Manganese in PDB 8ffd: Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)

The structure of Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form), PDB code: 8ffd was solved by S.Lovell, 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)	48.86 / 2.20
Space group	P 21 3 1
Cell size a, b, c (Å), α, β, γ (°)	223.914, 223.914, 223.914, 90, 90, 90
R / Rfree (%)	17 / 22.4

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>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) (pdb code 8ffd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form), PDB code: 8ffd:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in the Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:42.2 occ:1.00 O E:HOH302 2.1 25.9 1.0 OE2 A:GLU68 2.2 40.1 1.0 OD2 A:ASP64 2.2 56.8 1.0 NE2 E:HIS37 2.3 24.3 1.0 OD1 A:ASP64 2.4 45.2 1.0 O A:HOH392 2.6 45.2 1.0 CG A:ASP64 2.6 45.6 1.0 CD A:GLU68 3.2 40.2 1.0 CD2 E:HIS37 3.2 29.2 1.0 CE1 E:HIS37 3.3 26.9 1.0 OE1 A:GLU68 3.7 43.3 1.0 O A:HOH397 3.7 52.6 1.0 OE2 E:GLU53 3.9 35.4 1.0 OH E:TYR56 3.9 31.8 1.0 O K:HOH356 4.1 57.9 1.0 CB A:ASP64 4.2 37.7 1.0 CG A:GLU68 4.3 29.2 1.0 CE1 E:HIS49 4.4 35.3 1.0 ND1 E:HIS37 4.4 25.4 1.0 CG E:HIS37 4.4 27.0 1.0 NE2 E:HIS49 4.4 28.8 1.0 CD1 E:TRP38 4.4 24.7 1.0 NE1 E:TRP38 4.5 27.7 1.0 CE2 E:TYR56 4.7 32.4 1.0 CZ E:TYR56 4.8 32.9 1.0 CD E:GLU53 4.9 31.6 1.0 O A:HOH404 5.0 47.7 1.0

Manganese binding site 2 out of 16 in the Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:41.7 occ:1.00 O L:HOH334 2.1 24.9 1.0 OE2 B:GLU68 2.2 47.4 1.0 O B:HOH414 2.3 36.4 1.0 OD2 B:ASP64 2.3 49.3 1.0 OD1 B:ASP64 2.4 42.4 1.0 NE2 L:HIS37 2.5 27.1 1.0 CG B:ASP64 2.7 44.8 1.0 CD B:GLU68 3.2 39.1 1.0 CD2 L:HIS37 3.3 23.8 1.0 CE1 L:HIS37 3.6 27.3 1.0 OE1 B:GLU68 3.6 34.2 1.0 O B:HOH315 3.8 40.3 1.0 OH L:TYR56 4.1 42.6 1.0 CB B:ASP64 4.2 28.6 1.0 CG B:GLU68 4.3 45.0 1.0 CE1 L:HIS49 4.4 30.0 1.0 NE2 L:HIS49 4.5 21.3 1.0 CG L:HIS37 4.5 24.1 1.0 NE1 L:TRP38 4.5 21.9 1.0 OE2 L:GLU53 4.6 46.8 1.0 O B:HOH312 4.6 39.5 1.0 CD1 L:TRP38 4.6 19.4 1.0 ND1 L:HIS37 4.6 26.2 1.0 CE2 L:TYR56 4.8 25.1 1.0 CZ L:TYR56 4.9 25.2 1.0

