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Bromine in PDB 9eff: Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus.

Protein crystallography data

The structure of Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus., PDB code: 9eff was solved by R.Dhanaraju, G.Gonzalez-Gutierrez, S.D.Bell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.26 / 1.82
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.742, 136.051, 38.38, 90, 109.12, 90
R / Rfree (%) 20 / 22.8

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus. (pdb code 9eff). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus., PDB code: 9eff:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 9eff

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Bromine binding site 1 out of 8 in the Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br21

b:34.5
occ:1.00
 BR D:BRU21 0.0 34.5 1.0
C5 D:BRU21 1.9 25.1 1.0
C6 D:BRU21 2.9 29.9 1.0
C4 D:BRU21 2.9 26.5 1.0
O4 D:BRU21 3.1 24.8 1.0
O D:HOH109 3.3 32.7 1.0
C8 D:DA20 3.7 31.7 1.0
N7 D:DA20 3.9 31.4 1.0
O5' D:DA20 4.0 34.6 1.0
OP2 D:BRU21 4.0 27.3 1.0
N9 D:DA20 4.0 30.5 1.0
C3' D:DA20 4.1 29.3 1.0
CE A:LYS63 4.1 52.9 1.0
N1 D:BRU21 4.1 32.8 1.0
N3 D:BRU21 4.2 26.2 1.0
CD1 A:LEU68 4.2 31.8 1.0
NZ A:LYS63 4.2 54.1 1.0
C5 D:DA20 4.3 31.5 1.0
CD1 A:LEU61 4.3 23.9 1.0
C2' D:DA20 4.3 28.4 1.0
C4 D:DA20 4.4 29.6 1.0
CD2 A:LEU68 4.5 31.6 1.0
C7 D:DT22 4.5 25.9 1.0
C2 D:BRU21 4.6 30.5 1.0
C1' D:DA20 4.6 31.6 1.0
O4 D:DT22 4.8 22.9 1.0
O5' D:BRU21 4.9 31.0 1.0
C4' D:DA20 4.9 32.6 1.0
P D:BRU21 4.9 32.2 1.0
CG A:LEU68 5.0 28.2 1.0
O4' D:DA20 5.0 34.5 1.0

Bromine binding site 2 out of 8 in 9eff

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Bromine binding site 2 out of 8 in the Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br24

b:25.6
occ:1.00
 BR D:BRU24 0.0 25.6 1.0
C5 D:BRU24 1.9 17.5 1.0
C6 D:BRU24 2.8 24.4 1.0
C4 D:BRU24 2.9 21.9 1.0
O A:TYR41 3.0 19.8 1.0
O4 D:BRU24 3.1 19.2 1.0
O A:HOH266 3.3 21.2 1.0
CE A:LYS39 3.7 15.1 1.0
C8 D:DA23 3.8 20.1 1.0
NZ A:LYS39 3.8 19.6 1.0
N7 D:DA23 3.9 21.4 1.0
CG1 A:ILE43 4.1 21.9 1.0
O D:HOH116 4.1 18.6 1.0
C A:TYR41 4.1 21.4 1.0
N1 D:BRU24 4.1 23.8 1.0
N9 D:DA23 4.1 19.4 1.0
CD1 A:ILE43 4.1 27.2 1.0
N3 D:BRU24 4.1 24.7 1.0
C2' D:DA23 4.2 20.6 1.0
CD2 A:TYR41 4.2 29.0 1.0
N A:ILE43 4.3 19.1 1.0
C5 D:DA23 4.4 20.2 1.0
CA A:HIS42 4.4 16.7 1.0
C4 D:DA23 4.5 21.9 1.0
C2 D:BRU24 4.6 19.4 1.0
N A:HIS42 4.7 20.8 1.0
CE2 A:TYR41 4.7 38.4 1.0
C1' D:DA23 4.7 20.8 1.0
C A:HIS42 4.8 19.5 1.0
CB A:ILE43 4.9 21.2 1.0
O D:HOH126 4.9 18.0 1.0
CG A:TYR41 4.9 25.6 1.0
N7 D:DA25 5.0 18.3 1.0

Bromine binding site 3 out of 8 in 9eff

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Bromine binding site 3 out of 8 in the Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br42

b:56.7
occ:1.00
 BR E:BRU42 0.0 56.7 1.0
C5 E:BRU42 1.9 27.3 1.0
C6 E:BRU42 2.8 26.6 1.0
C4 E:BRU42 2.9 28.8 1.0
O4 E:BRU42 3.1 30.1 1.0
O E:HOH122 3.7 39.8 1.0
O A:HOH207 3.7 33.8 1.0
C2' E:DC41 3.8 35.5 1.0
C6 E:DC41 3.9 38.2 1.0
CG A:LYS46 4.1 50.1 1.0
OH A:TYR51 4.1 31.8 1.0
N1 E:BRU42 4.1 24.4 1.0
N1 E:DC41 4.1 37.6 1.0
C5 E:DC41 4.2 37.5 1.0
N3 E:BRU42 4.2 23.7 1.0
O E:HOH120 4.2 35.5 1.0
CB A:LYS46 4.4 42.0 1.0
C2 E:DC41 4.5 33.9 1.0
CZ A:TYR51 4.5 29.9 1.0
C1' E:DC41 4.5 37.7 1.0
C4 E:DC41 4.5 34.6 1.0
CE1 A:TYR51 4.6 27.6 1.0
C2 E:BRU42 4.6 25.0 1.0
N3 E:DC41 4.7 32.8 1.0
C3' E:DC41 4.8 39.1 1.0
ND2 A:ASN47 4.9 55.0 1.0
C7 E:DT43 4.9 20.9 1.0

