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Bromine in PDB 1n7a: Rip-Radiation-Damage Induced Phasing

Protein crystallography data

The structure of Rip-Radiation-Damage Induced Phasing, PDB code: 1n7a was solved by R.B.G.Ravelli, H.-K.S.Leiros, B.Pan, M.Caffrey, S.Mcsweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 31.233, 51.102, 70.651, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 15.6

Other elements in 1n7a:

The structure of Rip-Radiation-Damage Induced Phasing also contains other interesting chemical elements:

Potassium (K) 9 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Rip-Radiation-Damage Induced Phasing (pdb code 1n7a). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Rip-Radiation-Damage Induced Phasing, PDB code: 1n7a:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 1n7a

Go back to Bromine Binding Sites List in 1n7a
Bromine binding site 1 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2

b:6.9
occ:0.80
 BR A:BGM2 0.0 6.9 0.8
C8 A:BGM2 1.9 5.4 1.0
N7 A:BGM2 2.8 5.7 1.0
N9 A:BGM2 2.9 5.2 1.0
O E:HOH381 3.0 12.5 1.0
O4' A:BGM2 3.3 5.8 1.0
C1' A:BGM2 3.4 5.2 1.0
C2' A:BGM2 3.5 6.5 1.0
N3 E:U1 3.6 7.9 1.0
C5' A:BGM2 3.7 6.9 1.0
C2 E:U1 3.7 7.2 1.0
O2 E:U1 3.7 8.3 1.0
O B:HOH285 3.8 18.2 1.0
N2 D:BGM2 3.9 5.8 1.0
N2 B:BGM2 3.9 6.8 1.0
C5 A:BGM2 3.9 5.6 1.0
C4' A:BGM2 3.9 6.2 1.0
C4 A:BGM2 4.0 4.8 1.0
N7 A:A3 4.2 5.7 1.0
C3' A:BGM2 4.3 6.5 1.0
C4 E:U1 4.3 9.9 1.0
N1 E:U1 4.4 8.1 1.0
O2' A:U1 4.5 10.8 1.0
O2' E:U1 4.5 11.7 1.0
C2 B:BGM2 4.5 5.1 1.0
O A:HOH253 4.5 17.7 1.0
N3 B:BGM2 4.6 5.2 1.0
BR E:BGM2 4.6 6.7 0.8
C5 A:A3 4.7 4.7 1.0
O D:HOH292 4.7 17.3 1.0
O4 E:U1 4.8 11.8 1.0
C8 A:A3 4.8 6.0 1.0
N6 A:A3 4.9 6.4 1.0

Bromine binding site 2 out of 8 in 1n7a

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Bromine binding site 2 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br2

b:6.2
occ:0.80
 BR B:BGM2 0.0 6.2 0.8
C8 B:BGM2 1.9 5.0 1.0
N7 B:BGM2 2.8 4.8 1.0
N9 B:BGM2 2.9 5.1 1.0
O C:HOH382 3.0 10.7 1.0
O4' B:BGM2 3.4 6.5 1.0
C1' B:BGM2 3.4 6.5 1.0
C2' B:BGM2 3.5 7.0 1.0
N3 C:U1 3.6 5.5 1.0
C5' B:BGM2 3.6 8.1 1.0
O2 C:U1 3.6 7.0 1.0
C2 C:U1 3.6 6.0 1.0
O A:HOH311 3.8 21.4 1.0
N2 G:BGM2 3.9 6.1 1.0
C5 B:BGM2 3.9 4.5 1.0
N2 A:BGM2 4.0 5.9 1.0
C4' B:BGM2 4.0 6.8 1.0
C4 B:BGM2 4.0 5.2 1.0
N7 B:A3 4.1 4.2 1.0
C3' B:BGM2 4.3 6.9 1.0
O2' B:U1 4.4 11.6 1.0
C4 C:U1 4.4 7.3 1.0
N1 C:U1 4.5 5.8 1.0
O B:HOH257 4.6 19.7 1.0
C2 A:BGM2 4.6 4.6 1.0
BR C:BGM2 4.6 6.1 0.8
N3 A:BGM2 4.6 5.8 1.0
C5 B:A3 4.7 4.1 1.0
O2' C:U1 4.7 10.6 1.0
C8 B:A3 4.7 4.3 1.0
O4 C:U1 4.8 8.0 1.0
O G:HOH296 4.8 15.2 1.0
N6 B:A3 4.9 4.1 1.0
O5' B:BGM2 4.9 8.2 1.0

