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Sodium in PDB 1dps: The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna

Protein crystallography data

The structure of The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna, PDB code: 1dps was solved by R.A.Grant, D.J.Filman, S.E.Finkel, R.Kolter, J.M.Hogle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 134.410, 139.650, 118.110, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna (pdb code 1dps). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna, PDB code: 1dps:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 1dps

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Sodium binding site 1 out of 12 in the The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na168

b:34.8
occ:1.00
 O A:LYS140 2.3 20.9 1.0
O A:HOH219 2.6 21.6 1.0
O A:HOH235 2.7 27.5 1.0
O A:HOH211 2.7 23.6 1.0
OD1 A:ASP142 2.8 18.9 1.0
CG A:ASP142 3.4 18.8 1.0
C A:LYS140 3.5 20.9 1.0
OD2 A:ASP142 3.6 19.3 1.0
N A:ASP142 3.9 17.6 1.0
O A:HOH193 4.0 21.2 1.0
CA A:LYS140 4.4 21.8 1.0
N A:ASP141 4.4 19.7 1.0
CA A:ASP141 4.4 18.7 1.0
C A:ASP141 4.5 18.2 1.0
CB A:ASP142 4.5 17.9 1.0
CA A:ASP142 4.6 17.3 1.0
OE2 A:GLU25 4.6 25.2 1.0
O A:HOH236 4.8 19.6 1.0
CB A:LYS140 4.8 22.9 1.0
O A:HOH238 4.9 26.2 1.0

Sodium binding site 2 out of 12 in 1dps

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Sodium binding site 2 out of 12 in the The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na168

b:13.7
occ:1.00
 O B:LYS140 2.4 20.3 1.0
O B:HOH221 2.6 24.3 1.0
OD1 B:ASP142 2.7 18.5 1.0
O B:HOH245 2.7 28.4 1.0
O B:HOH213 2.8 19.5 1.0
CG B:ASP142 3.4 18.1 1.0
C B:LYS140 3.6 20.6 1.0
OD2 B:ASP142 3.6 18.6 1.0
N B:ASP142 3.9 17.4 1.0
O B:HOH194 4.1 21.1 1.0
CA B:ASP141 4.4 18.7 1.0
N B:ASP141 4.4 19.6 1.0
CB B:ASP142 4.5 17.2 1.0
OE2 B:GLU25 4.5 24.0 1.0
CA B:LYS140 4.5 21.4 1.0
C B:ASP141 4.5 17.9 1.0
O B:HOH246 4.6 17.5 1.0
CA B:ASP142 4.7 17.0 1.0
O G:HOH219 4.7 21.4 1.0
CB B:LYS140 4.8 22.9 1.0

Sodium binding site 3 out of 12 in 1dps

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Sodium binding site 3 out of 12 in the The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na168

b:12.8
occ:1.00
 O C:LYS140 2.3 19.0 1.0
O C:HOH228 2.6 30.7 1.0
O C:HOH221 2.6 23.1 1.0
O C:HOH239 2.7 30.4 1.0
OD1 C:ASP142 2.8 16.7 1.0
CG C:ASP142 3.4 16.1 1.0
C C:LYS140 3.5 19.1 1.0
OD2 C:ASP142 3.6 16.2 1.0
N C:ASP142 3.9 16.5 1.0
O C:HOH202 4.1 15.2 1.0
OE2 C:GLU25 4.4 24.9 1.0
CA C:ASP141 4.4 17.6 1.0
N C:ASP141 4.4 18.3 1.0
CA C:LYS140 4.4 19.9 1.0
C C:ASP141 4.6 17.2 1.0
CB C:ASP142 4.6 15.9 1.0
O C:HOH273 4.6 46.3 1.0
O C:HOH241 4.6 17.1 1.0
CA C:ASP142 4.7 15.9 1.0
O H:HOH219 4.7 15.6 1.0
CB C:LYS140 4.8 21.2 1.0

