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Cadmium in PDB 1rj4: Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+

Protein crystallography data

The structure of Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+, PDB code: 1rj4 was solved by M.Hothorn, I.D'angelo, J.A.Marquez, S.Greiner, K.Scheffzek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.67 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.170, 95.639, 126.191, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+ (pdb code 1rj4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+, PDB code: 1rj4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 1rj4

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Cadmium binding site 1 out of 8 in the Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd148

b:28.8
occ:1.00
O6 A:BTB156 2.1 27.4 1.0
O8 A:BTB156 2.2 42.8 1.0
O3 A:BTB156 2.3 28.1 1.0
O4 A:BTB156 2.3 35.6 1.0
N A:BTB156 2.3 24.6 1.0
OE2 A:GLU113 2.4 22.5 1.0
OE1 A:GLU113 2.4 26.9 1.0
CD A:GLU113 2.7 18.1 1.0
C2 A:BTB156 2.9 28.4 1.0
C3 A:BTB156 3.0 27.7 1.0
C4 A:BTB156 3.1 36.7 1.0
C6 A:BTB156 3.1 27.0 1.0
C5 A:BTB156 3.2 32.9 1.0
C8 A:BTB156 3.3 30.9 1.0
C7 A:BTB156 3.4 30.2 1.0
OD1 A:ASP110 3.7 28.6 1.0
O A:HOH161 4.0 22.2 1.0
O A:HOH189 4.0 27.4 1.0
CG A:GLU113 4.3 29.6 1.0
O A:HOH289 4.3 31.7 1.0
OH A:TYR117 4.3 30.2 1.0
O A:HOH320 4.4 40.9 1.0
C1 A:BTB156 4.5 31.3 1.0
OG A:SER76 4.5 19.6 1.0
CG A:ASP110 4.5 33.9 1.0
OE1 C:GLU87 4.9 22.7 1.0

Cadmium binding site 2 out of 8 in 1rj4

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Cadmium binding site 2 out of 8 in the Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd152

b:27.8
occ:1.00
OD2 A:ASP137 2.2 30.2 1.0
O B:HOH333 2.4 18.4 1.0
NE2 A:HIS133 2.4 26.6 1.0
O A:HOH334 2.5 34.0 1.0
OD1 A:ASP137 2.6 21.8 1.0
CG A:ASP137 2.7 28.5 1.0
CE1 A:HIS133 3.3 19.8 1.0
CD2 A:HIS133 3.4 26.0 1.0
OE1 A:GLN112 4.2 29.8 1.0
CB A:ASP137 4.3 20.3 1.0
CB A:SER108 4.4 23.3 1.0
ND1 A:HIS133 4.5 24.4 1.0
OG A:SER108 4.5 27.9 1.0
CG A:HIS133 4.5 22.9 1.0
C B:THR11 4.6 17.9 1.0
N B:PRO12 4.6 20.1 1.0
CA B:PRO12 4.8 21.3 1.0
O B:THR11 4.8 18.7 1.0
CB B:PRO12 4.8 25.1 1.0
CD B:PRO12 4.8 21.0 1.0
CD A:GLN112 4.9 28.7 1.0
NH2 B:ARG144 4.9 54.7 1.0
O A:HOH335 5.0 28.6 1.0

Cadmium binding site 3 out of 8 in 1rj4

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Cadmium binding site 3 out of 8 in the Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd150

b:27.5
occ:1.00
O3 B:BTB157 2.0 28.7 1.0
O6 B:BTB157 2.1 34.9 1.0
O8 B:BTB157 2.3 34.8 1.0
OE2 B:GLU113 2.3 24.3 1.0
OE1 B:GLU113 2.3 24.2 1.0
N B:BTB157 2.3 22.5 1.0
O4 B:BTB157 2.4 32.1 1.0
CD B:GLU113 2.6 20.5 1.0
C2 B:BTB157 3.1 27.3 1.0
C3 B:BTB157 3.1 33.1 1.0
C6 B:BTB157 3.1 31.9 1.0
C5 B:BTB157 3.2 30.5 1.0
C8 B:BTB157 3.2 25.1 1.0
C4 B:BTB157 3.3 30.8 1.0
C7 B:BTB157 3.3 22.2 1.0
OD1 B:ASP110 4.0 24.9 1.0
O B:HOH177 4.1 33.9 1.0
CG B:GLU113 4.2 24.8 1.0
OH B:TYR117 4.2 27.7 1.0
OG B:SER76 4.5 26.9 1.0
C1 B:BTB157 4.6 25.1 1.0
O B:HOH389 4.8 43.2 1.0
CG B:ASP110 4.9 30.1 1.0
O B:HOH283 4.9 36.5 1.0

Cadmium binding site 4 out of 8 in 1rj4

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Cadmium binding site 4 out of 8 in the Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd151

b:29.4
occ:1.00
O B:HOH190 2.2 31.3 1.0
OD2 B:ASP137 2.3 28.4 1.0
O B:HOH321 2.3 24.4 1.0
O B:HOH280 2.4 37.8 1.0
NE2 B:HIS133 2.4 22.4 1.0
O B:HOH384 2.6 37.2 1.0
OD1 B:ASP137 2.7 25.1 1.0
CG B:ASP137 2.8 30.6 1.0
CE1 B:HIS133 3.3 24.0 1.0
CD2 B:HIS133 3.4 26.8 1.0
OG B:SER108 4.0 35.3 1.0
OE1 B:GLN112 4.3 32.1 1.0
CB B:ASP137 4.3 22.0 1.0
ND1 B:HIS133 4.5 23.2 1.0
CG B:HIS133 4.5 24.7 1.0
O A:THR11 4.5 21.6 1.0
C A:THR11 4.6 20.2 1.0
N A:PRO12 4.6 19.7 1.0
CA A:PRO12 4.6 21.7 1.0
CB A:PRO12 4.7 22.0 1.0
CB B:SER108 4.8 25.5 1.0

