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Cadmium in PDB 2qth: Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus in Complex with Gdp

Protein crystallography data

The structure of Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus in Complex with Gdp, PDB code: 2qth was solved by H.Wu, L.Sun, S.J.Brouns, S.Fu, Z.Rao, J.Van Der Oost, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.30 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.991, 72.403, 96.016, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus in Complex with Gdp (pdb code 2qth). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus in Complex with Gdp, PDB code: 2qth:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 2qth

Go back to Cadmium Binding Sites List in 2qth
Cadmium binding site 1 out of 4 in the Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:27.1
occ:1.00
OE2 A:GLU92 2.2 28.2 1.0
OE1 A:GLU92 2.4 24.9 1.0
O A:HOH528 2.4 30.1 1.0
O A:HOH624 2.6 34.8 1.0
CD A:GLU92 2.6 22.4 1.0
NH2 A:ARG111 4.0 21.0 1.0
CG A:GLU92 4.1 23.6 1.0
OE2 A:GLU82 4.5 49.9 1.0
O A:HOH511 4.5 30.9 1.0
NZ A:LYS2 4.6 52.1 1.0
CZ A:ARG111 4.9 20.4 1.0
CB A:GLU92 4.9 21.8 1.0

Cadmium binding site 2 out of 4 in 2qth

Go back to Cadmium Binding Sites List in 2qth
Cadmium binding site 2 out of 4 in the Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:32.7
occ:1.00
OD2 A:ASP232 2.2 33.9 1.0
O A:HOH560 2.2 39.7 1.0
NE2 A:HIS97 2.3 24.7 1.0
O A:HOH584 2.4 35.1 1.0
O A:HOH543 2.5 37.0 1.0
O A:HOH505 2.5 33.3 1.0
OD1 A:ASP232 2.7 23.9 1.0
CG A:ASP232 2.7 26.8 1.0
CD2 A:HIS97 3.1 20.7 1.0
CE1 A:HIS97 3.3 22.9 1.0
CB A:ASP232 4.1 26.3 1.0
OG1 A:THR193 4.2 28.8 1.0
O A:HOH565 4.2 46.8 1.0
O A:THR233 4.2 29.0 1.0
CG A:HIS97 4.3 24.5 1.0
NZ A:LYS217 4.4 47.5 1.0
ND1 A:HIS97 4.4 23.4 1.0
O A:HOH514 4.4 27.0 1.0
O A:HOH538 4.5 28.5 1.0
MG A:MG501 4.6 40.5 1.0
C A:THR233 4.9 29.0 1.0

Cadmium binding site 3 out of 4 in 2qth

Go back to Cadmium Binding Sites List in 2qth
Cadmium binding site 3 out of 4 in the Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:38.2
occ:1.00
OE2 A:GLU283 2.2 33.7 1.0
OE1 A:GLU283 2.5 28.9 1.0
CD A:GLU283 2.7 32.4 1.0
O A:HOH595 2.7 36.4 1.0
CG A:GLU283 4.2 28.3 1.0
CB A:GLU283 5.0 29.5 1.0
CB A:SER280 5.0 26.3 1.0

Cadmium binding site 4 out of 4 in 2qth

Go back to Cadmium Binding Sites List in 2qth
Cadmium binding site 4 out of 4 in the Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus in Complex with Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:49.3
occ:1.00
OE1 A:GLU108 2.3 43.0 1.0
OE2 A:GLU108 2.6 37.6 1.0
CD A:GLU108 2.8 35.1 1.0
CG A:GLU108 4.3 28.9 1.0
CD2 A:LEU112 4.5 32.0 1.0
NE A:ARG152 4.7 43.9 1.0
O A:HOH517 4.8 24.4 1.0
CG A:LEU112 4.9 29.2 1.0

Reference:

H.Wu, L.Sun, S.J.Brouns, S.Fu, J.Akerboom, X.Li, C.Zhang, Z.Rao, J.Van Der Oost. Crystal Structure of A Gtp-Binding Protein From the Hyperthermophilic Archaeon Sulfolobus Solfataricus. To Be Published.
Page generated: Fri Aug 28 13:05:55 2020
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