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Bromine in PDB 1d7w: Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0

Enzymatic activity of Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0

All present enzymatic activity of Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0, PDB code: 1d7w was solved by T.J.Fiedler, R.E.Fenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.338, 63.324, 92.263, 90.00, 97.41, 90.00
R / Rfree (%) 21.5 / 27

Other elements in 1d7w:

The structure of Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0 also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Calcium (Ca) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0 (pdb code 1d7w). 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 Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0, PDB code: 1d7w:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 1d7w

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Bromine binding site 1 out of 8 in the Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0


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 Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1601

b:6.9
occ:1.00
O A:HOH652A 3.2 7.2 1.0
N C:VAL327 3.3 4.7 1.0
N A:TRP32 3.4 7.0 1.0
CB C:ASN326 3.5 4.3 1.0
CH2 C:TRP436 3.6 6.0 1.0
N C:ASN326 3.7 3.7 1.0
CZ2 C:TRP436 3.8 6.5 1.0
CA A:ARG31 3.9 7.9 1.0
CA C:ASN326 3.9 3.8 1.0
CB C:VAL327 3.9 3.9 1.0
O A:VAL30 4.0 4.9 1.0
CD2 C:LEU430 4.0 3.2 1.0
C C:ASN326 4.1 3.2 1.0
CG1 C:VAL327 4.1 4.0 1.0
N A:LEU33 4.1 3.8 1.0
C A:ARG31 4.1 8.5 1.0
CD A:ARG31 4.2 6.3 1.0
CA C:VAL327 4.2 5.0 1.0
CA A:TRP32 4.3 6.2 1.0
CB A:TRP32 4.4 7.9 1.0
O A:LEU33 4.4 6.2 1.0
C C:ALA325 4.5 3.2 1.0
CB A:ARG31 4.6 8.3 1.0
NH1 A:ARG31 4.6 3.5 1.0
CB C:ALA325 4.7 2.7 1.0
C A:TRP32 4.7 6.3 1.0
CG C:ASN326 4.8 4.8 1.0
CG A:ARG31 4.9 7.9 1.0
CZ3 C:TRP436 4.9 6.8 1.0
C A:VAL30 4.9 6.2 1.0
N A:ARG31 4.9 6.7 1.0

Bromine binding site 2 out of 8 in 1d7w

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Bromine binding site 2 out of 8 in the Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0


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 Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br758

b:22.3
occ:0.65
O C:ASN348 3.0 30.9 1.0
N C:THR544 3.4 10.7 1.0
NH1 C:ARG382 3.4 18.8 1.0
CG2 C:ILE543 3.7 11.9 1.0
OG1 C:THR544 3.8 13.4 1.0
N C:THR545 3.8 9.3 1.0
CA C:ILE543 3.8 12.0 1.0
C C:ASN348 4.0 27.5 1.0
C C:ILE543 4.1 12.0 1.0
CB C:THR545 4.2 16.0 1.0
CA C:ASN348 4.2 27.5 1.0
CD C:ARG382 4.3 15.9 1.0
CB C:ILE543 4.3 12.1 1.0
CA C:THR544 4.3 10.9 1.0
CE1 C:TYR350 4.4 19.3 1.0
O C:THR545 4.4 12.0 1.0
C C:THR544 4.5 9.3 1.0
CA C:THR545 4.5 13.0 1.0
CB C:ASN348 4.6 30.4 1.0
CZ C:ARG382 4.6 18.1 1.0
OG1 C:THR545 4.6 20.9 1.0
O C:GLY542 4.6 11.8 1.0
CB C:THR544 4.7 10.5 1.0
CD1 C:TYR350 4.7 17.8 1.0
NE C:ARG382 4.9 19.9 1.0
CG1 C:ILE543 4.9 9.9 1.0
C C:THR545 5.0 12.4 1.0

Bromine binding site 3 out of 8 in 1d7w

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Bromine binding site 3 out of 8 in the Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0


