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Cadmium in PDB 4jc6: Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization

Protein crystallography data

The structure of Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization, PDB code: 4jc6 was solved by A.Frick, M.Jarva, M.Nyblom, M.Ekvall, P Uzdavinys, S.Tornroth-Horsefield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.90 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.546, 141.818, 186.515, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.7

Other elements in 4jc6:

The structure of Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization also contains other interesting chemical elements:

Mercury (Hg) 32 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Cadmium atom in the Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization (pdb code 4jc6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 17 binding sites of Cadmium where determined in the Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization, PDB code: 4jc6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 17 in 4jc6

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Cadmium binding site 1 out of 17 in the Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:30.6
occ:0.99
 OE2 A:GLU31 2.3 28.4 1.0
OD2 A:ASP28 2.4 33.2 1.0
O A:HOH401 2.4 8.1 1.0
O A:HOH402 2.4 12.0 1.0
OD1 A:ASP28 2.5 34.4 1.0
OE1 A:GLU31 2.7 28.4 1.0
CG A:ASP28 2.8 31.8 1.0
CD A:GLU31 2.8 28.7 1.0
NE A:ARG118 4.1 26.4 1.0
CB A:ASP28 4.3 29.2 1.0
OG A:SER115 4.3 28.8 1.0
NH2 A:ARG118 4.3 27.1 1.0
CG A:GLU31 4.3 28.0 1.0
N A:GLU31 4.3 29.3 1.0
CA A:GLY30 4.4 29.5 1.0
CB A:SER115 4.4 28.2 1.0
N A:GLY30 4.6 28.5 1.0
C A:GLY30 4.6 31.4 1.0
CZ A:ARG118 4.7 27.3 1.0
N A:ASP28 4.7 34.4 1.0
N A:SER115 4.8 29.9 1.0
CA A:ASP28 4.9 29.6 1.0
CD A:ARG118 5.0 25.4 1.0

Cadmium binding site 2 out of 17 in 4jc6

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Cadmium binding site 2 out of 17 in the Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:33.8
occ:0.66
 O A:HOH480 2.3 36.3 1.0
O A:HOH408 2.4 26.8 1.0
O A:ALA267 2.5 46.2 1.0
OG1 A:THR183 2.5 29.0 1.0
O A:HOH421 2.5 22.7 1.0
O A:HOH481 2.6 41.6 1.0
C A:ALA267 3.4 49.7 1.0
NZ A:LYS113 3.4 52.4 1.0
CB A:THR183 3.6 25.5 1.0
CA A:ALA267 3.7 48.0 1.0
O A:PHE180 4.1 26.1 1.0
O A:THR183 4.2 25.1 1.0
CE1 A:HIS260 4.4 33.4 1.0
CG2 A:THR183 4.4 22.8 1.0
CB A:ALA267 4.4 48.9 1.0
O A:ILE269 4.5 47.6 1.0
CE A:LYS113 4.5 51.2 1.0
N A:ALA268 4.5 48.8 1.0
O A:ALA266 4.5 38.6 1.0
C A:THR183 4.6 26.3 1.0
CA A:THR183 4.7 24.3 1.0
N A:ALA267 4.9 42.6 1.0
NE2 A:HIS260 5.0 33.9 1.0
CB A:PRO185 5.0 35.7 1.0

Cadmium binding site 3 out of 17 in 4jc6

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Cadmium binding site 3 out of 17 in the Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:26.8
occ:0.71
 O A:HOH478 2.0 39.9 1.0
O A:HOH453 2.4 34.7 1.0
O A:HOH404 2.5 19.0 1.0
O A:HOH477 2.6 16.8 1.0
O A:HOH434 2.6 23.0 1.0
O A:HOH476 2.6 17.1 1.0
NZ A:LYS138 4.0 34.9 1.0
O A:PHE233 4.1 28.6 1.0
OD1 A:ASN146 4.1 30.8 1.0
ND2 A:ASN146 4.4 28.9 1.0
CG A:ASN146 4.4 31.2 1.0
CE A:LYS138 4.8 34.3 1.0

Cadmium binding site 4 out of 17 in 4jc6

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Cadmium binding site 4 out of 17 in the Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:35.9
occ:0.97
 OE2 B:GLU31 2.1 33.8 1.0
OD2 B:ASP28 2.4 36.3 1.0
OD1 B:ASP28 2.4 35.1 1.0
O B:HOH402 2.4 15.0 1.0
O B:HOH401 2.5 11.8 1.0
CG B:ASP28 2.7 34.3 1.0
CD B:GLU31 2.8 33.7 1.0
OE1 B:GLU31 2.9 30.9 1.0
NE B:ARG118 4.1 30.6 1.0
NH2 B:ARG118 4.2 31.9 1.0
CB B:ASP28 4.2 34.6 1.0
OG B:SER115 4.3 30.9 1.0
CG B:GLU31 4.3 33.2 1.0
CA B:GLY30 4.3 32.8 1.0
N B:GLU31 4.3 34.3 1.0
CB B:SER115 4.5 30.9 1.0
N B:GLY30 4.6 33.3 1.0
C B:GLY30 4.6 34.3 1.0
CZ B:ARG118 4.6 31.1 1.0
N B:ASP28 4.8 37.0 1.0
N B:SER115 4.9 34.5 1.0
CA B:ASP28 4.9 34.1 1.0

