Magnesium in PDB 8w1f: Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound)

The structure of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound), PDB code: 8w1f was solved by S.Lovell, L.Liu, S.Seibold, K.P.Battaile, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.27 / 3.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	215.79, 215.79, 277.54, 90, 90, 90
R / Rfree (%)	17.9 / 20.4

The structure of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound) also contains other interesting chemical elements:

Iron

(Fe)

24 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 37;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound) (pdb code 8w1f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 37 binding sites of Magnesium where determined in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound), PDB code: 8w1f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 37 in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:65.0 occ:1.00 OD2 A:ASP168 2.1 69.2 1.0 OE1 A:GLU75 2.7 88.5 1.0 OE1 A:GLU72 2.7 72.6 1.0 NE2 A:HIS76 2.8 67.6 1.0 CD A:GLU75 3.3 98.9 1.0 CG A:ASP168 3.3 69.2 1.0 OE2 A:GLU75 3.3 97.8 1.0 CD2 A:HIS76 3.4 67.3 1.0 OE2 A:GLU72 3.4 80.8 1.0 CD A:GLU72 3.5 75.8 1.0 OE2 A:GLU164 3.6 87.8 1.0 CE1 A:HIS76 3.9 65.6 1.0 OD1 A:ASP168 4.1 71.8 1.0 CB A:ASP168 4.3 64.5 1.0 CG A:GLU164 4.3 71.6 1.0 CD2 A:HIS165 4.4 63.3 1.0 CD A:GLU164 4.4 74.5 1.0 CG A:GLU75 4.6 89.4 1.0 CG A:HIS76 4.7 59.6 1.0 OE1 A:GLN79 4.7 70.6 1.0 ND1 A:HIS76 4.9 61.7 1.0 CG A:GLU72 5.0 62.2 1.0

Magnesium binding site 2 out of 37 in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:60.4 occ:1.00 OD1 A:ASP171 2.3 79.5 1.0 CG A:ASP171 3.6 70.4 1.0 OD1 A:ASP167 4.1 67.8 1.0 CA A:ASP171 4.3 62.3 1.0 OD2 A:ASP171 4.4 60.7 1.0 N A:ASP171 4.5 60.7 1.0 OG1 J:THR62 4.5 72.6 1.0 CB A:ASP171 4.5 63.9 1.0 O G:MET92 5.0 64.4 1.0 C A:ALA170 5.0 63.4 1.0

Magnesium binding site 3 out of 37 in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:67.9 occ:1.00 CD A:ARG103 3.4 99.5 1.0 ND2 A:ASN101 3.6 73.6 1.0 OE1 F:GLU106 3.7 86.5 1.0 OD1 A:ASN101 3.9 68.5 1.0 OE2 F:GLU106 3.9 79.8 1.0 O F:TYR113 4.0 63.3 1.0 CG A:ARG103 4.1 94.1 1.0 CG A:ASN101 4.2 66.4 1.0 CD F:GLU106 4.2 83.3 1.0 NE A:ARG103 4.4 116.7 1.0 CB A:ARG103 4.6 75.3 1.0 CD2 F:TYR113 5.0 55.9 1.0

Magnesium binding site 4 out of 37 in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:63.2 occ:1.00 OD2 B:ASP168 2.1 64.8 1.0 OE1 B:GLU72 2.7 73.9 1.0 NE2 B:HIS76 2.7 64.0 1.0 OE1 B:GLU75 2.7 87.3 1.0 OE2 B:GLU75 3.0 100.4 1.0 OE2 B:GLU72 3.1 79.8 1.0 CD B:GLU75 3.2 99.1 1.0 CD B:GLU72 3.3 71.8 1.0 CG B:ASP168 3.3 63.3 1.0 CD2 B:HIS76 3.4 63.7 1.0 OE2 B:GLU164 3.6 79.7 1.0 CE1 B:HIS76 3.8 61.6 1.0 OD1 B:ASP168 4.1 68.5 1.0 CB B:ASP168 4.2 57.9 1.0 CG B:GLU164 4.4 68.9 1.0 CD B:GLU164 4.5 69.0 1.0 CD2 B:HIS165 4.6 63.0 1.0 CG B:GLU75 4.7 92.3 1.0 CG B:HIS76 4.7 59.3 1.0 CG B:GLU72 4.8 58.6 1.0 ND1 B:HIS76 4.9 54.4 1.0 OE1 B:GLN79 5.0 73.3 1.0

Magnesium binding site 5 out of 37 in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:68.4 occ:1.00 OD1 B:ASP171 2.3 75.1 1.0 CG B:ASP171 3.6 70.7 1.0 OD1 B:ASP167 3.7 66.7 1.0 OD2 B:ASP171 4.3 69.3 1.0 CA B:ASP171 4.5 65.1 1.0 N B:ASP171 4.5 58.3 1.0 CB B:ASP171 4.6 61.8 1.0 O A:MET92 4.7 57.8 1.0 CG B:ASP167 4.7 61.0 1.0 O B:ASP167 4.8 58.4 1.0 CB B:ALA170 4.9 59.4 1.0 C B:ALA170 4.9 54.4 1.0 OG1 F:THR62 5.0 67.1 1.0