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 Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br889

b:21.2
occ:0.73
N C:PHE213 3.3 12.1 1.0
N C:GLN201 3.4 12.3 1.0
OD1 C:ASN200 3.6 13.8 1.0
O C:HOH1218A 3.7 18.3 1.0
CG C:ASN200 3.7 9.9 1.0
CA C:ASN200 3.7 10.6 1.0
CA C:PRO212 3.9 9.4 1.0
ND2 C:ASN200 4.0 6.8 1.0
CB C:PHE213 4.0 8.6 1.0
CD1 C:PHE213 4.1 9.7 1.0
C C:PRO212 4.1 12.9 1.0
C C:ASN200 4.1 12.1 1.0
CB C:PRO212 4.1 9.5 1.0
CA C:PHE213 4.2 11.4 1.0
CG C:PHE213 4.3 11.0 1.0
CB C:ASN200 4.3 8.6 1.0
CA C:GLN201 4.4 15.9 1.0
CB C:GLN201 4.5 15.9 1.0
N C:ARG202 4.6 18.4 1.0
O C:PHE213 4.7 11.8 1.0
CG C:GLN201 4.7 16.8 1.0
O C:VAL199 4.8 12.3 1.0
N C:ASN200 4.8 10.1 1.0
C C:GLN201 4.9 18.0 1.0
C C:PHE213 5.0 12.4 1.0

Bromine binding site 4 out of 8 in 1d7w

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Bromine binding site 4 out of 8 in the Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0


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 Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br957

b:29.0
occ:0.51
O A:HOH843A 3.0 18.0 1.0
O C:HOH946A 3.4 15.4 1.0
CG C:GLU242 3.7 7.1 1.0
CG C:ARG239 3.9 7.4 1.0
O C:HOH967A 4.0 24.1 1.0
CD C:ARG239 4.1 7.6 1.0
CZ C:PHE407 4.2 12.1 1.0
CZ C:PHE366 4.2 12.6 1.0
O C:HOH845A 4.3 6.0 1.0
CB C:GLU242 4.4 8.0 1.0
CE1 C:PHE407 4.5 10.2 1.0
CB C:ARG239 4.5 6.1 1.0
CMA A:HEM605 4.5 6.2 1.0
C3A A:HEM605 4.7 6.0 1.0
CE1 C:PHE366 4.8 13.1 1.0
CD C:GLU242 4.9 9.3 1.0
O A:HOH947A 4.9 13.8 1.0

Bromine binding site 5 out of 8 in 1d7w

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Bromine binding site 5 out of 8 in the Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0


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 Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br2601

b:10.4
occ:1.00
N B:TRP32 3.3 6.3 1.0
N D:VAL327 3.3 4.7 1.0
O B:HOH652B 3.4 5.2 1.0
CH2 D:TRP436 3.6 5.3 1.0
CB D:ASN326 3.7 3.8 1.0
N D:ASN326 3.8 4.4 1.0
CB D:VAL327 3.8 3.5 1.0
CZ2 D:TRP436 3.9 6.2 1.0
CA B:ARG31 3.9 7.0 1.0
CA D:ASN326 4.0 3.1 1.0
CG1 D:VAL327 4.0 4.0 1.0
O B:VAL30 4.0 6.9 1.0
C B:ARG31 4.1 6.7 1.0
N B:LEU33 4.1 5.4 1.0
C D:ASN326 4.1 4.0 1.0
CA D:VAL327 4.1 7.3 1.0
CD2 D:LEU430 4.2 3.2 1.0
CB B:TRP32 4.2 9.2 1.0
CA B:TRP32 4.2 6.8 1.0
CD B:ARG31 4.2 9.1 1.0
O B:LEU33 4.4 11.2 1.0
C D:ALA325 4.6 6.3 1.0
CB D:ALA325 4.6 5.3 1.0
NH1 B:ARG31 4.6 5.0 1.0
CB B:ARG31 4.6 6.9 1.0
C B:TRP32 4.7 6.5 1.0
CZ3 D:TRP436 4.9 8.3 1.0
C B:VAL30 4.9 4.1 1.0
N B:ARG31 4.9 5.8 1.0
CG B:TRP32 4.9 11.5 1.0
CG B:ARG31 5.0 10.2 1.0
CA D:ALA325 5.0 7.3 1.0
CG D:ASN326 5.0 3.6 1.0

Bromine binding site 6 out of 8 in 1d7w

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Bromine binding site 6 out of 8 in the Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0


