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Bromine in PDB 4yem: Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement

Enzymatic activity of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement

All present enzymatic activity of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement:
3.2.1.17;

Protein crystallography data

The structure of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement, PDB code: 4yem was solved by I.G.Shabalin, Z.Dauter, M.Jaskolski, W.Minor, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.29 / 1.47
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.580, 78.580, 37.290, 90.00, 90.00, 90.00
R / Rfree (%) 10.5 / 15.6

Other elements in 4yem:

The structure of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement also contains other interesting chemical elements:

Platinum (Pt) 3 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Bromine atom in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement (pdb code 4yem). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 19 binding sites of Bromine where determined in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement, PDB code: 4yem:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 19 in 4yem

Go back to Bromine Binding Sites List in 4yem
Bromine binding site 1 out of 19 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br202

b:19.4
occ:0.85
 PT A:PT201 2.5 17.3 0.8
ND1 A:HIS15 3.2 19.3 1.0
OD1 A:ASN93 3.5 18.0 0.6
CL A:CL223 3.5 29.6 0.8
BR A:BR204 3.5 23.3 0.1
CB A:HIS15 3.7 12.8 1.0
CG A:HIS15 3.7 13.5 1.0
CG A:ASN93 3.8 14.4 0.6
CG2 A:THR89 3.8 11.8 1.0
CG1 A:VAL92 3.8 13.9 1.0
O A:THR89 3.9 10.2 1.0
CB A:VAL92 4.0 10.2 1.0
ND2 A:ASN93 4.0 17.5 0.6
O A:HIS15 4.0 15.7 1.0
CE1 A:HIS15 4.1 18.6 1.0
CA A:THR89 4.1 10.4 1.0
N A:ASN93 4.3 9.7 1.0
O A:HOH301 4.4 26.9 1.0
NZ A:LYS96 4.4 18.2 1.0
CA A:HIS15 4.4 12.7 1.0
CB A:THR89 4.4 11.5 1.0
C A:THR89 4.5 10.5 1.0
CB A:ASN93 4.7 13.0 0.4
C A:HIS15 4.7 13.8 1.0
OG1 A:THR89 4.7 14.1 1.0
CA A:ASN93 4.8 10.6 0.4
CD2 A:HIS15 4.8 14.0 1.0
CB A:ASN93 4.8 12.7 0.6
CA A:ASN93 4.8 10.2 0.6
C A:VAL92 4.8 10.1 1.0
BR A:BR203 4.9 23.9 0.8
CA A:VAL92 5.0 9.4 1.0
NE2 A:HIS15 5.0 18.5 1.0
CG2 A:VAL92 5.0 11.7 1.0

Bromine binding site 2 out of 19 in 4yem

Go back to Bromine Binding Sites List in 4yem
Bromine binding site 2 out of 19 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br203

b:23.9
occ:0.85
 PT A:PT201 2.5 17.3 0.8
ND1 A:HIS15 3.2 19.3 1.0
CL A:CL223 3.4 29.6 0.8
NH1 A:ARG14 3.6 26.3 1.0
CE1 A:HIS15 3.6 18.6 1.0
O A:HOH330 3.7 30.2 1.0
O A:ARG14 3.8 16.1 1.0
CA A:HIS15 4.0 12.7 1.0
CG A:HIS15 4.1 13.5 1.0
CG A:ARG14 4.3 19.4 1.0
C A:ARG14 4.3 12.6 1.0
BR A:BR204 4.4 23.3 0.1
CZ A:ARG14 4.4 23.4 1.0
N A:HIS15 4.5 12.3 1.0
O A:HOH321 4.5 28.9 1.0
O A:HOH368 4.6 32.5 1.0
CB A:HIS15 4.6 12.8 1.0
NE2 A:HIS15 4.6 18.5 1.0
CD2 A:HIS15 4.9 14.0 1.0
BR A:BR202 4.9 19.4 0.8
NE A:ARG14 5.0 25.5 1.0

Bromine binding site 3 out of 19 in 4yem

Go back to Bromine Binding Sites List in 4yem
Bromine binding site 3 out of 19 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br204

b:23.3
occ:0.15
 CL A:CL223 1.4 29.6 0.8
PT A:PT201 3.1 17.3 0.8
O A:HOH301 3.4 26.9 1.0
BR A:BR202 3.5 19.4 0.8
PT A:PT218 3.7 17.0 0.1
NZ A:LYS96 3.8 18.2 1.0
O A:HIS15 4.0 15.7 1.0
BR A:BR203 4.4 23.9 0.8
OD1 A:ASN93 4.5 18.0 0.6
C A:HIS15 4.7 13.8 1.0
CA A:HIS15 4.9 12.7 1.0