Manganese binding site 3 out of 16 in the Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn201 b:46.5 occ:1.00 O J:HOH328 2.2 25.2 1.0 OE2 C:GLU68 2.2 51.1 1.0 OD1 C:ASP64 2.2 57.4 1.0 OD2 C:ASP64 2.3 52.6 1.0 NE2 J:HIS37 2.4 30.4 1.0 CG C:ASP64 2.6 52.6 1.0 O J:HOH384 2.8 37.7 1.0 CD2 J:HIS37 3.2 33.3 1.0 CD C:GLU68 3.2 53.8 1.0 CE1 J:HIS37 3.4 35.5 1.0 OE1 C:GLU68 3.7 46.7 1.0 OH J:TYR56 4.1 44.2 1.0 CB C:ASP64 4.1 29.0 1.0 OE2 J:GLU53 4.2 40.7 1.0 O A:HOH329 4.3 52.4 1.0 NE2 J:HIS49 4.3 35.9 1.0 CE1 J:HIS49 4.4 32.6 1.0 CG C:GLU68 4.4 40.9 1.0 CG J:HIS37 4.4 33.5 1.0 ND1 J:HIS37 4.5 38.0 1.0 CD1 J:TRP38 4.6 37.5 1.0 NE1 J:TRP38 4.6 38.1 1.0 O C:HOH320 4.9 39.2 1.0 CE2 J:TYR56 4.9 33.0 1.0 O C:ASP64 5.0 33.9 1.0 CZ J:TYR56 5.0 43.8 1.0

Manganese binding site 4 out of 16 in the Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn201 b:44.3 occ:1.00 OE2 D:GLU68 2.1 47.3 1.0 O F:HOH327 2.2 29.0 1.0 OD2 D:ASP64 2.3 59.3 1.0 OD1 D:ASP64 2.3 48.3 1.0 NE2 F:HIS37 2.4 39.3 1.0 CG D:ASP64 2.7 42.4 1.0 O D:HOH397 2.9 47.8 1.0 CD D:GLU68 3.1 46.9 1.0 CD2 F:HIS37 3.3 32.0 1.0 CE1 F:HIS37 3.4 36.4 1.0 OE1 D:GLU68 3.6 38.3 1.0 O D:HOH406 3.8 51.8 1.0 OH F:TYR56 4.0 39.8 1.0 OE2 F:GLU53 4.1 46.5 1.0 CB D:ASP64 4.2 31.5 1.0 CG D:GLU68 4.2 40.8 1.0 NE2 F:HIS49 4.4 28.2 1.0 CE1 F:HIS49 4.4 30.2 1.0 CG F:HIS37 4.5 44.5 1.0 ND1 F:HIS37 4.5 40.5 1.0 NE1 F:TRP38 4.5 35.2 1.0 CD1 F:TRP38 4.5 28.9 1.0 CE2 F:TYR56 4.7 34.1 1.0 O D:HOH322 4.8 39.0 1.0 CZ F:TYR56 4.9 36.2 1.0 O D:HOH405 4.9 48.7 1.0 O D:ASP64 5.0 31.8 1.0

Manganese binding site 5 out of 16 in the Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn201 b:41.7 occ:1.00 OE2 E:GLU68 2.2 46.0 1.0 O A:HOH325 2.2 25.1 1.0 OD2 E:ASP64 2.3 41.0 1.0 OD1 E:ASP64 2.3 46.5 1.0 NE2 A:HIS37 2.4 23.5 1.0 O E:HOH401 2.5 30.8 1.0 CG E:ASP64 2.7 44.2 1.0 CD E:GLU68 3.1 42.0 1.0 CE1 A:HIS37 3.3 22.6 1.0 CD2 A:HIS37 3.4 30.6 1.0 OE1 E:GLU68 3.5 39.9 1.0 O E:HOH374 3.8 43.5 1.0 OH A:TYR56 4.0 35.0 1.0 OE2 A:GLU53 4.2 50.5 1.0 CB E:ASP64 4.2 38.5 1.0 CE1 A:HIS49 4.3 32.9 1.0 CG E:GLU68 4.4 35.1 1.0 NE2 A:HIS49 4.4 28.4 1.0 ND1 A:HIS37 4.4 25.3 1.0 CD1 A:TRP38 4.5 25.8 1.0 CG A:HIS37 4.6 25.5 1.0 NE1 A:TRP38 4.6 28.1 1.0 O E:ASP64 5.0 25.5 1.0 CZ A:TYR56 5.0 34.8 1.0 CE2 A:TYR56 5.0 26.6 1.0

