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Chlorine in PDB 7ni3: Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3

Enzymatic activity of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3

All present enzymatic activity of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3:
1.11.2.2;

Protein crystallography data

The structure of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3, PDB code: 7ni3 was solved by T.Sjogren, T.Inghardt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.61 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.66, 63.64, 111.03, 90, 97.15, 90
R / Rfree (%) 17.5 / 22.4

Other elements in 7ni3:

The structure of Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3 also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3 (pdb code 7ni3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3, PDB code: 7ni3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 7ni3

Go back to Chlorine Binding Sites List in 7ni3
Chlorine binding site 1 out of 5 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3


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 Native Human Myeloperoxidase in Complex with Cpd 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:23.3
occ:1.00
 O A:HOH342 2.9 21.3 1.0
N3 C:UE8602 3.1 30.5 1.0
NE2 A:GLN91 3.4 5.0 1.0
CG C:GLU242 3.4 12.4 1.0
CE1 A:HIS95 3.5 5.2 1.0
CD C:GLU242 3.6 11.4 1.0
NE2 A:HIS95 3.6 5.2 1.0
S5 C:UE8602 3.7 41.3 1.0
CB C:GLU242 3.7 9.0 1.0
C4 C:UE8602 3.8 35.5 1.0
OE1 C:GLU242 3.9 13.0 1.0
CB C:ARG239 3.9 3.7 1.0
CD C:ARG239 3.9 5.1 1.0
O1 C:UE8602 3.9 12.2 1.0
C2 C:UE8602 3.9 24.1 1.0
CHB A:HEM201 4.0 8.7 1.0
OE2 C:GLU242 4.0 10.2 1.0
C1B A:HEM201 4.1 8.3 1.0
CG C:ARG239 4.1 8.4 1.0
C4A A:HEM201 4.2 8.3 1.0
NA A:HEM201 4.4 8.3 1.0
C2B A:HEM201 4.5 8.4 1.0
NB A:HEM201 4.5 7.9 1.0
CD A:GLN91 4.6 13.6 1.0
ND1 A:HIS95 4.7 6.2 1.0
C3A A:HEM201 4.7 8.8 1.0
C1A A:HEM201 4.9 8.4 1.0
CMB A:HEM201 4.9 10.1 1.0
O C:ARG239 4.9 10.1 1.0
CD2 C:LEU246 4.9 11.1 1.0
CG A:GLN91 4.9 7.6 1.0
NE C:ARG239 4.9 8.3 1.0
CD2 A:HIS95 5.0 6.4 1.0

Chlorine binding site 2 out of 5 in 7ni3

Go back to Chlorine Binding Sites List in 7ni3
Chlorine binding site 2 out of 5 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3


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 Native Human Myeloperoxidase in Complex with Cpd 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:11.1
occ:1.00
 N B:TRP32 3.2 10.2 1.0
O B:HOH324 3.3 3.0 1.0
N D:VAL327 3.3 6.1 1.0
CH2 D:TRP436 3.6 12.1 1.0
CA B:ARG31 3.7 7.7 1.0
CB D:ASN326 3.7 9.2 1.0
N D:ASN326 3.7 8.2 1.0
CG1 D:VAL327 3.8 5.3 1.0
CB D:VAL327 3.8 6.8 1.0
CZ2 D:TRP436 3.8 12.8 1.0
C B:ARG31 3.9 11.5 1.0
CA D:ASN326 4.0 8.1 1.0
C D:ASN326 4.1 10.0 1.0
O B:VAL30 4.1 9.8 1.0
CA D:VAL327 4.1 5.0 1.0
CA B:TRP32 4.2 11.2 1.0
N B:LEU33 4.2 5.3 1.0
CB B:ARG31 4.2 9.4 1.0
CB B:TRP32 4.2 11.2 1.0
CD2 D:LEU430 4.3 3.0 1.0
CG B:ARG31 4.4 14.2 1.0
CB D:ALA325 4.4 5.7 1.0
C D:ALA325 4.5 11.0 1.0
O B:LEU33 4.6 6.6 1.0
N B:ARG31 4.7 7.7 1.0
CZ3 D:TRP436 4.8 11.3 1.0
C B:TRP32 4.8 12.3 1.0
CG B:TRP32 4.8 13.0 1.0
CD B:ARG31 4.8 18.3 1.0
NH1 B:ARG31 4.8 8.3 1.0
CA D:ALA325 4.8 5.3 1.0
C B:VAL30 4.8 10.0 1.0
CG D:ASN326 4.9 18.9 1.0

Chlorine binding site 3 out of 5 in 7ni3

Go back to Chlorine Binding Sites List in 7ni3
Chlorine binding site 3 out of 5 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3


