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Magnesium 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:

Potassium (K) 1 atom
Calcium (Ca) 2 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 26 binding sites of Magnesium where determined in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution, PDB code: 5owo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 26 in 5owo

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Magnesium binding site 1 out of 26 in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg304

b:49.0
occ:1.00
O A:ASP106 2.7 26.9 1.0
O A:HOH471 2.8 36.9 1.0
O A:HOH468 2.8 32.9 1.0
CE1 A:HIS108 3.1 34.5 1.0
CB A:ASN104 3.1 32.2 1.0
ND1 A:HIS108 3.5 34.9 1.0
C A:ASP106 3.7 26.3 1.0
CD2 A:LEU78 3.7 26.7 1.0
OD1 A:ASN104 3.7 44.5 1.0
N A:ASP106 3.7 23.0 1.0
CG A:ASN104 3.8 38.3 1.0
C A:ASN104 3.8 23.8 1.0
O A:ASN104 3.8 21.9 1.0
CB A:ASP106 3.8 33.4 1.0
CA A:ASN104 3.9 24.7 1.0
CA A:ASP106 4.0 29.1 1.0
CB A:LEU78 4.0 22.4 1.0
N A:ASN104 4.2 19.6 1.0
NE2 A:HIS108 4.2 35.1 1.0
O C:HOH426 4.4 38.0 1.0
CG A:LEU78 4.4 24.3 1.0
OD2 A:ASP106 4.4 48.0 1.0
N A:ILE105 4.5 21.3 1.0
C A:ILE105 4.6 24.1 1.0
OE1 A:GLU80 4.7 31.7 1.0
CG A:ASP106 4.7 42.1 1.0
CG A:HIS108 4.8 28.3 1.0
O A:LEU78 4.9 19.1 1.0
N A:ILE107 4.9 27.7 1.0
ND2 A:ASN104 4.9 31.8 1.0

Magnesium binding site 2 out of 26 in 5owo

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Magnesium binding site 2 out of 26 in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
A:Mg305

b:41.8
occ:1.00
N A:ALA51 3.1 20.8 1.0
CB A:ALA51 3.4 22.5 1.0
O3 A:GOL301 3.4 26.9 1.0
N A:ALA50 3.4 29.2 1.0
CB A:PRO49 3.7 35.8 1.0
CA A:ALA51 3.8 20.4 1.0
CE1 C:PHE98 3.8 26.0 1.0
C A:ALA50 4.0 19.8 1.0
CA A:ALA50 4.0 25.9 1.0
CB A:ALA50 4.0 29.0 1.0
C A:PRO49 4.0 32.9 1.0
CA A:PRO49 4.2 33.7 1.0
CZ C:PHE98 4.3 23.7 1.0
C3 A:GOL301 4.5 34.9 1.0
C1 A:GOL301 4.6 43.4 1.0
CD1 C:PHE98 4.6 26.6 1.0
CG A:PRO49 4.8 33.0 1.0
O A:PRO49 4.9 27.4 1.0

Magnesium binding site 3 out of 26 in 5owo

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Magnesium binding site 3 out of 26 in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 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:Mg306

b:48.2
occ:1.00
O A:HOH458 2.6 26.1 1.0
CG2 A:THR83 2.8 29.3 1.0
O A:LYS112 3.1 30.2 1.0
CB A:THR83 3.2 32.2 1.0
C A:LYS112 3.7 33.8 1.0
ND2 A:ASN114 3.7 28.3 1.0
OE2 A:GLU142 3.8 48.1 1.0
OE1 A:GLU142 3.8 55.7 1.0
N A:THR83 3.9 21.1 1.0
CD A:GLU142 4.1 43.3 1.0
CA A:THR83 4.2 26.6 1.0
CA A:LYS112 4.2 37.3 1.0
OG1 A:THR83 4.3 49.9 1.0
CB A:LYS112 4.3 46.8 1.0
NH1 A:ARG81 4.4 23.0 1.0
N A:SER113 4.5 26.1 1.0
C A:SER82 4.6 21.4 1.0
O A:ARG81 4.8 18.9 1.0
CA A:SER113 4.9 26.2 1.0
CG A:LYS112 4.9 51.4 1.0

