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

Protein crystallography data

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

Other elements in 8w1f:

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

Magnesium (Mg) 37 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iron 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 Iron atom.
In total 24 binding sites of Iron where determined in the Crystal Structure of Dps-Like Protein PA4880 From Pseudomonas Aeruginosa (Dodecamer, Mg Bound), PDB code: 8w1f:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 24 in 8w1f

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Iron binding site 1 out of 24 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 Iron with other atoms in the Fe 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:Fe207

b:76.2
occ:1.00
 OE1 A:GLU80 2.0 68.1 1.0
OE2 A:GLU162 2.0 72.1 1.0
OE1 A:GLU47 2.0 64.3 1.0
ND1 A:HIS83 2.2 60.8 1.0
CD A:GLU47 2.6 64.7 1.0
OE2 A:GLU47 2.6 69.4 1.0
CD A:GLU162 3.0 66.1 1.0
CE1 A:HIS83 3.1 65.2 1.0
CD A:GLU80 3.1 63.8 1.0
CG A:HIS83 3.3 63.4 1.0
OE1 A:GLU162 3.5 67.1 1.0
CB A:HIS83 3.7 64.5 1.0
OE2 A:GLU80 3.7 69.7 1.0
CA A:GLU80 4.0 57.7 1.0
CG A:GLU47 4.1 64.3 1.0
FE A:FE2208 4.1 68.4 1.0
CG2 A:ILE158 4.1 61.8 1.0
CG A:GLU162 4.2 63.7 1.0
NE2 A:HIS83 4.3 67.2 1.0
CG A:GLU80 4.3 59.8 1.0
CB A:GLU80 4.4 58.7 1.0
CD2 A:HIS83 4.4 67.5 1.0
O A:GLU80 4.6 61.4 1.0
CB A:GLU47 4.8 59.6 1.0
C A:GLU80 4.9 59.8 1.0
N A:GLU80 4.9 57.1 1.0
O A:GLN79 4.9 61.0 1.0

Iron binding site 2 out of 24 in 8w1f

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Iron binding site 2 out of 24 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 Iron with other atoms in the Fe 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:Fe208

b:68.4
occ:1.00
 OE2 A:GLU80 2.0 69.7 1.0
OE1 A:GLU162 2.1 67.1 1.0
ND1 A:HIS165 2.2 58.9 1.0
OE1 A:GLU130 2.3 66.0 1.0
OE2 A:GLU130 2.4 61.0 1.0
CD A:GLU130 2.7 63.4 1.0
CD A:GLU80 3.0 63.8 1.0
CD A:GLU162 3.0 66.1 1.0
CE1 A:HIS165 3.1 60.5 1.0
CG A:HIS165 3.3 57.4 1.0
OE1 A:GLU80 3.4 68.1 1.0
OE2 A:GLU162 3.4 72.1 1.0
CB A:HIS165 3.6 58.6 1.0
FE A:FE2207 4.1 76.2 1.0
CG A:GLU130 4.2 59.3 1.0
CA A:GLU162 4.2 61.0 1.0
NE2 A:HIS165 4.2 62.9 1.0
CG A:GLU162 4.3 63.7 1.0
CG A:GLU80 4.3 59.8 1.0
CD2 A:HIS165 4.4 63.3 1.0
CB A:GLU162 4.4 62.3 1.0
OH A:TYR54 4.7 58.3 1.0
CE2 A:TYR54 4.7 61.3 1.0
N A:GLU162 4.9 61.1 1.0
CB A:GLU130 4.9 61.2 1.0

