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Bromine in PDB 2x3h: Coliphage K5A Lyase

Enzymatic activity of Coliphage K5A Lyase

All present enzymatic activity of Coliphage K5A Lyase:
4.2.2.7;

Protein crystallography data

The structure of Coliphage K5A Lyase, PDB code: 2x3h was solved by J.E.Thompson, M.Pourhossein, M.Goldrick, T.Hudson, J.P.Derrick, I.S.Roberts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.18 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.530, 130.400, 145.740, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.3

Bromine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Bromine atom in the Coliphage K5A Lyase (pdb code 2x3h). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 12 binding sites of Bromine where determined in the Coliphage K5A Lyase, PDB code: 2x3h:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 12 in 2x3h

Go back to Bromine Binding Sites List in 2x3h
Bromine binding site 1 out of 12 in the Coliphage K5A Lyase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Coliphage K5A Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1505

b:11.7
occ:1.00
 N A:ASP424 3.4 6.5 1.0
NZ B:LYS418 3.4 5.2 1.0
CE B:LYS418 3.8 4.3 1.0
CB A:ILE403 3.8 5.1 1.0
O A:ASP424 3.9 6.9 1.0
CA A:GLY423 4.0 4.8 1.0
CD A:LYS404 4.0 9.5 1.0
CD B:LYS418 4.1 3.5 1.0
CG2 A:ILE403 4.1 6.5 1.0
CG A:LYS404 4.1 7.4 1.0
CB A:ASP424 4.1 9.9 1.0
C A:GLY423 4.2 6.0 1.0
CA A:ASP424 4.2 8.2 1.0
CG1 A:ILE403 4.3 4.2 1.0
C A:ASP424 4.4 7.1 1.0
CE A:LYS404 4.7 13.7 1.0
CG A:ASP424 4.9 12.8 1.0
CA A:ILE403 5.0 4.9 1.0

Bromine binding site 2 out of 12 in 2x3h

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Bromine binding site 2 out of 12 in the Coliphage K5A Lyase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Coliphage K5A Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1506

b:18.4
occ:1.00
 O A:HOH2008 3.1 15.4 1.0
O B:HOH2005 3.2 10.7 1.0
O B:HOH2004 3.2 13.2 1.0
N A:LYS15 3.3 10.6 1.0
CA A:LYS15 3.8 11.8 1.0
C A:HIS14 4.3 9.8 1.0
CE1 B:TYR20 4.4 11.1 1.0
CD1 B:TYR20 4.4 10.5 1.0
CA A:HIS14 4.5 8.7 1.0
CD B:LYS8 4.6 16.1 1.0
CG A:LYS15 4.6 14.8 1.0
N A:GLY16 4.7 13.1 1.0
C A:LYS15 4.8 12.9 1.0
OE1 B:GLU10 4.9 12.0 1.0
CE B:LYS8 4.9 17.8 1.0
CB A:LYS15 4.9 13.0 1.0
CG B:LYS8 5.0 14.6 1.0

Bromine binding site 3 out of 12 in 2x3h

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Bromine binding site 3 out of 12 in the Coliphage K5A Lyase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Coliphage K5A Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1507

b:28.1
occ:1.00
 O A:HOH2228 2.8 16.7 1.0
OG A:SER436 3.1 8.5 1.0
O B:VAL427 3.6 8.1 1.0
O A:SER436 3.6 5.0 1.0
CG A:GLN438 3.6 4.9 1.0
C A:SER436 3.7 5.1 1.0
N B:VAL427 3.7 5.6 1.0
CB B:ALA426 3.8 5.4 1.0
CD A:GLN438 3.8 6.1 1.0
N A:SER437 3.8 4.4 1.0
CB A:SER436 3.9 6.8 1.0
C B:VAL427 3.9 5.8 1.0
OE1 A:GLN438 4.0 8.2 1.0
CA A:SER437 4.0 4.8 1.0
CA B:ALA426 4.0 5.2 1.0
C A:SER437 4.1 4.4 1.0
N A:GLN438 4.1 4.3 1.0
C B:ALA426 4.2 5.4 1.0
CB A:GLN438 4.3 4.0 1.0
NE2 A:GLN438 4.4 5.8 1.0
CA A:SER436 4.4 5.7 1.0
N B:SER428 4.4 4.7 1.0
CB B:SER428 4.5 5.8 1.0
CA B:VAL427 4.5 5.8 1.0
CA B:SER428 4.7 4.3 1.0
O A:SER437 4.7 5.7 1.0
O A:HOH2237 4.7 14.4 1.0
CA A:GLN438 4.8 3.6 1.0

