Magnesium in PDB 7arr: The De Novo Designed Hybrid Alpha/Beta-Miniprotein

Protein crystallography data

The structure of The De Novo Designed Hybrid Alpha/Beta-Miniprotein, PDB code: 7arr was solved by M.Bejger, P.Fortuna, M.Drewniak-Switalska, W.Rypniewski, L.Berlicki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.02 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 30.937, 32.068, 43.087, 114.16, 91.88, 109.86
R / Rfree (%) 12.9 / 16.1

Other elements in 7arr:

The structure of The De Novo Designed Hybrid Alpha/Beta-Miniprotein also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein (pdb code 7arr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein, PDB code: 7arr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7arr

Go back to Magnesium Binding Sites List in 7arr
Magnesium binding site 1 out of 4 in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The De Novo Designed Hybrid Alpha/Beta-Miniprotein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:7.4
occ:0.70
O A:HOH272 2.1 12.1 1.0
O A:HOH254 2.1 11.6 1.0
O A:HOH205 2.1 9.8 1.0
O A:HOH250 2.1 12.5 1.0
OE2 A:GLU22 2.1 9.6 1.0
O A:HOH258 2.1 12.3 1.0
CD A:GLU22 3.1 9.1 1.0
OE1 A:GLU22 3.4 8.7 1.0
O A:HOH213 3.9 26.6 0.5
O A:HOH268 4.2 14.9 1.0
O A:HOH262 4.2 13.3 1.0
O D:HOH256 4.3 28.9 1.0
CG A:GLU22 4.4 8.7 1.0
OH D:TYR25 4.5 15.8 1.0

Magnesium binding site 2 out of 4 in 7arr

Go back to Magnesium Binding Sites List in 7arr
Magnesium binding site 2 out of 4 in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The De Novo Designed Hybrid Alpha/Beta-Miniprotein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:20.9
occ:0.50
OE2 B:GLU22 2.0 13.9 0.8
O B:HOH239 2.1 23.6 1.0
O B:HOH273 2.2 22.4 1.0
O B:HOH206 2.5 21.4 1.0
O B:HOH254 2.6 38.0 0.7
O C:HOH129 2.6 25.0 1.0
CD B:GLU22 3.0 14.3 0.8
OE1 B:GLU22 3.3 19.8 0.8
OE2 B:GLU22 4.2 14.2 0.2
CD B:GLU22 4.2 12.9 0.2
CG B:GLU22 4.3 11.3 0.8
CG B:GLU22 4.3 11.9 0.2
O B:HOH213 4.4 21.2 1.0
OE1 B:GLU22 4.8 15.7 0.2
OH C:TYR25 4.9 11.8 1.0

Magnesium binding site 3 out of 4 in 7arr

Go back to Magnesium Binding Sites List in 7arr
Magnesium binding site 3 out of 4 in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The De Novo Designed Hybrid Alpha/Beta-Miniprotein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:20.1
occ:0.50
MG D:MG101 0.0 20.1 0.5
O D:HOH263 1.8 42.2 1.0
O D:HOH254 1.9 18.6 0.5
MG D:MG101 2.3 22.8 0.5
O C:HOH161 2.4 41.2 1.0
O D:HOH210 2.6 81.6 1.0
O D:HOH244 2.7 42.3 1.0
O D:HOH245 3.5 46.1 0.5
OE1 D:GLU3 3.9 29.3 1.0
O D:HOH237 4.1 37.2 1.0
O C:HOH117 4.1 15.9 1.0
O C:HOH119 4.3 23.0 0.7
OE2 D:GLU3 4.4 19.3 1.0
O D:HOH209 4.4 20.2 1.0
CD D:GLU3 4.5 17.4 1.0
O A:HOH204 4.9 18.4 1.0

Magnesium binding site 4 out of 4 in 7arr

Go back to Magnesium Binding Sites List in 7arr
Magnesium binding site 4 out of 4 in the The De Novo Designed Hybrid Alpha/Beta-Miniprotein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The De Novo Designed Hybrid Alpha/Beta-Miniprotein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:22.8
occ:0.50
MG D:MG101 0.0 22.8 0.5
O D:HOH210 1.7 81.6 1.0
O C:HOH161 2.0 41.2 1.0
O C:HOH117 2.2 15.9 1.0
MG D:MG101 2.3 20.1 0.5
O C:HOH119 2.3 23.0 0.7
O D:HOH254 2.5 18.6 0.5
O D:HOH237 3.0 37.2 1.0
O C:HOH119 3.7 15.2 0.3
O D:HOH228 3.8 23.2 1.0
O D:HOH263 4.0 42.2 1.0
O A:HOH204 4.2 18.4 1.0
O A:HOH226 4.2 13.1 1.0
OE1 D:GLU3 4.2 29.3 1.0
OE2 C:GLU22 4.3 10.4 1.0
OE1 C:GLU22 4.4 11.0 1.0
O D:HOH244 4.6 42.3 1.0
OE2 D:GLU3 4.6 19.3 1.0
CD C:GLU22 4.8 8.3 1.0
CD D:GLU3 4.9 17.4 1.0
O C:HOH122 4.9 24.6 1.0
O D:HOH245 5.0 46.1 0.5

Reference:

M.Bejger, P.Fortuna, M.Drewniak-Switalska, J.Plewka, W.Rypniewski, L.Berlicki. A Computationally Designed Beta-Amino Acid-Containing Miniprotein. Chem.Commun.(Camb.) V. 57 6015 2021.
ISSN: ESSN 1364-548X
PubMed: 34032224
DOI: 10.1039/D1CC02192C
Page generated: Sat Aug 21 16:19:51 2021

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