Bromine binding site 3 out of 8 in 1n7a

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Bromine binding site 3 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br2

b:6.1
occ:0.80
 BR C:BGM2 0.0 6.1 0.8
C8 C:BGM2 1.9 4.6 1.0
N7 C:BGM2 2.8 4.6 1.0
N9 C:BGM2 2.9 4.7 1.0
O B:HOH383 3.0 11.5 1.0
O4' C:BGM2 3.4 5.8 1.0
C1' C:BGM2 3.4 4.8 1.0
C2' C:BGM2 3.5 6.1 1.0
N3 B:U1 3.6 6.9 1.0
O2 B:U1 3.6 7.0 1.0
C5' C:BGM2 3.6 7.4 1.0
C2 B:U1 3.6 6.3 1.0
O G:HOH296 3.8 15.2 1.0
N2 G:BGM2 3.9 6.1 1.0
C5 C:BGM2 3.9 4.3 1.0
N2 A:BGM2 4.0 5.9 1.0
C4' C:BGM2 4.0 5.7 1.0
C4 C:BGM2 4.0 4.2 1.0
N7 C:A3 4.2 4.9 1.0
C3' C:BGM2 4.3 6.2 1.0
C4 B:U1 4.4 7.5 1.0
N1 B:U1 4.4 6.2 1.0
O2' B:U1 4.4 11.6 1.0
O2' C:U1 4.5 10.6 1.0
C2 G:BGM2 4.6 4.6 1.0
BR B:BGM2 4.6 6.2 0.8
N3 G:BGM2 4.6 4.4 1.0
O C:HOH235 4.7 14.3 1.0
O A:HOH311 4.8 21.4 1.0
O4 B:U1 4.8 8.5 1.0
C5 C:A3 4.8 4.3 1.0
C8 C:A3 4.8 5.2 1.0
N6 C:A3 4.9 5.3 1.0
O5' C:BGM2 5.0 8.4 1.0
C6 B:U1 5.0 7.5 1.0

Bromine binding site 4 out of 8 in 1n7a

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Bromine binding site 4 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br2

b:6.2
occ:0.80
 BR D:BGM2 0.0 6.2 0.8
C8 D:BGM2 1.9 4.8 1.0
N7 D:BGM2 2.8 4.7 1.0
N9 D:BGM2 2.9 5.4 1.0
O D:HOH384 3.0 12.6 1.0
O4' D:BGM2 3.3 6.2 1.0
C1' D:BGM2 3.4 5.6 1.0
C2' D:BGM2 3.5 6.6 1.0
N3 F:U1 3.6 8.2 1.0
C5' D:BGM2 3.6 7.5 1.0
O2 F:U1 3.6 8.1 1.0
C2 F:U1 3.7 7.8 1.0
O E:HOH371 3.7 18.9 1.0
N2 H:BGM2 3.9 5.7 1.0
C5 D:BGM2 3.9 5.2 1.0
C4' D:BGM2 3.9 6.2 1.0
N2 E:BGM2 4.0 5.8 1.0
C4 D:BGM2 4.0 5.3 1.0
N7 D:A3 4.1 5.7 1.0
O2' D:U1 4.2 11.4 1.0
C3' D:BGM2 4.3 6.2 1.0
C4 F:U1 4.3 9.4 1.0
N1 F:U1 4.5 9.3 1.0
C2 E:BGM2 4.6 5.5 1.0
N3 E:BGM2 4.6 5.5 1.0
O2' F:U1 4.6 13.8 1.0
C5 D:A3 4.7 5.2 1.0
BR F:BGM2 4.7 6.3 0.8
O4 F:U1 4.7 11.8 1.0
O H:HOH308 4.8 14.8 1.0
C8 D:A3 4.8 5.9 1.0
N6 D:A3 4.8 5.8 1.0
O5' D:BGM2 5.0 8.4 1.0

