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Magnesium in PDB 4lsi: Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr

Protein crystallography data

The structure of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr, PDB code: 4lsi was solved by D.Balasundaresan, L.Blachowicz, B.Roux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.74 / 2.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 202.094, 116.559, 53.592, 90.00, 97.00, 90.00
R / Rfree (%) 19 / 24.5

Other elements in 4lsi:

The structure of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr also contains other interesting chemical elements:

Bromine (Br) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr (pdb code 4lsi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr, PDB code: 4lsi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4lsi

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Magnesium binding site 1 out of 8 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:43.6
occ:1.00
 O A:GLN203 2.5 51.0 1.0
O A:GLY206 2.5 59.4 1.0
O A:GLU201 3.0 42.0 1.0
C A:GLY206 3.6 51.9 1.0
C A:GLN203 3.7 45.2 1.0
C A:GLU201 3.9 41.4 1.0
CA A:ASN207 4.2 50.1 1.0
CB A:ASN207 4.3 53.5 1.0
O A:PRO204 4.3 52.7 1.0
N A:ASN207 4.4 50.1 1.0
N A:GLN203 4.4 49.9 1.0
CA A:GLU201 4.4 49.4 1.0
OE1 A:GLU201 4.4 57.0 1.0
C A:PRO204 4.5 50.8 1.0
CA A:GLN203 4.6 48.7 1.0
O A:GLN200 4.6 39.0 1.0
N A:PRO204 4.6 44.3 1.0
CA A:PRO204 4.6 50.2 1.0
C A:ALA202 4.7 49.9 1.0
N A:GLY206 4.7 42.2 1.0
OD1 A:ASN207 4.7 56.2 1.0
CA A:GLY206 4.7 47.5 1.0
C A:LEU205 4.8 41.3 1.0
O A:LEU205 4.8 39.5 1.0
N A:ALA202 4.9 45.2 1.0
NH1 A:ARG196 5.0 54.5 1.0

Magnesium binding site 2 out of 8 in 4lsi

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Magnesium binding site 2 out of 8 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:39.4
occ:1.00
 O A:ILE318 2.4 46.7 1.0
O A:SER328 2.6 35.4 1.0
O A:HOH595 2.7 42.4 1.0
O A:ASN316 2.8 38.3 1.0
O A:HOH557 2.8 55.4 1.0
C A:ILE318 3.6 47.6 1.0
C A:SER328 3.6 32.9 1.0
C A:ASN316 3.7 36.9 1.0
CB A:SER328 3.8 40.2 1.0
CA A:SER328 4.0 36.4 1.0
N A:ILE318 4.0 41.6 1.0
C A:GLN317 4.1 41.5 1.0
CA A:GLN317 4.3 39.6 1.0
N A:GLN317 4.3 37.3 1.0
CA A:ILE318 4.5 42.4 1.0
N A:ASP319 4.5 49.2 1.0
CB A:ASN316 4.5 30.1 1.0
O A:GLN317 4.5 41.7 1.0
CA A:ASP319 4.5 53.1 1.0
OG A:SER328 4.6 41.8 1.0
CA A:ASN316 4.7 33.5 1.0
CG A:ASN316 4.8 27.7 1.0
N A:ASP329 4.8 34.4 1.0
OD1 A:ASN316 5.0 29.4 1.0
OD1 A:ASP330 5.0 32.2 1.0

Magnesium binding site 3 out of 8 in 4lsi

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Magnesium binding site 3 out of 8 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:33.8
occ:1.00
 O B:GLN203 2.4 33.5 1.0
O B:GLY206 2.4 47.2 1.0
O B:GLU201 2.8 39.9 1.0
O B:HOH601 2.8 41.4 1.0
O B:HOH673 2.9 51.3 1.0
C B:GLY206 3.6 40.0 1.0
C B:GLN203 3.6 33.5 1.0
C B:GLU201 3.8 38.3 1.0
N B:GLN203 4.3 39.4 1.0
CA B:ASN207 4.3 35.5 1.0
N B:ASN207 4.4 39.7 1.0
C B:PRO204 4.4 40.1 1.0
CA B:GLU201 4.4 37.3 1.0
CB B:ASN207 4.5 41.4 1.0
O B:PRO204 4.5 33.1 1.0
CA B:GLN203 4.5 37.0 1.0
N B:PRO204 4.6 33.8 1.0
CA B:PRO204 4.6 37.7 1.0
C B:ALA202 4.6 43.7 1.0
OE1 B:GLU201 4.6 37.7 1.0
N B:GLY206 4.7 36.8 1.0
O B:GLN200 4.7 31.6 1.0
CA B:GLY206 4.7 36.6 1.0
N B:ALA202 4.7 36.1 1.0
C B:LEU205 4.8 37.8 1.0
N B:LEU205 4.8 40.2 1.0
CA B:ALA202 5.0 42.0 1.0

