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Calcium 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:

Magnesium (Mg) 10 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, Reduced, 2 Mol/Asu, with Bound Nadh (pdb code 3iam). 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, Reduced, 2 Mol/Asu, with Bound Nadh, PDB code: 3iam:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3iam

Go back to Calcium Binding Sites List in 3iam
Calcium binding site 1 out of 2 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 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, Reduced, 2 Mol/Asu, with Bound Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Ca204

b:36.5
occ:1.00
 O 7:GLY64 2.6 53.0 1.0
OE1 7:GLU32 3.1 66.7 1.0
OD1 3:ASP165 3.4 59.0 1.0
OE2 7:GLU34 3.4 53.0 1.0
ND1 3:HIS168 3.5 49.2 1.0
OG 7:SER60 3.7 56.2 1.0
C 7:GLY64 3.7 54.2 1.0
CB 3:HIS168 4.1 46.2 1.0
CD 7:GLU32 4.1 66.7 1.0
CG 3:HIS168 4.2 45.6 1.0
O 3:LYS166 4.3 47.6 1.0
CA 7:GLY64 4.3 53.6 1.0
CB 7:SER60 4.3 57.6 1.0
CG 3:ASP165 4.5 55.8 1.0
CD 7:GLU34 4.5 52.5 1.0
CE1 3:HIS168 4.5 51.4 1.0
OE2 7:GLU32 4.7 67.1 1.0
CG 7:PRO66 4.7 59.0 1.0
OE1 7:GLU34 4.7 53.8 1.0
CA 3:HIS168 4.8 41.7 1.0
OD2 3:ASP165 4.8 54.9 1.0
N 7:GLU65 4.8 53.5 1.0
CD 7:PRO66 4.9 56.2 1.0

Calcium binding site 2 out of 2 in 3iam

Go back to Calcium Binding Sites List in 3iam
Calcium binding site 2 out of 2 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 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, Reduced, 2 Mol/Asu, with Bound Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca204

b:32.5
occ:1.00
 O H:GLY64 2.8 53.1 1.0
OE1 H:GLU32 3.2 65.8 1.0
OD1 C:ASP165 3.2 60.5 1.0
OE2 H:GLU34 3.2 54.2 1.0
ND1 C:HIS168 3.5 49.9 1.0
OG H:SER60 3.9 56.1 1.0
CB C:HIS168 3.9 45.8 1.0
C H:GLY64 3.9 55.1 1.0
O C:LYS166 4.1 48.1 1.0
CG C:HIS168 4.2 45.6 1.0
CD H:GLU32 4.2 66.3 1.0
CG C:ASP165 4.3 56.0 1.0
CD H:GLU34 4.3 53.7 1.0
CB H:SER60 4.6 57.0 1.0
CA H:GLY64 4.6 53.9 1.0
CA C:HIS168 4.6 41.7 1.0
CE1 C:HIS168 4.6 51.7 1.0
OE1 H:GLU34 4.6 54.7 1.0
OD2 C:ASP165 4.7 54.7 1.0
CG H:PRO66 4.7 59.0 1.0
OE2 H:GLU32 4.8 66.1 1.0
O C:HIS167 4.9 43.9 1.0
CD H:PRO66 4.9 56.6 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 Dec 12 04:15:19 2020

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