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Bromine in PDB 1f5m: Structure of the Gaf Domain

Protein crystallography data

The structure of Structure of the Gaf Domain, PDB code: 1f5m was solved by Y.S.Ho, L.M.Burden, J.H.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 500.00 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.640, 73.640, 162.480, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 24.6

Bromine Binding Sites:

The binding sites of Bromine atom in the Structure of the Gaf Domain (pdb code 1f5m). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the Structure of the Gaf Domain, PDB code: 1f5m:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 1f5m

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Bromine binding site 1 out of 9 in the Structure of the Gaf Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of the Gaf Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br501

b:43.0
occ:1.00
CG A:PRO120 3.7 23.4 1.0
O A:LYS118 3.9 24.9 1.0
C A:LYS118 4.0 22.6 1.0
CD A:PRO120 4.0 23.8 1.0
CA A:LYS118 4.2 22.1 1.0
N A:PRO120 4.2 23.8 1.0
N A:TYR119 4.5 23.9 1.0
O A:ASN117 4.6 25.1 1.0
CA A:PRO120 4.6 25.1 1.0
CB A:PRO120 4.7 23.3 1.0
C A:TYR119 4.7 23.5 1.0

Bromine binding site 2 out of 9 in 1f5m

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Bromine binding site 2 out of 9 in the Structure of the Gaf Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of the Gaf Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br503

b:61.2
occ:1.00
O A:HOH644 2.8 41.9 1.0
N A:GLN95 3.4 26.5 1.0
O A:HOH663 3.5 36.8 1.0
CG A:GLN95 3.8 35.1 1.0
CB A:LYS98 3.9 26.4 1.0
CB A:GLN95 3.9 28.9 1.0
O A:HOH566 3.9 34.9 1.0
CD1 A:ILE123 4.0 29.2 1.0
CG A:LYS98 4.0 27.3 1.0
CA A:ILE94 4.1 24.5 1.0
C A:ILE94 4.2 26.9 1.0
CA A:GLN95 4.2 27.3 1.0
O A:MET93 4.5 27.3 1.0
CG2 A:ILE94 4.6 19.7 1.0
O A:HOH638 4.7 42.9 1.0
O A:GLN95 4.9 24.7 1.0
CB A:ILE94 4.9 23.2 1.0
CD A:GLN95 4.9 39.0 1.0

Bromine binding site 3 out of 9 in 1f5m

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Bromine binding site 3 out of 9 in the Structure of the Gaf Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of the Gaf Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br505

b:95.7
occ:1.00
O A:HOH516 3.1 26.5 1.0
OD1 A:ASN174 3.3 25.5 1.0
CG A:LYS175 3.6 34.8 1.0
O A:LYS171 3.7 25.8 1.0
CA A:LYS171 3.9 26.7 1.0
CD A:LYS175 4.1 41.0 1.0
CB A:LYS171 4.1 26.3 1.0
CG A:LYS171 4.1 32.2 1.0
CB A:ASN174 4.2 20.3 1.0
CG A:ASN174 4.2 21.1 1.0
C A:LYS171 4.2 26.1 1.0
CE A:LYS175 4.4 42.0 1.0
OD1 A:ASN140 4.6 33.1 1.0
O A:HOH599 4.6 45.9 1.0
N A:LYS175 4.8 25.5 1.0
O A:ILE138 4.8 29.8 1.0
CB A:LYS175 4.9 31.6 1.0

Bromine binding site 4 out of 9 in 1f5m

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Bromine binding site 4 out of 9 in the Structure of the Gaf Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of the Gaf Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br507

b:67.5
occ:1.00
O A:HOH605 3.1 40.4 1.0
N A:THR144 3.1 29.3 1.0
O A:HOH539 3.2 28.0 1.0
CA A:LYS143 3.7 34.1 1.0
ND2 A:ASN78 3.7 53.4 1.0
CB A:LYS143 3.8 35.2 1.0
C A:LYS143 3.9 32.8 1.0
CE A:LYS108 3.9 32.1 1.0
CB A:THR144 4.0 27.9 1.0
CA A:THR144 4.1 27.7 1.0
CE A:LYS143 4.1 42.8 1.0
CD A:LYS143 4.2 41.8 1.0
OG1 A:THR144 4.2 24.9 1.0
NZ A:LYS108 4.3 36.0 1.0
CE2 A:PHE96 4.3 26.8 1.0
O A:THR144 4.5 27.9 1.0
CG A:LYS143 4.6 39.3 1.0
C A:THR144 4.8 26.2 1.0
CD A:LYS108 4.9 29.0 1.0
O A:ALA105 4.9 25.8 1.0

