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Calcium in PDB 5owo: Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution

Protein crystallography data

The structure of Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution, PDB code: 5owo was solved by L.Urnavicius, C.K.Lau, M.M.Elshenawy, E.Morales-Rios, C.Motz, A.Yildiz, A.P.Carter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.78 / 1.79
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.242, 175.560, 50.444, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.9

Other elements in 5owo:

The structure of Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 26 atoms
Potassium (K) 1 atom
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution (pdb code 5owo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution, PDB code: 5owo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5owo

Go back to Calcium Binding Sites List in 5owo
Calcium binding site 1 out of 2 in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca312

b:21.6
occ:1.00
OD1 A:ASN102 2.4 28.1 1.0
O A:HOH420 2.4 21.0 1.0
OD1 C:ASN102 2.4 26.7 1.0
O C:HOH415 2.4 22.1 1.0
OE1 A:GLU58 2.5 23.4 1.0
OE1 C:GLU58 2.5 27.4 1.0
OE2 C:GLU58 2.5 21.8 1.0
OE2 A:GLU58 2.6 25.8 1.0
CD C:GLU58 2.9 24.9 1.0
CD A:GLU58 2.9 24.4 1.0
CG A:ASN102 3.4 27.9 1.0
CG C:ASN102 3.5 28.9 1.0
O A:HOH447 4.2 22.1 1.0
O C:HOH435 4.3 20.4 1.0
CB A:ASN102 4.3 22.8 1.0
ND2 A:ASN102 4.4 35.1 1.0
CB C:ASN102 4.4 21.3 1.0
ND2 C:ASN102 4.4 33.9 1.0
CG A:GLU58 4.4 26.5 1.0
CG C:GLU58 4.5 24.2 1.0
O A:HOH443 4.5 28.0 1.0
O C:HOH434 4.5 30.6 1.0
O A:TYR101 4.5 18.8 1.0
O C:TYR101 4.6 17.8 1.0
O A:HOH446 4.6 34.2 1.0
CA A:ASN102 4.8 20.2 1.0
O C:HOH436 4.8 38.5 1.0
CA C:ASN102 4.8 18.2 1.0

Calcium binding site 2 out of 2 in 5owo

Go back to Calcium Binding Sites List in 5owo
Calcium binding site 2 out of 2 in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca305

b:45.7
occ:0.50
OD1 D:ASN102 2.5 23.0 1.0
O D:HOH412 2.5 23.0 1.0
OE2 D:GLU58 2.7 24.2 1.0
OE1 D:GLU58 2.7 30.9 1.0
CD D:GLU58 3.1 28.0 1.0
CG D:ASN102 3.5 26.8 1.0
K D:K306 3.9 0.0 0.5
O D:HOH453 4.2 20.5 1.0
CB D:ASN102 4.3 21.7 1.0
ND2 D:ASN102 4.4 28.2 1.0
O D:TYR101 4.5 17.6 1.0
O D:HOH421 4.5 30.9 1.0
CG D:GLU58 4.6 31.4 1.0
CA D:ASN102 4.7 19.2 1.0
O D:HOH418 4.7 32.9 1.0

Reference:

L.Urnavicius, C.K.Lau, M.M.Elshenawy, E.Morales-Rios, C.Motz, A.Yildiz, A.P.Carter. Cryo-Em Shows How Dynactin Recruits Two Dyneins For Faster Movement. Nature V. 554 202 2018.
ISSN: ESSN 1476-4687
PubMed: 29420470
DOI: 10.1038/NATURE25462
Page generated: Sat Dec 12 05:41:48 2020

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