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 Native Human Myeloperoxidase in Complex with Cpd 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:25.1
occ:1.00
 N3 D:UE82201 3.0 38.1 1.0
NE2 B:GLN91 3.0 12.5 1.0
O B:HOH327 3.1 12.9 1.0
CG D:GLU242 3.4 13.1 1.0
CD D:GLU242 3.4 23.8 1.0
CE1 B:HIS95 3.5 12.0 1.0
NE2 B:HIS95 3.6 12.2 1.0
OE2 D:GLU242 3.7 17.2 1.0
OE1 D:GLU242 3.7 12.6 1.0
CHB B:HEM202 3.7 12.4 1.0
C1B B:HEM202 3.8 12.0 1.0
S5 D:UE82201 3.8 39.1 1.0
O1 D:UE82201 3.8 30.6 1.0
CB D:GLU242 3.8 9.8 1.0
C2 D:UE82201 3.8 35.1 1.0
C4 D:UE82201 3.9 40.4 1.0
CD D:ARG239 4.0 13.1 1.0
C4A B:HEM202 4.0 12.1 1.0
CB D:ARG239 4.1 8.0 1.0
NB B:HEM202 4.2 11.7 1.0
C2B B:HEM202 4.2 12.1 1.0
CG D:ARG239 4.3 15.3 1.0
CD B:GLN91 4.3 22.6 1.0
NA B:HEM202 4.3 12.1 1.0
C3A B:HEM202 4.6 12.6 1.0
CMB B:HEM202 4.7 13.8 1.0
C4B B:HEM202 4.7 11.9 1.0
ND1 B:HIS95 4.7 13.5 1.0
C3B B:HEM202 4.8 12.3 1.0
CG B:GLN91 4.8 14.7 1.0
C1A B:HEM202 4.9 12.2 1.0
FE B:HEM202 4.9 12.0 1.0
CD2 D:LEU246 4.9 13.7 1.0
CD2 B:HIS95 4.9 12.5 1.0

Chlorine binding site 4 out of 5 in 7ni3

Go back to Chlorine Binding Sites List in 7ni3
Chlorine binding site 4 out of 5 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3


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 Native Human Myeloperoxidase in Complex with Cpd 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl601

b:6.5
occ:0.96
 N A:TRP32 3.1 7.3 1.0
O A:HOH338 3.2 3.0 1.0
N C:VAL327 3.3 3.1 1.0
CH2 C:TRP436 3.5 8.7 1.0
CA A:ARG31 3.7 6.9 1.0
N C:ASN326 3.8 5.6 1.0
CZ2 C:TRP436 3.8 8.5 1.0
CG1 C:VAL327 3.8 6.2 1.0
CB C:VAL327 3.8 7.2 1.0
CB C:ASN326 3.8 4.1 1.0
C A:ARG31 3.9 11.3 1.0
N A:LEU33 4.0 5.5 1.0
CA A:TRP32 4.1 6.2 1.0
CB A:TRP32 4.1 5.1 1.0
CA C:ASN326 4.1 5.2 1.0
CA C:VAL327 4.1 3.8 1.0
C C:ASN326 4.1 7.7 1.0
O A:VAL30 4.2 6.1 1.0
CD2 C:LEU430 4.3 6.6 1.0
CB A:ARG31 4.3 4.6 1.0
CB C:ALA325 4.4 4.2 1.0
C C:ALA325 4.5 9.1 1.0
O A:LEU33 4.5 8.2 1.0
C A:TRP32 4.6 9.5 1.0
CG A:ARG31 4.6 9.8 1.0
CG A:TRP32 4.7 6.0 1.0
CZ3 C:TRP436 4.7 8.2 1.0
N A:ARG31 4.8 6.8 1.0
CA C:ALA325 4.8 4.0 1.0
NH1 A:ARG31 4.9 4.0 1.0
C A:VAL30 4.9 8.8 1.0
CD A:ARG31 5.0 3.0 1.0

Chlorine binding site 5 out of 5 in 7ni3

Go back to Chlorine Binding Sites List in 7ni3
Chlorine binding site 5 out of 5 in the Crystal Structure of Native Human Myeloperoxidase in Complex with Cpd 3


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 Native Human Myeloperoxidase in Complex with Cpd 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl604

b:31.8
occ:0.96
 NE C:ARG382 3.2 37.8 1.0
N C:THR544 3.5 14.1 1.0
NH2 C:ARG382 3.6 31.1 1.0
O C:ASN348 3.8 32.0 1.0
CA C:ILE543 3.8 11.0 1.0
CZ C:ARG382 3.8 40.9 1.0
OG1 C:THR544 3.9 15.6 1.0
N C:THR545 3.9 15.4 1.0
CG2 C:ILE543 4.0 9.6 1.0
CA C:ASN348 4.1 24.9 1.0
C C:ILE543 4.2 15.7 1.0
CD C:ARG382 4.2 33.2 1.0
CE1 C:TYR350 4.3 25.5 1.0
C C:ASN348 4.3 31.1 1.0
CB C:ILE543 4.3 11.9 1.0
CB C:ASN348 4.4 25.7 1.0
CA C:THR544 4.4 14.8 1.0
CB C:THR545 4.4 23.0 1.0
O C:THR545 4.5 19.4 1.0
O C:GLY542 4.6 21.2 1.0
C C:THR544 4.6 19.1 1.0
O C:HOH954 4.7 32.9 1.0
CG1 C:ILE543 4.7 11.4 1.0
CA C:THR545 4.7 15.2 1.0
CB C:THR544 4.8 19.8 1.0
CD1 C:TYR350 4.8 26.9 1.0
OG1 C:THR545 4.9 23.1 1.0
N C:ILE543 4.9 13.9 1.0

Reference:

T.Inghardt, T.Antonsson, C.Ericsson, D.Hovdal, P.Johannesson, C.Johansson, U.Jurva, J.Kajanus, B.Kull, E.Michaelsson, A.Pettersen, T.Sjogren, H.Sorensen, K.Westerlund, E.L.Lindstedt. Discovery of AZD4831, A Mechanism-Based Irreversible Inhibitor of Myeloperoxidase, As A Potential Treatment For Heart Failure with Preserved Ejection Fraction. J.Med.Chem. V. 65 11485 2022.
ISSN: ISSN 0022-2623
PubMed: 36005476
DOI: 10.1021/ACS.JMEDCHEM.1C02141
Page generated: Tue Jul 30 00:55:25 2024

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