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Magnesium in PDB 7r5p: Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron

Protein crystallography data

The structure of Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron, PDB code: 7r5p was solved by S.Morera, A.Vigouroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.24 / 1.68
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.575, 77.996, 115.225, 90, 95.83, 90
R / Rfree (%) 17.9 / 21.1

Other elements in 7r5p:

The structure of Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron also contains other interesting chemical elements:

Copper (Cu) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron (pdb code 7r5p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron, PDB code: 7r5p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7r5p

Go back to Magnesium Binding Sites List in 7r5p
Magnesium binding site 1 out of 6 in the Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:27.4
occ:1.00
 O A:HOH318 2.0 25.7 1.0
O A:HOH327 2.1 25.9 1.0
OD2 A:ASP92 2.1 28.8 1.0
O A:HOH302 2.2 25.9 1.0
O A:HOH311 2.2 20.1 1.0
OE1 A:GLU43 2.3 24.0 1.0
CG A:ASP92 3.1 29.0 1.0
CD A:GLU43 3.2 36.0 1.0
OD1 A:ASP92 3.3 31.0 1.0
OE2 A:GLU43 3.5 28.1 1.0
OE2 A:GLU2 3.8 26.2 1.0
OD1 A:ASP45 4.2 22.5 1.0
O A:HOH367 4.2 38.5 1.0
O A:HOH320 4.4 28.2 1.0
OD2 A:ASP45 4.4 33.8 1.0
CB A:ASP92 4.5 18.2 1.0
CG A:GLU43 4.6 23.1 1.0
CG A:ASP45 4.7 29.2 1.0
CG2 A:VAL19 4.7 20.7 1.0
ND1 A:HIS95 4.7 14.7 1.0
CG A:HIS95 4.7 12.8 1.0
CD2 A:LEU21 4.8 25.4 1.0
CB A:HIS95 5.0 11.0 1.0

Magnesium binding site 2 out of 6 in 7r5p

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Magnesium binding site 2 out of 6 in the Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:47.5
occ:1.00
 O B:HOH326 1.9 12.9 0.5
O B:HOH327 1.9 43.6 1.0
OD2 B:ASP92 2.2 30.6 1.0
O B:HOH301 2.2 26.8 1.0
O B:HOH304 2.4 23.1 0.5
OE1 B:GLU43 2.4 27.9 1.0
CG B:ASP92 3.2 28.3 1.0
CD B:GLU43 3.4 37.6 1.0
OD1 B:ASP92 3.5 30.0 1.0
OE2 B:GLU43 3.6 32.2 1.0
OE2 B:GLU2 3.8 58.2 1.0
OD1 B:ASP45 3.9 31.9 1.0
OD2 B:ASP45 4.1 37.2 1.0
O B:HOH348 4.3 40.4 1.0
CG B:ASP45 4.4 30.1 1.0
CB B:ASP92 4.5 21.8 1.0
CG B:HIS95 4.6 16.5 1.0
ND1 B:HIS95 4.6 19.6 1.0
CG2 B:VAL19 4.7 21.3 1.0
CB B:HIS95 4.7 12.7 1.0
CG B:GLU43 4.7 26.6 1.0

Magnesium binding site 3 out of 6 in 7r5p

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Magnesium binding site 3 out of 6 in the Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:55.6
occ:1.00
 OD2 C:ASP92 2.1 53.2 1.0
OE1 C:GLU43 2.2 29.6 1.0
OE2 C:GLU2 2.8 67.2 1.0
O C:HOH331 3.1 38.8 1.0
CD C:GLU43 3.1 46.0 1.0
CG C:ASP92 3.2 46.5 1.0
OE2 C:GLU43 3.4 30.5 1.0
OD1 C:ASP92 3.5 44.0 1.0
CD C:GLU2 3.7 78.2 1.0
OE1 C:GLU2 4.1 80.5 1.0
OD1 C:ASP45 4.1 49.9 1.0
OD2 C:ASP45 4.2 52.0 1.0
CG2 C:VAL19 4.4 32.2 1.0
O C:HOH342 4.5 61.4 1.0
CB C:ASP92 4.5 35.1 1.0
CG C:GLU43 4.5 34.8 1.0
CG C:ASP45 4.6 48.6 1.0
CB C:GLU43 4.9 24.7 1.0
CG C:HIS95 5.0 25.0 1.0
CG C:GLU2 5.0 57.4 1.0
ND1 C:HIS95 5.0 28.4 1.0