Magnesium binding site 4 out of 8 in 4lsi

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Magnesium binding site 4 out of 8 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:47.5
occ:1.00
 O B:ILE318 2.3 35.4 1.0
O B:ASN316 2.6 33.6 1.0
O B:SER328 2.7 33.2 1.0
O B:HOH600 2.8 34.8 1.0
C B:ILE318 3.4 35.8 1.0
C B:ASN316 3.5 30.9 1.0
C B:SER328 3.7 31.2 1.0
C B:GLN317 3.8 32.9 1.0
N B:ILE318 3.9 31.8 1.0
CA B:GLN317 3.9 33.8 1.0
CB B:SER328 4.0 36.7 1.0
N B:GLN317 4.0 31.0 1.0
CA B:SER328 4.1 34.3 1.0
O B:GLN317 4.2 31.1 1.0
CA B:ILE318 4.3 35.7 1.0
CB B:ASN316 4.4 28.5 1.0
N B:ASP319 4.4 42.9 1.0
CA B:ASP319 4.4 49.2 1.0
CA B:ASN316 4.6 30.7 1.0
OG B:SER328 4.6 35.2 1.0
CG B:ASN316 4.7 27.5 1.0
OD1 B:ASN316 4.9 30.6 1.0
N B:ASP329 4.9 31.2 1.0
CB B:ILE318 4.9 33.4 1.0

Magnesium binding site 5 out of 8 in 4lsi

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Magnesium binding site 5 out of 8 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:35.4
occ:0.77
 O C:ASN207 2.2 44.9 1.0
OD1 C:ASN236 2.3 33.4 1.0
OD1 C:ASN252 2.4 38.3 1.0
O C:HOH593 2.4 30.0 1.0
O C:HOH588 2.4 38.3 1.0
CG C:ASN236 3.1 30.9 1.0
ND2 C:ASN236 3.2 28.1 1.0
CG C:ASN252 3.3 36.9 1.0
C C:ASN207 3.3 40.6 1.0
CB C:ASN252 3.6 33.8 1.0
O C:HOH549 3.7 47.9 1.0
CA C:ASN252 4.0 33.7 1.0
N C:ASN207 4.0 44.2 1.0
CA C:ASN207 4.2 44.1 1.0
O C:ASN252 4.2 35.6 1.0
N C:GLY208 4.2 40.1 1.0
CA C:GLY208 4.4 38.8 1.0
O C:HOH546 4.4 52.2 1.0
ND2 C:ASN252 4.5 36.6 1.0
CB C:ASN236 4.5 30.5 1.0
C C:ASN252 4.6 32.1 1.0
CB C:ASN207 4.6 49.0 1.0

Magnesium binding site 6 out of 8 in 4lsi

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Magnesium binding site 6 out of 8 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:31.5
occ:0.85
 OD2 C:ASP74 2.5 26.5 1.0
O C:HOH636 2.7 34.3 1.0
OD1 C:ASN69 2.7 27.1 1.0
O B:HOH532 2.8 27.9 1.0
CG C:ASP74 3.3 32.8 1.0
CB C:ASP74 3.5 30.8 1.0
CG C:ASN69 3.5 23.7 1.0
CA C:ASN69 3.7 24.4 1.0
CB C:ASN69 3.7 24.7 1.0
O C:ASP74 3.9 31.5 1.0
NH1 B:ARG163 4.2 22.4 1.0
OG1 C:THR77 4.2 34.0 1.0
CB C:THR77 4.2 35.7 1.0
O C:ASN68 4.3 21.6 1.0
O C:HOH594 4.5 28.1 1.0
OD1 C:ASP74 4.5 32.7 1.0
N C:SER70 4.6 26.0 1.0
CG2 C:THR77 4.6 37.4 1.0
ND2 C:ASN69 4.6 24.7 1.0
N C:ASN69 4.7 24.0 1.0
C C:ASP74 4.7 27.9 1.0
CA C:ASP74 4.7 29.8 1.0
C C:ASN69 4.7 25.4 1.0
C C:ASN68 4.9 23.0 1.0