Manganese binding site 6 out of 16 in the Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn201 b:49.0 occ:1.00 O F:HOH330 2.1 36.7 1.0 OE2 F:GLU68 2.2 57.6 1.0 OD1 F:ASP64 2.2 47.5 1.0 O D:HOH310 2.2 27.1 1.0 OD2 F:ASP64 2.2 58.8 1.0 NE2 D:HIS37 2.4 32.1 1.0 CG F:ASP64 2.6 50.8 1.0 CD2 D:HIS37 3.2 22.7 1.0 CD F:GLU68 3.3 51.7 1.0 CE1 D:HIS37 3.5 32.5 1.0 OE1 F:GLU68 3.9 49.8 1.0 OH D:TYR56 3.9 37.5 1.0 CB F:ASP64 4.1 39.5 1.0 OE2 D:GLU53 4.2 47.9 1.0 CG F:GLU68 4.4 45.9 1.0 NE1 D:TRP38 4.4 27.1 1.0 CG D:HIS37 4.4 31.6 1.0 CE1 D:HIS49 4.4 32.9 1.0 CD1 D:TRP38 4.4 29.9 1.0 NE2 D:HIS49 4.5 36.7 1.0 ND1 D:HIS37 4.5 28.0 1.0 O F:HOH328 4.6 50.8 1.0 O F:ASP64 4.8 39.5 1.0 CZ D:TYR56 4.9 30.5 1.0 CA F:ASP64 4.9 34.4 1.0 CE2 D:TYR56 4.9 23.0 1.0

Manganese binding site 7 out of 16 in the Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn201 b:48.1 occ:1.00 OE2 G:GLU68 2.2 48.6 1.0 O I:HOH333 2.3 29.5 1.0 OD2 G:ASP64 2.3 42.8 1.0 OD1 G:ASP64 2.4 44.9 1.0 NE2 I:HIS37 2.4 25.6 1.0 O I:HOH414 2.5 33.5 1.0 CG G:ASP64 2.7 31.4 1.0 CD G:GLU68 3.1 45.6 1.0 CD2 I:HIS37 3.4 23.5 1.0 CE1 I:HIS37 3.4 34.2 1.0 OE1 G:GLU68 3.5 27.9 1.0 OH I:TYR56 4.0 37.2 1.0 CB G:ASP64 4.2 32.5 1.0 CE1 I:HIS49 4.2 29.6 1.0 CG G:GLU68 4.3 40.0 1.0 NE2 I:HIS49 4.4 26.8 1.0 ND1 I:HIS37 4.5 32.7 1.0 CG I:HIS37 4.5 39.5 1.0 NE1 I:TRP38 4.6 20.6 1.0 OE2 I:GLU53 4.6 48.3 1.0 CD1 I:TRP38 4.6 24.2 1.0 O G:ASP64 4.9 28.4 1.0 CE2 I:TYR56 5.0 32.1 1.0 CZ I:TYR56 5.0 27.4 1.0

Manganese binding site 8 out of 16 in the Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn201 b:41.1 occ:1.00 OE2 H:GLU68 2.2 33.2 1.0 O K:HOH311 2.2 28.9 1.0 OD2 H:ASP64 2.3 48.9 1.0 OD1 H:ASP64 2.3 44.4 1.0 NE2 K:HIS37 2.3 25.1 1.0 O K:HOH373 2.7 42.3 1.0 CG H:ASP64 2.7 41.7 1.0 CD H:GLU68 3.1 41.5 1.0 CD2 K:HIS37 3.2 24.7 1.0 CE1 K:HIS37 3.4 27.6 1.0 OE1 H:GLU68 3.5 28.1 1.0 OH K:TYR56 3.9 33.9 1.0 OE2 K:GLU53 4.0 46.6 1.0 O H:HOH435 4.1 44.4 1.0 O B:HOH356 4.1 40.4 1.0 CB H:ASP64 4.2 35.7 1.0 CG H:GLU68 4.3 40.1 1.0 NE2 K:HIS49 4.4 28.3 1.0 CE1 K:HIS49 4.4 26.1 1.0 CG K:HIS37 4.4 19.8 1.0 ND1 K:HIS37 4.5 30.4 1.0 CD1 K:TRP38 4.5 23.2 1.0 NE1 K:TRP38 4.5 20.6 1.0 O H:HOH316 4.5 40.9 1.0 CE2 K:TYR56 4.8 21.9 1.0 CZ K:TYR56 4.9 26.4 1.0 O K:HOH327 5.0 47.6 1.0