Bromine binding site 4 out of 19 in 4yem

Go back to Bromine Binding Sites List in 4yem
Bromine binding site 4 out of 19 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br205

b:19.9
occ:0.60
 PT A:PT224 2.1 21.1 0.1
O A:HOH318 3.3 26.4 0.7
N A:ILE88 3.5 10.9 1.0
CG1 A:ILE88 3.7 12.8 1.0
NE2 A:HIS15 3.7 18.5 1.0
O A:HOH435 3.9 24.9 1.0
CA A:ASP87 4.0 13.1 1.0
OD1 A:ASP87 4.0 18.2 1.0
NH2 A:ARG14 4.1 27.4 1.0
CB A:ALA11 4.2 11.6 1.0
C A:ASP87 4.2 12.8 1.0
O A:SER86 4.3 15.4 1.0
CD2 A:HIS15 4.3 14.0 1.0
CB A:ILE88 4.4 10.9 1.0
CA A:ILE88 4.4 10.7 1.0
CZ A:PHE3 4.5 14.1 1.0
CG2 A:ILE88 4.5 12.8 1.0
CG A:ASP87 4.6 20.5 1.0
CD1 A:ILE88 4.6 13.1 1.0
CB A:ASP87 4.8 16.1 1.0
CE1 A:HIS15 4.8 18.6 1.0
CE2 A:PHE3 5.0 12.8 1.0

Bromine binding site 5 out of 19 in 4yem

Go back to Bromine Binding Sites List in 4yem
Bromine binding site 5 out of 19 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br206

b:10.8
occ:0.80
 OH A:TYR23 3.2 8.7 1.0
O A:HOH328 3.4 12.2 1.0
CE2 A:TYR23 3.8 6.8 1.0
CZ A:TYR23 3.8 7.3 1.0
CA A:GLY104 4.1 7.6 1.0
O A:ARG21 4.6 11.0 1.0
N A:GLY104 4.7 8.9 1.0
CD2 A:TYR23 5.0 7.4 1.0

Bromine binding site 6 out of 19 in 4yem

Go back to Bromine Binding Sites List in 4yem
Bromine binding site 6 out of 19 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br207

b:15.0
occ:0.80
 O A:HOH468 3.2 41.4 1.0
OG A:SER24 3.2 13.4 1.0
N A:GLY26 3.3 8.9 1.0
CB A:SER24 3.6 12.1 1.0
CA A:GLY26 3.6 9.9 1.0
CA A:GLN121 3.7 14.5 1.0
CD1 A:ILE124 3.8 23.6 1.0
CB A:GLN121 3.9 19.5 1.0
N A:GLN121 4.0 13.5 1.0
CG A:GLN121 4.1 24.1 1.0
CG1 A:ILE124 4.2 17.1 1.0
N A:LEU25 4.3 8.6 1.0
CG2 A:VAL120 4.3 13.9 1.0
C A:VAL120 4.4 13.3 1.0
O A:VAL120 4.4 11.7 1.0
C A:SER24 4.5 9.5 1.0
C A:LEU25 4.5 8.7 1.0
CA A:SER24 4.6 9.6 1.0
C A:GLY26 4.7 8.3 1.0
CA A:LEU25 4.8 9.0 1.0
N A:ASN27 4.9 7.8 1.0
C A:GLN121 4.9 12.9 1.0
O A:SER24 4.9 10.2 1.0

Bromine binding site 7 out of 19 in 4yem

Go back to Bromine Binding Sites List in 4yem
Bromine binding site 7 out of 19 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br208

b:19.3
occ:0.80
 O A:HOH412 3.3 10.4 1.0
O A:THR69 3.4 10.8 1.0
N A:THR69 3.5 9.3 1.0
OG A:SER72 3.5 11.5 1.0
C A:GLY67 3.7 11.3 1.0
OD1 A:ASN65 3.7 15.9 1.0
N A:ARG68 3.7 9.4 1.0
CA A:GLY67 3.8 11.5 1.0
N A:GLY67 3.9 10.4 1.0
C A:THR69 3.9 10.1 1.0
BR A:BR212 3.9 31.6 0.4
O A:HOH419 4.0 12.7 1.0
CA A:THR69 4.1 9.4 1.0
O A:GLY67 4.3 14.2 1.0
C A:ARG68 4.5 11.4 1.0
CB A:THR69 4.5 9.5 1.0
OD1 A:ASP66 4.5 8.7 1.0
CA A:ARG68 4.5 10.4 0.5
CA A:ARG68 4.6 10.4 0.5
N A:PRO70 4.7 11.9 1.0
O A:HOH363 4.7 15.0 0.5
NA A:NA219 4.8 10.6 1.0
CB A:SER72 4.8 10.8 1.0
CG A:ASN65 4.9 11.2 1.0
C A:ASP66 5.0 10.1 1.0