Magnesium binding site 4 out of 6 in 7r5p

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Magnesium binding site 4 out of 6 in the Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:37.5
occ:1.00
 O D:HOH301 2.2 29.0 1.0
O D:HOH324 2.2 33.6 1.0
OD2 D:ASP92 2.3 35.1 1.0
OE1 D:GLU43 2.3 28.1 1.0
O D:HOH303 2.4 41.6 1.0
CD D:GLU43 3.2 41.4 1.0
CG D:ASP92 3.3 34.5 1.0
OE2 D:GLU43 3.5 38.0 1.0
OE2 D:GLU2 3.6 34.4 1.0
OD1 D:ASP92 3.6 34.9 1.0
O D:HOH305 3.8 38.0 1.0
OD1 D:ASP45 4.2 37.5 1.0
CD2 D:LEU21 4.2 34.9 1.0
OD2 D:ASP45 4.3 50.0 1.0
CG2 D:VAL19 4.5 19.2 1.0
O D:HOH357 4.6 46.2 1.0
CB D:ASP92 4.6 25.9 1.0
CG D:GLU43 4.6 32.7 1.0
CG D:ASP45 4.7 39.5 1.0
CD D:GLU2 4.8 47.6 1.0
CG D:HIS95 4.9 19.5 1.0
ND1 D:HIS95 4.9 21.8 1.0

Magnesium binding site 5 out of 6 in 7r5p

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Magnesium binding site 5 out of 6 in the Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:25.3
occ:1.00
 O E:HOH307 1.9 26.7 1.0
O E:HOH328 2.1 29.4 1.0
O E:HOH305 2.1 23.9 1.0
OD2 E:ASP92 2.2 31.1 1.0
OE1 E:GLU43 2.2 21.5 1.0
O E:HOH301 2.3 28.8 1.0
CD E:GLU43 3.2 31.5 1.0
CG E:ASP92 3.2 33.7 1.0
OE2 E:GLU43 3.5 28.5 1.0
OD1 E:ASP92 3.6 32.1 1.0
OE1 E:GLU2 3.6 22.8 1.0
O E:HOH366 4.0 37.7 1.0
OD1 E:ASP45 4.1 36.5 1.0
OD2 E:ASP45 4.2 39.3 1.0
CB E:ASP92 4.5 27.0 1.0
O E:HOH342 4.6 34.5 1.0
CG E:GLU43 4.6 21.8 1.0
CG2 E:VAL19 4.6 20.0 1.0
CG E:ASP45 4.6 36.3 1.0
CD2 E:LEU21 4.8 23.0 1.0
CD E:GLU2 4.9 41.6 1.0
CG E:HIS95 4.9 19.1 1.0
CB E:GLU43 4.9 15.1 1.0
ND1 E:HIS95 5.0 21.6 1.0

Magnesium binding site 6 out of 6 in 7r5p

Go back to Magnesium Binding Sites List in 7r5p
Magnesium binding site 6 out of 6 in the Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Strep-Tag Ftra-P19 From Rubrivivax Gelatinosus in Complex with Copper and Iron within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:46.9
occ:0.50
 O F:HOH336 2.0 40.1 1.0
OD2 F:ASP92 2.2 47.5 1.0
O F:HOH309 2.3 37.2 1.0
O F:HOH306 2.3 40.9 1.0
OE1 F:GLU43 2.3 31.1 1.0
CG F:ASP92 3.2 42.6 1.0
CD F:GLU43 3.3 44.1 1.0
OD1 F:ASP92 3.5 44.8 1.0
OE2 F:GLU43 3.5 38.8 1.0
OD1 F:ASP45 4.1 38.0 1.0
OE1 F:GLU2 4.1 60.5 1.0
OD2 F:ASP45 4.4 50.3 1.0
CB F:ASP92 4.6 26.6 1.0
CG F:HIS95 4.6 20.8 1.0
CD2 F:LEU21 4.7 37.2 1.0
CG F:GLU43 4.7 36.2 1.0
ND1 F:HIS95 4.7 22.3 1.0
CG F:ASP45 4.7 39.6 1.0
CG2 F:VAL19 4.8 26.9 1.0
CB F:HIS95 4.9 16.9 1.0

Reference:

A.S.Steunou, A.Vigouroux, M.Aumont-Nicaise, S.Plancqueel, A.Boussac, S.Ouchane, S.Morera. New Insights Into the Mechanism of Iron Transport Through the Bacterial Ftr System Present in Pathogens. Febs J. V. 289 6286 2022.
ISSN: ISSN 1742-464X
PubMed: 35527501
DOI: 10.1111/FEBS.16476
Page generated: Thu Oct 3 07:28:24 2024

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