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Cadmium 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

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 9 in 1dl5

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Cadmium binding site 1 out of 9 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd601

b:18.6
occ:0.42
CL A:CL603 2.2 33.4 0.4
ND1 B:HIS312 2.2 28.5 1.0
CL A:CL604 2.6 15.5 0.6
CE1 B:HIS312 3.2 27.3 1.0
CG B:HIS312 3.2 23.3 1.0
CB B:HIS312 3.5 21.7 1.0
CG B:GLN289 3.9 37.1 1.0
CA B:HIS312 4.2 18.2 1.0
NE2 B:HIS312 4.3 25.8 1.0
O B:HOH1893 4.3 34.8 1.0
CD2 B:HIS312 4.3 23.9 1.0
N B:ILE313 4.7 17.1 1.0
O B:ILE313 4.7 18.9 1.0
CD B:GLN289 4.8 40.4 1.0
CB B:GLN289 4.9 26.2 1.0

Cadmium binding site 2 out of 9 in 1dl5

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Cadmium binding site 2 out of 9 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd621

b:21.4
occ:0.46
CL A:CL623 2.2 23.3 0.5
CL A:CL622 2.4 15.2 0.5
CD2 B:HIS238 2.4 31.3 1.0
CG B:HIS238 3.2 25.2 1.0
CB B:HIS238 3.5 20.8 1.0
NE2 B:HIS238 3.6 35.0 1.0
ND1 B:HIS238 4.4 33.7 1.0
N B:HIS238 4.5 16.3 1.0
CA B:HIS238 4.6 14.9 1.0
CE1 B:HIS238 4.6 32.2 1.0

Cadmium binding site 3 out of 9 in 1dl5

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Cadmium binding site 3 out of 9 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd641

b:25.8
occ:0.51
OD1 A:ASP272 2.5 37.1 1.0
O A:HOH925 2.7 32.1 1.0
O A:HOH926 2.7 22.7 1.0
OD2 A:ASP272 2.8 46.3 1.0
CG A:ASP272 3.0 43.5 1.0
O A:HOH842 3.9 34.3 1.0
OD1 A:ASP271 4.0 29.8 1.0
CA A:ARG236 4.1 29.4 1.0
N A:SER237 4.1 26.5 1.0
OG A:SER237 4.2 30.1 1.0
N A:ARG236 4.3 28.9 1.0
CB A:ASP272 4.5 39.0 1.0
C A:ARG236 4.5 27.3 1.0
N A:ASP272 4.9 34.5 1.0
N A:HIS238 5.0 24.6 1.0

Cadmium binding site 4 out of 9 in 1dl5

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Cadmium binding site 4 out of 9 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd650

b:12.3
occ:0.15
OD2 A:ASP16 2.2 35.1 1.0
CG A:ASP16 2.9 28.4 1.0
OD1 A:ASP16 3.0 28.8 1.0
O A:HOH860 3.9 40.7 1.0
O A:HOH753 3.9 27.5 1.0
NZ A:LYS10 4.4 33.8 1.0
CB A:ASP16 4.4 25.0 1.0
CE A:LYS10 5.0 33.4 1.0

Cadmium binding site 5 out of 9 in 1dl5

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Cadmium binding site 5 out of 9 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd651

b:21.1
occ:0.18
OD2 B:ASP74 2.5 31.9 1.0
OD1 B:ASP74 2.5 27.2 1.0
CG B:ASP74 2.8 31.8 1.0
CB B:ASP74 4.3 26.9 1.0
CG B:LYS75 4.8 31.7 1.0
N B:LYS75 4.8 24.5 1.0
CD2 B:HIS17 4.8 35.2 1.0
CD B:LYS75 4.9 36.5 1.0

Cadmium binding site 6 out of 9 in 1dl5

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Cadmium binding site 6 out of 9 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd701

b:16.7
occ:1.00
OE2 A:GLU253 2.2 13.9 1.0
CL B:CL702 2.5 19.9 1.0
CL B:CL703 2.5 18.7 1.0
OE1 A:GLU253 2.6 16.4 1.0
CD A:GLU253 2.8 18.3 1.0
NH2 A:ARG220 3.7 32.5 1.0
N A:ASP255 3.9 18.6 1.0
N A:GLY256 4.3 14.1 1.0
CG A:GLU253 4.3 16.2 1.0
CA A:ASP255 4.5 16.7 1.0
O A:GLU253 4.5 14.5 1.0
CZ A:ARG220 4.6 31.8 1.0
C A:ILE254 4.7 14.5 1.0
CA A:ILE254 4.8 17.9 1.0
C A:ASP255 4.9 18.3 1.0
C A:GLU253 4.9 12.3 1.0
NE A:ARG220 5.0 29.7 1.0