Magnesium binding site 7 out of 8 in 4lsi

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Magnesium binding site 7 out of 8 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:31.8
occ:1.00
 O C:GLY206 2.5 46.4 1.0
O C:GLN203 2.5 35.9 1.0
O C:HOH606 2.7 48.8 1.0
O C:HOH676 2.9 40.5 1.0
O C:GLU201 2.9 43.5 1.0
C C:GLY206 3.6 43.1 1.0
C C:GLN203 3.7 35.2 1.0
C C:GLU201 3.9 38.3 1.0
O C:PRO204 4.2 39.3 1.0
N C:GLN203 4.3 41.1 1.0
CA C:ASN207 4.4 44.1 1.0
N C:ASN207 4.4 44.2 1.0
C C:PRO204 4.4 42.6 1.0
CA C:GLU201 4.5 38.9 1.0
CB C:ASN207 4.6 49.0 1.0
CA C:GLN203 4.6 37.6 1.0
C C:ALA202 4.6 40.2 1.0
CA C:GLY206 4.6 42.5 1.0
O C:GLN200 4.6 29.2 1.0
N C:GLY206 4.6 35.1 1.0
N C:PRO204 4.7 37.0 1.0
O C:LEU205 4.7 38.9 1.0
NH2 C:ARG196 4.7 38.7 1.0
OE1 C:GLU201 4.7 41.8 1.0
C C:LEU205 4.7 36.8 1.0
CA C:PRO204 4.7 41.6 1.0
O C:HOH681 4.8 41.7 1.0
N C:ALA202 4.8 40.3 1.0
CA C:ALA202 5.0 39.2 1.0

Magnesium binding site 8 out of 8 in 4lsi

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Magnesium binding site 8 out of 8 in the Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ion Selectivity of Ompf Porin Soaked in 0.3M Kbr within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg405

b:31.3
occ:1.00
 O C:ILE318 2.5 38.3 1.0
O C:SER328 2.6 29.2 1.0
O C:ASN316 2.7 29.7 1.0
O C:HOH565 3.1 47.1 1.0
O C:HOH529 3.3 39.8 1.0
C C:ILE318 3.6 38.1 1.0
C C:ASN316 3.6 32.6 1.0
C C:SER328 3.7 31.0 1.0
CB C:SER328 4.0 36.0 1.0
C C:GLN317 4.0 35.4 1.0
N C:ILE318 4.0 32.6 1.0
CA C:SER328 4.1 31.2 1.0
CA C:GLN317 4.2 33.3 1.0
N C:GLN317 4.3 34.0 1.0
O C:GLN317 4.4 30.1 1.0
CA C:ILE318 4.5 36.9 1.0
CB C:ASN316 4.5 26.4 1.0
OG C:SER328 4.5 38.9 1.0
N C:ASP319 4.5 43.0 1.0
CA C:ASP319 4.6 47.6 1.0
CA C:ASN316 4.7 29.3 1.0
CG C:ASN316 4.8 27.2 1.0
N C:ASP329 4.8 29.4 1.0
OD1 C:ASN316 4.9 29.8 1.0

Reference:

B.Dhakshnamoorthy, B.K.Ziervogel, L.Blachowicz, B.Roux. A Structural Study of Ion Permeation in Ompf Porin From Anomalous X-Ray Diffraction and Molecular Dynamics Simulations. J.Am.Chem.Soc. V. 135 16561 2013.
ISSN: ISSN 0002-7863
PubMed: 24106986
DOI: 10.1021/JA407783A
Page generated: Mon Aug 19 20:06:15 2024

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