Sodium binding site 4 out of 12 in 1dps

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Sodium binding site 4 out of 12 in the The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na168

b:35.3
occ:1.00
 O D:HOH227 2.0 31.2 1.0
O D:LYS140 2.3 19.7 1.0
O D:HOH220 2.4 30.9 1.0
O D:HOH263 3.1 54.0 1.0
OD1 D:ASP142 3.3 19.2 1.0
C D:LYS140 3.5 19.4 1.0
CG D:ASP142 3.7 17.7 1.0
OD2 D:ASP142 3.7 18.1 1.0
N D:ASP142 4.0 17.0 1.0
O D:HOH201 4.0 26.2 1.0
OE2 D:GLU25 4.3 27.6 1.0
CA D:ASP141 4.3 18.1 1.0
N D:ASP141 4.3 18.4 1.0
CA D:LYS140 4.4 20.0 1.0
C D:ASP141 4.5 17.9 1.0
O D:HOH233 4.7 27.2 1.0
CB D:ASP142 4.7 17.1 1.0
O D:HOH234 4.8 19.9 1.0
CB D:LYS140 4.8 20.6 1.0
CA D:ASP142 4.8 16.5 1.0

Sodium binding site 5 out of 12 in 1dps

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Sodium binding site 5 out of 12 in the The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na168

b:33.4
occ:1.00
 O E:LYS140 2.1 20.3 1.0
O E:HOH267 2.4 40.2 1.0
O E:HOH216 2.5 30.7 1.0
O E:HOH236 3.0 23.9 1.0
OD1 E:ASP142 3.1 19.6 1.0
C E:LYS140 3.3 20.5 1.0
CG E:ASP142 3.5 18.6 1.0
OD2 E:ASP142 3.6 19.3 1.0
N E:ASP142 3.8 17.6 1.0
O E:HOH199 4.1 19.3 1.0
CA E:ASP141 4.2 18.1 1.0
N E:ASP141 4.2 19.4 1.0
OE2 E:GLU25 4.2 27.6 1.0
CA E:LYS140 4.3 21.5 1.0
C E:ASP141 4.4 17.9 1.0
O E:HOH238 4.5 20.0 1.0
O E:HOH239 4.5 21.8 1.0
CB E:ASP142 4.5 17.8 1.0
CB E:LYS140 4.6 23.0 1.0
CA E:ASP142 4.6 17.5 1.0

Sodium binding site 6 out of 12 in 1dps

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Sodium binding site 6 out of 12 in the The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na168

b:16.0
occ:1.00
 O F:LYS140 2.3 19.4 1.0
O F:HOH219 2.5 18.1 1.0
O F:HOH227 2.6 24.9 1.0
O F:HOH250 2.7 23.4 1.0
OD1 F:ASP142 2.7 17.8 1.0
O F:HOH276 2.8 55.8 1.0
CG F:ASP142 3.3 17.0 1.0
OD2 F:ASP142 3.4 17.4 1.0
C F:LYS140 3.5 19.4 1.0
N F:ASP142 3.8 16.6 1.0
O F:HOH200 4.2 21.1 1.0
CA F:ASP141 4.2 17.7 1.0
N F:ASP141 4.3 18.2 1.0
OE2 F:GLU25 4.4 24.0 1.0
O F:HOH252 4.4 18.0 1.0
CB F:ASP142 4.4 16.3 1.0
C F:ASP141 4.4 17.0 1.0
CA F:LYS140 4.5 20.5 1.0
CA F:ASP142 4.6 16.0 1.0
O F:HOH254 4.6 18.0 1.0
CB F:LYS140 4.9 21.7 1.0

Sodium binding site 7 out of 12 in 1dps

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Sodium binding site 7 out of 12 in the The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na168

b:24.3
occ:1.00
 O G:LYS140 2.3 20.2 1.0
O G:HOH232 2.6 35.9 1.0
OD1 G:ASP142 2.8 19.2 1.0
O G:HOH225 2.8 24.4 1.0
O G:HOH242 2.9 25.8 1.0
CG G:ASP142 3.4 18.6 1.0
C G:LYS140 3.5 20.5 1.0
OD2 G:ASP142 3.6 19.2 1.0
N G:ASP142 4.0 17.3 1.0
O G:HOH210 4.1 19.9 1.0
CA G:LYS140 4.4 21.5 1.0
N G:ASP141 4.4 19.4 1.0
CA G:ASP141 4.4 18.4 1.0
OE2 G:GLU25 4.5 26.7 1.0
C G:ASP141 4.6 17.8 1.0
CB G:ASP142 4.6 17.4 1.0
O G:HOH244 4.7 15.9 1.0
CB G:LYS140 4.7 23.0 1.0
CA G:ASP142 4.7 17.1 1.0
O L:HOH232 4.9 19.5 1.0

