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Chlorine in PDB 1dl5: Protein-L-Isoaspartate O-Methyltransferase

Enzymatic activity of Protein-L-Isoaspartate O-Methyltransferase

All present enzymatic activity of Protein-L-Isoaspartate O-Methyltransferase:
2.1.1.77;

Protein crystallography data

The structure of Protein-L-Isoaspartate O-Methyltransferase, PDB code: 1dl5 was solved by M.M.Skinner, J.M.Puvathingal, R.L.Walter, A.M.Friedman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.060, 98.910, 76.860, 90.00, 105.66, 90.00
R / Rfree (%) 18.2 / 20.3

Other elements in 1dl5:

The structure of Protein-L-Isoaspartate O-Methyltransferase also contains other interesting chemical elements:

Cadmium (Cd) 9 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Protein-L-Isoaspartate O-Methyltransferase (pdb code 1dl5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Protein-L-Isoaspartate O-Methyltransferase, PDB code: 1dl5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 1dl5

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Chlorine binding site 1 out of 10 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:33.4
occ:0.44
 CD A:CD601 2.2 18.6 0.4
O B:ILE313 3.1 18.9 1.0
CL A:CL604 3.3 15.5 0.6
CB B:HIS312 3.3 21.7 1.0
ND1 B:HIS312 3.5 28.5 1.0
CG B:HIS312 3.8 23.3 1.0
CG B:GLN289 3.8 37.1 1.0
N B:ILE313 4.0 17.1 1.0
C B:ILE313 4.1 20.2 1.0
CD B:GLN289 4.3 40.4 1.0
CA B:HIS312 4.3 18.2 1.0
C B:HIS312 4.5 17.3 1.0
OE1 B:GLN289 4.5 43.8 1.0
CE1 B:HIS312 4.6 27.3 1.0
CA B:ILE313 4.7 16.6 1.0
CB B:GLN289 4.9 26.2 1.0
NE2 B:GLN289 4.9 44.6 1.0
CD2 B:HIS312 5.0 23.9 1.0

Chlorine binding site 2 out of 10 in 1dl5

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Chlorine binding site 2 out of 10 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:15.5
occ:0.55
 CD A:CD601 2.6 18.6 0.4
CG B:GLN289 3.0 37.1 1.0
N B:ILE313 3.2 17.1 1.0
CB B:GLN289 3.2 26.2 1.0
CL A:CL603 3.3 33.4 0.4
CA B:HIS312 3.5 18.2 1.0
CB B:HIS312 3.7 21.7 1.0
ND1 B:HIS312 3.8 28.5 1.0
O B:ILE313 3.8 18.9 1.0
C B:HIS312 3.8 17.3 1.0
O B:ASN285 3.8 17.9 1.0
CD2 B:LEU286 3.9 18.9 1.0
CA B:ILE313 4.2 16.6 1.0
CG B:HIS312 4.2 23.3 1.0
CA B:LEU286 4.2 16.0 1.0
CB B:ILE313 4.3 17.7 1.0
C B:ASN285 4.4 16.7 1.0
CD B:GLN289 4.4 40.4 1.0
C B:ILE313 4.5 20.2 1.0
O B:SER311 4.5 15.2 1.0
O B:HOH1893 4.5 34.8 1.0
N B:LEU286 4.5 16.2 1.0
CA B:GLN289 4.7 22.3 1.0
N B:HIS312 4.7 13.5 1.0
CG1 B:ILE313 4.8 18.0 1.0
CE1 B:HIS312 4.9 27.3 1.0
CG B:LEU286 4.9 18.7 1.0
OE1 B:GLN289 5.0 43.8 1.0

Chlorine binding site 3 out of 10 in 1dl5

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Chlorine binding site 3 out of 10 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl622

b:15.2
occ:0.51
 CD A:CD621 2.4 21.4 0.5
CA B:ARG236 3.4 16.9 1.0
C B:ARG236 3.5 18.5 1.0
CB B:HIS238 3.6 20.8 1.0
N B:ILE239 3.7 14.1 1.0
N B:HIS238 3.7 16.3 1.0
O B:ARG236 3.7 19.4 1.0
CG1 B:ILE239 3.8 16.2 1.0
CB B:ARG236 3.8 18.4 1.0
CD2 B:HIS238 3.9 31.3 1.0
CA B:HIS238 4.1 14.9 1.0
N B:SER237 4.1 18.1 1.0
CG B:HIS238 4.1 25.2 1.0
CD1 B:ILE239 4.2 17.1 1.0
C B:HIS238 4.3 14.3 1.0
CB B:ILE239 4.4 14.8 1.0
CL A:CL623 4.4 23.3 0.5
CG B:ARG236 4.6 23.1 1.0
CA B:ILE239 4.6 14.6 1.0
C B:SER237 4.6 16.1 1.0
N B:ARG236 4.7 15.8 1.0
CA B:SER237 4.9 18.6 1.0