Cadmium binding site 5 out of 17 in 4jc6

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Cadmium binding site 5 out of 17 in the Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:37.4
occ:0.67
 O B:HOH460 2.1 41.1 1.0
O B:HOH408 2.4 24.8 1.0
O B:HOH405 2.4 26.7 1.0
O B:HOH461 2.5 51.3 1.0
OG1 B:THR183 2.5 28.0 1.0
O B:ALA267 2.6 55.1 1.0
C B:ALA267 3.5 51.5 1.0
CB B:THR183 3.5 25.9 1.0
CA B:ALA267 3.8 51.1 1.0
O B:PHE180 4.1 29.5 1.0
O B:THR183 4.3 29.0 1.0
CG2 B:THR183 4.3 25.8 1.0
CE B:LYS113 4.4 51.2 1.0
CB B:ALA267 4.4 47.3 1.0
CE1 B:HIS260 4.4 40.2 1.0
O B:ILE269 4.5 55.2 1.0
NZ B:LYS113 4.5 56.2 1.0
O B:ALA266 4.6 42.0 1.0
C B:THR183 4.6 28.0 1.0
CA B:THR183 4.6 26.8 1.0
N B:ALA268 4.7 52.3 1.0
CB B:PRO185 4.9 38.8 1.0
N B:ALA267 5.0 46.6 1.0

Cadmium binding site 6 out of 17 in 4jc6

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Cadmium binding site 6 out of 17 in the Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd302

b:32.0
occ:0.97
 OE2 C:GLU31 2.1 31.3 1.0
OD2 C:ASP28 2.2 29.6 1.0
O C:HOH402 2.5 12.0 1.0
O C:HOH401 2.5 6.4 1.0
OD1 C:ASP28 2.5 31.6 1.0
CG C:ASP28 2.7 29.9 1.0
CD C:GLU31 2.8 31.9 1.0
OE1 C:GLU31 2.8 29.9 1.0
NE C:ARG118 4.2 26.0 1.0
O C:HOH440 4.2 40.7 1.0
CB C:ASP28 4.2 27.7 1.0
CA C:GLY30 4.2 29.6 1.0
CG C:GLU31 4.3 30.2 1.0
OG C:SER115 4.3 31.3 1.0
N C:GLU31 4.3 27.8 1.0
NH2 C:ARG118 4.4 31.1 1.0
CB C:SER115 4.5 28.5 1.0
N C:GLY30 4.5 30.0 1.0
C C:GLY30 4.5 29.9 1.0
O C:HOH471 4.7 63.5 1.0
N C:ASP28 4.7 32.6 1.0
CZ C:ARG118 4.8 28.7 1.0
N C:SER115 4.9 28.6 1.0
CA C:ASP28 4.9 29.9 1.0
O C:ASP28 5.0 27.7 1.0

Cadmium binding site 7 out of 17 in 4jc6

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Cadmium binding site 7 out of 17 in the Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd303

b:37.5
occ:0.66
 O C:HOH475 2.3 51.5 1.0
O C:HOH476 2.3 45.5 1.0
O C:HOH474 2.4 36.5 1.0
O C:HOH412 2.4 22.4 1.0
OG1 C:THR183 2.5 27.4 1.0
O C:ALA267 2.5 50.6 1.0
C C:ALA267 3.4 52.3 1.0
CB C:THR183 3.6 24.0 1.0
CA C:ALA267 3.7 51.2 1.0
O C:PHE180 4.2 24.7 1.0
NZ C:LYS113 4.3 55.0 1.0
CB C:ALA267 4.4 49.5 1.0
O C:THR183 4.4 27.0 1.0
O C:ILE269 4.4 54.8 1.0
CG2 C:THR183 4.4 24.0 1.0
O C:ALA266 4.5 46.9 1.0
CE1 C:HIS260 4.5 39.5 1.0
CE C:LYS113 4.6 56.6 1.0
N C:ALA268 4.6 52.6 1.0
C C:THR183 4.6 26.2 1.0
CA C:THR183 4.7 23.9 1.0
CB C:PRO185 4.8 39.0 1.0
N C:ALA267 4.9 43.2 1.0
CA C:PRO185 4.9 37.9 1.0