Sodium binding site 8 out of 12 in 1dps

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Sodium binding site 8 out of 12 in the The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na168

b:12.0
occ:1.00
 O H:LYS140 2.3 18.4 1.0
O H:HOH266 2.4 31.1 1.0
O H:HOH234 2.6 21.4 1.0
O H:HOH226 2.6 16.8 1.0
OD1 H:ASP142 2.7 16.4 1.0
O H:HOH240 2.7 23.9 1.0
CG H:ASP142 3.3 16.4 1.0
C H:LYS140 3.5 18.2 1.0
OD2 H:ASP142 3.6 16.8 1.0
N H:ASP142 3.9 15.7 1.0
O H:HOH207 4.2 17.1 1.0
CA H:ASP141 4.4 16.7 1.0
N H:ASP141 4.4 17.3 1.0
OE2 H:GLU25 4.4 21.7 1.0
CA H:LYS140 4.5 19.1 1.0
CB H:ASP142 4.5 15.5 1.0
C H:ASP141 4.5 16.2 1.0
O H:HOH242 4.6 14.6 1.0
CA H:ASP142 4.6 15.2 1.0
O J:HOH222 4.7 16.4 1.0
CB H:LYS140 4.8 20.2 1.0

Sodium binding site 9 out of 12 in 1dps

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Sodium binding site 9 out of 12 in the The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na168

b:18.4
occ:1.00
 O I:LYS140 2.4 21.5 1.0
O I:HOH241 2.6 40.1 1.0
O I:HOH169 2.7 23.2 1.0
OD1 I:ASP142 2.8 20.9 1.0
O I:HOH235 2.9 23.7 1.0
CG I:ASP142 3.5 20.3 1.0
C I:LYS140 3.6 21.2 1.0
OD2 I:ASP142 3.7 20.3 1.0
N I:ASP142 4.1 19.1 1.0
O I:HOH217 4.2 21.9 1.0
CA I:LYS140 4.4 21.8 1.0
N I:ASP141 4.5 20.3 1.0
OE2 I:GLU25 4.5 26.0 1.0
CA I:ASP141 4.5 19.9 1.0
CB I:ASP142 4.7 19.5 1.0
C I:ASP141 4.7 19.5 1.0
CB I:LYS140 4.8 23.1 1.0
CA I:ASP142 4.8 18.9 1.0
O I:HOH171 4.9 22.2 1.0
O I:HOH173 4.9 20.8 1.0

Sodium binding site 10 out of 12 in 1dps

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Sodium binding site 10 out of 12 in the The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na168

b:12.8
occ:1.00
 O J:LYS140 2.3 17.6 1.0
O J:HOH274 2.5 33.9 1.0
O J:HOH228 2.5 14.3 1.0
O J:HOH236 2.6 30.6 1.0
OD1 J:ASP142 2.7 15.3 1.0
O J:HOH173 2.7 24.9 1.0
CG J:ASP142 3.3 15.2 1.0
C J:LYS140 3.5 17.6 1.0
OD2 J:ASP142 3.6 15.4 1.0
N J:ASP142 3.8 15.3 1.0
O J:HOH212 4.0 17.5 1.0
CA J:ASP141 4.3 16.3 1.0
N J:ASP141 4.3 16.9 1.0
OE2 J:GLU25 4.4 21.2 1.0
C J:ASP141 4.4 15.9 1.0
O J:HOH283 4.4 39.0 1.0
CA J:LYS140 4.4 18.5 1.0
CB J:ASP142 4.5 15.2 1.0
O J:HOH175 4.5 15.9 1.0
CA J:ASP142 4.6 15.2 1.0
O J:HOH176 4.7 15.4 1.0
CB J:LYS140 4.8 19.8 1.0

Reference:

R.A.Grant, D.J.Filman, S.E.Finkel, R.Kolter, J.M.Hogle. The Crystal Structure of Dps, A Ferritin Homolog That Binds and Protects Dna. Nat.Struct.Biol. V. 5 294 1998.
ISSN: ISSN 1072-8368
PubMed: 9546221
DOI: 10.1038/NSB0498-294
Page generated: Sun Oct 6 18:18:43 2024

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