Magnesium binding site 6 out of 37 in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:64.7 occ:1.00 OD2 C:ASP168 2.2 67.0 1.0 NE2 C:HIS76 2.6 69.9 1.0 OE1 C:GLU72 2.7 77.9 1.0 OE1 C:GLU75 2.9 94.8 1.0 CD2 C:HIS76 3.3 67.1 1.0 OE2 C:GLU72 3.3 86.3 1.0 CD C:GLU75 3.4 100.8 1.0 OE2 C:GLU75 3.4 103.5 1.0 CD C:GLU72 3.4 75.2 1.0 CG C:ASP168 3.4 68.5 1.0 OE2 C:GLU164 3.5 90.5 1.0 CE1 C:HIS76 3.8 67.8 1.0 OD1 C:ASP168 4.3 73.5 1.0 CB C:ASP168 4.3 70.7 1.0 CD2 C:HIS165 4.3 66.5 1.0 CG C:GLU164 4.4 72.7 1.0 CD C:GLU164 4.4 79.5 1.0 CG C:HIS76 4.5 60.6 1.0 OE1 C:GLN79 4.6 75.1 1.0 CG C:GLU75 4.6 84.9 1.0 ND1 C:HIS76 4.7 60.3 1.0 CG C:GLU72 4.9 60.4 1.0 NE2 C:HIS165 4.9 62.6 1.0

Magnesium binding site 7 out of 37 in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:60.0 occ:1.00 OD1 C:ASP171 2.1 81.4 1.0 CG C:ASP171 3.3 74.6 1.0 OD2 C:ASP171 3.9 74.9 1.0 OD1 C:ASP167 4.0 74.0 1.0 OG1 K:THR62 4.4 83.6 1.0 CG2 K:THR62 4.5 69.3 1.0 CB C:ASP171 4.5 64.9 1.0 CA C:ASP171 4.6 65.5 1.0 O D:MET92 4.6 69.0 1.0 CB K:THR62 4.8 72.8 1.0 N C:ASP171 4.9 64.0 1.0 CE D:MET92 5.0 63.9 1.0

Magnesium binding site 8 out of 37 in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:77.4 occ:1.00 ND2 C:ASN101 3.2 72.0 1.0 CD C:ARG103 3.5 109.9 1.0 OE1 B:GLU106 3.7 95.6 1.0 OE2 B:GLU106 3.8 80.7 1.0 OD1 C:ASN101 3.9 74.2 1.0 O B:TYR113 4.0 63.0 1.0 CG C:ASN101 4.0 68.1 1.0 CG C:ARG103 4.1 104.9 1.0 CD B:GLU106 4.2 88.4 1.0 NE C:ARG103 4.8 123.6 1.0 CD1 B:TYR113 4.9 59.1 1.0 CB C:ARG103 5.0 90.0 1.0

Magnesium binding site 9 out of 37 in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:62.4 occ:1.00 OD2 D:ASP168 2.2 71.6 1.0 OE1 D:GLU72 2.5 82.0 1.0 NE2 D:HIS76 2.7 71.1 1.0 OE1 D:GLU75 2.7 94.3 1.0 OE2 D:GLU72 3.0 91.5 1.0 CD D:GLU72 3.1 80.6 1.0 CD2 D:HIS76 3.4 64.8 1.0 CG D:ASP168 3.4 70.0 1.0 OE2 D:GLU164 3.6 89.6 1.0 CD D:GLU75 3.6 95.3 1.0 CE1 D:HIS76 3.8 68.2 1.0 OE2 D:GLU75 3.9 92.1 1.0 OD1 D:ASP168 4.2 73.1 1.0 CB D:ASP168 4.3 69.0 1.0 CD D:GLU164 4.5 75.8 1.0 CG D:GLU164 4.6 77.0 1.0 CG D:HIS76 4.6 59.9 1.0 CG D:GLU72 4.6 63.4 1.0 CD2 D:HIS165 4.7 66.2 1.0 ND1 D:HIS76 4.8 63.5 1.0 CG D:GLU75 4.9 80.3 1.0 OE1 D:GLN79 5.0 74.9 1.0

Magnesium binding site 10 out of 37 in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:66.2 occ:1.00 OD1 D:ASP171 2.3 84.0 1.0 CG D:ASP171 3.5 75.4 1.0 OD1 D:ASP167 4.1 76.5 1.0 OD2 D:ASP171 4.1 73.0 1.0 OG1 E:THR62 4.5 77.9 1.0 CA D:ASP171 4.6 64.9 1.0 CB D:ASP171 4.6 62.8 1.0 O H:MET92 4.8 60.9 1.0 CG2 E:THR62 4.8 66.3 1.0 N D:ASP171 4.9 61.1 1.0 CB E:THR62 5.0 78.8 1.0

N.Rajapaksha, H.Yao, A.Cook, S.Seibold, L.Liu, K.P.Battaile, L.Fontenot, F.Donnarumma, S.Lovell, M.Rivera. Pseudomonas Aeruginosa Gene PA4880 Encodes A Dps-Like Protein with A Dps Fold, Bacterioferritin-Type Ferroxidase Centers, and Endonuclease Activity Front Mol Biosci 2024.
ISSN: ESSN 2296-889X
DOI: 10.3389/FMOLB.2024.1390745