Bromine binding site 4 out of 12 in 2x3h

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Bromine binding site 4 out of 12 in the Coliphage K5A Lyase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Coliphage K5A Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1508

b:26.1
occ:1.00
 O A:HOH2118 3.0 21.0 1.0
O A:HOH2119 3.1 16.0 1.0
O A:HOH2134 3.2 13.2 1.0
N A:THR232 3.5 7.7 1.0
O A:THR232 3.8 9.9 1.0
CA A:GLY231 3.8 5.9 1.0
CE A:LYS260 4.0 17.2 1.0
CG2 A:THR232 4.1 8.0 1.0
C A:GLY231 4.1 6.4 1.0
CD A:LYS260 4.2 14.9 1.0
CG A:LYS260 4.4 12.9 1.0
CA A:THR232 4.5 8.4 1.0
O A:ASN230 4.5 6.5 1.0
NZ A:LYS260 4.5 19.2 1.0
C A:THR232 4.6 9.4 1.0
OH A:TYR229 4.7 11.6 1.0
CB A:THR232 4.9 8.4 1.0
O A:HOH2145 5.0 12.2 1.0

Bromine binding site 5 out of 12 in 2x3h

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Bromine binding site 5 out of 12 in the Coliphage K5A Lyase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Coliphage K5A Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1509

b:25.9
occ:1.00
 O A:HOH2149 2.9 13.7 1.0
N A:SER334 3.3 6.6 1.0
O A:HOH2055 3.4 16.7 1.0
O A:CYS301 3.6 8.9 1.0
OG A:SER334 3.6 9.5 1.0
CA A:TYR333 3.7 5.3 1.0
CB A:ASP302 3.7 10.9 1.0
C A:CYS301 3.8 8.0 1.0
CB A:TYR333 3.9 5.0 1.0
C A:TYR333 4.0 6.1 1.0
CA A:ASP302 4.0 9.5 1.0
N A:ASP302 4.0 8.5 1.0
CB A:SER334 4.1 8.8 1.0
N A:CYS301 4.2 7.5 1.0
CA A:SER334 4.3 7.0 1.0
CA A:CYS301 4.6 7.5 1.0
N A:GLY300 4.7 5.7 1.0
C A:GLY300 4.7 7.1 1.0
CA A:GLY300 4.8 6.5 1.0
O A:SER332 4.9 7.0 1.0
CG A:ASP302 4.9 12.5 1.0
N A:TYR333 5.0 6.3 1.0

Bromine binding site 6 out of 12 in 2x3h

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Bromine binding site 6 out of 12 in the Coliphage K5A Lyase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Coliphage K5A Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1505

b:17.2
occ:1.00
 N B:ASP424 3.4 7.5 1.0
NZ C:LYS418 3.4 5.8 1.0
CE C:LYS418 3.7 4.9 1.0
CB B:ILE403 3.8 4.0 1.0
CD B:LYS404 3.9 12.4 1.0
O B:ASP424 3.9 7.6 1.0
CG2 B:ILE403 3.9 5.7 1.0
CA B:GLY423 4.0 5.3 1.0
CD C:LYS418 4.0 4.7 1.0
CG B:LYS404 4.1 9.0 1.0
C B:GLY423 4.2 5.9 1.0
CA B:ASP424 4.3 9.2 1.0
CG1 B:ILE403 4.3 4.9 1.0
OD1 B:ASP424 4.4 21.9 1.0
C B:ASP424 4.4 8.3 1.0
CB B:ASP424 4.5 14.3 1.0
CE B:MET406 4.8 14.5 1.0
CE B:LYS404 4.8 16.6 1.0
CG B:ASP424 4.9 17.4 1.0

Bromine binding site 7 out of 12 in 2x3h

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Bromine binding site 7 out of 12 in the Coliphage K5A Lyase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Coliphage K5A Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1506

b:20.4
occ:1.00
 O B:HOH2126 3.3 16.0 1.0
O B:HOH2129 3.3 19.9 1.0
O B:HOH2128 3.3 8.9 1.0
N B:THR232 3.4 7.2 1.0
O B:HOH2144 3.7 20.7 1.0
O B:THR232 3.8 9.5 1.0
CA B:GLY231 3.8 6.6 1.0
CE B:LYS260 4.0 13.3 1.0
C B:GLY231 4.0 6.3 1.0
CG2 B:THR232 4.1 9.1 1.0
CD B:LYS260 4.1 10.6 1.0
NZ B:LYS260 4.2 15.5 1.0
CA B:THR232 4.4 7.9 1.0
O B:ASN230 4.5 7.5 1.0
CG B:LYS260 4.5 9.2 1.0
C B:THR232 4.6 9.1 1.0
CB B:THR232 4.8 8.1 1.0
OH B:TYR229 4.8 12.0 1.0
N B:GLY231 5.0 6.2 1.0