Bromine binding site 5 out of 8 in 1n7a

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Bromine binding site 5 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br2

b:6.7
occ:0.80
 BR E:BGM2 0.0 6.7 0.8
C8 E:BGM2 1.9 4.9 1.0
N7 E:BGM2 2.8 5.1 1.0
N9 E:BGM2 2.9 4.9 1.0
O A:HOH385 3.1 13.2 1.0
O4' E:BGM2 3.3 5.8 1.0
C1' E:BGM2 3.4 5.8 1.0
C2' E:BGM2 3.5 6.8 1.0
N3 A:U1 3.6 7.0 1.0
C5' E:BGM2 3.6 7.2 1.0
C2 A:U1 3.7 6.4 1.0
O2 A:U1 3.7 6.7 1.0
O D:HOH292 3.7 17.3 1.0
N2 B:BGM2 3.9 6.8 1.0
C5 E:BGM2 3.9 4.8 1.0
C4' E:BGM2 4.0 7.4 1.0
N2 D:BGM2 4.0 5.8 1.0
C4 E:BGM2 4.0 5.4 1.0
N7 E:A3 4.1 4.7 1.0
O2' E:U1 4.3 11.7 1.0
C4 A:U1 4.3 7.8 1.0
C3' E:BGM2 4.3 6.5 1.0
N1 A:U1 4.4 7.3 1.0
C2 D:BGM2 4.6 5.1 1.0
N3 D:BGM2 4.6 5.0 1.0
BR A:BGM2 4.6 6.9 0.8
O2' A:U1 4.7 10.8 1.0
O4 A:U1 4.7 8.3 1.0
O E:HOH266 4.7 17.5 1.0
C8 E:A3 4.7 5.0 1.0
C5 E:A3 4.7 3.6 1.0
O B:HOH285 4.7 18.2 1.0
N6 E:A3 4.9 4.9 1.0
O5' E:BGM2 5.0 9.0 1.0

Bromine binding site 6 out of 8 in 1n7a

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Bromine binding site 6 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br2

b:6.3
occ:0.80
 BR F:BGM2 0.0 6.3 0.8
C8 F:BGM2 1.9 5.7 1.0
N7 F:BGM2 2.8 4.9 1.0
N9 F:BGM2 2.9 5.2 1.0
O F:HOH386 3.1 12.4 1.0
O4' F:BGM2 3.3 5.9 1.0
C1' F:BGM2 3.4 5.1 1.0
C2' F:BGM2 3.5 5.4 1.0
N3 D:U1 3.6 6.3 1.0
C2 D:U1 3.6 5.5 1.0
O2 D:U1 3.6 5.7 1.0
C5' F:BGM2 3.6 7.7 1.0
O H:HOH308 3.8 14.8 1.0
C5 F:BGM2 3.9 4.9 1.0
C4' F:BGM2 3.9 7.0 1.0
N2 E:BGM2 3.9 5.8 1.0
N2 H:BGM2 4.0 5.7 1.0
C4 F:BGM2 4.0 4.5 1.0
N7 F:A3 4.2 3.8 1.0
C3' F:BGM2 4.3 5.2 1.0
O2' F:U1 4.3 13.8 1.0
C4 D:U1 4.3 6.1 1.0
N1 D:U1 4.4 5.5 1.0
O2' D:U1 4.5 11.4 1.0
C2 H:BGM2 4.6 4.1 1.0
N3 H:BGM2 4.6 4.7 1.0
O E:HOH371 4.6 18.9 1.0
BR D:BGM2 4.7 6.2 0.8
O F:HOH247 4.7 14.8 1.0
C5 F:A3 4.8 3.3 1.0
O4 D:U1 4.8 7.3 1.0
C8 F:A3 4.8 3.8 1.0
N6 F:A3 4.9 4.8 1.0
C6 D:U1 5.0 7.3 1.0
O5' F:BGM2 5.0 8.7 1.0

