Atomistry » Calcium » PDB 3hzb-3iit » 3i9v
Atomistry »
  Calcium »
    PDB 3hzb-3iit »
      3i9v »

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: Sat Jul 13 11:25:34 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy