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Chlorine in PDB 4dl1: Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog

Enzymatic activity of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog

All present enzymatic activity of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog:
1.11.2.2;

Protein crystallography data

The structure of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog, PDB code: 4dl1 was solved by F.Vajdos, A.Varghese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 128.49 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.829, 242.636, 151.505, 90.00, 91.19, 90.00
R / Rfree (%) 19 / 24.6

Other elements in 4dl1:

The structure of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Calcium (Ca) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog (pdb code 4dl1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog, PDB code: 4dl1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4dl1

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Chlorine binding site 1 out of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1601

b:16.0
occ:1.00
O A:HOH1704 2.9 11.6 1.0
N A:TRP32 3.1 10.8 1.0
N C:VAL327 3.3 11.8 1.0
CA A:ARG31 3.6 13.2 1.0
CB C:ASN326 3.7 12.7 1.0
N C:ASN326 3.7 13.0 1.0
CB C:VAL327 3.8 10.9 1.0
CH2 C:TRP436 3.8 8.7 1.0
C A:ARG31 3.9 10.9 1.0
CG1 C:VAL327 3.9 13.9 1.0
O A:VAL30 4.0 10.8 1.0
CA C:ASN326 4.1 12.6 1.0
CZ2 C:TRP436 4.1 7.6 1.0
CA C:VAL327 4.1 12.1 1.0
CA A:TRP32 4.1 12.4 1.0
CB A:TRP32 4.1 13.7 1.0
C C:ASN326 4.1 11.1 1.0
N A:LEU33 4.2 11.3 1.0
CD2 C:LEU430 4.3 8.5 1.0
CB A:ARG31 4.3 15.2 1.0
C C:ALA325 4.5 13.6 1.0
CB C:ALA325 4.5 11.2 1.0
O A:LEU33 4.5 14.4 1.0
CG A:ARG31 4.6 16.3 1.0
C A:TRP32 4.6 11.7 1.0
CD A:ARG31 4.7 19.7 1.0
N A:ARG31 4.7 14.3 1.0
NH1 A:ARG31 4.8 13.8 1.0
CG A:TRP32 4.8 13.4 1.0
C A:VAL30 4.8 13.3 1.0
CA C:ALA325 4.9 12.5 1.0
CG C:ASN326 5.0 13.7 1.0
CZ3 C:TRP436 5.0 13.7 1.0

Chlorine binding site 2 out of 8 in 4dl1

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Chlorine binding site 2 out of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:14.7
occ:1.00
O B:HOH305 3.1 12.8 1.0
N B:TRP32 3.2 14.6 1.0
N D:VAL327 3.3 15.4 1.0
CB D:ASN326 3.6 15.2 1.0
CA B:ARG31 3.6 16.2 1.0
CH2 D:TRP436 3.7 15.4 1.0
N D:ASN326 3.7 17.6 1.0
CG1 D:VAL327 3.8 14.7 1.0
CB D:VAL327 3.9 14.5 1.0
C B:ARG31 3.9 15.9 1.0
CA D:ASN326 4.0 16.8 1.0
CZ2 D:TRP436 4.1 13.9 1.0
O B:VAL30 4.1 17.7 1.0
C D:ASN326 4.2 16.4 1.0
CD2 D:LEU430 4.2 18.0 1.0
CA D:VAL327 4.2 14.2 1.0
N B:LEU33 4.2 16.3 1.0
CA B:TRP32 4.2 14.7 1.0
CB B:ARG31 4.2 16.7 1.0
CB B:TRP32 4.3 16.3 1.0
CG B:ARG31 4.4 20.9 1.0
C D:ALA325 4.5 16.6 1.0
CB D:ALA325 4.5 14.4 1.0
O B:LEU33 4.5 13.4 1.0
NH1 B:ARG31 4.6 16.7 1.0
C B:TRP32 4.7 14.7 1.0
N B:ARG31 4.7 15.8 1.0
CG B:TRP32 4.8 18.3 1.0
CD B:ARG31 4.8 18.1 1.0
CZ3 D:TRP436 4.8 10.9 1.0
C B:VAL30 4.9 16.1 1.0
CG D:ASN326 4.9 13.2 1.0
CA D:ALA325 4.9 16.0 1.0