Iron binding site 3 out of 24 in 8w1f

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Iron binding site 3 out of 24 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 Iron with other atoms in the Fe 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
B:Fe206

b:71.7
occ:1.00
 OE2 B:GLU162 2.0 70.4 1.0
OE1 B:GLU80 2.0 63.1 1.0
OE1 B:GLU47 2.1 63.7 1.0
ND1 B:HIS83 2.1 58.5 1.0
CD B:GLU47 2.7 60.1 1.0
OE2 B:GLU47 2.7 65.7 1.0
CE1 B:HIS83 2.9 60.3 1.0
CD B:GLU162 3.1 67.2 1.0
CD B:GLU80 3.1 62.2 1.0
CG B:HIS83 3.3 58.5 1.0
OE1 B:GLU162 3.5 69.3 1.0
OE2 B:GLU80 3.6 67.3 1.0
CB B:HIS83 3.7 59.1 1.0
FE B:FE2207 3.9 66.2 1.0
CG2 B:ILE158 4.0 55.2 1.0
CA B:GLU80 4.1 58.6 1.0
NE2 B:HIS83 4.1 62.1 1.0
CG B:GLU47 4.2 63.5 1.0
CD2 B:HIS83 4.3 62.6 1.0
CG B:GLU162 4.3 59.8 1.0
CG B:GLU80 4.3 60.4 1.0
CB B:GLU80 4.4 58.3 1.0
O B:GLU80 4.8 57.9 1.0
N B:GLU80 4.8 57.6 1.0
O B:GLN79 4.9 61.7 1.0
CB B:GLU47 4.9 60.4 1.0
C B:GLU80 5.0 59.5 1.0

Iron binding site 4 out of 24 in 8w1f

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Iron binding site 4 out of 24 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 Iron with other atoms in the Fe 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:Fe207

b:66.2
occ:1.00
 OE1 B:GLU162 2.0 69.3 1.0
OE2 B:GLU80 2.0 67.3 1.0
ND1 B:HIS165 2.3 61.5 1.0
OE1 B:GLU130 2.4 67.0 1.0
OE2 B:GLU130 2.4 68.1 1.0
CD B:GLU130 2.7 63.0 1.0
CD B:GLU80 3.0 62.2 1.0
CD B:GLU162 3.0 67.2 1.0
CE1 B:HIS165 3.2 59.9 1.0
OE1 B:GLU80 3.3 63.1 1.0
OE2 B:GLU162 3.4 70.4 1.0
CG B:HIS165 3.5 63.3 1.0
CB B:HIS165 3.8 61.4 1.0
FE B:FE2206 3.9 71.7 1.0
CG B:GLU130 4.2 56.7 1.0
CG B:GLU162 4.3 59.8 1.0
CG B:GLU80 4.3 60.4 1.0
NE2 B:HIS165 4.4 60.5 1.0
CA B:GLU162 4.4 61.5 1.0
CB B:GLU162 4.5 62.4 1.0
CD2 B:HIS165 4.5 63.0 1.0
CE2 B:TYR54 4.6 58.6 1.0
OH B:TYR54 4.7 54.3 1.0
CB B:GLU130 5.0 59.4 1.0

Iron binding site 5 out of 24 in 8w1f

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Iron binding site 5 out of 24 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 Iron with other atoms in the Fe 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
C:Fe209

b:77.7
occ:1.00
 OE1 C:GLU47 1.9 67.8 1.0
OE2 C:GLU162 1.9 72.5 1.0
OE1 C:GLU80 2.0 71.8 1.0
ND1 C:HIS83 2.3 66.3 1.0
CD C:GLU47 2.6 68.0 1.0
OE2 C:GLU47 2.7 70.7 1.0
CD C:GLU162 3.0 69.1 1.0
CE1 C:HIS83 3.1 68.8 1.0
CD C:GLU80 3.1 67.4 1.0
CG C:HIS83 3.4 68.0 1.0
OE1 C:GLU162 3.4 69.2 1.0
OE2 C:GLU80 3.7 70.4 1.0
CB C:HIS83 3.8 69.2 1.0
FE C:FE2210 4.0 77.5 1.0
CG2 C:ILE158 4.1 66.8 1.0
CG C:GLU47 4.1 64.8 1.0
CA C:GLU80 4.1 62.6 1.0
CG C:GLU162 4.2 63.8 1.0
NE2 C:HIS83 4.3 70.0 1.0
CG C:GLU80 4.4 63.6 1.0
CB C:GLU80 4.4 61.4 1.0
CD2 C:HIS83 4.5 73.6 1.0
CB C:GLU47 4.7 60.8 1.0
O C:GLU80 4.8 63.0 1.0
N C:GLU80 4.9 61.1 1.0
C C:GLU80 5.0 60.0 1.0
CE2 C:TYR137 5.0 70.8 1.0
O C:GLN79 5.0 66.2 1.0

