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Cadmium in PDB 1uxk: Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface

Enzymatic activity of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface

All present enzymatic activity of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface:
1.1.1.37;

Protein crystallography data

The structure of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface, PDB code: 1uxk was solved by A.Bjork, B.Dalhus, D.Mantzilas, V.G.H.Eijsink, R.Sirevag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.405, 105.405, 102.305, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 21.4

Other elements in 1uxk:

The structure of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 6 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface (pdb code 1uxk). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface, PDB code: 1uxk:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 1uxk

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Cadmium binding site 1 out of 10 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1308

b:16.6
occ:1.00
 OD2 A:ASP200 2.2 15.7 1.0
OD1 A:ASP200 2.4 11.8 1.0
CG A:ASP200 2.7 13.7 1.0
CB A:ASP200 4.2 15.8 1.0
O A:HOH2212 4.3 27.8 1.0
NA C:NA1315 4.7 30.5 1.0

Cadmium binding site 2 out of 10 in 1uxk

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Cadmium binding site 2 out of 10 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1309

b:20.1
occ:1.00
 OE2 A:GLU195 2.1 26.8 1.0
O A:HOH2206 2.3 19.6 1.0
O C:GLU281 2.4 16.0 1.0
CL C:CL1312 2.5 25.0 1.0
CD A:GLU195 3.2 28.7 1.0
C C:GLU281 3.4 17.3 1.0
CG A:GLU195 3.9 26.2 1.0
OE1 A:GLU195 4.1 28.8 1.0
N C:GLU281 4.1 15.8 1.0
CA C:GLU281 4.2 15.5 1.0
N C:LEU282 4.3 17.2 1.0
CB C:GLU281 4.4 17.7 1.0
O C:HOH2292 4.5 19.1 1.0
CD C:PRO283 4.5 22.9 1.0
CA C:LEU282 4.5 17.2 1.0
O A:HOH2203 4.5 53.7 1.0
O A:HOH2204 4.6 31.9 1.0
O A:GLU195 4.6 21.9 1.0
O C:HOH2286 4.8 34.5 1.0

Cadmium binding site 3 out of 10 in 1uxk

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Cadmium binding site 3 out of 10 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1310

b:24.9
occ:1.00
 O A:HOH2168 2.3 30.7 1.0
OE1 A:GLU159 2.4 19.9 1.0
OE2 A:GLU159 2.6 27.5 1.0
O A:HOH2170 2.8 32.7 1.0
CD A:GLU159 2.8 20.3 1.0
NE A:ARG201 4.1 27.9 1.0
CG A:GLU159 4.3 19.4 1.0
NH1 A:ARG201 4.5 31.9 1.0
CZ A:ARG201 4.8 31.3 1.0
CA A:GLU159 4.8 16.7 1.0
O A:HOH2169 5.0 42.7 1.0
CB A:GLU159 5.0 16.0 1.0
O A:GLU159 5.0 15.9 1.0

Cadmium binding site 4 out of 10 in 1uxk

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Cadmium binding site 4 out of 10 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1311

b:28.5
occ:0.95
 OE1 A:GLU178 2.2 32.7 1.0
O A:HOH2077 2.4 16.8 1.0
CL A:CL1313 2.5 26.2 1.0
O A:HOH2142 2.5 12.4 1.0
CD A:GLU178 3.0 31.2 1.0
OE2 A:GLU178 3.2 33.8 1.0
CB A:PRO121 4.3 23.1 1.0
O A:HOH2184 4.4 39.8 1.0
CG A:GLU178 4.4 28.1 1.0
OD2 A:ASP123 4.4 23.6 1.0
N A:ASP123 4.6 20.9 1.0
CB A:ASP123 4.6 22.6 1.0
N A:HIS175 4.6 21.5 1.0
CA A:PRO121 4.7 22.8 1.0
N A:LEU122 4.7 22.7 1.0
CG A:ASP123 4.7 23.6 1.0
C A:PRO121 4.8 22.7 1.0
CA A:GLY174 4.9 19.3 1.0
CG2 A:VAL299 4.9 23.5 1.0
CB A:GLU178 4.9 23.1 1.0
CD2 A:HIS175 4.9 24.1 1.0

Cadmium binding site 5 out of 10 in 1uxk

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Cadmium binding site 5 out of 10 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1312

b:25.0
occ:0.90
 ND1 A:HIS175 2.1 18.4 1.0
OD1 A:ASP148 2.3 16.0 1.0
O A:HOH2314 2.4 18.3 1.0
O A:HOH2185 2.5 13.5 1.0
O A:HOH2162 2.5 7.8 1.0
OD2 A:ASP148 2.7 17.1 1.0
CG A:ASP148 2.9 16.6 1.0
CE1 A:HIS175 2.9 23.5 1.0
CG A:HIS175 3.3 24.1 1.0
CB A:HIS175 3.8 23.0 1.0
CA A:HIS175 4.0 22.3 1.0
NE2 A:HIS175 4.1 22.1 1.0
O A:HOH2159 4.3 16.3 1.0
CD2 A:HIS175 4.3 24.1 1.0
CB A:ASP148 4.4 13.1 1.0
O A:ALA144 4.4 13.6 1.0
NH1 A:ARG151 4.5 14.3 1.0
O7N A:NAD1307 4.6 22.9 1.0
CD2 A:LEU147 4.6 12.9 1.0
O A:HOH2139 4.7 38.1 1.0
O A:HOH2231 4.8 30.4 1.0
N A:HIS175 4.9 21.5 1.0
N A:GLY176 4.9 22.0 1.0
CA A:ASP148 5.0 12.5 1.0

