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Bromine in PDB 1d2v: Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5

Enzymatic activity of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5

All present enzymatic activity of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5, PDB code: 1d2v was solved by T.J.Fiedler, C.A.Davey, R.E.Fenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.155, 63.488, 92.476, 90.00, 97.36, 90.00
R / Rfree (%) 24.3 / 29.6

Other elements in 1d2v:

The structure of Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 (pdb code 1d2v). 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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5, PDB code: 1d2v:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 1d2v

Go back to Bromine Binding Sites List in 1d2v
Bromine binding site 1 out of 8 in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5


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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br601

b:6.7
occ:1.00
N A:TRP32 3.3 4.3 1.0
O A:HOH652A 3.3 2.0 1.0
N C:VAL327 3.4 2.0 1.0
CB C:ASN326 3.6 4.2 1.0
CH2 C:TRP436 3.6 4.3 1.0
N C:ASN326 3.7 4.2 1.0
CZ2 C:TRP436 3.8 2.6 1.0
CA A:ARG31 3.8 7.3 1.0
CB C:VAL327 3.9 4.8 1.0
CG1 C:VAL327 3.9 3.6 1.0
CA C:ASN326 4.0 4.7 1.0
O A:VAL30 4.0 5.0 1.0
C A:ARG31 4.0 6.7 1.0
N A:LEU33 4.1 5.2 1.0
CD2 C:LEU430 4.1 6.3 1.0
C C:ASN326 4.1 2.0 1.0
CD A:ARG31 4.2 7.2 1.0
CA A:TRP32 4.2 5.3 1.0
CB A:TRP32 4.2 6.5 1.0
CA C:VAL327 4.2 2.8 1.0
O A:LEU33 4.3 3.7 1.0
C C:ALA325 4.6 4.7 1.0
CB A:ARG31 4.6 9.7 1.0
CB C:ALA325 4.6 2.5 1.0
C A:TRP32 4.7 6.5 1.0
NH1 A:ARG31 4.7 3.2 1.0
N A:ARG31 4.9 6.0 1.0
C A:VAL30 4.9 5.7 1.0
CG C:ASN326 4.9 4.9 1.0
CZ3 C:TRP436 4.9 3.4 1.0
CG A:TRP32 4.9 6.7 1.0
CG A:ARG31 5.0 10.4 1.0
CA C:ALA325 5.0 5.2 1.0

Bromine binding site 2 out of 8 in 1d2v

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Bromine binding site 2 out of 8 in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5


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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br758

b:16.2
occ:0.55
N C:THR544 3.3 9.6 1.0
NH1 C:ARG382 3.5 17.0 1.0
CG2 C:ILE543 3.5 12.1 1.0
O C:ASN348 3.5 22.4 1.0
N C:THR545 3.7 8.3 1.0
CA C:ILE543 3.8 10.4 1.0
O C:HOH777A 3.8 24.7 1.0
CD C:ARG382 3.9 16.3 1.0
C C:ILE543 4.0 9.4 1.0
OG1 C:THR544 4.0 8.3 1.0
O C:THR545 4.1 10.9 1.0
CB C:ILE543 4.2 12.5 1.0
C C:ASN348 4.2 21.0 1.0
CA C:ASN348 4.2 19.9 1.0
CE1 C:TYR350 4.3 17.1 1.0
CA C:THR544 4.3 9.9 1.0
CB C:ASN348 4.4 18.9 1.0
CZ C:ARG382 4.5 17.8 1.0
C C:THR544 4.5 8.8 1.0
CA C:THR545 4.6 11.2 1.0
CB C:THR545 4.6 14.8 1.0
NE C:ARG382 4.6 20.0 1.0
O C:GLY542 4.7 10.7 1.0
C C:THR545 4.8 10.4 1.0
CG1 C:ILE543 4.8 9.3 1.0
CB C:THR544 4.8 10.4 1.0
CD1 C:TYR350 4.8 17.0 1.0
CG C:ARG382 4.9 14.5 1.0
N C:ILE543 5.0 9.1 1.0

Bromine binding site 3 out of 8 in 1d2v

Go back to Bromine Binding Sites List in 1d2v
Bromine binding site 3 out of 8 in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5