Cadmium binding site 5 out of 8 in 1rj4

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Cadmium binding site 5 out of 8 in the Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd153

b:35.8
occ:1.00
O8 C:BTB158 2.0 47.3 1.0
OE2 C:GLU113 2.3 42.4 1.0
O6 C:BTB158 2.3 32.1 1.0
N C:BTB158 2.3 27.6 1.0
O4 C:BTB158 2.5 37.3 1.0
OE1 C:GLU113 2.5 26.4 1.0
O3 C:BTB158 2.6 42.2 1.0
CD C:GLU113 2.8 39.9 1.0
C2 C:BTB158 3.1 35.5 1.0
C8 C:BTB158 3.1 37.5 1.0
C4 C:BTB158 3.2 37.3 1.0
C6 C:BTB158 3.3 31.7 1.0
C3 C:BTB158 3.3 35.1 1.0
C7 C:BTB158 3.3 35.6 1.0
C5 C:BTB158 3.3 33.8 1.0
O A:HOH226 3.7 32.8 1.0
OD1 C:ASP110 3.9 33.9 1.0
O C:HOH380 4.1 40.0 1.0
CG C:GLU113 4.3 43.2 1.0
OH C:TYR117 4.3 40.1 1.0
OG C:SER76 4.5 28.8 1.0
C1 C:BTB158 4.6 31.4 1.0
OE1 A:GLU87 4.6 41.8 1.0
CG C:ASP110 4.7 34.7 1.0

Cadmium binding site 6 out of 8 in 1rj4

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Cadmium binding site 6 out of 8 in the Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd155

b:93.2
occ:1.00
OD2 C:ASP137 2.3 38.0 1.0
NE2 C:HIS133 2.5 48.9 1.0
CG C:ASP137 3.2 38.0 1.0
O C:HOH336 3.3 54.4 1.0
CE1 C:HIS133 3.4 47.6 1.0
CD2 C:HIS133 3.5 44.1 1.0
OD1 C:ASP137 3.5 36.4 1.0
OE1 C:GLN112 4.1 57.9 1.0
OG C:SER108 4.2 37.1 1.0
ND1 C:HIS133 4.5 44.3 1.0
CB C:ASP137 4.6 34.3 1.0
CG C:HIS133 4.6 40.3 1.0
CD C:GLN112 4.7 50.0 1.0
NE2 C:GLN112 4.8 54.7 1.0

Cadmium binding site 7 out of 8 in 1rj4

Go back to Cadmium Binding Sites List in 1rj4
Cadmium binding site 7 out of 8 in the Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd149

b:31.1
occ:1.00
O3 D:BTB159 2.1 31.2 1.0
O8 D:BTB159 2.1 31.4 1.0
O6 D:BTB159 2.2 24.0 1.0
N D:BTB159 2.3 22.3 1.0
OE1 D:GLU113 2.4 28.8 1.0
OE2 D:GLU113 2.4 23.0 1.0
O4 D:BTB159 2.4 30.9 1.0
CD D:GLU113 2.7 31.1 1.0
C2 D:BTB159 3.1 25.8 1.0
C8 D:BTB159 3.1 28.2 1.0
C3 D:BTB159 3.1 28.3 1.0
C6 D:BTB159 3.2 22.4 1.0
C5 D:BTB159 3.2 24.4 1.0
C4 D:BTB159 3.3 30.8 1.0
C7 D:BTB159 3.3 24.0 1.0
OD1 D:ASP110 4.0 27.2 1.0
OH D:TYR117 4.1 26.9 1.0
O D:HOH184 4.1 40.1 1.0
CG D:GLU113 4.3 29.7 1.0
O D:HOH242 4.4 35.4 1.0
O D:HOH267 4.4 33.0 1.0
OG D:SER76 4.5 22.7 1.0
C1 D:BTB159 4.6 21.9 1.0
O D:HOH265 4.7 36.7 1.0
CG D:ASP110 4.8 28.6 1.0

Cadmium binding site 8 out of 8 in 1rj4

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Cadmium binding site 8 out of 8 in the Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of A Cell Wall Invertase Inhibitor From Tobacco in Complex with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd154

b:40.0
occ:1.00
NE2 D:HIS133 2.4 34.2 1.0
OD2 D:ASP137 2.4 21.9 1.0
O D:HOH313 2.5 49.1 1.0
O D:HOH294 3.0 45.0 1.0
CG D:ASP137 3.3 28.8 1.0
CE1 D:HIS133 3.3 35.6 1.0
CD2 D:HIS133 3.4 32.3 1.0
OD1 D:ASP137 3.4 26.0 1.0
O D:HOH348 4.0 40.9 1.0
OG D:SER108 4.3 36.5 1.0
OE1 D:GLN112 4.4 46.0 1.0
ND1 D:HIS133 4.4 33.4 1.0
CG D:HIS133 4.5 31.4 1.0
CB D:ASP137 4.7 19.2 1.0
CD D:GLN112 5.0 39.6 1.0
NE2 D:GLN112 5.0 32.7 1.0

Reference:

M.Hothorn, I.D'angelo, J.A.Marquez, S.Greiner, K.Scheffzek. The Invertase Inhibitor Nt-Cif From Tobacco: A Highly Thermostable Four-Helix Bundle with An Unusual N-Terminal Extension J.Mol.Biol. V. 335 987 2004.
ISSN: ISSN 0022-2836
PubMed: 14698293
DOI: 10.1016/J.JMB.2003.10.066
Page generated: Wed Oct 28 09:56:14 2020
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