEU274 3.8 54.6 1.0
O C:HIS298 4.2 57.4 1.0
NH1 C:ARG243 4.3 64.0 1.0
OE1 C:GLU299 4.3 60.6 1.0
O C:GLU299 4.3 60.0 1.0
CB C:ASP302 4.4 63.9 1.0
ND1 C:HIS298 4.4 55.6 1.0
CE1 C:HIS298 4.6 56.7 1.0
CA C:LEU274 4.6 52.4 1.0
N C:LEU274 4.7 55.8 1.0
N C:LEU275 4.8 50.5 1.0
CB C:LEU274 4.8 50.9 1.0
CA C:GLU299 4.9 60.6 1.0
CA C:LEU275 4.9 51.9 1.0
C C:GLU299 5.0 58.4 1.0

Calcium binding site 6 out of 16 in 3ias

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Calcium binding site 6 out of 16 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca201

b:43.5
occ:1.00
 OE2 G:GLU71 3.8 56.2 1.0
NH1 E:ARG163 4.2 52.6 1.0
OE1 G:GLU71 4.2 55.8 1.0
CD G:GLU71 4.4 56.0 1.0
OE1 C:GLU273 4.5 66.2 1.0

Calcium binding site 7 out of 16 in 3ias

Go back to Calcium Binding Sites List in 3ias
Calcium binding site 7 out of 16 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:1.0
occ:1.00
 OD1 B:ASP9 3.4 89.4 1.0
OD2 B:ASP9 3.6 82.0 1.0
CG B:ASP9 4.0 86.3 1.0

Calcium binding site 8 out of 16 in 3ias

Go back to Calcium Binding Sites List in 3ias
Calcium binding site 8 out of 16 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca203

b:55.9
occ:1.00
 O H:GLY64 2.9 63.9 1.0
OE1 H:GLU32 3.0 80.9 1.0
CB C:HIS168 3.6 57.0 1.0
OD1 C:ASP165 3.6 71.5 1.0
OG H:SER60 3.7 65.0 1.0
C H:GLY64 3.8 63.1 1.0
ND1 C:HIS168 3.8 60.9 1.0
OE2 H:GLU34 3.8 62.4 1.0
CG C:HIS168 3.9 56.8 1.0
CA H:GLY64 4.1 63.5 1.0
CD H:GLU32 4.2 79.7 1.0
CA C:HIS168 4.4 57.1 1.0
CB H:SER60 4.4 63.2 1.0
CG C:ASP165 4.6 65.8 1.0
O C:LYS166 4.7 61.1 1.0
OE2 H:GLU32 4.8 84.3 1.0
CG H:PRO66 4.8 58.3 1.0
CE1 C:HIS168 4.8 65.5 1.0
OD2 C:ASP165 4.9 65.6 1.0
N H:GLU65 4.9 60.7 1.0
CD H:GLU34 5.0 61.7 1.0

Calcium binding site 9 out of 16 in 3ias

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Calcium binding site 9 out of 16 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca788

b:50.6
occ:1.00
 O L:LEU274 2.6 55.8 1.0
OD1 L:ASP302 2.6 54.7 1.0
OD2 L:ASP302 2.7 53.5 1.0
CG L:ASP302 3.0 58.1 1.0
C L:LEU274 3.8 55.3 1.0
NH1 L:ARG243 3.8 62.2 1.0
OE1 L:GLU299 4.4 60.9 1.0
CB L:ASP302 4.6 63.5 1.0
N L:LEU274 4.7 56.2 1.0
N L:LEU275 4.7 52.6 1.0
CA L:LEU275 4.7 52.4 1.0
ND1 L:HIS298 4.7 57.4 1.0
CZ L:ARG243 4.7 69.3 1.0
CA L:LEU274 4.7 52.7 1.0
O L:HIS298 4.8 58.0 1.0
O L:GLU299 4.8 61.6 1.0
NH2 L:ARG243 4.8 74.8 1.0
CE1 L:HIS298 4.8 57.0 1.0

Calcium binding site 10 out of 16 in 3ias

Go back to Calcium Binding Sites List in 3ias
Calcium binding site 10 out of 16 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca201

b:40.1
occ:1.00
 OE2 P:GLU71 3.8 56.5 1.0
OE1 P:GLU71 4.3 57.2 1.0
NH1 N:ARG163 4.3 51.8 1.0
OE1 L:GLU273 4.4 67.8 1.0
CD P:GLU71 4.4 57.0 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 Jul 13 11:29:00 2024

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