Chlorine binding site 4 out of 10 in 1dl5

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Chlorine binding site 4 out of 10 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl623

b:23.3
occ:0.51
 CD A:CD621 2.2 21.4 0.5
CD2 B:HIS238 3.0 31.3 1.0
NE2 B:HIS238 3.3 35.0 1.0
O B:HOH1919 3.7 12.3 1.0
CG B:HIS238 4.2 25.2 1.0
CL A:CL622 4.4 15.2 0.5
CE1 B:HIS238 4.6 32.2 1.0

Chlorine binding site 5 out of 10 in 1dl5

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Chlorine binding site 5 out of 10 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl702

b:19.9
occ:1.00
 CD B:CD701 2.5 16.7 1.0
OE2 A:GLU253 3.5 13.9 1.0
NH2 A:ARG220 3.7 32.5 1.0
CL B:CL703 4.0 18.7 1.0
O A:HOH932 4.3 33.1 1.0
CD A:GLU253 4.6 18.3 1.0
CZ A:ARG220 4.7 31.8 1.0
OE1 A:GLU253 4.9 16.4 1.0

Chlorine binding site 6 out of 10 in 1dl5

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Chlorine binding site 6 out of 10 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl703

b:18.7
occ:1.00
 CD B:CD701 2.5 16.7 1.0
N A:ASP255 3.3 18.6 1.0
CA A:ILE254 3.7 17.9 1.0
OE2 A:GLU253 3.7 13.9 1.0
OE1 A:GLU253 3.8 16.4 1.0
NH2 A:ARG220 3.9 32.5 1.0
CL B:CL702 4.0 19.9 1.0
O A:GLU253 4.0 14.5 1.0
NE A:ARG220 4.0 29.7 1.0
O A:HOH876 4.0 45.9 1.0
C A:ILE254 4.0 14.5 1.0
CZ A:ARG220 4.0 31.8 1.0
CD A:GLU253 4.1 18.3 1.0
CA A:ASP255 4.3 16.7 1.0
OD1 A:ASP255 4.4 21.2 1.0
CD1 A:ILE254 4.5 25.7 1.0
N A:ILE254 4.6 16.4 1.0
CG2 A:ILE254 4.6 23.4 1.0
C A:GLU253 4.6 12.3 1.0
CB A:ILE254 4.7 20.9 1.0
NH1 A:ARG220 4.8 28.6 1.0
CD A:ARG220 4.8 27.9 1.0

Chlorine binding site 7 out of 10 in 1dl5

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Chlorine binding site 7 out of 10 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl722

b:27.5
occ:1.00
 CD B:CD721 2.0 46.9 1.0
OE1 A:GLU284 2.2 37.5 1.0
OE2 A:GLU284 2.8 41.0 1.0
CD A:GLU284 2.8 37.0 1.0
O B:HOH1926 3.3 20.0 1.0
O A:HOH930 3.4 16.2 1.0
CL B:CL723 3.4 23.9 0.9
NH1 A:ARG230 3.8 53.5 1.0
CE1 B:HIS312 4.1 27.3 1.0
CG A:GLU284 4.3 32.5 1.0
ND2 B:ASN285 4.3 24.4 1.0
CZ A:ARG230 4.5 49.0 1.0
O B:HOH1807 4.6 41.7 1.0
NH2 A:ARG230 4.7 52.3 1.0
CB A:PRO281 4.7 14.9 1.0
CA A:PRO281 4.8 14.8 1.0
NE2 B:HIS312 4.8 25.8 1.0