Iron binding site 6 out of 24 in 8w1f

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Iron binding site 6 out of 24 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 Iron with other atoms in the Fe 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:Fe210

b:77.5
occ:1.00
 OE1 C:GLU162 2.0 69.2 1.0
OE2 C:GLU80 2.0 70.4 1.0
ND1 C:HIS165 2.3 67.1 1.0
OE1 C:GLU130 2.4 66.2 1.0
OE2 C:GLU130 2.4 68.9 1.0
CD C:GLU130 2.7 66.6 1.0
CD C:GLU162 2.9 69.1 1.0
CD C:GLU80 3.0 67.4 1.0
CE1 C:HIS165 3.2 65.8 1.0
OE2 C:GLU162 3.3 72.5 1.0
OE1 C:GLU80 3.4 71.8 1.0
CG C:HIS165 3.4 63.4 1.0
CB C:HIS165 3.8 63.2 1.0
FE C:FE2209 4.0 77.7 1.0
CG C:GLU162 4.2 63.8 1.0
CG C:GLU130 4.2 64.5 1.0
CA C:GLU162 4.2 63.5 1.0
NE2 C:HIS165 4.3 62.6 1.0
CG C:GLU80 4.4 63.6 1.0
CB C:GLU162 4.4 65.7 1.0
CD2 C:HIS165 4.5 66.5 1.0
CE2 C:TYR54 4.6 63.3 1.0
OH C:TYR54 4.7 66.7 1.0
CB C:GLU130 5.0 65.5 1.0
N C:GLU162 5.0 62.2 1.0

Iron binding site 7 out of 24 in 8w1f

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Iron binding site 7 out of 24 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 Iron with other atoms in the Fe 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
D:Fe208

b:82.4
occ:1.00
 OE2 D:GLU162 2.0 69.5 1.0
OE1 D:GLU47 2.0 64.5 1.0
OE1 D:GLU80 2.1 70.5 1.0
ND1 D:HIS83 2.2 64.7 1.0
CD D:GLU47 2.8 65.3 1.0
OE2 D:GLU47 2.9 73.4 1.0
CD D:GLU162 2.9 69.6 1.0
CE1 D:HIS83 3.0 68.1 1.0
CD D:GLU80 3.0 68.2 1.0
OE1 D:GLU162 3.3 69.3 1.0
CG D:HIS83 3.3 66.5 1.0
OE2 D:GLU80 3.4 70.7 1.0
CB D:HIS83 3.8 72.5 1.0
FE D:FE2209 4.0 76.6 1.0
CG2 D:ILE158 4.1 64.1 1.0
CA D:GLU80 4.1 65.5 1.0
NE2 D:HIS83 4.2 70.0 1.0
CG D:GLU162 4.2 66.2 1.0
CG D:GLU47 4.2 67.9 1.0
CG D:GLU80 4.3 66.7 1.0
CD2 D:HIS83 4.4 70.4 1.0
CB D:GLU80 4.4 66.0 1.0
O D:GLU80 4.8 57.2 1.0
CB D:GLU47 4.9 64.9 1.0
N D:GLU80 4.9 62.4 1.0
O D:GLN79 4.9 67.2 1.0

Iron binding site 8 out of 24 in 8w1f

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Iron binding site 8 out of 24 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 Iron with other atoms in the Fe 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
D:Fe209