Cadmium binding site 7 out of 9 in 1dl5

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Cadmium binding site 7 out of 9 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd721

b:46.9
occ:1.00
CL B:CL722 2.0 27.5 1.0
O A:HOH930 2.3 16.2 1.0
CL B:CL723 2.4 23.9 0.9
O B:HOH1926 2.5 20.0 1.0
OD1 A:ASP279 3.3 27.8 1.0
OE1 A:GLU284 3.8 37.5 1.0
OE2 A:GLU284 3.9 41.0 1.0
CD A:GLU284 4.1 37.0 1.0
CE1 B:HIS312 4.2 27.3 1.0
ND2 A:ASN229 4.2 25.1 1.0
CG A:ASP279 4.2 23.8 1.0
NE2 B:HIS312 4.3 25.8 1.0
O B:HOH1744 4.3 31.9 1.0
CB A:ASP279 4.5 22.2 1.0
O B:HOH1807 4.7 41.7 1.0
CA A:ASP279 4.7 18.4 1.0
NH1 A:ARG230 4.7 53.5 1.0
CD A:PRO281 4.8 17.6 1.0
N A:ALA280 4.8 15.5 1.0
N A:PRO281 4.8 15.6 1.0
CB A:PRO281 4.9 14.9 1.0
CA A:PRO281 5.0 14.8 1.0

Cadmium binding site 8 out of 9 in 1dl5

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Cadmium binding site 8 out of 9 in the Protein-L-Isoaspartate O-Methyltransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd741

b:21.2
occ:0.96
OD1 B:ASP279 2.2 18.6 1.0
CL B:CL743 2.4 20.5 0.9
CL B:CL742 2.4 20.7 0.9
OE1 B:GLU284 2.6 22.4 1.0
OE2 B:GLU284 2.8 36.3 1.0
CG B:ASP279 2.9 17.8 1.0
OD2 B:ASP279 2.9 16.8 1.0
CD B:GLU284 3.1 30.5 1.0
O A:HOH749 4.3 25.1 1.0
CB B:ASP279 4.4 16.4 1.0
N B:PRO281 4.5 13.2 1.0
CD B:PRO281 4.6 16.1 1.0
CB B:PRO281 4.6 13.1 1.0
CA B:PRO281 4.6 13.8 1.0
CG B:GLU284 4.6 27.5 1.0
O A:HOH717 4.6 34.8 1.0
N B:ALA280 4.7 13.3 1.0
O A:HOH709 4.7 24.2 1.0
NH2 B:ARG230 4.8 27.9 1.0
NE B:ARG230 4.8 27.5 1.0
ND2 B:ASN229 4.8 20.2 1.0
CB A:PHE310 4.9 14.5 1.0
ND2 A:ASN285 4.9 20.0 1.0
CA B:ASP279 5.0 15.3 1.0

Cadmium binding site 9 out of 9 in 1dl5

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


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Protein-L-Isoaspartate O-Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd761

b:23.6
occ:0.90
OE2 B:GLU217 2.3 24.8 1.0
O B:HOH1927 2.4 17.4 1.0
O B:HOH1928 2.5 21.0 1.0
O B:HOH1929 2.6 33.6 1.0
O B:HOH1766 2.8 34.2 1.0
CD B:GLU217 3.3 25.7 1.0
OE1 B:GLU217 3.6 21.1 1.0
O B:HOH1702 3.7 35.5 1.0
O B:HOH1790 4.3 25.7 1.0
O B:GLY213 4.4 13.3 1.0
O B:HOH1864 4.5 27.3 1.0
O B:HOH1783 4.6 30.6 1.0
CG B:GLU217 4.6 20.9 1.0
O B:HOH1844 4.8 36.5 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 Aug 28 11:43:53 2020
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