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Cadmium in PDB 4pl9: Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana

Enzymatic activity of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana

All present enzymatic activity of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana:
2.7.13.3;

Protein crystallography data

The structure of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana, PDB code: 4pl9 was solved by S.Panneerselvam, J.Mueller-Dieckmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.56 / 1.90
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.260, 83.120, 91.930, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 18.2

Other elements in 4pl9:

The structure of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Cadmium atom in the Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana (pdb code 4pl9). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 11 binding sites of Cadmium where determined in the Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana, PDB code: 4pl9:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 11 in 4pl9

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Cadmium binding site 1 out of 11 in the Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd601

b:37.4
occ:1.00
 OD1 A:ASN470 2.3 34.5 1.0
O1A A:ADP613 2.3 31.8 1.0
O2B A:ADP613 2.5 39.3 1.0
O A:HOH723 2.5 31.6 1.0
OD1 A:ASN466 2.5 27.8 0.5
O A:HOH726 2.5 40.5 1.0
HD22 A:ASN470 2.8 31.3 1.0
CG A:ASN470 3.1 31.2 1.0
ND2 A:ASN470 3.3 31.3 1.0
PB A:ADP613 3.3 38.4 1.0
PA A:ADP613 3.4 35.2 1.0
O3A A:ADP613 3.5 36.9 1.0
HD22 A:ASN466 3.5 42.8 0.5
CG A:ASN466 3.5 38.7 0.5
HA3 A:GLY547 3.6 34.3 1.0
HZ2 A:LYS473 3.7 43.2 1.0
O1B A:ADP613 3.8 34.0 1.0
HZ1 A:LYS473 3.8 43.2 1.0
ND2 A:ASN466 3.9 29.6 0.5
CD A:CD602 3.9 49.5 0.5
HE2 A:PHE474 4.1 41.6 1.0
HD21 A:ASN470 4.1 31.3 1.0
H A:GLY547 4.2 38.6 1.0
NZ A:LYS473 4.2 43.2 1.0
O5' A:ADP613 4.3 34.9 1.0
HD3 A:LYS473 4.3 45.5 1.0
O A:ASN466 4.5 35.4 1.0
HA A:ASN470 4.5 29.9 1.0
HD2 A:LYS473 4.5 45.5 1.0
CA A:GLY547 4.5 34.3 1.0
HB3 A:ASN466 4.5 31.3 0.5
O2A A:ADP613 4.6 38.2 1.0
CB A:ASN470 4.6 27.3 1.0
O3B A:ADP613 4.7 39.7 1.0
N A:GLY547 4.8 38.6 1.0
HD21 A:ASN466 4.8 42.8 0.5
HZ3 A:LYS473 4.8 43.2 1.0
CD A:LYS473 4.8 45.5 1.0
HA A:ASN466 4.8 38.0 0.5
HG A:LEU548 4.9 32.5 1.0
H3' A:ADP613 4.9 36.5 1.0
CB A:ASN466 4.9 32.0 0.5
CE2 A:PHE474 5.0 41.6 1.0
HA A:ASN466 5.0 38.0 0.5
CA A:ASN470 5.0 29.9 1.0
H A:LEU548 5.0 32.4 1.0

Cadmium binding site 2 out of 11 in 4pl9

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Cadmium binding site 2 out of 11 in the Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd602

b:49.5
occ:0.50
 O1B A:ADP613 2.3 34.0 1.0
O A:HOH723 2.4 31.6 1.0
HZ1 A:LYS473 3.0 43.2 1.0
PB A:ADP613 3.5 38.4 1.0
HZ3 A:LYS473 3.5 43.2 1.0
NZ A:LYS473 3.6 43.2 1.0
HA2 A:GLY545 3.7 55.4 1.0
O A:HOH726 3.8 40.5 1.0
HZ2 A:LYS473 3.8 43.2 1.0
O2B A:ADP613 3.8 39.3 1.0
H A:LEU546 3.8 49.1 1.0
CD A:CD601 3.9 37.4 1.0
O3A A:ADP613 4.3 36.9 1.0
H A:GLY547 4.4 38.6 1.0
HA3 A:GLY545 4.4 55.4 1.0
CA A:GLY545 4.5 55.4 1.0
N A:LEU546 4.6 49.1 1.0
O3B A:ADP613 4.7 39.7 1.0
CE A:LYS473 5.0 51.2 1.0