Chlorine binding site 3 out of 8 in 4dl1

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Chlorine binding site 3 out of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1601

b:18.7
occ:1.00
N E:TRP32 3.2 16.6 1.0
O E:HOH1702 3.2 13.7 1.0
N G:VAL327 3.3 15.1 1.0
N G:ASN326 3.6 15.2 1.0
CH2 G:TRP436 3.6 19.0 1.0
CB G:ASN326 3.7 15.7 1.0
CA E:ARG31 3.7 17.3 1.0
CG1 G:VAL327 3.8 11.6 1.0
CB G:VAL327 3.9 18.5 1.0
C E:ARG31 3.9 17.7 1.0
CA G:ASN326 4.0 13.9 1.0
CZ2 G:TRP436 4.0 17.2 1.0
N E:LEU33 4.0 15.8 1.0
C G:ASN326 4.1 13.5 1.0
CA E:TRP32 4.1 17.6 1.0
O E:VAL30 4.1 14.7 1.0
CB E:TRP32 4.1 18.5 1.0
CA G:VAL327 4.2 14.3 1.0
CB E:ARG31 4.3 19.4 1.0
CD2 G:LEU430 4.4 10.7 1.0
CB G:ALA325 4.4 17.2 1.0
O E:LEU33 4.5 18.1 1.0
C G:ALA325 4.5 17.1 1.0
C E:TRP32 4.6 17.1 1.0
CG E:ARG31 4.6 22.5 1.0
NH1 E:ARG31 4.8 18.1 1.0
CZ3 G:TRP436 4.8 17.5 1.0
N E:ARG31 4.8 18.0 1.0
CG E:TRP32 4.9 18.2 1.0
CA G:ALA325 4.9 18.4 1.0
C E:VAL30 4.9 14.9 1.0
CG G:ASN326 4.9 19.3 1.0
CD E:ARG31 5.0 23.6 1.0

Chlorine binding site 4 out of 8 in 4dl1

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Chlorine binding site 4 out of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl201

b:25.8
occ:1.00
N H:VAL327 3.1 19.7 1.0
N F:TRP32 3.2 24.7 1.0
O F:HOH322 3.2 22.5 1.0
CB H:ASN326 3.7 22.9 1.0
CB H:VAL327 3.7 22.4 1.0
CA F:ARG31 3.7 23.4 1.0
N H:ASN326 3.8 21.6 1.0
CH2 H:TRP436 3.8 26.1 1.0
C F:ARG31 3.9 24.2 1.0
CA H:VAL327 4.0 20.2 1.0
CA H:ASN326 4.0 21.5 1.0
CG1 H:VAL327 4.0 17.6 1.0
C H:ASN326 4.0 22.3 1.0
N F:LEU33 4.0 23.4 1.0
O F:VAL30 4.1 20.8 1.0
CB F:TRP32 4.1 22.4 1.0
CA F:TRP32 4.1 23.3 1.0
CZ2 H:TRP436 4.2 23.8 1.0
CD2 H:LEU430 4.3 19.4 1.0
CB H:ALA325 4.4 17.7 1.0
CB F:ARG31 4.4 25.2 1.0
C H:ALA325 4.4 18.7 1.0
O F:LEU33 4.5 21.4 1.0
CD F:ARG31 4.5 27.2 1.0
C F:TRP32 4.6 24.7 1.0
CG F:TRP32 4.8 18.6 1.0
CA H:ALA325 4.8 18.1 1.0
N F:ARG31 4.8 22.1 1.0
CG F:ARG31 4.8 28.1 1.0
NH1 F:ARG31 4.8 19.3 1.0
C F:VAL30 4.9 19.0 1.0
CZ3 H:TRP436 4.9 27.4 1.0
CG H:ASN326 4.9 23.7 1.0