Manganese binding site 9 out of 16 in the Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn201 b:42.7 occ:1.00 OE2 I:GLU68 2.2 37.9 1.0 O G:HOH315 2.3 27.2 1.0 OD2 I:ASP64 2.3 53.1 1.0 OD1 I:ASP64 2.3 40.3 1.0 O G:HOH383 2.4 35.2 1.0 NE2 G:HIS37 2.4 26.2 1.0 CG I:ASP64 2.7 42.5 1.0 CD I:GLU68 3.1 41.1 1.0 CD2 G:HIS37 3.2 20.1 1.0 OE1 I:GLU68 3.4 39.0 1.0 O I:HOH346 3.4 43.6 1.0 CE1 G:HIS37 3.5 31.9 1.0 OH G:TYR56 4.1 43.3 1.0 CE1 G:HIS49 4.2 31.1 1.0 CB I:ASP64 4.2 33.7 1.0 NE2 G:HIS49 4.3 26.5 1.0 OE2 G:GLU53 4.3 51.9 1.0 CG I:GLU68 4.4 34.2 1.0 CG G:HIS37 4.4 33.0 1.0 CD1 G:TRP38 4.5 17.6 1.0 ND1 G:HIS37 4.5 22.0 1.0 NE1 G:TRP38 4.6 22.1 1.0 O I:HOH444 4.6 51.0 1.0 O I:HOH342 4.8 36.3 1.0 CE2 G:TYR56 4.8 30.9 1.0 CZ G:TYR56 4.9 36.5 1.0

Manganese binding site 10 out of 16 in the Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Manganeese Bound Dps Protein (PA0962) From Pseudomonas Aeruginosa (Cubic Form) within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn201 b:51.5 occ:1.00 O C:HOH319 2.2 36.6 1.0 OE2 J:GLU68 2.2 44.6 1.0 OD2 J:ASP64 2.2 48.5 1.0 NE2 C:HIS37 2.3 22.8 1.0 OD1 J:ASP64 2.3 42.5 1.0 CG J:ASP64 2.6 43.6 1.0 O C:HOH386 2.7 47.6 1.0 CD J:GLU68 3.2 51.2 1.0 CE1 C:HIS37 3.2 28.8 1.0 CD2 C:HIS37 3.3 34.6 1.0 OE1 J:GLU68 3.7 50.9 1.0 O J:HOH354 3.7 48.4 1.0 OH C:TYR56 3.9 35.9 1.0 CB J:ASP64 4.1 36.2 1.0 CG J:GLU68 4.3 42.6 1.0 CE1 C:HIS49 4.3 32.8 1.0 ND1 C:HIS37 4.3 31.2 1.0 CG C:HIS37 4.4 24.5 1.0 NE2 C:HIS49 4.5 32.3 1.0 OE2 C:GLU53 4.6 50.9 1.0 CD1 C:TRP38 4.6 30.7 1.0 NE1 C:TRP38 4.6 33.4 1.0 CE2 C:TYR56 4.7 28.6 1.0 CZ C:TYR56 4.8 31.3 1.0

N.Rajapaksha, A.Soldano, H.Yao, F.Donnarumma, M.M.Kashipathy, S.Seibold, K.P.Battaile, S.Lovell, M.Rivera. Pseudomonas Aeruginosa Dps (PA0962) Functions in H2O2 Mediated Oxidative Stress Defense and Exhibits in Vitro Dna Cleaving Activity Int J Mol Sci V. 24 2023.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS24054669