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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br843

b:12.7
occ:0.44
O C:HOH957A 2.7 11.4 1.0
O A:HOH844A 3.1 8.6 1.0
CG C:GLU242 3.3 5.7 1.0
CE1 A:HIS95 3.5 5.8 1.0
NE2 A:HIS95 3.6 8.7 1.0
NE2 A:GLN91 3.6 8.4 1.0
CD C:GLU242 3.6 4.2 1.0
O C:HOH845A 3.6 2.0 1.0
CB C:GLU242 3.7 6.3 1.0
CHB A:HEM605 3.8 3.9 1.0
C1B A:HEM605 3.9 5.2 1.0
OE2 C:GLU242 3.9 9.3 1.0
CD C:ARG239 4.0 7.6 1.0
OE1 C:GLU242 4.0 4.9 1.0
CB C:ARG239 4.0 3.3 1.0
C4A A:HEM605 4.0 5.7 1.0
CG C:ARG239 4.2 6.8 1.0
NB A:HEM605 4.3 6.5 1.0
NA A:HEM605 4.4 6.6 1.0
C2B A:HEM605 4.5 4.6 1.0
C3A A:HEM605 4.5 4.7 1.0
CD A:GLN91 4.7 7.8 1.0
ND1 A:HIS95 4.8 6.0 1.0
CD2 A:HIS95 4.9 8.5 1.0
C1A A:HEM605 4.9 6.7 1.0
O C:ARG239 4.9 2.4 1.0
CMB A:HEM605 5.0 5.6 1.0
C4B A:HEM605 5.0 5.3 1.0

Bromine binding site 4 out of 8 in 1d2v

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Bromine binding site 4 out of 8 in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5


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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br889

b:24.4
occ:0.60
N C:PHE213 3.4 10.2 1.0
N C:GLN201 3.4 12.1 1.0
OD1 C:ASN200 3.5 13.0 1.0
CA C:PRO212 3.7 10.8 1.0
CG C:ASN200 3.7 12.0 1.0
CA C:ASN200 3.8 9.2 1.0
CB C:PRO212 3.9 9.7 1.0
C C:PRO212 4.0 9.6 1.0
ND2 C:ASN200 4.1 9.1 1.0
C C:ASN200 4.1 9.7 1.0
CD1 C:PHE213 4.2 7.5 1.0
CB C:PHE213 4.3 9.2 1.0
CB C:ASN200 4.3 9.0 1.0
CA C:PHE213 4.4 9.3 1.0
CB C:GLN201 4.4 16.2 1.0
CA C:GLN201 4.4 15.0 1.0
CG C:PHE213 4.5 9.4 1.0
N C:ARG202 4.6 15.1 1.0
O C:PHE213 4.7 8.8 1.0
CG C:GLN201 4.7 16.4 1.0
O C:VAL199 4.8 11.5 1.0
N C:ASN200 4.9 8.0 1.0
CG C:ARG202 5.0 23.5 1.0
C C:GLN201 5.0 16.1 1.0

Bromine binding site 5 out of 8 in 1d2v

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Bromine binding site 5 out of 8 in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5


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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br601

b:6.7
occ:1.00
N D:VAL327 3.3 2.0 1.0
N B:TRP32 3.3 5.4 1.0
O B:HOH652B 3.3 3.2 1.0
CB D:ASN326 3.6 5.8 1.0
CH2 D:TRP436 3.6 4.2 1.0
N D:ASN326 3.7 2.0 1.0
CB D:VAL327 3.8 3.2 1.0
CA B:ARG31 3.8 4.9 1.0
CZ2 D:TRP436 3.9 4.8 1.0
CG1 D:VAL327 3.9 2.2 1.0
CA D:ASN326 4.0 3.3 1.0
O B:VAL30 4.0 5.9 1.0
C B:ARG31 4.0 5.9 1.0
C D:ASN326 4.1 2.4 1.0
CA D:VAL327 4.1 2.6 1.0
N B:LEU33 4.1 6.2 1.0
CD2 D:LEU430 4.1 5.4 1.0
CA B:TRP32 4.3 6.1 1.0
CB B:TRP32 4.3 6.2 1.0
O B:LEU33 4.4 7.7 1.0
CD B:ARG31 4.4 5.1 1.0
C D:ALA325 4.5 5.0 1.0
CB D:ALA325 4.5 6.9 1.0
CB B:ARG31 4.6 4.7 1.0
C B:TRP32 4.7 5.9 1.0
N B:ARG31 4.8 6.7 1.0
C B:VAL30 4.8 4.8 1.0
NH1 B:ARG31 4.9 3.9 1.0
CZ3 D:TRP436 4.9 5.0 1.0
CG D:ASN326 4.9 4.9 1.0
CA D:ALA325 4.9 5.6 1.0
CG B:TRP32 4.9 8.8 1.0

Bromine binding site 6 out of 8 in 1d2v

Go back to Bromine Binding Sites List in 1d2v
Bromine binding site 6 out of 8 in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5