Cadmium binding site 3 out of 11 in 4pl9

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Cadmium binding site 3 out of 11 in the Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd603

b:36.1
occ:1.00
 N1 A:ADP613 2.4 37.5 1.0
OD2 A:ASP513 2.4 36.6 1.0
SG A:CYS573 2.4 33.1 1.0
CL A:CL612 2.4 37.4 1.0
OD1 A:ASP513 2.5 35.9 1.0
HN61 A:ADP613 2.7 31.9 1.0
CG A:ASP513 2.8 34.1 1.0
C6 A:ADP613 3.1 32.5 1.0
HB3 A:CYS573 3.1 30.4 1.0
H A:CYS573 3.1 31.7 1.0
C2 A:ADP613 3.2 32.6 1.0
N6 A:ADP613 3.2 31.9 1.0
H2 A:ADP613 3.3 32.6 1.0
CB A:CYS573 3.3 30.4 1.0
HG A:CYS573 3.3 33.1 1.0
N A:CYS573 3.4 31.7 1.0
HA2 A:GLY572 3.8 31.7 1.0
HA3 A:GLY515 3.8 44.6 1.0
H A:GLY515 3.9 42.0 1.0
CA A:CYS573 3.9 32.4 1.0
HD11 A:ILE518 3.9 34.0 1.0
C A:GLY572 4.0 36.7 1.0
HB2 A:CYS573 4.2 30.4 1.0
HN62 A:ADP613 4.2 31.9 1.0
HG13 A:ILE518 4.2 31.7 1.0
CB A:ASP513 4.3 37.5 1.0
CA A:GLY572 4.3 31.7 1.0
HB2 A:PHE474 4.4 32.2 1.0
C5 A:ADP613 4.4 34.3 1.0
O A:HOH738 4.4 32.6 1.0
N3 A:ADP613 4.4 33.4 1.0
HA3 A:GLY572 4.5 31.7 1.0
O A:CYS573 4.5 33.8 1.0
C A:CYS573 4.5 38.4 1.0
N A:GLY515 4.6 42.0 1.0
HB3 A:PHE474 4.6 32.2 1.0
CA A:GLY515 4.6 44.6 1.0
HB3 A:ASP513 4.6 37.5 1.0
CD1 A:ILE518 4.7 34.0 1.0
HG A:SER475 4.7 38.5 1.0
H A:GLY517 4.7 37.7 1.0
HB2 A:ASP513 4.7 37.5 1.0
H A:ASP513 4.7 32.5 1.0
HD12 A:ILE518 4.8 34.0 1.0
HA A:ALA471 4.8 31.0 1.0
HA A:CYS573 4.8 32.4 1.0
O A:GLY572 4.8 37.3 1.0
CG1 A:ILE518 4.9 31.7 1.0
C4 A:ADP613 4.9 38.0 1.0
CB A:PHE474 4.9 32.2 1.0

Cadmium binding site 4 out of 11 in 4pl9

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Cadmium binding site 4 out of 11 in the Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd604

b:32.5
occ:0.50
 OE1 A:GLU565 2.4 33.1 1.0
O A:HOH728 2.5 54.4 0.5
OE2 A:GLU565 2.5 35.6 1.0
CD A:GLU565 2.8 35.5 1.0
O A:HOH729 3.1 35.3 1.0
HE1 A:TRP563 3.7 26.2 1.0
HZ2 A:TRP563 3.7 30.3 1.0
HD13 A:ILE576 4.2 39.2 1.0
CG A:GLU565 4.3 32.9 1.0
NE1 A:TRP563 4.5 26.2 1.0
HD11 A:ILE576 4.5 39.2 1.0
CZ2 A:TRP563 4.5 30.3 1.0
HG2 A:GLU565 4.7 32.9 1.0
HG3 A:GLU565 4.7 32.9 1.0
CD1 A:ILE576 4.8 39.2 1.0
CE2 A:TRP563 4.9 29.6 1.0

Cadmium binding site 5 out of 11 in 4pl9

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Cadmium binding site 5 out of 11 in the Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd605

b:44.0
occ:1.00
 OE1 A:GLU451 2.4 39.4 1.0
OE2 A:GLU451 2.4 55.0 1.0
O A:HOH701 2.5 56.0 0.5
CD A:GLU451 2.7 39.0 1.0
HE2 A:PHE452 4.2 41.6 1.0
CG A:GLU451 4.3 38.5 1.0
O A:HOH709 4.5 33.3 1.0
HG3 A:GLU451 4.7 38.5 1.0
HG2 A:GLU451 4.7 38.5 1.0
HD22 A:ASN418 4.8 35.7 1.0
HB2 A:GLU451 4.8 37.4 1.0
HB3 A:GLU451 4.9 37.4 1.0
CB A:GLU451 5.0 37.4 1.0
CE2 A:PHE452 5.0 41.6 1.0

