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Cadmium in PDB 1uxj: 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: 1uxj 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 / 1.75
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.247, 105.247, 102.196, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 21.1

Other elements in 1uxj:

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) 3 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 1uxj). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 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: 1uxj:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 1uxj

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Cadmium binding site 1 out of 9 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:Cd1309

b:16.9
occ:1.00
OD1 A:ASP243 2.3 15.6 1.0
OE2 A:GLU277 2.3 15.2 1.0
O A:HOH2284 2.4 17.9 1.0
OE1 A:GLU277 2.5 15.8 1.0
CD A:GLU277 2.7 14.9 1.0
OD2 A:ASP243 2.8 17.6 1.0
CG A:ASP243 2.9 18.9 1.0
N A:ALA273 4.1 12.7 1.0
CG A:GLU277 4.2 15.0 1.0
O A:HOH2286 4.3 12.6 1.0
CB A:ASP243 4.3 16.2 1.0
NZ A:LYS245 4.4 28.3 1.0
O A:HOH2130 4.5 41.7 1.0
CB A:ALA273 4.5 14.8 1.0
CG A:LYS245 4.6 17.4 1.0
N A:GLY274 4.6 17.2 1.0
CA A:GLY272 4.6 11.4 1.0
C A:GLY272 4.7 12.8 1.0
O A:HOH2262 4.8 30.9 1.0
CD A:LYS245 4.8 20.9 1.0
CA A:ALA273 4.8 15.3 1.0
CA A:ASP243 5.0 15.3 1.0

Cadmium binding site 2 out of 9 in 1uxj

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Cadmium binding site 2 out of 9 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:Cd1310

b:20.3
occ:0.80
OE2 A:GLU195 2.1 33.0 1.0
O A:HOH2211 2.4 25.8 1.0
O C:GLU281 2.4 18.1 1.0
O C:HOH2278 2.6 18.2 1.0
CD A:GLU195 3.3 31.9 1.0
C C:GLU281 3.5 19.0 1.0
CG A:GLU195 4.0 29.1 1.0
N C:GLU281 4.1 17.8 1.0
CA C:GLU281 4.2 18.2 1.0
OE1 A:GLU195 4.3 32.1 1.0
CB C:GLU281 4.4 19.3 1.0
N C:LEU282 4.4 17.9 1.0
O C:HOH2279 4.6 25.4 1.0
O C:HOH2271 4.6 44.1 1.0
O A:HOH2209 4.6 34.6 1.0
O A:GLU195 4.7 23.3 1.0
CA C:LEU282 4.7 19.1 1.0
CD C:PRO283 4.8 26.0 1.0

Cadmium binding site 3 out of 9 in 1uxj

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Cadmium binding site 3 out of 9 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:Cd1311

b:26.8
occ:0.80
OE1 A:GLU178 2.1 36.0 1.0
O A:HOH2195 2.4 24.6 1.0
O A:HOH2154 2.5 14.2 1.0
CL A:CL1313 2.5 24.8 1.0
CD A:GLU178 3.0 31.8 1.0
OE2 A:GLU178 3.2 34.1 1.0
O A:HOH2191 4.3 39.1 1.0
OD2 A:ASP123 4.4 20.4 1.0
CG A:GLU178 4.4 28.5 1.0
CB A:PRO121 4.6 23.8 1.0
N A:ASP123 4.6 19.4 1.0
N A:HIS175 4.6 21.1 1.0
CB A:ASP123 4.6 21.0 1.0
N A:LEU122 4.7 21.4 1.0
CG A:ASP123 4.8 23.8 1.0
CA A:GLY174 4.8 18.6 1.0
CB A:GLU178 4.8 23.2 1.0
CA A:PRO121 4.9 22.2 1.0
CG2 A:VAL299 4.9 25.6 1.0
CD2 A:HIS175 4.9 23.0 1.0
C A:PRO121 4.9 22.4 1.0

Cadmium binding site 4 out of 9 in 1uxj

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Cadmium binding site 4 out of 9 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:Cd1312

b:25.9
occ:0.90
ND1 A:HIS175 2.1 17.6 1.0
OD1 A:ASP148 2.3 15.1 1.0
O A:HOH2168 2.4 18.9 1.0
O A:HOH2172 2.4 13.7 1.0
O A:HOH2173 2.7 9.1 1.0
OD2 A:ASP148 2.7 16.1 1.0
CE1 A:HIS175 2.8 23.6 1.0
CG A:ASP148 2.8 16.5 1.0
CG A:HIS175 3.3 23.6 1.0
CB A:HIS175 3.8 22.6 1.0
CA A:HIS175 4.0 22.5 1.0
NE2 A:HIS175 4.0 22.7 1.0
CD2 A:HIS175 4.2 23.0 1.0
O A:HOH2171 4.3 15.1 1.0
CB A:ASP148 4.3 13.2 1.0
O A:HOH2075 4.4 37.7 1.0
O A:HOH2153 4.4 30.6 1.0
O A:ALA144 4.4 13.2 1.0
NH1 A:ARG151 4.4 14.2 1.0
CE A:MET179 4.6 19.5 1.0
O7N A:NAD1308 4.6 22.8 1.0
CD2 A:LEU147 4.6 13.7 1.0
N A:HIS175 4.9 21.1 1.0
N A:GLY176 4.9 21.2 1.0
CA A:ASP148 5.0 11.7 1.0
N A:ASP148 5.0 13.3 1.0