b:76.6
occ:1.00
 OE1 D:GLU162 2.0 69.3 1.0
OE1 D:GLU130 2.2 68.5 1.0
OE2 D:GLU130 2.2 63.2 1.0
ND1 D:HIS165 2.2 64.8 1.0
OE2 D:GLU80 2.3 70.7 1.0
CD D:GLU130 2.5 65.3 1.0
CD D:GLU80 3.1 68.2 1.0
CE1 D:HIS165 3.1 66.7 1.0
CD D:GLU162 3.1 69.6 1.0
CG D:HIS165 3.3 63.4 1.0
OE1 D:GLU80 3.3 70.5 1.0
CB D:HIS165 3.6 63.4 1.0
OE2 D:GLU162 3.6 69.5 1.0
FE D:FE2208 4.0 82.4 1.0
CG D:GLU130 4.0 64.1 1.0
NE2 D:HIS165 4.3 64.0 1.0
CG D:GLU162 4.4 66.2 1.0
CG D:GLU80 4.4 66.7 1.0
CA D:GLU162 4.4 62.3 1.0
CD2 D:HIS165 4.4 66.2 1.0
CB D:GLU162 4.6 58.8 1.0
CE2 D:TYR54 4.6 58.6 1.0
OH D:TYR54 4.7 60.3 1.0
CB D:GLU130 4.8 63.4 1.0
CA D:GLU130 5.0 62.6 1.0

Iron binding site 9 out of 24 in 8w1f

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Iron binding site 9 out of 24 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 Iron with other atoms in the Fe 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
E:Fe208

b:74.1
occ:1.00
 OE1 E:GLU47 2.0 60.3 1.0
ND1 E:HIS83 2.0 60.7 1.0
OE2 E:GLU162 2.1 71.0 1.0
CD E:GLU47 2.5 60.0 1.0
OE2 E:GLU47 2.6 68.9 1.0
CG E:HIS83 2.9 59.2 1.0
CE1 E:HIS83 2.9 60.5 1.0
OE1 E:GLU80 3.0 66.4 1.0
CD E:GLU162 3.1 64.2 1.0
CB E:HIS83 3.3 59.5 1.0
CD E:GLU80 3.5 61.8 1.0
OE2 E:GLU80 3.7 65.8 1.0
OE1 E:GLU162 3.7 67.9 1.0
CG2 E:ILE158 3.8 58.8 1.0
CG E:GLU47 3.9 61.7 1.0
NE2 E:HIS83 4.0 63.1 1.0
CD2 E:HIS83 4.1 65.5 1.0
CA E:GLU80 4.1 60.5 1.0
CG E:GLU162 4.2 54.7 1.0
FE E:FE2209 4.3 78.6 1.0
O E:GLU80 4.6 54.4 1.0
CB E:GLU80 4.6 60.2 1.0
CG E:GLU80 4.6 57.8 1.0
CB E:GLU47 4.7 55.6 1.0
O E:GLN79 4.7 61.3 1.0
CA E:HIS83 4.8 57.3 1.0
C E:GLU80 4.9 54.8 1.0
N E:GLU80 4.9 56.6 1.0
CE2 E:TYR137 5.0 56.5 1.0

Iron binding site 10 out of 24 in 8w1f

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Iron binding site 10 out of 24 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 Iron with other atoms in the Fe 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
E:Fe209

b:78.6
occ:1.00
 OE1 E:GLU162 2.0 67.9 1.0
ND1 E:HIS165 2.2 61.0 1.0
OE1 E:GLU130 2.3 60.8 1.0
OE2 E:GLU80 2.4 65.8 1.0
OE2 E:GLU130 2.4 61.0 1.0
CD E:GLU130 2.7 59.8 1.0
OE1 E:GLU80 2.8 66.4 1.0
CD E:GLU162 2.8 64.2 1.0
CD E:GLU80 2.8 61.8 1.0
CE1 E:HIS165 3.0 62.7 1.0
OE2 E:GLU162 3.1 71.0 1.0
CG E:HIS165 3.4 57.9 1.0
CB E:HIS165 3.8 60.6 1.0
CG E:GLU162 4.2 54.7 1.0
CG E:GLU80 4.2 57.8 1.0
NE2 E:HIS165 4.2 57.4 1.0
CG E:GLU130 4.3 56.6 1.0
FE E:FE2208 4.3 74.1 1.0
CA E:GLU162 4.3 61.1 1.0
CD2 E:HIS165 4.4 61.5 1.0
CB E:GLU162 4.5 59.6 1.0
CE2 E:TYR54 4.6 55.6 1.0
OH E:TYR54 4.7 60.6 1.0

Reference:

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
Page generated: Sat Aug 10 18:48:09 2024

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