Cadmium binding site 8 out of 17 in 4jc6

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Cadmium binding site 8 out of 17 in the Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd303

b:30.8
occ:0.94
 OE2 D:GLU31 2.1 28.9 1.0
OD2 D:ASP28 2.2 28.4 1.0
O D:HOH402 2.5 14.5 1.0
O D:HOH401 2.5 9.5 1.0
OD1 D:ASP28 2.5 28.6 1.0
CG D:ASP28 2.7 30.2 1.0
CD D:GLU31 2.8 28.6 1.0
OE1 D:GLU31 2.8 30.2 1.0
NE D:ARG118 4.0 25.1 1.0
CB D:ASP28 4.2 29.0 1.0
OG D:SER115 4.2 27.3 1.0
NH2 D:ARG118 4.3 28.1 1.0
CG D:GLU31 4.3 29.6 1.0
CA D:GLY30 4.3 26.6 1.0
N D:GLU31 4.4 28.0 1.0
CB D:SER115 4.5 27.2 1.0
N D:GLY30 4.6 27.5 1.0
C D:GLY30 4.6 27.3 1.0
CZ D:ARG118 4.7 26.7 1.0
N D:ASP28 4.7 31.9 1.0
CA D:ASP28 4.9 30.2 1.0
N D:SER115 4.9 28.7 1.0

Cadmium binding site 9 out of 17 in 4jc6

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Cadmium binding site 9 out of 17 in the Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd304

b:34.4
occ:0.68
 O D:HOH473 2.2 39.8 1.0
O D:HOH404 2.4 25.8 1.0
OG1 D:THR183 2.4 29.1 1.0
O D:ALA267 2.5 45.6 1.0
O D:HOH437 2.5 45.2 1.0
O D:HOH408 2.6 20.9 1.0
C D:ALA267 3.5 44.7 1.0
CB D:THR183 3.5 25.5 1.0
NZ D:LYS113 3.7 56.9 1.0
CA D:ALA267 3.8 44.2 1.0
O D:PHE180 4.2 26.8 1.0
O D:THR183 4.3 27.7 1.0
CG2 D:THR183 4.3 24.1 1.0
CE1 D:HIS260 4.4 30.1 1.0
CB D:ALA267 4.5 45.2 1.0
O D:ILE269 4.5 47.1 1.0
O D:ALA266 4.5 35.2 1.0
CE D:LYS113 4.6 53.3 1.0
C D:THR183 4.6 26.0 1.0
CA D:THR183 4.7 24.9 1.0
N D:ALA268 4.7 43.5 1.0
CB D:PRO185 4.8 34.1 1.0
CA D:PRO185 5.0 34.9 1.0
N D:ALA267 5.0 37.0 1.0

Cadmium binding site 10 out of 17 in 4jc6

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Cadmium binding site 10 out of 17 in the Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Mercury Activation of the Plant Aquaporin SOPIP2;1 - Structural and Functional Characterization within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cd303

b:38.2
occ:1.00
 OE2 H:GLU31 2.2 36.1 1.0
OD2 H:ASP28 2.4 36.4 1.0
O H:HOH403 2.4 12.7 1.0
OD1 H:ASP28 2.5 34.9 1.0
O H:HOH402 2.5 14.3 1.0
CG H:ASP28 2.8 34.6 1.0
CD H:GLU31 2.9 35.2 1.0
OE1 H:GLU31 3.0 31.9 1.0
NE H:ARG118 4.1 32.0 1.0
OG H:SER115 4.2 34.2 1.0
NH2 H:ARG118 4.2 33.6 1.0
CB H:ASP28 4.3 33.9 1.0
CA H:GLY30 4.3 31.2 1.0
CG H:GLU31 4.4 36.2 1.0
N H:GLU31 4.4 33.2 1.0
N H:GLY30 4.6 31.2 1.0
CB H:SER115 4.6 33.6 1.0
C H:GLY30 4.6 32.3 1.0
CZ H:ARG118 4.6 32.1 1.0
N H:ASP28 4.8 38.5 1.0
N H:SER115 4.9 33.0 1.0
CA H:ASP28 5.0 34.2 1.0

Reference:

A.Frick, M.Jarva, M.Ekvall, P.Uzdavinys, M.Nyblom, S.Tornroth-Horsefield. Mercury Increases Water Permeability of A Plant Aquaporin Through A Non-Cysteine-Related Mechanism. Biochem.J. V. 454 491 2013.
ISSN: ISSN 0264-6021
PubMed: 23819815
DOI: 10.1042/BJ20130377
Page generated: Sat Dec 12 08:24:59 2020

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