Bromine binding site 8 out of 19 in 4yem

Go back to Bromine Binding Sites List in 4yem
Bromine binding site 8 out of 19 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br209

b:27.3
occ:0.35
 O A:HOH335 3.1 21.1 1.0
O A:HOH318 3.6 26.4 0.7
CB A:ALA10 4.1 13.9 1.0
C A:ALA10 4.2 10.6 1.0
O A:ALA10 4.2 11.1 1.0
N A:ALA11 4.2 10.7 1.0
CA A:ALA11 4.4 11.4 1.0
CD A:ARG14 4.4 23.3 1.0
NE A:ARG14 4.4 25.5 1.0
O A:HOH331 4.7 17.9 1.0
CA A:ALA10 4.8 11.2 1.0
CB A:ARG14 4.9 16.8 1.0
CB A:ALA11 4.9 11.6 1.0

Bromine binding site 9 out of 19 in 4yem

Go back to Bromine Binding Sites List in 4yem
Bromine binding site 9 out of 19 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br210

b:19.0
occ:0.25
 BR A:BR210 0.0 19.0 0.2
BR A:BR210 1.8 26.4 0.3
C2 A:DMS220 3.4 29.5 1.0
NE1 A:TRP63 3.4 11.0 1.0
O A:HOH442 3.7 25.5 0.6
O A:HOH342 3.9 39.6 1.0
OD2 A:ASP101 3.9 24.6 0.4
CZ2 A:TRP63 4.0 10.8 1.0
O A:HOH370 4.0 47.7 1.0
CE2 A:TRP63 4.0 10.2 1.0
CB A:ALA107 4.3 10.8 1.0
O A:HOH399 4.6 31.7 0.5
CD1 A:TRP63 4.6 10.5 1.0
CG2 A:ILE98 4.7 10.4 1.0
S A:DMS220 4.7 27.8 1.0
O A:HOH430 4.9 18.6 1.0
CA A:ALA107 4.9 8.7 1.0
OD2 A:ASP101 4.9 21.9 0.6
O A:DMS220 5.0 15.6 1.0
O A:ALA107 5.0 11.4 1.0

Bromine binding site 10 out of 19 in 4yem

Go back to Bromine Binding Sites List in 4yem
Bromine binding site 10 out of 19 in the Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Carboplatin Binding to Hewl in Nabr Crystallisation Conditions Studied at An X-Ray Wavelength of 0.9163A - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br210

b:26.4
occ:0.35
 BR A:BR210 0.0 26.4 0.3
BR A:BR210 1.8 19.0 0.2
O A:HOH399 3.3 31.7 0.5
O A:HOH430 3.4 18.6 1.0
NE1 A:TRP63 3.4 11.0 1.0
O A:HOH370 3.7 47.7 1.0
CD1 A:TRP62 3.9 22.1 1.0
C2 A:DMS220 3.9 29.5 1.0
O A:HOH342 4.0 39.6 1.0
NH2 A:ARG61 4.1 16.5 0.5
O A:HOH449 4.1 36.5 1.0
CD1 A:TRP63 4.3 10.5 1.0
CE2 A:TRP63 4.4 10.2 1.0
CG A:TRP62 4.6 18.1 1.0
CZ2 A:TRP63 4.6 10.8 1.0
CB A:TRP62 4.6 13.2 1.0
S A:DMS220 4.7 27.8 1.0
NE1 A:TRP62 4.8 25.3 1.0
O A:DMS220 4.8 15.6 1.0
CZ A:ARG61 4.9 15.8 0.5

Reference:

I.G.Shabalin, Z.Dauter, M.Jaskolski, W.Minor, A.Wlodawer. Crystallography and Chemistry Should Always Go Together: A Cautionary Tale of Protein Complexes with Cisplatin and Carboplatin To Be Published.
Page generated: Wed Jul 10 23:05:19 2024

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