Bromine binding site 7 out of 8 in 1n7a

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Bromine binding site 7 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Br2

b:6.0
occ:0.80
 BR G:BGM2 0.0 6.0 0.8
C8 G:BGM2 1.9 5.1 1.0
N7 G:BGM2 2.8 4.8 1.0
N9 G:BGM2 2.9 4.7 1.0
O H:HOH387 3.0 9.6 1.0
O4' G:BGM2 3.4 6.5 1.0
C1' G:BGM2 3.4 5.0 1.0
C2' G:BGM2 3.5 5.4 1.0
C5' G:BGM2 3.6 7.5 1.0
N3 H:U1 3.6 5.2 1.0
O2 H:U1 3.7 6.2 1.0
C2 H:U1 3.7 5.4 1.0
O C:HOH315 3.8 20.7 1.0
C5 G:BGM2 3.9 4.2 1.0
N2 F:BGM2 3.9 6.2 1.0
C4' G:BGM2 3.9 7.3 1.0
C4 G:BGM2 4.0 3.6 1.0
N2 C:BGM2 4.0 6.4 1.0
N7 G:A3 4.1 5.0 1.0
C3' G:BGM2 4.3 6.7 1.0
O2' G:U1 4.4 9.9 1.0
C4 H:U1 4.4 7.2 1.0
N1 H:U1 4.4 6.1 1.0
C2 C:BGM2 4.6 4.6 1.0
O2' H:U1 4.6 8.9 1.0
N3 C:BGM2 4.6 4.7 1.0
O G:HOH229 4.6 14.4 1.0
C5 G:A3 4.6 3.9 1.0
O F:HOH228 4.7 12.6 1.0
BR H:BGM2 4.7 5.5 0.8
C8 G:A3 4.8 4.8 1.0
N6 G:A3 4.8 5.5 1.0
O4 H:U1 4.9 7.7 1.0
O5' G:BGM2 4.9 7.9 1.0
C6 G:A3 5.0 3.4 1.0

Bromine binding site 8 out of 8 in 1n7a

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Bromine binding site 8 out of 8 in the Rip-Radiation-Damage Induced Phasing


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Rip-Radiation-Damage Induced Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br2

b:5.5
occ:0.80
 BR H:BGM2 0.0 5.5 0.8
C8 H:BGM2 1.9 4.3 1.0
N7 H:BGM2 2.8 4.2 1.0
N9 H:BGM2 2.9 4.2 1.0
O G:HOH388 3.1 8.8 1.0
O4' H:BGM2 3.4 4.8 1.0
C1' H:BGM2 3.4 4.7 1.0
C2' H:BGM2 3.5 6.2 1.0
C5' H:BGM2 3.6 6.4 1.0
O2 G:U1 3.6 6.2 1.0
C2 G:U1 3.6 6.0 1.0
N3 G:U1 3.6 7.0 1.0
O F:HOH228 3.8 12.6 1.0
C5 H:BGM2 3.9 4.2 1.0
N2 C:BGM2 3.9 6.4 1.0
C4' H:BGM2 3.9 5.8 1.0
N2 F:BGM2 4.0 6.2 1.0
C4 H:BGM2 4.0 4.8 1.0
N7 H:A3 4.2 6.0 1.0
C3' H:BGM2 4.3 5.6 1.0
N1 G:U1 4.4 7.0 1.0
C4 G:U1 4.4 7.5 1.0
O2' H:U1 4.5 8.9 1.0
O2' G:U1 4.5 9.9 1.0
O H:HOH219 4.6 12.6 1.0
C2 F:BGM2 4.6 5.0 1.0
N3 F:BGM2 4.6 5.1 1.0
BR G:BGM2 4.7 6.0 0.8
C5 H:A3 4.7 4.5 1.0
C8 H:A3 4.8 5.9 1.0
O C:HOH315 4.8 20.7 1.0
N6 H:A3 4.9 5.7 1.0
O4 G:U1 4.9 9.1 1.0
O5' H:BGM2 4.9 7.3 1.0
C1' G:U1 5.0 6.4 1.0

Reference:

R.B.G.Ravelli, H.-K.S.Leiros, B.Pan, M.Caffrey, S.Mcsweeney. Specific Radiation-Damage Can Be Used to Solve Macromolecular Crystal Structures Structure V. 11 217 2003.
ISSN: ISSN 0969-2126
PubMed: 12575941
DOI: 10.1016/S0969-2126(03)00006-6
Page generated: Wed Jul 10 17:00:05 2024

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