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Magnesium in PDB 4rh7: Crystal Structure of Human Cytoplasmic Dynein 2 Motor Domain in Complex with Adp.VI

Protein crystallography data

The structure of Crystal Structure of Human Cytoplasmic Dynein 2 Motor Domain in Complex with Adp.VI, PDB code: 4rh7 was solved by H.Schmidt, R.Zalyte, L.Urnavicius, A.P.Carter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.60 / 3.41
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 136.030, 487.150, 276.460, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28.5

Other elements in 4rh7:

The structure of Crystal Structure of Human Cytoplasmic Dynein 2 Motor Domain in Complex with Adp.VI also contains other interesting chemical elements:

Vanadium (V) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Cytoplasmic Dynein 2 Motor Domain in Complex with Adp.VI (pdb code 4rh7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Cytoplasmic Dynein 2 Motor Domain in Complex with Adp.VI, PDB code: 4rh7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4rh7

Go back to Magnesium Binding Sites List in 4rh7
Magnesium binding site 1 out of 2 in the Crystal Structure of Human Cytoplasmic Dynein 2 Motor Domain in Complex with Adp.VI


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Cytoplasmic Dynein 2 Motor Domain in Complex with Adp.VI within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4402

b:31.1
occ:1.00
O4G A:AOV4401 2.1 41.9 1.0
OG1 A:THR1696 2.2 64.1 1.0
O2B A:AOV4401 2.4 56.3 1.0
OD1 A:ASP1741 2.5 99.8 1.0
OD2 A:ASP1741 2.7 0.8 1.0
CB A:THR1696 2.9 68.7 1.0
CG A:ASP1741 2.9 0.2 1.0
O3B A:AOV4401 3.0 62.0 1.0
O2A A:AOV4401 3.1 65.8 1.0
PB A:AOV4401 3.2 64.4 1.0
OD2 A:ASP2071 3.3 0.3 1.0
CG2 A:THR1696 3.4 67.0 1.0
VG A:AOV4401 3.4 55.7 1.0
NH1 A:ARG2109 3.5 79.3 1.0
NH2 A:ARG2109 3.7 85.1 1.0
OE2 A:GLU1742 3.8 77.1 1.0
PA A:AOV4401 4.0 66.3 1.0
CZ A:ARG2109 4.0 81.9 1.0
CG A:ASP2071 4.1 0.8 1.0
O3A A:AOV4401 4.2 63.3 1.0
O1A A:AOV4401 4.2 69.1 1.0
CA A:THR1696 4.2 69.2 1.0
O3G A:AOV4401 4.3 57.0 1.0
CB A:ASP1741 4.4 0.3 1.0
OD1 A:ASP2071 4.4 0.2 1.0
N A:THR1696 4.5 69.2 1.0
O1B A:AOV4401 4.5 69.6 1.0
OG1 A:THR1790 4.6 81.2 1.0
NH1 A:ARG1867 4.6 77.5 1.0
O2G A:AOV4401 4.8 52.5 1.0
NZ A:LYS1695 4.8 83.2 1.0
CD A:GLU1742 5.0 83.4 1.0

Magnesium binding site 2 out of 2 in 4rh7

Go back to Magnesium Binding Sites List in 4rh7
Magnesium binding site 2 out of 2 in the Crystal Structure of Human Cytoplasmic Dynein 2 Motor Domain in Complex with Adp.VI


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Cytoplasmic Dynein 2 Motor Domain in Complex with Adp.VI within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4404

b:22.5
occ:1.00
O3G A:ATP4403 2.2 49.5 1.0
O2B A:ATP4403 2.3 54.6 1.0
OG A:SER1986 2.4 57.9 1.0
CB A:SER1986 2.5 56.5 1.0
OE2 A:GLU2095 2.5 58.7 1.0
OD2 A:ASP2055 3.1 82.7 1.0
PG A:ATP4403 3.3 54.1 1.0
PB A:ATP4403 3.4 55.3 1.0
CD A:GLU2095 3.4 63.2 1.0
O2G A:ATP4403 3.5 53.9 1.0
OE1 A:GLU2095 3.6 61.8 1.0
O1B A:ATP4403 3.7 51.6 1.0
CA A:SER1986 3.9 55.9 1.0
O3B A:ATP4403 3.9 54.5 1.0
CG2 A:THR2383 4.0 72.8 1.0
OH A:TYR2384 4.1 93.5 1.0
CG A:ASP2055 4.1 77.2 1.0
OD1 A:ASP2055 4.2 77.4 1.0
N A:SER1986 4.3 54.9 1.0
NH2 A:ARG2420 4.5 68.5 1.0
O2A A:ATP4403 4.5 53.3 1.0
O1G A:ATP4403 4.6 52.3 1.0
O3A A:ATP4403 4.7 54.2 1.0
CG A:GLU2095 4.8 66.5 1.0
C A:SER1986 4.9 58.1 1.0
PA A:ATP4403 4.9 59.4 1.0
O1A A:ATP4403 4.9 61.0 1.0

Reference:

H.Schmidt, R.Zalyte, L.Urnavicius, A.P.Carter. Structure of Human Cytoplasmic Dynein-2 Primed For Its Power Stroke Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE14023
Page generated: Mon Dec 14 19:30:45 2020

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