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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br758

b:18.1
occ:0.53
O D:ASN348 3.3 29.3 1.0
N D:THR544 3.4 18.3 1.0
CA D:ILE543 3.6 18.3 1.0
CG2 D:ILE543 3.7 18.3 1.0
N D:THR545 3.8 16.6 1.0
NH1 D:ARG382 3.9 18.0 1.0
C D:ILE543 4.0 19.1 1.0
CA D:ASN348 4.0 26.9 1.0
CB D:ILE543 4.1 19.5 1.0
C D:ASN348 4.1 27.8 1.0
OG1 D:THR544 4.2 22.6 1.0
CB D:ASN348 4.3 28.6 1.0
O D:THR545 4.3 12.9 1.0
CE1 D:TYR350 4.3 16.4 1.0
CG1 D:ILE543 4.3 19.2 1.0
CB D:THR545 4.3 16.5 1.0
CD D:ARG382 4.4 15.3 1.0
CA D:THR544 4.5 18.3 1.0
CA D:THR545 4.6 16.5 1.0
C D:THR544 4.6 16.8 1.0
O D:HOH1248B 4.7 23.9 1.0
N D:ILE543 4.8 19.3 1.0
O D:GLY542 4.9 20.1 1.0
CD1 D:TYR350 4.9 16.5 1.0
C D:THR545 4.9 13.7 1.0
CZ D:ARG382 4.9 11.8 1.0
OG1 D:THR545 5.0 20.1 1.0
CB D:THR544 5.0 20.5 1.0

Bromine binding site 7 out of 8 in 1d2v

Go back to Bromine Binding Sites List in 1d2v
Bromine binding site 7 out of 8 in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5


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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br843

b:12.6
occ:0.44
O D:HOH957B 2.9 15.3 1.0
O B:HOH844B 3.2 21.1 1.0
CE1 B:HIS95 3.3 6.7 1.0
NE2 B:GLN91 3.4 3.2 1.0
CG D:GLU242 3.4 9.3 1.0
NE2 B:HIS95 3.5 5.2 1.0
CD D:GLU242 3.6 9.7 1.0
O D:HOH845B 3.7 6.7 1.0
CB D:GLU242 3.7 9.0 1.0
CHB B:HEM605 3.8 5.8 1.0
OE1 D:GLU242 3.9 8.7 1.0
C1B B:HEM605 3.9 3.8 1.0
CD D:ARG239 4.0 5.5 1.0
C4A B:HEM605 4.0 8.5 1.0
CB D:ARG239 4.0 5.8 1.0
OE2 D:GLU242 4.1 8.6 1.0
CG D:ARG239 4.3 8.2 1.0
NB B:HEM605 4.3 5.5 1.0
NA B:HEM605 4.4 8.4 1.0
C2B B:HEM605 4.4 2.9 1.0
CD B:GLN91 4.6 4.9 1.0
C3A B:HEM605 4.6 6.6 1.0
ND1 B:HIS95 4.6 4.2 1.0
CMB B:HEM605 4.8 3.3 1.0
CD2 B:HIS95 4.8 5.0 1.0
NE D:ARG239 4.9 5.1 1.0
C4B B:HEM605 4.9 4.2 1.0
O D:ARG239 4.9 5.3 1.0
C1A B:HEM605 5.0 7.5 1.0
C3B B:HEM605 5.0 3.7 1.0
FE B:HEM605 5.0 9.3 1.0
CG B:GLN91 5.0 6.1 1.0

Bromine binding site 8 out of 8 in 1d2v

Go back to Bromine Binding Sites List in 1d2v
Bromine binding site 8 out of 8 in the Crystal Structure of Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5


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 Bromide-Bound Human Myeloperoxidase Isoform C at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br889

b:23.4
occ:0.60
N D:PHE213 3.4 11.5 1.0
N D:GLN201 3.5 19.1 1.0
ND2 D:ASN200 3.7 14.5 1.0
CA D:ASN200 3.8 16.4 1.0
CG D:ASN200 3.8 15.5 1.0
CA D:PRO212 3.9 13.8 1.0
OD1 D:ASN200 4.1 14.7 1.0
C D:ASN200 4.2 16.8 1.0
C D:PRO212 4.2 12.3 1.0
CD1 D:PHE213 4.2 10.7 1.0
CB D:PRO212 4.2 17.1 1.0
CB D:PHE213 4.2 10.6 1.0
CG D:ARG202 4.3 32.6 1.0
CB D:ASN200 4.4 14.9 1.0
CA D:PHE213 4.4 11.7 1.0
CA D:GLN201 4.4 23.5 1.0
CB D:GLN201 4.4 23.9 1.0
CG D:PHE213 4.5 8.0 1.0
O D:VAL199 4.7 15.2 1.0
N D:ARG202 4.8 25.2 1.0
C D:GLN201 4.9 25.5 1.0
N D:ASN200 4.9 16.1 1.0
CG D:GLN201 4.9 28.9 1.0
O D:PHE213 4.9 15.4 1.0

Reference:

T.J.Fiedler, C.A.Davey, R.E.Fenna. X-Ray Crystal Structure and Characterization of Halide-Binding Sites of Human Myeloperoxidase at 1.8 A Resolution. J.Biol.Chem. V. 275 11964 2000.
ISSN: ISSN 0021-9258
PubMed: 10766826
DOI: 10.1074/JBC.275.16.11964
Page generated: Sat Dec 12 01:59:45 2020

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