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Cadmium in PDB 4cl3: 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus

Enzymatic activity of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus

All present enzymatic activity of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus:
1.1.1.37;

Protein crystallography data

The structure of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus, PDB code: 4cl3 was solved by R.Talon, D.Madern, E.Girard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.701 / 1.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.226, 106.226, 102.566, 90.00, 90.00, 120.00
R / Rfree (%) 16.63 / 20.86

Other elements in 4cl3:

The structure of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus 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 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus (pdb code 4cl3). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 11 binding sites of Cadmium where determined in the 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus, PDB code: 4cl3:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 11 in 4cl3

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Cadmium binding site 1 out of 11 in the 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1310

b:20.4
occ:0.57
 O A:HOH2288 2.4 25.4 1.0
OE2 A:GLU165 2.4 20.5 1.0
OE1 A:GLU165 2.6 23.4 1.0
O A:HOH2285 2.6 39.4 1.0
O A:HOH2284 2.6 55.7 1.0
O A:HOH2466 2.7 51.4 1.0
O A:HOH2289 2.8 27.8 1.0
CD A:GLU165 2.8 27.4 1.0
O A:HOH2465 3.3 36.2 1.0
O A:HOH2287 3.9 34.3 1.0
OE1 D:GLU238 4.2 17.6 1.0
NZ D:LYS244 4.2 13.5 1.0
O A:HOH2271 4.2 35.3 1.0
CG A:GLU165 4.3 14.4 1.0
CE D:LYS244 4.4 16.7 1.0
OE2 D:GLU238 4.4 22.8 1.0
NH1 D:ARG246 4.5 16.7 1.0
CD D:GLU238 4.7 14.2 1.0
O A:HOH2286 4.9 36.5 1.0

Cadmium binding site 2 out of 11 in 4cl3

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Cadmium binding site 2 out of 11 in the 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1311

b:32.4
occ:0.30
 O A:HOH2057 2.6 35.1 1.0
OD2 A:ASP33 2.6 23.8 1.0
O A:ACT1317 2.6 19.5 0.3
OXT A:ACT1317 2.7 17.8 0.3
O A:HOH2467 3.0 42.6 1.0
C A:ACT1317 3.1 18.2 0.3
CG A:ASP33 3.2 30.2 1.0
OD1 A:ASP33 3.3 26.0 1.0
O A:HOH2020 3.6 35.0 1.0
CA A:GLY9 4.0 19.5 1.0
N A:ALA10 4.5 26.8 1.0
CB A:SER78 4.6 34.1 1.0
CB A:ASP33 4.6 22.8 1.0
CH3 A:ACT1317 4.6 17.4 0.3
C A:GLY9 4.8 28.7 1.0
N A:ILE34 4.8 21.0 1.0
CA A:SER78 4.9 25.4 1.0
CA A:ASP33 4.9 18.1 1.0
O A:HOH2155 4.9 51.5 1.0

Cadmium binding site 3 out of 11 in 4cl3

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Cadmium binding site 3 out of 11 in the 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1312

b:88.5
occ:0.40
 OD1 A:ASP90 2.7 65.5 1.0
O A:HOH2166 2.9 61.5 1.0
O A:HOH2468 2.9 58.8 1.0
O A:HOH2170 3.1 48.7 1.0
CG A:ASP90 3.5 71.9 1.0
OD2 A:ASP90 3.8 60.6 1.0
OG A:SER87 4.5 63.0 1.0
CG A:GLU89 4.6 65.0 1.0
CB A:ASP90 4.7 59.1 1.0
N A:ASP90 4.8 56.0 1.0
CA A:ASP90 4.8 61.8 1.0
OE1 A:GLU89 5.0 55.5 1.0

Cadmium binding site 4 out of 11 in 4cl3

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Cadmium binding site 4 out of 11 in the 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1313

b:16.9
occ:0.79
 OE1 A:GLU159 2.4 17.2 1.0
O A:HOH2274 2.4 31.3 1.0
OE2 A:GLU159 2.5 23.3 1.0
O A:HOH2272 2.6 27.8 1.0
CD A:GLU159 2.8 19.6 1.0
NH1 A:ARG201 3.7 22.4 1.0
CG A:GLU159 4.3 17.0 1.0
O A:GLU159 4.4 17.9 1.0
O A:HOH2273 4.5 21.1 1.0
CZ A:ARG201 4.6 31.1 1.0
CA A:GLU159 4.7 17.9 1.0
CD A:ARG201 4.9 28.9 1.0
O A:HOH2276 4.9 28.0 1.0
CB A:GLU159 5.0 16.4 1.0

Cadmium binding site 5 out of 11 in 4cl3

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Cadmium binding site 5 out of 11 in the 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1314

b:29.8
occ:0.10
 O A:HOH2469 2.7 57.7 1.0
OE1 D:GLU281 2.8 30.5 0.5
OE2 D:GLU281 2.9 29.8 0.5
CD D:GLU281 3.2 22.1 0.5
O D:HOH2395 3.8 40.1 1.0
O D:HOH2410 4.4 43.0 1.0
CG D:GLU281 4.7 16.8 0.5
NZ D:LYS278 4.9 28.0 1.0