Cadmium binding site 6 out of 11 in 4pl9

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Cadmium binding site 6 out of 11 in the Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd606

b:58.2
occ:0.48
 HZ3 A:LYS458 1.7 68.7 1.0
OE2 A:GLU413 2.4 64.1 1.0
OE1 A:GLU413 2.5 73.2 1.0
NZ A:LYS458 2.5 68.7 1.0
CD A:GLU413 2.8 62.6 1.0
HE2 A:LYS458 3.0 63.4 1.0
HZ2 A:LYS458 3.0 68.7 1.0
HE3 A:LYS458 3.0 63.4 1.0
HZ1 A:LYS458 3.0 68.7 1.0
CE A:LYS458 3.1 63.4 1.0
HH22 A:ARG459 4.2 55.2 1.0
CG A:GLU413 4.3 56.2 1.0
HH21 A:ARG459 4.3 55.2 1.0
NH2 A:ARG459 4.4 55.2 1.0
CD A:LYS458 4.6 62.0 1.0
HG2 A:GLU413 4.6 56.2 1.0
HG3 A:GLU413 4.7 56.2 1.0
HD2 A:LYS458 4.8 62.0 1.0
HB2 A:GLU413 4.9 41.8 1.0

Cadmium binding site 7 out of 11 in 4pl9

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Cadmium binding site 7 out of 11 in the Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd607

b:68.1
occ:0.55
 OE2 A:GLU559 2.5 69.2 1.0
OE1 A:GLU559 2.5 65.2 1.0
CD A:GLU559 2.8 61.0 1.0
HE3 A:LYS580 3.6 63.2 1.0
CG A:GLU559 4.3 48.5 1.0
HZ3 A:LYS580 4.4 70.3 1.0
CE A:LYS580 4.4 63.2 1.0
HE2 A:LYS580 4.6 63.2 1.0
HG2 A:GLU559 4.6 48.5 1.0
NZ A:LYS580 4.8 70.3 1.0
HG3 A:GLU559 4.8 48.5 1.0
HB3 A:GLU559 4.9 40.4 1.0
HZ1 A:LYS580 4.9 70.3 1.0

Cadmium binding site 8 out of 11 in 4pl9

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Cadmium binding site 8 out of 11 in the Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd608

b:81.5
occ:0.53
 OE1 A:GLU457 2.5 61.8 1.0
OE2 A:GLU457 2.5 59.5 1.0
CD A:GLU457 2.8 46.7 1.0
O A:HOH725 3.9 56.4 1.0
O A:HOH760 3.9 56.0 1.0
HB2 A:PHE417 4.0 35.2 1.0
HB3 A:PHE417 4.2 35.2 1.0
CG A:GLU457 4.4 40.7 1.0
O A:HOH767 4.4 60.1 1.0
CB A:PHE417 4.6 35.2 1.0
HG2 A:GLU457 4.7 40.7 1.0
HG3 A:GLU457 4.8 40.7 1.0

Cadmium binding site 9 out of 11 in 4pl9

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Cadmium binding site 9 out of 11 in the Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd609

b:0.7
occ:0.64
 HD1 A:HIS504 1.8 77.2 1.0
ND1 A:HIS504 2.5 77.2 1.0
O A:HOH792 2.6 73.3 1.0
HB2 A:HIS504 3.1 57.2 1.0
CE1 A:HIS504 3.3 79.3 1.0
CG A:HIS504 3.4 72.0 1.0
HE1 A:HIS504 3.5 79.3 1.0
H A:HIS504 3.5 43.2 1.0
HA A:SER503 3.6 54.0 1.0
CB A:HIS504 3.7 57.2 1.0
N A:HIS504 3.9 43.2 1.0
O A:HOH731 4.4 53.8 1.0
NE2 A:HIS504 4.4 84.2 1.0
CA A:HIS504 4.4 39.6 1.0
CA A:SER503 4.5 54.0 1.0
CD2 A:HIS504 4.5 76.7 1.0
HB3 A:HIS504 4.5 57.2 1.0
C A:SER503 4.5 47.1 1.0
HD3 A:LYS580 4.7 57.1 1.0

Cadmium binding site 10 out of 11 in 4pl9

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Cadmium binding site 10 out of 11 in the Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of the Catalytic Domain of ETR1 From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd610

b:0.8
occ:0.83
 HE2 A:HIS504 1.6 84.2 1.0
NE2 A:HIS504 2.4 84.2 1.0
O A:HOH757 2.6 62.8 1.0
O A:HOH799 2.6 65.0 1.0
CD2 A:HIS504 3.3 76.7 1.0
HD2 A:HIS504 3.3 76.7 1.0
CE1 A:HIS504 3.5 79.3 1.0
HE1 A:HIS504 3.7 79.3 1.0
CG A:HIS504 4.5 72.0 1.0
ND1 A:HIS504 4.5 77.2 1.0
HA3 A:GLY582 5.0 37.6 1.0

Reference:

H.Mayerhofer, S.Panneerselvam, H.Kaljunen, A.Tuukkanen, H.D.Mertens, J.Mueller-Dieckmann. Structural Model of the Cytosolic Domain of the Plant Ethylene Receptor 1 (ETR1). J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25451923
DOI: 10.1074/JBC.M114.587667
Page generated: Fri Jul 19 17:50:02 2024

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