Magnesium binding site 4 out of 26 in 5owo

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Magnesium binding site 4 out of 26 in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 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:Mg307

b:65.2
occ:1.00
O3 A:GOL303 2.3 77.2 1.0
C3 A:GOL303 3.1 83.8 1.0
C1 A:GOL303 4.1 83.0 1.0
C2 A:GOL303 4.2 79.2 1.0
O1 A:GOL303 4.4 77.3 1.0
O2 A:GOL303 4.8 84.8 1.0

Magnesium binding site 5 out of 26 in 5owo

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Magnesium binding site 5 out of 26 in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 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:Mg308

b:62.0
occ:1.00
CB A:PHE152 3.7 22.6 1.0
CG2 A:VAL157 3.8 21.5 1.0
CB D:PHE152 3.8 19.4 1.0
CG2 D:VAL157 3.9 19.8 1.0
CG A:PHE152 4.1 26.7 1.0
CD1 A:LEU138 4.1 44.9 1.0
CG D:PHE152 4.2 22.0 1.0
CD1 A:PHE152 4.3 28.0 1.0
CD1 D:PHE152 4.5 23.8 1.0
CD2 D:LEU138 4.6 38.1 1.0
CD2 A:LEU138 4.6 38.0 1.0
CD2 A:PHE152 4.8 28.1 1.0
CA A:PHE152 4.8 18.3 1.0
C A:PHE152 4.9 18.8 1.0
CD2 D:PHE152 4.9 23.4 1.0
O A:PHE152 4.9 18.0 1.0
O D:PHE152 5.0 20.1 1.0
C D:PHE152 5.0 18.7 1.0

Magnesium binding site 6 out of 26 in 5owo

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Magnesium binding site 6 out of 26 in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 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:Mg309

b:48.9
occ:1.00
N A:LYS59 3.0 24.8 1.0
OE1 C:GLU80 3.4 35.1 1.0
CG A:LYS59 3.4 47.5 1.0
CA A:GLU58 3.5 26.2 1.0
OE2 C:GLU80 3.6 43.8 1.0
C A:GLU58 3.7 26.4 1.0
CD C:GLU80 3.8 32.3 1.0
CB A:LYS59 3.8 35.7 1.0
O A:HOH463 3.9 36.0 1.0
CA A:LYS59 4.0 28.7 1.0
O A:GLU57 4.1 25.0 1.0
NE2 C:HIS108 4.3 32.2 1.0
CB A:GLU58 4.4 26.6 1.0
N A:GLU58 4.5 25.0 1.0
OG C:SER82 4.5 30.7 1.0
CD A:LYS59 4.6 62.2 1.0
CG A:GLU58 4.6 26.5 1.0
C A:GLU57 4.7 29.1 1.0
O C:HOH418 4.7 21.6 1.0
O A:HOH426 4.8 25.3 1.0
NZ A:LYS59 4.8 63.8 1.0
O A:GLU58 4.9 23.4 1.0
OG C:SER113 5.0 30.1 1.0

Magnesium binding site 7 out of 26 in 5owo

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Magnesium binding site 7 out of 26 in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 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:Mg310

b:72.0
occ:1.00
O A:HOH459 1.8 32.1 1.0
O A:LEU135 2.7 24.9 1.0
OG1 D:THR139 3.2 19.7 1.0
CG2 A:VAL137 3.4 27.9 1.0
C A:LEU135 3.5 21.5 1.0
O A:HOH417 3.5 36.3 1.0
O A:SER132 3.7 36.0 1.0
CG2 D:THR139 3.7 25.0 1.0
O A:HOH437 3.7 42.7 1.0
CA A:ARG136 3.8 18.0 1.0
O D:HOH445 3.8 41.4 1.0
N A:VAL137 3.8 18.7 1.0
CB D:THR139 3.8 21.2 1.0
O D:HOH450 3.9 30.1 1.0
C A:ARG136 4.0 20.0 1.0
N A:ARG136 4.0 18.6 1.0
CB A:VAL137 4.1 24.0 1.0
CB A:LEU135 4.3 21.2 1.0
O D:LEU41 4.4 24.4 1.0
CA A:LEU135 4.4 20.7 1.0
CD2 D:LEU41 4.6 26.4 1.0
CA A:VAL137 4.6 19.9 1.0
C A:SER132 4.7 28.8 1.0
O A:ARG136 4.8 18.9 1.0
N A:LEU135 4.8 20.2 1.0
O D:HOH462 5.0 33.2 1.0