Chlorine binding site 5 out of 8 in 4dl1

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Chlorine binding site 5 out of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl1601

b:14.1
occ:1.00
N I:TRP32 3.2 15.9 1.0
O I:HOH1767 3.2 7.2 1.0
N K:VAL327 3.2 14.2 1.0
CB K:ASN326 3.5 12.0 1.0
CH2 K:TRP436 3.7 14.8 1.0
CA I:ARG31 3.7 16.7 1.0
N K:ASN326 3.7 14.0 1.0
CB K:VAL327 3.8 18.1 1.0
C I:ARG31 3.9 15.8 1.0
CA K:ASN326 3.9 12.9 1.0
CG1 K:VAL327 4.0 19.0 1.0
C K:ASN326 4.0 12.6 1.0
CZ2 K:TRP436 4.0 13.8 1.0
N I:LEU33 4.0 16.2 1.0
O I:VAL30 4.1 14.3 1.0
CA K:VAL327 4.1 15.4 1.0
CA I:TRP32 4.2 16.3 1.0
CB I:TRP32 4.2 16.2 1.0
CB I:ARG31 4.2 17.9 1.0
CD2 K:LEU430 4.4 9.2 1.0
O I:LEU33 4.4 16.4 1.0
CG I:ARG31 4.5 22.4 1.0
C K:ALA325 4.5 14.8 1.0
CB K:ALA325 4.5 13.8 1.0
C I:TRP32 4.6 17.2 1.0
NH1 I:ARG31 4.7 14.7 1.0
CG K:ASN326 4.8 14.6 1.0
N I:ARG31 4.8 15.9 1.0
CD I:ARG31 4.8 17.5 1.0
CZ3 K:TRP436 4.8 18.2 1.0
C I:VAL30 4.9 15.6 1.0
CA K:ALA325 4.9 14.4 1.0
CG I:TRP32 4.9 17.8 1.0

Chlorine binding site 6 out of 8 in 4dl1

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Chlorine binding site 6 out of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl201

b:20.5
occ:1.00
N J:TRP32 3.2 20.0 1.0
O J:HOH358 3.2 8.2 1.0
N L:VAL327 3.3 18.2 1.0
CB L:ASN326 3.6 19.8 1.0
CH2 L:TRP436 3.6 18.8 1.0
CA J:ARG31 3.7 20.9 1.0
CB L:VAL327 3.8 18.9 1.0
N L:ASN326 3.8 17.2 1.0
C J:ARG31 3.9 20.5 1.0
CG1 L:VAL327 4.0 12.1 1.0
CZ2 L:TRP436 4.0 23.9 1.0
O J:VAL30 4.1 23.0 1.0
CA L:ASN326 4.1 18.7 1.0
CA L:VAL327 4.1 15.4 1.0
N J:LEU33 4.1 18.2 1.0
CB J:TRP32 4.2 18.3 1.0
CA J:TRP32 4.2 18.0 1.0
C L:ASN326 4.2 18.5 1.0
CD2 L:LEU430 4.3 22.1 1.0
CB J:ARG31 4.4 21.6 1.0
CB L:ALA325 4.4 15.1 1.0
O J:LEU33 4.5 20.9 1.0
CD J:ARG31 4.5 26.5 1.0
C L:ALA325 4.5 15.2 1.0
C J:TRP32 4.7 19.8 1.0
N J:ARG31 4.8 20.8 1.0
NH1 J:ARG31 4.8 19.5 1.0
CZ3 L:TRP436 4.8 22.6 1.0
CG J:TRP32 4.8 14.0 1.0
C J:VAL30 4.8 19.3 1.0
CA L:ALA325 4.9 15.6 1.0
CG J:ARG31 4.9 27.2 1.0
CG L:ASN326 4.9 20.4 1.0

