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Sodium in PDB 4s0n: Crystal Structure of Hltf Hiran Domain Bound to Dna

Protein crystallography data

The structure of Crystal Structure of Hltf Hiran Domain Bound to Dna, PDB code: 4s0n was solved by D.A.Chavez, B.F.Eichman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.72 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.026, 74.211, 66.180, 90.00, 113.68, 90.00
R / Rfree (%) 15.3 / 18.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hltf Hiran Domain Bound to Dna (pdb code 4s0n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Hltf Hiran Domain Bound to Dna, PDB code: 4s0n:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4s0n

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Sodium binding site 1 out of 4 in the Crystal Structure of Hltf Hiran Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Hltf Hiran Domain Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:21.3
occ:1.00
 O A:LEU70 2.3 20.2 1.0
O A:TYR73 2.3 20.1 1.0
O A:HOH342 2.4 28.0 1.0
O A:HOH301 2.4 21.7 1.0
O A:HOH366 2.4 32.2 1.0
O A:HOH377 2.4 34.9 1.0
C A:LEU70 3.4 17.9 1.0
C A:TYR73 3.4 18.2 1.0
O A:HOH370 4.1 34.5 1.0
CA A:LEU70 4.2 17.3 1.0
N A:TYR73 4.2 17.6 1.0
N A:THR74 4.2 18.7 1.0
O A:HOH405 4.3 46.0 1.0
CA A:THR74 4.3 19.3 1.0
CA A:TYR73 4.3 17.4 1.0
O A:HOH400 4.3 63.7 1.0
N A:ARG71 4.3 19.4 1.0
CB A:LEU70 4.3 18.5 1.0
CA A:ARG71 4.4 21.2 1.0
O A:GLY75 4.5 20.3 1.0
O A:HOH410 4.5 48.8 1.0
C A:ARG71 4.6 20.8 1.0
O A:HOH380 4.6 40.2 1.0
C A:THR74 4.7 17.7 1.0
O A:VAL108 4.7 15.7 1.0
CB A:TYR73 4.8 18.0 1.0
N A:GLY75 4.9 16.8 1.0
O A:ARG71 5.0 24.4 1.0
N A:TYR72 5.0 19.1 1.0

Sodium binding site 2 out of 4 in 4s0n

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Sodium binding site 2 out of 4 in the Crystal Structure of Hltf Hiran Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Hltf Hiran Domain Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:25.9
occ:1.00
 O B:HOH448 2.3 37.1 1.0
O B:TYR73 2.4 24.3 1.0
O B:LEU70 2.4 19.9 1.0
O B:HOH464 2.5 24.1 1.0
O B:HOH367 2.5 34.4 1.0
O B:HOH403 2.5 39.9 1.0
C B:LEU70 3.4 18.2 1.0
C B:TYR73 3.5 22.6 1.0
O B:HOH404 4.0 60.6 1.0
CA B:LEU70 4.2 19.1 1.0
N B:TYR73 4.2 21.6 1.0
N B:ARG71 4.2 18.4 1.0
CA B:ARG71 4.3 19.6 1.0
CB B:LEU70 4.3 19.4 1.0
N B:THR74 4.3 24.8 1.0
CA B:TYR73 4.3 21.1 1.0
CA B:THR74 4.3 26.5 1.0
O B:GLY75 4.6 30.8 1.0
O B:HOH405 4.6 49.9 1.0
C B:ARG71 4.6 19.3 1.0
C B:THR74 4.7 27.0 1.0
O B:VAL108 4.8 19.3 1.0
CB B:TYR73 4.8 20.3 1.0
N B:TYR72 4.9 20.4 1.0
O B:ARG71 5.0 21.5 1.0

Sodium binding site 3 out of 4 in 4s0n

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Sodium binding site 3 out of 4 in the Crystal Structure of Hltf Hiran Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Hltf Hiran Domain Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:19.2
occ:1.00
 O C:LEU70 2.3 19.4 1.0
O C:HOH302 2.3 22.4 1.0
O C:HOH328 2.4 29.4 1.0
O C:TYR73 2.4 20.4 1.0
O C:HOH338 2.5 31.6 1.0
O C:HOH410 2.5 25.3 1.0
C C:LEU70 3.4 16.8 1.0
C C:TYR73 3.4 17.0 1.0
O C:HOH349 3.7 47.1 1.0
O C:HOH396 3.9 30.7 1.0
CA C:LEU70 4.1 17.0 1.0
CB C:LEU70 4.2 16.9 1.0
CA C:THR74 4.2 18.4 1.0
N C:THR74 4.2 16.9 1.0
O C:HOH343 4.2 30.9 1.0
N C:TYR73 4.2 18.7 1.0
O C:HOH313 4.3 24.3 1.0
CA C:TYR73 4.3 16.8 1.0
N C:ARG71 4.4 18.6 1.0
CA C:ARG71 4.5 19.3 1.0
O C:VAL108 4.7 17.4 1.0
C C:ARG71 4.7 19.5 1.0
CB C:TYR73 4.8 17.5 1.0
C C:THR74 4.8 17.6 1.0
O C:HOH345 4.8 40.4 1.0
O C:GLY75 4.9 25.8 1.0
O C:HOH309 5.0 20.9 1.0
O C:ARG71 5.0 21.9 1.0

Sodium binding site 4 out of 4 in 4s0n

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Sodium binding site 4 out of 4 in the Crystal Structure of Hltf Hiran Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Hltf Hiran Domain Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:38.5
occ:1.00
 O D:TYR73 2.3 41.3 1.0
O D:LEU70 2.3 36.8 1.0
O D:HOH311 2.4 28.2 1.0
O D:HOH368 2.5 61.8 1.0
O D:HOH317 2.5 46.3 1.0
O D:HOH319 2.6 33.0 1.0
C D:TYR73 3.4 39.9 1.0
C D:LEU70 3.5 35.4 1.0
O D:HOH348 4.0 31.7 1.0
CA D:LEU70 4.2 33.2 1.0
N D:TYR73 4.2 39.7 1.0
N D:THR74 4.3 39.3 1.0
CA D:TYR73 4.3 40.8 1.0
CB D:LEU70 4.4 31.0 1.0
CA D:THR74 4.4 39.1 1.0
O D:GLY75 4.4 27.5 1.0
N D:ARG71 4.4 38.6 1.0
CA D:ARG71 4.5 40.5 1.0
O D:VAL108 4.6 32.5 1.0
C D:ARG71 4.7 40.5 1.0
C D:THR74 4.8 34.5 1.0
CB D:TYR73 4.8 42.1 1.0
O D:HOH313 5.0 28.5 1.0

Reference:

A.C.Kile, D.A.Chavez, J.Bacal, S.Eldirani, D.Korzhnev, I.Bezsonova, B.F.Eichman, K.A.Cimprich. Hltf S Ancient Hiran Domain Binds 3′-Dna Ends to Drive Replication Fork Reversal Mol.Cell 2015.
ISSN: ISSN 1097-2765
Page generated: Mon Oct 7 18:23:54 2024

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