Magnesium binding site 8 out of 26 in 5owo

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Magnesium binding site 8 out of 26 in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 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:Mg311

b:52.0
occ:1.00
OD1 A:ASN199 2.2 31.9 1.0
O A:HIS195 3.3 23.9 1.0
CG A:ASN199 3.3 29.3 1.0
OE1 A:GLN198 3.3 35.3 1.0
CA A:HIS195 3.8 24.3 1.0
CB A:HIS195 3.8 24.8 1.0
CB A:GLN198 3.8 27.9 1.0
ND2 A:ASN199 3.9 33.0 1.0
C A:HIS195 3.9 24.5 1.0
N A:ASN199 4.2 28.3 1.0
ND1 A:HIS195 4.2 27.2 1.0
CG A:HIS195 4.3 23.8 1.0
CD A:GLN198 4.4 30.6 1.0
CB A:ASN199 4.5 27.6 1.0
C A:GLN198 4.6 26.2 1.0
CA A:ASN199 4.6 30.0 1.0
CG A:GLN198 4.7 26.8 1.0
CA A:GLN198 4.8 28.0 1.0

Magnesium binding site 9 out of 26 in 5owo

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Magnesium binding site 9 out of 26 in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:51.6
occ:1.00
O B:PRO72 2.5 32.0 1.0
O3 B:GOL302 3.0 76.4 1.0
O1 B:GOL302 3.2 71.8 1.0
C3 B:GOL302 3.3 77.5 1.0
C1 B:GOL302 3.3 81.3 1.0
C B:PRO72 3.4 30.4 1.0
NE2 B:HIS75 3.7 30.9 1.0
CA B:PRO72 3.8 35.9 1.0
C2 B:GOL302 3.8 84.0 1.0
CB B:PRO72 3.9 40.1 1.0
CD2 B:HIS75 3.9 29.6 1.0
CA B:PRO123 3.9 32.1 1.0
CB B:PRO123 4.0 36.6 1.0
CG B:PRO123 4.1 35.0 1.0
O2 B:GOL302 4.6 79.1 1.0
N B:GLN73 4.6 32.7 1.0
O B:HOH414 4.6 54.0 1.0
N B:PRO123 4.6 31.3 1.0
CE1 B:HIS75 4.8 34.1 1.0
O B:PRO123 4.9 28.2 1.0
C B:PRO123 5.0 27.4 1.0
CD B:PRO123 5.0 36.0 1.0

Magnesium binding site 10 out of 26 in 5owo

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Magnesium binding site 10 out of 26 in the Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Human Cytoplasmic Dynein N-Terminus Dimerization Domain at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:42.5
occ:1.00
OE1 B:GLU190 2.8 29.7 1.0
O B:SER154 3.0 18.1 1.0
O B:HOH455 3.3 40.4 1.0
OE2 B:GLU190 3.4 32.4 1.0
CD B:GLU190 3.5 31.5 1.0
OG B:SER154 3.6 26.3 1.0
CB B:ALA158 3.6 21.8 1.0
O B:HOH411 3.7 33.0 1.0
C B:SER154 3.8 17.7 1.0
CA B:SER154 3.8 19.0 1.0
CB B:SER154 4.3 20.7 1.0
CD B:PRO159 4.6 20.4 1.0
O B:ILE153 4.9 16.2 1.0
CG B:GLU190 4.9 28.0 1.0
CA B:ALA158 5.0 18.4 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: Mon Dec 14 21:02:10 2020

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