Bromine binding site 4 out of 8 in 9eff

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Bromine binding site 4 out of 8 in the Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br49

b:34.8
occ:1.00
 BR E:BRU49 0.0 34.8 1.0
C5 E:BRU49 1.9 20.7 1.0
C6 E:BRU49 2.9 22.7 1.0
C4 E:BRU49 2.9 23.0 1.0
O4 E:BRU49 3.1 20.6 1.0
O A:LEU68 3.1 30.5 1.0
CB A:LEU68 3.7 28.6 1.0
O E:HOH109 3.7 35.4 1.0
O A:HOH211 3.8 26.8 1.0
C A:LEU68 3.8 30.2 1.0
NE1 A:TRP70 3.9 22.9 1.0
C2' E:DA48 3.9 32.9 1.0
C8 E:DA48 4.0 22.5 1.0
CD1 A:TRP70 4.0 19.5 1.0
N1 E:BRU49 4.1 26.9 1.0
N7 E:DA48 4.1 23.3 1.0
N9 E:DA48 4.1 23.2 1.0
N3 E:BRU49 4.1 21.7 1.0
CA A:LEU68 4.2 34.4 1.0
OP2 E:BRU49 4.2 35.7 1.0
CG A:LEU68 4.2 28.2 1.0
C5 E:DA48 4.3 18.3 1.0
C4 E:DA48 4.3 20.3 1.0
N A:LEU68 4.4 35.5 1.0
O A:HOH235 4.4 33.8 1.0
CD2 A:LEU68 4.4 31.6 1.0
O E:HOH123 4.6 39.0 1.0
C2 E:BRU49 4.6 27.1 1.0
C1' E:DA48 4.7 27.4 1.0
O E:HOH107 4.7 37.5 1.0
C3' E:DA48 4.8 27.6 1.0
N A:LYS69 4.9 24.2 1.0
N3 E:DA48 5.0 22.6 1.0

Bromine binding site 5 out of 8 in 9eff

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Bromine binding site 5 out of 8 in the Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br21

b:38.9
occ:1.00
 BR C:BRU21 0.0 38.9 1.0
C5 C:BRU21 1.9 31.7 1.0
C6 C:BRU21 2.9 32.2 1.0
C4 C:BRU21 3.0 33.5 1.0
O4 C:BRU21 3.2 31.9 1.0
O C:HOH107 3.4 29.5 1.0
O B:HOH204 3.7 33.4 1.0
C8 C:DA20 3.7 40.9 1.0
N7 C:DA20 3.8 39.8 1.0
OP2 C:BRU21 3.9 35.8 1.0
O5' C:DA20 4.0 42.1 1.0
CD1 B:LEU68 4.0 30.7 1.0
N9 C:DA20 4.1 41.4 1.0
C3' C:DA20 4.1 39.7 1.0
N1 C:BRU21 4.1 34.8 1.0
C5 C:DA20 4.2 38.6 1.0
N3 C:BRU21 4.2 32.5 1.0
CD1 B:LEU61 4.2 24.9 1.0
C4 C:DA20 4.3 42.8 1.0
C2' C:DA20 4.4 40.3 1.0
CD2 B:LEU68 4.4 33.2 1.0
NZ B:LYS63 4.6 56.5 1.0
C2 C:BRU21 4.7 37.9 1.0
C7 C:DT22 4.7 27.1 1.0
C1' C:DA20 4.8 41.6 1.0
CG B:LEU68 4.8 29.2 1.0
C6 C:DA20 4.9 38.4 1.0
P C:BRU21 4.9 37.9 1.0
O4 C:DT22 4.9 28.5 1.0
O5' C:BRU21 4.9 38.9 1.0
CE B:LYS63 4.9 43.8 1.0