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 Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br758

b:19.5
occ:0.55
N D:THR544 3.4 21.4 1.0
O D:ASN348 3.5 31.5 1.0
N D:THR545 3.7 18.7 1.0
CG2 D:ILE543 3.7 15.6 1.0
NH1 D:ARG382 3.7 20.7 1.0
CA D:ILE543 3.7 20.4 1.0
OG1 D:THR544 4.0 24.7 1.0
CB D:THR545 4.0 19.1 1.0
C D:ILE543 4.1 22.6 1.0
CE1 D:TYR350 4.1 17.6 1.0
CA D:ASN348 4.1 28.7 1.0
CD D:ARG382 4.1 19.6 1.0
OG1 D:THR545 4.1 22.6 1.0
CB D:ILE543 4.2 19.3 1.0
C D:ASN348 4.3 29.3 1.0
O D:THR545 4.4 16.6 1.0
CA D:THR545 4.4 17.7 1.0
CA D:THR544 4.4 20.5 1.0
CB D:ASN348 4.5 30.1 1.0
C D:THR544 4.5 18.4 1.0
CG1 D:ILE543 4.6 18.4 1.0
CD1 D:TYR350 4.7 20.0 1.0
O D:HOH1248B 4.7 25.0 1.0
O D:GLY542 4.7 21.9 1.0
CZ D:ARG382 4.8 16.0 1.0
CB D:THR544 4.9 22.7 1.0
C D:THR545 4.9 15.2 1.0
N D:ILE543 4.9 22.8 1.0
NE D:ARG382 4.9 19.9 1.0

Bromine binding site 7 out of 8 in 1d7w

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Bromine binding site 7 out of 8 in the Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0


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 Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br889

b:22.5
occ:0.63
N D:GLN201 3.3 25.1 1.0
N D:PHE213 3.5 18.7 1.0
ND2 D:ASN200 3.8 20.3 1.0
CA D:ASN200 3.9 23.3 1.0
CA D:PRO212 3.9 19.7 1.0
CG D:ASN200 3.9 22.1 1.0
C D:ASN200 4.1 25.2 1.0
CB D:PRO212 4.1 21.5 1.0
OD1 D:ASN200 4.1 21.2 1.0
CB D:GLN201 4.1 25.1 1.0
C D:PRO212 4.2 20.2 1.0
CA D:GLN201 4.2 25.2 1.0
CB D:PHE213 4.3 18.9 1.0
CD1 D:PHE213 4.4 19.7 1.0
CA D:PHE213 4.5 19.5 1.0
CB D:ASN200 4.5 21.1 1.0
N D:ARG202 4.5 25.3 1.0
CG D:GLN201 4.6 29.9 1.0
CG D:ARG202 4.6 33.9 1.0
CG D:PHE213 4.6 19.4 1.0
O D:PHE213 4.8 21.8 1.0
C D:GLN201 4.8 25.3 1.0
O D:VAL199 4.9 21.3 1.0
N D:ASN200 5.0 22.9 1.0

Bromine binding site 8 out of 8 in 1d7w

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Bromine binding site 8 out of 8 in the Crystal Structure of Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0


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 Human Myeloperoxidase Isoform C Complexed with Cyanide and Bromide at pH 4.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br957

b:28.6
occ:0.51
O B:HOH843B 3.3 26.5 1.0
O D:HOH946B 3.4 23.6 1.0
CG D:ARG239 3.8 8.2 1.0
CG D:GLU242 3.9 10.5 1.0
CD D:ARG239 4.2 8.0 1.0
CZ D:PHE366 4.2 13.8 1.0
CZ D:PHE407 4.2 16.1 1.0
CE1 D:PHE407 4.4 15.4 1.0
CB D:ARG239 4.5 11.4 1.0
CMA B:HEM605 4.5 7.9 1.0
O B:HOH845B 4.6 16.1 1.0
CB D:GLU242 4.6 8.1 1.0
CE1 D:PHE366 4.6 14.0 1.0
C3A B:HEM605 4.9 8.9 1.0
O B:HOH947B 4.9 21.3 1.0

Reference:

M.Blair-Johnson, T.Fiedler, R.Fenna. Human Myeloperoxidase: Structure of A Cyanide Complex and Its Interaction with Bromide and Thiocyanate Substrates at 1.9 A Resolution. Biochemistry V. 40 13990 2001.
ISSN: ISSN 0006-2960
PubMed: 11705390
DOI: 10.1021/BI0111808
Page generated: Sun Jan 24 08:27:02 2021

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