Chlorine binding site 8 out of 10 in 1dl5

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Chlorine binding site 8 out of 10 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl723

b:23.9
occ:0.87
 CD B:CD721 2.4 46.9 1.0
N A:ALA280 3.2 15.5 1.0
OE2 A:GLU284 3.4 41.0 1.0
CL B:CL722 3.4 27.5 1.0
CD A:GLU284 3.5 37.0 1.0
OE1 A:GLU284 3.8 37.5 1.0
C A:ALA280 3.8 14.6 1.0
N A:PRO281 3.8 15.6 1.0
CA A:ASP279 3.9 18.4 1.0
CG2 A:ILE276 4.0 18.1 1.0
O A:HOH930 4.0 16.2 1.0
ND2 A:ASN229 4.0 25.1 1.0
C A:ASP279 4.0 14.1 1.0
CA A:ALA280 4.0 16.3 1.0
OD1 A:ASP279 4.0 27.8 1.0
O B:HOH1926 4.1 20.0 1.0
CG A:GLU284 4.1 32.5 1.0
CD1 A:ILE276 4.2 26.0 1.0
O A:ALA280 4.2 16.5 1.0
CD A:PRO281 4.3 17.6 1.0
CB A:ASP279 4.4 22.2 1.0
CA A:PRO281 4.4 14.8 1.0
O A:GLY278 4.5 18.1 1.0
CB A:ALA280 4.6 17.2 1.0
CG A:ASP279 4.7 23.8 1.0
CB A:ILE276 5.0 19.6 1.0
CG A:ASN229 5.0 28.2 1.0
CB A:PRO281 5.0 14.9 1.0

Chlorine binding site 9 out of 10 in 1dl5

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Chlorine binding site 9 out of 10 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl742

b:20.7
occ:0.95
 CD B:CD741 2.4 21.2 1.0
NE B:ARG230 3.2 27.5 1.0
O A:HOH749 3.3 25.1 1.0
ND2 B:ASN229 3.5 20.2 1.0
OD2 B:ASP279 3.6 16.8 1.0
OH A:TYR194 3.6 24.7 1.0
OD1 B:ASP279 3.8 18.6 1.0
CD B:ARG230 3.9 23.0 1.0
OE1 B:GLU284 3.9 22.4 1.0
CG B:ASP279 4.0 17.8 1.0
OD1 B:ASN229 4.0 17.6 1.0
CG B:ASN229 4.1 17.9 1.0
CZ B:ARG230 4.1 26.6 1.0
NH2 B:ARG230 4.2 27.9 1.0
CL B:CL743 4.3 20.5 0.9
O A:HOH717 4.3 34.8 1.0
OE2 B:GLU284 4.3 36.3 1.0
CD B:GLU284 4.5 30.5 1.0
CG B:ARG230 4.7 21.0 1.0
CZ A:TYR194 4.9 19.9 1.0
O A:HOH873 5.0 47.4 1.0
ND1 A:HIS312 5.0 22.2 1.0

Chlorine binding site 10 out of 10 in 1dl5

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Chlorine binding site 10 out of 10 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl743

b:20.5
occ:0.93
 CD B:CD741 2.4 21.2 1.0
O A:HOH709 3.2 24.2 1.0
ND2 A:ASN285 3.3 20.0 1.0
OD1 B:ASP279 3.7 18.6 1.0
CB B:PRO281 3.8 13.1 1.0
OE1 B:GLU284 3.8 22.4 1.0
OD2 B:ASP279 3.8 16.8 1.0
CB A:PHE310 3.9 14.5 1.0
CG B:ASP279 4.1 17.8 1.0
CD2 A:PHE310 4.3 17.0 1.0
CL B:CL742 4.3 20.7 0.9
CG A:ASN285 4.3 21.8 1.0
CG B:PRO281 4.4 15.2 1.0
CA A:GLU282 4.4 15.2 1.0
OE2 B:GLU284 4.5 36.3 1.0
CB A:ASN285 4.5 19.3 1.0
CB A:GLU282 4.5 14.8 1.0
O A:HOH749 4.5 25.1 1.0
CD B:GLU284 4.5 30.5 1.0
CG A:PHE310 4.5 16.2 1.0
CA B:PRO281 4.5 13.8 1.0
CD B:PRO281 4.5 16.1 1.0
O A:HOH726 4.6 20.6 1.0
O A:HOH717 4.8 34.8 1.0
N B:PRO281 4.9 13.2 1.0

Reference:

M.M.Skinner, J.M.Puvathingal, R.L.Walter, A.M.Friedman. Crystal Structure of Protein Isoaspartyl Methyltransferase: A Catalyst For Protein Repair. Structure Fold.Des. V. 8 1189 2000.
ISSN: ISSN 0969-2126
PubMed: 11080641
DOI: 10.1016/S0969-2126(00)00522-0
Page generated: Fri Jul 19 21:35:58 2024

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