Bromine binding site 6 out of 8 in 9eff

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Bromine binding site 6 out of 8 in the Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br24

b:31.4
occ:1.00
 BR C:BRU24 0.0 31.4 1.0
C5 C:BRU24 1.9 22.4 1.0
C6 C:BRU24 2.8 24.6 1.0
C4 C:BRU24 2.9 24.6 1.0
O B:TYR41 3.0 24.1 1.0
O4 C:BRU24 3.1 25.0 1.0
CD1 B:ILE43 3.5 39.4 1.0
O C:HOH114 3.6 26.1 1.0
CE B:LYS39 3.6 24.9 1.0
NZ B:LYS39 3.7 20.9 1.0
C8 C:DA23 3.7 23.5 1.0
N7 C:DA23 3.9 23.0 1.0
N1 C:BRU24 4.1 30.0 1.0
C B:TYR41 4.1 25.7 1.0
N3 C:BRU24 4.1 27.1 1.0
N9 C:DA23 4.1 27.0 1.0
O C:HOH113 4.2 21.9 1.0
C2' C:DA23 4.2 26.7 1.0
N B:ILE43 4.3 25.4 1.0
C5 C:DA23 4.3 23.3 1.0
CA B:HIS42 4.4 25.0 1.0
CD2 B:TYR41 4.4 31.6 1.0
CG1 B:ILE43 4.4 33.8 1.0
C4 C:DA23 4.5 24.3 1.0
C2 C:BRU24 4.6 29.6 1.0
N B:HIS42 4.7 24.4 1.0
C B:HIS42 4.8 25.7 1.0
C1' C:DA23 4.8 26.1 1.0
O C:HOH122 4.8 21.9 1.0
CE2 B:TYR41 4.9 39.4 1.0
CB B:ILE43 5.0 30.2 1.0
CD B:LYS39 5.0 21.5 1.0

Bromine binding site 7 out of 8 in 9eff

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Bromine binding site 7 out of 8 in the Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br42

b:69.0
occ:1.00
 BR F:BRU42 0.0 69.0 1.0
C5 F:BRU42 1.9 39.0 1.0
C6 F:BRU42 2.9 35.8 1.0
C4 F:BRU42 2.9 34.0 1.0
O4 F:BRU42 3.1 35.0 1.0
C2' F:DC41 3.7 42.3 1.0
C6 F:DC41 3.8 45.9 1.0
O F:HOH111 4.0 42.1 1.0
CG B:LYS46 4.0 44.3 1.0
N1 F:DC41 4.0 45.5 1.0
C5 F:DC41 4.1 45.0 1.0
OH B:TYR51 4.1 40.9 1.0
N1 F:BRU42 4.1 34.4 1.0
N3 F:BRU42 4.2 32.7 1.0
CB B:LYS46 4.4 41.3 1.0
CE2 B:TYR51 4.5 34.9 1.0
C2 F:DC41 4.5 46.9 1.0
C1' F:DC41 4.5 44.9 1.0
C4 F:DC41 4.5 42.8 1.0
O5' F:DC41 4.5 57.4 1.0
CZ B:TYR51 4.5 36.8 1.0
C2 F:BRU42 4.6 34.3 1.0
N3 F:DC41 4.7 44.8 1.0
C3' F:DC41 4.8 44.8 1.0
C7 F:DT43 5.0 31.6 1.0

Bromine binding site 8 out of 8 in 9eff

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Bromine binding site 8 out of 8 in the Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of A Nucleoid-Associated Protein (Ubp) Bound to Dna From Sulfolobus Islandicus. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br49

b:36.1
occ:1.00
 BR F:BRU49 0.0 36.1 1.0
C5 F:BRU49 1.9 24.4 1.0
C6 F:BRU49 2.9 27.9 1.0
C4 F:BRU49 2.9 24.0 1.0
O4 F:BRU49 3.1 26.5 1.0
O B:LEU68 3.1 25.7 1.0
O F:HOH104 3.6 35.3 1.0
CB B:LEU68 3.7 25.6 1.0
OP2 F:BRU49 3.8 32.7 1.0
NE1 B:TRP70 3.9 25.2 1.0
C B:LEU68 3.9 28.2 1.0
C2' F:DA48 3.9 28.2 1.0
O F:HOH110 4.0 29.4 1.0
C8 F:DA48 4.0 24.4 1.0
CD1 B:TRP70 4.0 19.7 1.0
N9 F:DA48 4.0 27.9 1.0
N1 F:BRU49 4.1 29.8 1.0
N3 F:BRU49 4.1 28.2 1.0
N7 F:DA48 4.2 20.5 1.0
C4 F:DA48 4.2 26.0 1.0
CG B:LEU68 4.3 29.2 1.0
C5 F:DA48 4.3 25.4 1.0
CA B:LEU68 4.3 27.8 1.0
CD2 B:LEU68 4.4 33.2 1.0
C3' F:DA48 4.4 28.5 1.0
N B:LEU68 4.5 32.8 1.0
C1' F:DA48 4.6 31.9 1.0
O F:HOH121 4.6 40.0 1.0
C2 F:BRU49 4.6 32.0 1.0
N3 F:DA48 4.8 24.7 1.0
P F:BRU49 5.0 38.8 1.0
C6 F:DA48 5.0 22.4 1.0

Reference:

R.Dhanaraju, R.Y.Samson, X.Feng, A.Costa, G.Gonzalez-Gutierrez, S.D.Bell. Identification and Characterization of An Archaeal Nucleoid-Associated Protein That Plays An Essential Role in Dna Replication Initiation. To Be Published.
Page generated: Mon Jul 7 12:47:25 2025

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