Magnesium in PDB 6h7x: First X-Ray Structure of Full-Length Human Ruvb-Like 2.

Enzymatic activity of First X-Ray Structure of Full-Length Human Ruvb-Like 2.

All present enzymatic activity of First X-Ray Structure of Full-Length Human Ruvb-Like 2.:
3.6.4.12;

Protein crystallography data

The structure of First X-Ray Structure of Full-Length Human Ruvb-Like 2., PDB code: 6h7x was solved by S.Silva, J.Brito, P.Matias, T.Bandeiras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.27 / 2.89
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 123.023, 123.023, 60.880, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 23.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the First X-Ray Structure of Full-Length Human Ruvb-Like 2. (pdb code 6h7x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the First X-Ray Structure of Full-Length Human Ruvb-Like 2., PDB code: 6h7x:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6h7x

Go back to Magnesium Binding Sites List in 6h7x
Magnesium binding site 1 out of 3 in the First X-Ray Structure of Full-Length Human Ruvb-Like 2.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of First X-Ray Structure of Full-Length Human Ruvb-Like 2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:38.3
occ:1.00
NH2 A:ARG336 3.3 41.3 1.0
O2 A:PEG1005 3.4 79.4 1.0
OD2 A:ASP305 3.5 42.6 1.0
C3 A:PEG1005 3.7 78.8 1.0
CB A:ASP305 3.9 32.3 1.0
CZ A:ARG336 3.9 42.0 1.0
CG A:ASP305 4.2 38.7 1.0
O A:HOH1115 4.3 39.6 1.0
NH1 A:ARG336 4.5 44.6 1.0
NE A:ARG336 4.5 40.0 1.0
C4 A:PEG1005 4.6 77.3 1.0
N A:GLY337 4.6 34.1 1.0
CE1 A:PHE109 4.7 30.0 1.0
C2 A:PEG1005 4.7 79.6 1.0
CB A:ARG336 4.9 34.8 1.0
CA A:GLY337 4.9 30.1 1.0

Magnesium binding site 2 out of 3 in 6h7x

Go back to Magnesium Binding Sites List in 6h7x
Magnesium binding site 2 out of 3 in the First X-Ray Structure of Full-Length Human Ruvb-Like 2.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of First X-Ray Structure of Full-Length Human Ruvb-Like 2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:31.9
occ:1.00
OG A:SER398 3.0 31.4 1.0
O A:HOH1132 3.2 26.5 1.0
N A:GLU436 3.5 44.3 1.0
CB A:SER398 3.6 32.7 1.0
CB A:ASP435 3.7 32.2 1.0
CB A:TYR401 3.9 30.1 1.0
NH2 A:ARG400 3.9 66.5 1.0
CB A:GLU436 4.0 54.5 1.0
CG A:GLU436 4.1 58.8 1.0
N A:SER398 4.3 40.8 1.0
CA A:ASP435 4.3 30.4 1.0
C A:THR397 4.3 47.1 1.0
CD A:GLU436 4.4 61.3 1.0
CA A:GLU436 4.4 51.3 1.0
CB A:THR397 4.4 48.6 1.0
C A:ASP435 4.4 35.1 1.0
CG A:TYR401 4.5 28.8 1.0
CA A:SER398 4.6 36.4 1.0
O A:THR397 4.6 50.0 1.0
OE2 A:GLU436 4.6 61.2 1.0
OD2 A:ASP435 4.8 35.4 1.0
CG A:ASP435 4.8 34.7 1.0
CA A:THR397 4.8 49.3 1.0
OE1 A:GLU436 4.8 62.1 1.0
CZ A:ARG400 4.9 63.9 1.0
OG1 A:THR397 5.0 48.0 1.0

Magnesium binding site 3 out of 3 in 6h7x

Go back to Magnesium Binding Sites List in 6h7x
Magnesium binding site 3 out of 3 in the First X-Ray Structure of Full-Length Human Ruvb-Like 2.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of First X-Ray Structure of Full-Length Human Ruvb-Like 2. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:45.1
occ:1.00
OD2 A:ASP366 3.1 55.7 1.0
N A:GLN49 3.7 39.6 1.0
OG1 A:THR360 3.8 42.0 1.0
O A:PRO361 3.8 32.1 1.0
NE2 A:GLN49 4.3 32.4 1.0
CG A:ASP366 4.3 55.3 1.0
CA A:GLN49 4.3 39.2 1.0
CA A:TYR362 4.4 47.0 1.0
CD A:GLN49 4.4 32.9 1.0
N A:SER363 4.4 40.9 1.0
OE1 A:GLN49 4.5 33.8 1.0
C A:PRO361 4.6 34.5 1.0
CD1 A:TYR362 4.6 49.1 1.0
CA A:GLY48 4.7 36.0 1.0
O A:THR360 4.7 40.2 1.0
C A:GLY48 4.7 36.2 1.0
N A:TYR362 4.9 41.8 1.0
C A:TYR362 4.9 46.5 1.0

Reference:

S.T.N.Silva, J.A.Brito, R.Arranz, C.O.S.Sorzano, C.Ebel, J.Doutch, M.D.Tully, J.M.Carazo, J.L.Carrascosa, P.M.Matias, T.M.Bandeiras. X-Ray Structure of Full-Length Human Ruvb-Like 2 - Mechanistic Insights Into Coupling Between Atp Binding and Mechanical Action. Sci Rep V. 8 13726 2018.
ISSN: ESSN 2045-2322
PubMed: 30213962
DOI: 10.1038/S41598-018-31997-Z
Page generated: Mon Dec 14 22:47:46 2020

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