Bromine binding site 5 out of 9 in 1f5m

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Bromine binding site 5 out of 9 in the Structure of the Gaf Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Structure of the Gaf Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br502

b:51.1
occ:1.00
N B:SER16 3.6 37.1 1.0
CB B:TYR15 3.7 37.2 1.0
CA B:TYR15 3.9 36.4 1.0
CD1 B:LEU19 4.3 35.7 1.0
CD2 B:LEU19 4.3 34.7 1.0
C B:TYR15 4.3 36.9 1.0
CB B:SER16 4.4 36.4 1.0
CG B:LEU19 4.5 36.0 1.0
CA B:SER16 4.6 38.3 1.0
O B:HOH593 4.8 36.7 1.0
OG B:SER16 4.9 38.6 1.0

Bromine binding site 6 out of 9 in 1f5m

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Bromine binding site 6 out of 9 in the Structure of the Gaf Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Structure of the Gaf Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br504

b:63.4
occ:1.00
N B:GLN95 3.3 30.0 1.0
CB B:GLN95 3.7 34.4 1.0
CD1 B:ILE123 3.7 26.6 1.0
O B:HOH622 3.8 47.6 1.0
O B:HOH602 3.9 44.9 1.0
CA B:ILE94 4.0 24.9 1.0
C B:ILE94 4.1 27.7 1.0
CA B:GLN95 4.1 29.8 1.0
CB B:LYS98 4.2 28.3 1.0
CG2 B:ILE94 4.5 21.1 1.0
O B:MET93 4.5 23.1 1.0
CG B:LYS98 4.6 31.5 1.0
O B:HOH660 4.6 50.6 1.0
O B:GLN95 4.8 27.5 1.0
CB B:ILE94 4.8 23.2 1.0
CG B:GLN95 5.0 40.4 1.0
N B:ILE94 5.0 24.6 1.0

Bromine binding site 7 out of 9 in 1f5m

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Bromine binding site 7 out of 9 in the Structure of the Gaf Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Structure of the Gaf Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br506

b:74.8
occ:1.00
O B:HOH518 3.0 24.7 1.0
O B:HOH633 4.3 41.2 1.0
O B:HOH650 4.4 37.3 1.0
CB B:ASP159 4.6 24.1 1.0
O B:HOH671 4.7 25.9 1.0
OD1 B:ASP159 4.9 26.2 1.0

Bromine binding site 8 out of 9 in 1f5m

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Bromine binding site 8 out of 9 in the Structure of the Gaf Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Structure of the Gaf Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br508

b:89.0
occ:1.00
O B:HOH570 3.0 28.6 1.0
OE2 B:GLU22 3.2 43.6 1.0
CD B:LYS21 3.6 28.7 1.0
CG2 B:VAL161 3.9 26.5 1.0
O B:HOH585 4.1 40.7 1.0
CG1 B:VAL161 4.1 27.0 1.0
CB B:VAL161 4.2 24.4 1.0
CG B:LYS21 4.3 29.5 1.0
CB B:LYS21 4.3 33.1 1.0
CD B:GLU22 4.4 46.1 1.0
O B:HOH590 4.4 30.4 1.0
CE B:LYS21 4.5 27.9 1.0
NZ B:LYS21 4.6 21.9 1.0

Bromine binding site 9 out of 9 in 1f5m

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Bromine binding site 9 out of 9 in the Structure of the Gaf Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Structure of the Gaf Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br509

b:94.5
occ:1.00
O B:HOH569 2.9 28.3 1.0
CD1 B:LEU29 3.9 23.5 1.0
CB B:LYS168 3.9 26.1 1.0
CD1 B:LEU172 4.0 21.8 1.0
CG B:LEU172 4.1 24.8 1.0
CD2 B:LEU172 4.3 27.5 1.0
CG B:LYS168 4.3 28.3 1.0
CD B:LYS168 4.4 30.9 1.0
O B:LYS168 4.5 24.4 1.0
O B:HOH530 4.7 37.3 1.0
CG B:LEU29 4.7 23.9 1.0
CD2 B:LEU29 4.7 22.3 1.0
CB B:LEU29 4.7 23.4 1.0
C B:LYS168 4.8 25.5 1.0
CA B:LYS168 4.8 24.9 1.0

Reference:

Y.S.Ho, L.M.Burden, J.H.Hurley. Structure of the Gaf Domain, A Ubiquitous Signaling Motif and A New Class of Cyclic Gmp Receptor. Embo J. V. 19 5288 2000.
ISSN: ISSN 0261-4189
PubMed: 11032796
DOI: 10.1093/EMBOJ/19.20.5288
Page generated: Sat Dec 12 02:00:39 2020

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