Chlorine binding site 7 out of 8 in 4dl1

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Chlorine binding site 7 out of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl1601

b:18.3
occ:1.00
O M:HOH1709 2.9 15.0 1.0
N O:VAL327 3.2 19.5 1.0
N M:TRP32 3.2 15.5 1.0
CA M:ARG31 3.5 17.8 1.0
N O:ASN326 3.6 18.1 1.0
CB O:ASN326 3.6 17.9 1.0
CB O:VAL327 3.8 19.3 1.0
CH2 O:TRP436 3.8 16.0 1.0
C M:ARG31 3.9 18.0 1.0
CG1 O:VAL327 3.9 17.3 1.0
CA O:ASN326 3.9 17.6 1.0
C O:ASN326 3.9 18.4 1.0
CA O:VAL327 4.0 17.7 1.0
O M:VAL30 4.0 13.7 1.0
CZ2 O:TRP436 4.1 16.4 1.0
CB M:ARG31 4.2 20.1 1.0
CA M:TRP32 4.2 17.6 1.0
N M:LEU33 4.2 17.5 1.0
CD2 O:LEU430 4.3 12.5 1.0
CB M:TRP32 4.4 19.4 1.0
C O:ALA325 4.4 17.7 1.0
CB O:ALA325 4.5 17.5 1.0
O M:LEU33 4.6 16.7 1.0
CG M:ARG31 4.6 20.9 1.0
N M:ARG31 4.6 19.4 1.0
C M:TRP32 4.8 17.5 1.0
C M:VAL30 4.8 18.1 1.0
CD M:ARG31 4.8 21.5 1.0
NH1 M:ARG31 4.8 20.1 1.0
CA O:ALA325 4.8 17.7 1.0
CG O:ASN326 4.9 20.9 1.0
CG M:TRP32 5.0 21.2 1.0

Chlorine binding site 8 out of 8 in 4dl1

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Chlorine binding site 8 out of 8 in the Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Human Myeloperoxidase with Covalent Thioxanthine Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl201

b:21.0
occ:1.00
O N:HOH332 3.0 21.0 1.0
N N:TRP32 3.2 22.4 1.0
N P:VAL327 3.4 22.7 1.0
CH2 P:TRP436 3.6 30.5 1.0
CA N:ARG31 3.7 21.5 1.0
CB P:ASN326 3.7 23.2 1.0
N P:ASN326 3.8 21.4 1.0
CG1 P:VAL327 3.8 20.5 1.0
CB P:VAL327 3.8 24.1 1.0
CZ2 P:TRP436 3.9 29.2 1.0
C N:ARG31 3.9 22.1 1.0
N N:LEU33 4.1 24.9 1.0
CA P:ASN326 4.1 22.6 1.0
CA N:TRP32 4.1 23.6 1.0
O N:VAL30 4.2 22.5 1.0
CB N:TRP32 4.2 23.4 1.0
CA P:VAL327 4.2 22.9 1.0
C P:ASN326 4.2 23.3 1.0
CB N:ARG31 4.2 20.9 1.0
CD2 P:LEU430 4.3 20.8 1.0
O N:LEU33 4.5 21.1 1.0
CB P:ALA325 4.5 15.5 1.0
C P:ALA325 4.6 20.7 1.0
C N:TRP32 4.6 23.9 1.0
CG N:ARG31 4.6 24.0 1.0
NH1 N:ARG31 4.7 20.1 1.0
N N:ARG31 4.8 20.9 1.0
CZ3 P:TRP436 4.8 31.4 1.0
CG N:TRP32 4.8 24.7 1.0
CD N:ARG31 4.8 27.2 1.0
C N:VAL30 4.9 19.7 1.0
CA P:ALA325 4.9 18.7 1.0
CG P:ASN326 4.9 21.9 1.0

Reference:

K.F.Geoghegan, A.H.Varghese, X.Feng, A.J.Bessire, J.J.Conboy, R.B.Ruggeri, K.Ahn, S.N.Spath, S.V.Filippov, S.J.Conrad, P.A.Carpino, C.R.Guimaraes, F.F.Vajdos. Deconstruction of Activity-Dependent Covalent Modification of Heme in Human Neutrophil Myeloperoxidase By Multistage Mass Spectrometry (Ms(4)). Biochemistry V. 51 2065 2012.
ISSN: ISSN 0006-2960
PubMed: 22352991
DOI: 10.1021/BI201872J
Page generated: Sun Jul 21 12:10:44 2024

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