Cadmium binding site 5 out of 9 in 1uxj

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Cadmium binding site 5 out of 9 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
C:Cd1311

b:25.4
occ:0.90
OE1 C:GLU178 2.1 34.5 1.0
O C:HOH2181 2.3 13.9 1.0
O C:HOH2137 2.5 8.3 1.0
CL C:CL1314 2.5 25.6 1.0
CD C:GLU178 2.9 32.5 1.0
OE2 C:GLU178 3.1 36.1 1.0
O C:HOH2180 4.1 46.9 1.0
CG C:GLU178 4.3 28.4 1.0
OD2 C:ASP123 4.3 21.4 1.0
CB C:PRO121 4.4 22.8 1.0
N C:ASP123 4.5 20.1 1.0
N C:HIS175 4.5 22.7 1.0
CB C:ASP123 4.6 19.3 1.0
N C:LEU122 4.7 21.4 1.0
CG C:ASP123 4.7 21.9 1.0
CD2 C:HIS175 4.7 25.7 1.0
CA C:PRO121 4.8 22.4 1.0
C C:PRO121 4.8 21.5 1.0
CA C:GLY174 4.8 19.7 1.0
CB C:GLU178 4.8 23.9 1.0

Cadmium binding site 6 out of 9 in 1uxj

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Cadmium binding site 6 out of 9 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
C:Cd1312

b:25.2
occ:1.00
O C:HOH2161 2.1 32.1 1.0
OE1 C:GLU159 2.3 17.4 1.0
OE2 C:GLU159 2.5 23.9 1.0
CD C:GLU159 2.7 17.9 1.0
NH1 C:ARG201 3.6 29.9 1.0
CG C:GLU159 4.2 16.8 1.0
O C:HOH2159 4.3 42.0 1.0
CZ C:ARG201 4.4 31.3 1.0
O C:GLU159 4.6 17.7 1.0
CD C:ARG201 4.7 28.0 1.0
CA C:GLU159 4.8 16.7 1.0
NE C:ARG201 4.8 28.9 1.0
CB C:GLU159 4.9 17.1 1.0
O C:HOH2160 5.0 30.3 1.0

Cadmium binding site 7 out of 9 in 1uxj

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Cadmium binding site 7 out of 9 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:Cd1313

b:24.8
occ:0.80
ND1 C:HIS175 2.1 23.6 1.0
OD1 C:ASP148 2.4 19.5 1.0
O C:HOH2312 2.4 21.8 1.0
O C:HOH2176 2.5 13.6 1.0
O C:HOH2153 2.6 11.2 1.0
OD2 C:ASP148 2.7 21.2 1.0
CE1 C:HIS175 2.8 24.1 1.0
CG C:ASP148 2.9 17.2 1.0
CG C:HIS175 3.3 26.0 1.0
CB C:HIS175 3.9 25.1 1.0
CA C:HIS175 4.0 24.8 1.0
NE2 C:HIS175 4.1 24.1 1.0
O C:HOH2064 4.2 37.9 1.0
CD2 C:HIS175 4.3 25.7 1.0
O C:HOH2152 4.3 20.4 1.0
CB C:ASP148 4.4 16.2 1.0
NH1 C:ARG151 4.4 16.4 1.0
O C:ALA144 4.5 15.6 1.0
O C:HOH2132 4.5 35.3 1.0
O7N C:NAD1310 4.5 22.9 1.0
CE C:MET179 4.5 21.1 1.0
CD2 C:LEU147 4.7 16.4 1.0
N C:HIS175 4.8 22.7 1.0
N C:GLY176 4.9 25.7 1.0

Cadmium binding site 8 out of 9 in 1uxj

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Cadmium binding site 8 out of 9 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:Cd1316

b:28.6
occ:0.70
O C:HOH2021 2.4 27.0 1.0
O A:HOH2064 4.5 48.3 1.0
OE1 C:GLU25 4.5 23.1 1.0

Cadmium binding site 9 out of 9 in 1uxj

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Cadmium binding site 9 out of 9 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:Cd1317

b:29.4
occ:0.70
O C:HOH2085 2.3 25.7 1.0
O C:HOH2195 2.3 25.1 1.0
O C:HOH2196 4.3 30.5 1.0
OE1 C:GLU195 4.5 25.4 1.0
OE2 C:GLU195 4.6 26.9 1.0
CD C:GLU195 4.9 25.6 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: Wed Oct 28 09:56:25 2020
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