Cadmium binding site 6 out of 10 in 1uxk

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Cadmium binding site 6 out of 10 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1317

b:26.6
occ:0.75
 O A:HOH2250 2.3 23.4 1.0
O A:HOH2251 2.3 20.6 1.0
O C:HOH2176 2.4 24.9 1.0
O A:HOH2247 2.5 13.9 1.0
NZ A:LYS24 4.0 25.3 1.0
OE1 A:GLU238 4.1 16.0 1.0
NE2 C:GLN165 4.3 17.0 1.0
O C:HOH2067 4.3 28.9 1.0
OE2 A:GLU238 4.4 17.1 1.0
O C:HOH2175 4.4 25.4 1.0
OE1 A:GLN235 4.6 20.4 1.0
OE1 C:GLN165 4.6 15.6 1.0
CD A:GLU238 4.6 13.7 1.0
O A:HOH2256 4.7 22.9 1.0
CE A:LYS24 4.8 28.0 1.0
CD C:GLN165 4.9 17.1 1.0

Cadmium binding site 7 out of 10 in 1uxk

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Cadmium binding site 7 out of 10 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1310

b:28.0
occ:0.90
 ND1 C:HIS175 2.1 23.4 1.0
OD1 C:ASP148 2.4 21.5 1.0
O C:HOH2153 2.4 23.7 1.0
O C:HOH2156 2.5 18.4 1.0
O C:HOH2159 2.6 9.2 1.0
OD2 C:ASP148 2.8 25.1 1.0
CE1 C:HIS175 2.9 24.0 1.0
CG C:ASP148 2.9 20.6 1.0
CG C:HIS175 3.3 27.6 1.0
CB C:HIS175 3.8 26.3 1.0
CA C:HIS175 4.0 26.9 1.0
NE2 C:HIS175 4.1 27.0 1.0
CD2 C:HIS175 4.3 27.1 1.0
CB C:ASP148 4.4 17.8 1.0
O C:HOH2234 4.4 20.7 1.0
N7N C:NAD1309 4.4 23.3 1.0
NH1 C:ARG151 4.4 15.5 1.0
O C:ALA144 4.5 16.5 1.0
CE C:MET179 4.6 25.3 1.0
CD2 C:LEU147 4.8 15.6 1.0
N C:HIS175 4.8 25.6 1.0
N C:GLY176 4.9 27.5 1.0
CA C:ASP148 5.0 16.6 1.0

Cadmium binding site 8 out of 10 in 1uxk

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Cadmium binding site 8 out of 10 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1311

b:29.6
occ:1.00
 OE1 C:GLU178 2.0 28.0 1.0
O C:HOH2190 2.4 13.1 1.0
O C:HOH2139 2.4 10.8 1.0
O C:HOH2136 2.5 8.1 1.0
CD C:GLU178 2.9 29.8 1.0
OE2 C:GLU178 3.1 31.5 1.0
O C:HOH2183 4.1 44.1 1.0
CG C:GLU178 4.3 25.9 1.0
CB C:PRO121 4.4 24.3 1.0
OD2 C:ASP123 4.5 21.2 1.0
N C:ASP123 4.5 21.4 1.0
O C:HOH2314 4.5 38.5 1.0
CB C:ASP123 4.5 20.8 1.0
N C:HIS175 4.5 25.6 1.0
N C:LEU122 4.7 21.6 1.0
CG C:ASP123 4.7 21.7 1.0
CA C:PRO121 4.8 22.9 1.0
C C:PRO121 4.8 22.4 1.0
CA C:GLY174 4.8 22.1 1.0
CB C:GLU178 4.8 23.7 1.0
CD2 C:HIS175 4.8 27.1 1.0
CG2 C:VAL299 4.9 22.0 1.0

Cadmium binding site 9 out of 10 in 1uxk

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Cadmium binding site 9 out of 10 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1313

b:25.3
occ:0.70
 O C:HOH2254 2.2 21.5 1.0
O A:HOH2178 2.4 26.1 1.0
O C:HOH2253 2.5 26.2 1.0
OE1 C:GLU238 4.1 18.4 1.0
NZ C:LYS24 4.1 31.0 1.0
NE2 A:GLN165 4.2 14.8 1.0
O A:HOH2175 4.3 39.8 1.0
OE2 C:GLU238 4.4 19.4 1.0
OE1 A:GLN165 4.5 16.2 1.0
CD C:GLU238 4.7 16.8 1.0
OE1 C:GLN235 4.7 20.1 1.0
O C:HOH2264 4.8 23.6 1.0
CD A:GLN165 4.8 14.1 1.0

Cadmium binding site 10 out of 10 in 1uxk

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Cadmium binding site 10 out of 10 in the Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1314

b:22.8
occ:0.80
 O C:HOH2270 2.3 28.2 1.0
O C:HOH2289 2.4 10.5 1.0
O C:HOH2290 2.4 19.6 1.0
O C:HOH2129 2.4 22.4 1.0
O C:HOH2291 4.2 22.2 1.0
O C:HOH2293 4.4 25.0 1.0
OE2 C:GLU281 4.5 21.6 1.0
NE2 C:GLN257 4.5 21.1 1.0
O C:ILE279 4.5 17.2 1.0

Reference:

A.Bjork, B.Dalhus, D.Mantzilas, R.Sirevag, V.G.H.Eijsink. Large Improvement in the Thermal Stability of A Tetrameric Malate Dehydrogenase By Single Point Mutations at the Dimer-Dimer Interface. J.Mol.Biol. V. 341 1215 2004.
ISSN: ISSN 0022-2836
PubMed: 15321717
DOI: 10.1016/J.JMB.2004.06.079
Page generated: Sun Jan 24 09:42:50 2021

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