Bromine binding site 8 out of 12 in 2x3h

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Bromine binding site 8 out of 12 in the Coliphage K5A Lyase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Coliphage K5A Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br1505

b:18.6
occ:1.00
 O C:HOH2116 3.2 11.5 1.0
O C:HOH2130 3.3 8.1 1.0
O C:HOH2115 3.4 18.3 1.0
N C:THR232 3.6 6.3 1.0
CA C:GLY231 3.9 6.2 1.0
O C:THR232 3.9 7.7 1.0
CE C:LYS260 4.0 15.8 1.0
C C:GLY231 4.2 6.1 1.0
CD C:LYS260 4.2 13.3 1.0
CG2 C:THR232 4.2 7.4 1.0
CG C:LYS260 4.3 11.3 1.0
O C:ASN230 4.5 6.8 1.0
CA C:THR232 4.5 7.3 1.0
C C:THR232 4.7 8.6 1.0
OH C:TYR229 4.8 10.6 1.0
NZ C:LYS260 4.9 17.0 1.0
CB C:THR232 4.9 7.7 1.0
O C:HOH2147 4.9 11.5 1.0

Bromine binding site 9 out of 12 in 2x3h

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Bromine binding site 9 out of 12 in the Coliphage K5A Lyase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Coliphage K5A Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br1506

b:23.1
occ:1.00
 N C:GLY337 3.3 6.7 1.0
N C:ALA313 3.4 6.0 1.0
CA C:THR312 3.7 5.5 1.0
CA C:GLY337 3.9 5.3 1.0
CB C:THR312 4.0 6.1 1.0
N C:THR336 4.0 5.3 1.0
O C:HOH2178 4.0 11.7 1.0
C C:THR312 4.1 5.4 1.0
O C:ALA313 4.3 5.8 1.0
CG2 C:THR312 4.3 7.8 1.0
C C:THR336 4.3 6.9 1.0
CB C:ALA335 4.4 6.0 1.0
NH2 C:ARG310 4.4 19.9 1.0
CA C:THR336 4.4 6.8 1.0
CB C:THR336 4.5 8.3 1.0
CA C:ALA313 4.5 5.8 1.0
O C:GLN311 4.6 6.8 1.0
CB C:ALA313 4.6 7.0 1.0
C C:ALA335 4.7 5.4 1.0
C C:ALA313 4.8 6.2 1.0
N C:THR312 4.9 5.8 1.0
CA C:ALA335 5.0 5.2 1.0

Bromine binding site 10 out of 12 in 2x3h

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Bromine binding site 10 out of 12 in the Coliphage K5A Lyase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Coliphage K5A Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br1507

b:25.5
occ:1.00
 O C:HOH2223 3.0 22.0 1.0
N C:ASP424 3.3 9.8 1.0
NZ A:LYS418 3.4 9.1 1.0
CE A:LYS418 3.6 9.2 1.0
O C:ASP424 3.7 9.3 1.0
CD C:LYS404 3.8 14.5 1.0
CB C:ILE403 3.8 6.4 1.0
CA C:GLY423 3.8 6.7 1.0
CG2 C:ILE403 3.9 7.5 1.0
CD A:LYS418 4.0 8.0 1.0
C C:GLY423 4.0 8.3 1.0
CG C:LYS404 4.1 11.1 1.0
CA C:ASP424 4.2 11.1 1.0
C C:ASP424 4.3 9.8 1.0
CG1 C:ILE403 4.3 6.7 1.0
CB C:ASP424 4.5 15.7 1.0
CE C:LYS404 4.8 17.6 1.0
CB C:LYS404 5.0 8.4 1.0

Reference:

J.E.Thompson, M.Pourhossein, A.Waterhouse, T.Hudson, M.Goldrick, J.P.Derrick, I.S.Roberts. The K5 Lyase Kfla Combines A Viral Tail Spike Structure with A Bacterial Polysaccharide Lyase Mechanism. J.Biol.Chem. V. 285 23963 2010.
ISSN: ISSN 0021-9258
PubMed: 20519506
DOI: 10.1074/JBC.M110.127571
Page generated: Wed Jul 10 18:54:43 2024

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