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Cadmium in PDB 1ur5: Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface

Enzymatic activity of Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface

All present enzymatic activity of Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface:
1.1.1.37;

Protein crystallography data

The structure of Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface, PDB code: 1ur5 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 (°) 105.575, 105.575, 102.531, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface (pdb code 1ur5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface, PDB code: 1ur5:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 1ur5

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Cadmium binding site 1 out of 6 in the Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge 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 Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1309

b:27.7
occ:0.50
OE1 A:GLU178 2.1 28.8 1.0
O A:HOH2156 2.2 20.3 1.0
O A:HOH2157 2.3 25.5 1.0
CL A:CL1312 2.7 25.9 1.0
CD A:GLU178 3.0 26.1 1.0
OE2 A:GLU178 3.3 30.8 1.0
O A:HOH2116 4.1 28.9 1.0
OD2 A:ASP123 4.3 20.3 1.0
CG A:GLU178 4.4 24.5 1.0
CB A:PRO121 4.5 24.2 1.0
N A:ASP123 4.6 17.1 1.0
CB A:ASP123 4.7 18.4 1.0
N A:LEU122 4.7 19.8 1.0
CA A:PRO121 4.8 23.0 1.0
CG2 A:VAL299 4.8 21.0 1.0
CG A:ASP123 4.8 21.8 1.0
CB A:GLU178 4.8 18.8 1.0
C A:PRO121 4.9 20.9 1.0
N A:HIS175 4.9 21.6 1.0
CA A:GLY174 4.9 19.9 1.0

Cadmium binding site 2 out of 6 in 1ur5

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Cadmium binding site 2 out of 6 in the Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge 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 Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1310

b:36.4
occ:0.45
O C:HOH2203 2.4 37.2 1.0
OE1 A:GLU165 2.4 26.4 1.0
OE2 A:GLU165 2.5 26.5 1.0
CD A:GLU165 2.8 25.3 1.0
O C:HOH2211 3.1 42.6 1.0
OE1 C:GLU238 4.1 29.6 1.0
CG A:GLU165 4.3 20.2 1.0
NZ C:LYS244 4.4 21.5 1.0
CE C:LYS244 4.5 21.2 1.0
NH1 C:ARG246 4.6 17.6 1.0
OE2 C:GLU238 4.8 28.8 1.0
O C:HOH2210 4.8 31.8 1.0
CD C:GLU238 4.8 27.7 1.0

Cadmium binding site 3 out of 6 in 1ur5

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Cadmium binding site 3 out of 6 in the Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge 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 Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1311

b:15.5
occ:1.00
OD2 A:ASP200 2.4 15.2 1.0
OD1 A:ASP200 2.4 12.5 1.0
CG A:ASP200 2.7 14.4 1.0
CB A:ASP200 4.2 14.0 1.0
O A:HOH2180 4.3 21.1 1.0

Cadmium binding site 4 out of 6 in 1ur5

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Cadmium binding site 4 out of 6 in the Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge 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 Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1310

b:28.3
occ:0.65
OE1 C:GLU178 2.1 29.0 1.0
O C:HOH2083 2.3 21.7 1.0
O C:HOH2113 2.4 20.9 1.0
O C:HOH2115 2.5 10.3 1.0
CD C:GLU178 2.9 28.2 1.0
OE2 C:GLU178 3.1 31.2 1.0
CG C:GLU178 4.3 26.1 1.0
NH2 C:ARG88 4.3 40.1 1.0
OD2 C:ASP123 4.3 20.5 1.0
CB C:PRO121 4.4 23.7 1.0
O C:HOH2111 4.4 28.5 1.0
N C:ASP123 4.5 17.4 1.0
N C:LEU122 4.6 21.0 1.0
CB C:ASP123 4.7 17.4 1.0
CA C:PRO121 4.7 22.9 1.0
C C:PRO121 4.8 22.2 1.0
CB C:GLU178 4.8 23.1 1.0
CG C:ASP123 4.8 17.9 1.0
N C:HIS175 4.9 23.0 1.0
CA C:GLY174 4.9 20.8 1.0

Cadmium binding site 5 out of 6 in 1ur5

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Cadmium binding site 5 out of 6 in the Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge 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 Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1311

b:53.0
occ:0.50
O A:HOH2212 2.3 38.2 1.0
OE1 C:GLU165 2.6 25.9 1.0
OE2 C:GLU165 2.7 23.3 1.0
CD C:GLU165 3.0 23.5 1.0
O A:HOH2209 3.4 39.7 1.0
O A:HOH2211 3.6 38.8 1.0
OE1 A:GLU238 4.0 24.4 1.0
CG C:GLU165 4.5 19.9 1.0
CE A:LYS244 4.5 22.3 1.0
NZ A:LYS244 4.6 23.0 1.0
OE2 A:GLU238 4.6 27.7 1.0
NH1 A:ARG246 4.6 17.8 1.0
CD A:GLU238 4.7 24.5 1.0
O A:HOH2088 5.0 40.9 1.0

Cadmium binding site 6 out of 6 in 1ur5

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Cadmium binding site 6 out of 6 in the Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge 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 Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer/Dimer Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1312

b:25.9
occ:0.60
O C:HOH2140 2.4 37.5 1.0
OE1 C:GLU159 2.4 23.9 1.0
OE2 C:GLU159 2.6 29.2 1.0
CD C:GLU159 2.8 24.5 1.0
O C:HOH2137 3.6 34.4 1.0
O C:HOH2136 3.8 36.7 1.0
CG C:GLU159 4.3 21.6 1.0
NE C:ARG201 4.5 33.6 1.0
O C:GLU159 4.6 18.9 1.0
CA C:GLU159 4.6 16.9 1.0
O C:HOH2139 4.7 32.3 1.0
CB C:GLU159 4.9 17.7 1.0
NH2 C:ARG201 4.9 36.3 1.0

Reference:

A.Bjork, B.Dalhus, D.Mantzilas, V.G.H.Eijsink, R.Sirevag. Stabilization of A Tetrameric Malate Dehydrogenase By Introduction of A Disulfide Bridge at the Dimer-Dimer Interface J.Mol.Biol. V. 334 811 2003.
ISSN: ISSN 0022-2836
PubMed: 14636605
DOI: 10.1016/J.JMB.2003.10.006
Page generated: Fri Aug 28 12:27:25 2020
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