Cadmium binding site 6 out of 11 in 4cl3

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Cadmium binding site 6 out of 11 in the 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd1310

b:20.4
occ:0.60
 OE2 D:GLU165 2.4 21.7 1.0
O A:HOH2383 2.5 24.4 1.0
O D:HOH2447 2.5 45.0 1.0
O D:HOH2297 2.5 33.2 1.0
OE1 D:GLU165 2.5 22.5 1.0
O A:HOH2382 2.7 32.4 1.0
CD D:GLU165 2.8 19.8 1.0
O D:HOH2288 4.1 35.9 1.0
O A:HOH2381 4.2 36.7 1.0
O A:HOH2380 4.2 37.3 1.0
OE1 A:GLU238 4.2 21.4 1.0
CG D:GLU165 4.3 15.0 1.0
OE2 A:GLU238 4.4 20.3 1.0
NZ A:LYS244 4.5 14.9 1.0
CE A:LYS244 4.6 17.2 1.0
NH1 A:ARG246 4.6 16.1 1.0
CD A:GLU238 4.7 19.9 1.0
O D:HOH2298 4.8 40.5 1.0
O A:HOH2037 5.0 60.9 1.0

Cadmium binding site 7 out of 11 in 4cl3

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Cadmium binding site 7 out of 11 in the 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd1311

b:37.1
occ:0.25
 OD2 D:ASP33 2.7 22.6 1.0
O D:ACT1318 2.7 17.6 0.4
OXT D:ACT1318 2.7 17.8 0.4
C D:ACT1318 3.2 17.3 0.4
OD1 D:ASP33 3.2 22.7 1.0
CG D:ASP33 3.2 35.7 1.0
C4 D:PEG1319 3.3 37.0 0.7
O D:HOH2173 3.3 45.2 1.0
O D:HOH2448 3.4 55.6 1.0
O4 D:PEG1319 3.8 36.2 0.7
CA D:GLY9 4.4 15.2 1.0
O D:HOH2449 4.4 45.3 1.0
OG D:SER78 4.5 24.2 1.0
C3 D:PEG1319 4.5 38.1 0.7
CB D:ASP33 4.6 17.6 1.0
N D:ILE34 4.6 20.2 1.0
CH3 D:ACT1318 4.6 15.9 0.4
N D:ALA10 4.8 18.1 1.0
CA D:ASP33 5.0 15.3 1.0

Cadmium binding site 8 out of 11 in 4cl3

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Cadmium binding site 8 out of 11 in the 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd1312

b:28.8
occ:0.50
 OD1 D:ASP90 2.5 39.3 1.0
O D:HOH2183 2.6 37.3 0.5
OE2 D:GLU89 2.6 48.4 1.0
CG D:ASP90 3.5 55.2 1.0
CD D:GLU89 3.5 43.0 1.0
CG D:GLU89 3.7 45.1 1.0
OD2 D:ASP90 3.8 44.0 1.0
OG D:SER87 4.2 43.5 1.0
OE1 D:GLU89 4.7 43.3 1.0
CB D:ASP90 4.8 40.0 1.0
N D:ASP90 4.9 37.5 1.0
CA D:ASP90 5.0 37.1 1.0

Cadmium binding site 9 out of 11 in 4cl3

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Cadmium binding site 9 out of 11 in the 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd1313

b:16.9
occ:1.00
 O D:HOH2338 2.4 21.6 1.0
OD2 D:ASP200 2.4 16.3 1.0
OD1 D:ASP200 2.4 16.0 1.0
CG D:ASP200 2.7 15.7 1.0
CB D:ASP200 4.3 14.9 1.0
O D:HOH2139 4.5 37.5 1.0
O D:HOH2337 4.5 19.9 1.0

Cadmium binding site 10 out of 11 in 4cl3

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Cadmium binding site 10 out of 11 in the 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of 1.70 A Resolution Structure of the Malate Dehydrogenase From Chloroflexus Aurantiacus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd1314

b:42.9
occ:0.37
 OE2 D:GLU36 2.5 48.6 1.0
OE1 D:GLU36 2.7 45.1 1.0
CD D:GLU36 2.8 55.3 1.0
O D:HOH2055 3.8 52.0 1.0
CG D:GLU36 4.2 30.9 1.0
O D:HOH2057 4.4 39.5 1.0

Reference:

R.Talon, N.Coquelle, D.Madern, E.Girard. An Experimental Point of View on Hydration/Solvation in Halophilic Proteins. Front.Microbiol. V. 5 66 2014.
ISSN: ISSN 1664-302X
PubMed: 24600446
DOI: 10.3389/FMICB.2014.00066
Page generated: Fri Jul 19 17:08:11 2024

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