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

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: Tue Jul 8 13:17:05 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy