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Calcium in PDB 2r8z: Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion

Enzymatic activity of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion

All present enzymatic activity of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion:
3.1.3.45;

Protein crystallography data

The structure of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion, PDB code: 2r8z was solved by O.V.Tsodikov, P.Aggarwal, J.R.Rubin, J.A.Stuckey, R.W.Woodard, T.Biswas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.370, 156.908, 114.051, 90.00, 96.54, 90.00
R / Rfree (%) 18.4 / 23.1

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion (pdb code 2r8z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion, PDB code: 2r8z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 2r8z

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Calcium binding site 1 out of 16 in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:18.3
occ:1.00
 OD2 A:ASP32 2.2 36.5 1.0
O A:HOH204 2.2 28.8 1.0
OD2 A:ASP125 2.2 26.4 1.0
O4 A:PO4202 2.3 31.3 1.0
O A:ASP34 2.3 28.1 1.0
O A:HOH203 2.4 22.1 1.0
CG A:ASP32 3.0 33.7 1.0
OD1 A:ASP32 3.2 38.0 1.0
CG A:ASP125 3.3 27.6 1.0
C A:ASP34 3.5 28.4 1.0
O A:HOH310 3.7 43.1 1.0
P A:PO4202 3.8 31.4 1.0
OD1 A:ASP125 3.8 27.3 1.0
OD2 A:ASP129 4.1 31.2 1.0
CA A:ASP34 4.2 28.9 1.0
O2 A:PO4202 4.3 29.4 1.0
CB A:ASP34 4.3 29.1 1.0
O3 A:PO4202 4.3 28.5 1.0
N A:ASP34 4.3 29.0 1.0
O A:HOH376 4.3 28.8 1.0
CB A:ASP32 4.4 31.6 1.0
O A:HOH205 4.4 24.7 1.0
N A:GLY35 4.5 28.1 1.0
CB A:ASP125 4.5 27.2 1.0
O1 A:PO4202 4.6 29.5 1.0
N A:ASP125 4.6 27.2 1.0
CA A:GLY35 4.7 28.2 1.0
N A:ASP126 4.8 27.5 1.0
CB A:ASP126 4.8 27.3 1.0
CG2 D:VAL56 4.9 28.9 1.0
CA A:ASP125 5.0 27.5 1.0
CG A:ASP129 5.0 30.6 1.0

Calcium binding site 2 out of 16 in 2r8z

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Calcium binding site 2 out of 16 in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:22.9
occ:1.00
 OD2 B:ASP125 2.2 28.3 1.0
O A:HOH302 2.2 33.8 1.0
OD2 B:ASP32 2.3 38.8 1.0
O4 B:PO4203 2.3 44.8 1.0
O B:ASP34 2.3 30.7 1.0
O B:HOH205 2.4 18.5 1.0
CG B:ASP125 3.3 29.3 1.0
CG B:ASP32 3.5 35.2 1.0
C B:ASP34 3.5 30.7 1.0
OD1 B:ASP125 3.7 30.1 1.0
P B:PO4203 3.8 43.9 1.0
O B:HOH204 3.9 41.1 1.0
OD2 B:ASP129 4.1 30.1 1.0
CB B:ASP32 4.1 33.3 1.0
CA B:ASP34 4.3 31.0 1.0
CB B:ASP34 4.3 31.1 1.0
N B:ASP34 4.4 31.1 1.0
O B:HOH206 4.4 31.5 1.0
O2 B:PO4203 4.4 44.3 1.0
OD1 B:ASP32 4.4 38.4 1.0
O3 B:PO4203 4.4 43.9 1.0
CB B:ASP125 4.5 29.1 1.0
OG A:SER187 4.5 47.6 1.0
N B:GLY35 4.6 30.0 1.0
N B:ASP125 4.6 29.4 1.0
O1 B:PO4203 4.6 43.9 1.0
CB B:ASP126 4.7 28.4 1.0
N B:ASP126 4.8 28.8 1.0
CA B:GLY35 4.8 29.8 1.0
CA B:ASP125 4.9 29.1 1.0
CG B:ASP129 5.0 31.1 1.0

Calcium binding site 3 out of 16 in 2r8z

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Calcium binding site 3 out of 16 in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:21.0
occ:1.00
 OD2 C:ASP32 2.1 37.0 1.0
O C:HOH205 2.2 23.7 1.0
O4 C:PO4204 2.2 35.4 1.0
OD2 C:ASP125 2.2 29.4 1.0
O C:HOH206 2.3 19.4 1.0
O C:ASP34 2.3 28.4 1.0
CG C:ASP32 3.0 35.1 1.0
CG C:ASP125 3.3 29.0 1.0
OD1 C:ASP32 3.3 39.5 1.0
C C:ASP34 3.5 28.3 1.0
O C:HOH211 3.7 33.6 1.0
P C:PO4204 3.7 35.3 1.0
OD1 C:ASP125 3.7 30.8 1.0
OD2 C:ASP129 4.1 32.1 1.0
CA C:ASP34 4.2 28.8 1.0
CB C:ASP34 4.3 28.6 1.0
O2 C:PO4204 4.3 33.8 1.0
O B:HOH207 4.3 26.0 1.0
N C:ASP34 4.3 28.8 1.0
O3 C:PO4204 4.4 32.9 1.0
CB C:ASP32 4.4 32.9 1.0
O C:HOH356 4.5 35.5 1.0
CB C:ASP125 4.5 29.0 1.0
O1 C:PO4204 4.5 32.8 1.0
N C:GLY35 4.6 28.0 1.0
CB C:ASP126 4.7 27.9 1.0
N C:ASP125 4.8 28.5 1.0
CA C:GLY35 4.8 27.7 1.0
N C:ASP126 4.9 28.5 1.0
CG C:ASP129 5.0 31.4 1.0
OD1 C:ASP129 5.0 31.9 1.0
CG2 B:VAL56 5.0 30.5 1.0

Calcium binding site 4 out of 16 in 2r8z

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Calcium binding site 4 out of 16 in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca204

b:17.6
occ:1.00
 OD2 D:ASP32 2.0 37.2 1.0
O C:HOH207 2.2 29.2 1.0
OD2 D:ASP125 2.2 30.8 1.0
O D:ASP34 2.3 27.5 1.0
O4 D:PO4205 2.3 33.2 1.0
O D:HOH209 2.4 17.3 1.0
CG D:ASP32 3.1 34.0 1.0
CG D:ASP125 3.3 30.2 1.0
C D:ASP34 3.5 27.9 1.0
OD1 D:ASP32 3.5 39.1 1.0
O D:HOH352 3.7 29.9 1.0
OD1 D:ASP125 3.8 31.2 1.0
P D:PO4205 3.8 31.8 1.0
OD2 D:ASP129 4.2 28.3 1.0
CA D:ASP34 4.2 28.2 1.0
CB D:ASP32 4.3 31.7 1.0
N D:ASP34 4.3 28.4 1.0
CB D:ASP34 4.3 28.1 1.0
O2 D:PO4205 4.4 30.7 1.0
OG C:SER187 4.4 43.2 1.0
O3 D:PO4205 4.5 30.0 1.0
O D:HOH210 4.5 18.4 1.0
N D:GLY35 4.5 27.2 1.0
CB D:ASP125 4.6 29.2 1.0
O1 D:PO4205 4.6 31.0 1.0
N D:ASP125 4.6 28.7 1.0
CA D:GLY35 4.7 27.1 1.0
N D:ASP126 4.8 28.5 1.0
CB D:ASP126 4.8 28.3 1.0
CG2 C:VAL56 4.8 29.3 1.0
CB C:SER187 4.9 43.9 1.0
CA D:ASP125 5.0 28.9 1.0

Calcium binding site 5 out of 16 in 2r8z

Go back to Calcium Binding Sites List in 2r8z
Calcium binding site 5 out of 16 in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca205

b:17.1
occ:1.00
 OD1 E:ASP32 2.2 34.0 1.0
OD2 E:ASP125 2.2 28.4 1.0
O4 E:PO4206 2.2 31.2 1.0
O H:HOH210 2.3 19.9 1.0
O E:ASP34 2.3 28.8 1.0
O E:HOH208 2.3 20.9 1.0
CG E:ASP32 3.0 33.1 1.0
OD2 E:ASP32 3.3 37.9 1.0
CG E:ASP125 3.3 28.0 1.0
C E:ASP34 3.5 28.5 1.0
P E:PO4206 3.7 31.8 1.0
OD1 E:ASP125 3.8 28.1 1.0
O E:HOH290 3.8 29.6 1.0
OD2 E:ASP129 4.1 30.9 1.0
O2 E:PO4206 4.2 29.1 1.0
CA E:ASP34 4.2 28.8 1.0
CB E:ASP34 4.3 28.7 1.0
N E:ASP34 4.3 29.1 1.0
CB E:ASP32 4.4 31.7 1.0
O3 E:PO4206 4.4 29.6 1.0
OG H:SER187 4.4 53.5 1.0
CB E:ASP125 4.5 27.9 1.0
O1 E:PO4206 4.5 29.1 1.0
N E:GLY35 4.6 27.8 1.0
O E:HOH209 4.6 28.3 1.0
N E:ASP125 4.6 27.7 1.0
CB E:ASP126 4.7 28.9 1.0
N E:ASP126 4.8 28.8 1.0
CA E:GLY35 4.8 27.4 1.0
CG2 H:VAL56 4.9 27.6 1.0
CA E:ASP125 4.9 28.1 1.0
OD1 E:ASP129 5.0 31.1 1.0
CG E:ASP129 5.0 30.3 1.0

Calcium binding site 6 out of 16 in 2r8z

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Calcium binding site 6 out of 16 in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca206

b:22.0
occ:1.00
 OD2 F:ASP125 2.2 29.5 1.0
O4 F:PO4207 2.3 38.5 1.0
O F:HOH238 2.3 26.8 1.0
O F:ASP34 2.4 29.1 1.0
O F:HOH252 2.5 20.5 1.0
OD1 F:ASP32 2.8 37.2 1.0
CG F:ASP125 3.3 28.8 1.0
C F:ASP34 3.5 29.4 1.0
CG F:ASP32 3.6 34.3 1.0
P F:PO4207 3.7 38.4 1.0
OD1 F:ASP125 3.8 28.5 1.0
CB F:ASP32 3.8 32.0 1.0
O F:HOH286 3.8 15.8 1.0
CB F:ASP34 4.0 30.2 1.0
OD2 F:ASP129 4.2 32.7 1.0
CA F:ASP34 4.2 30.0 1.0
O F:HOH235 4.3 20.5 1.0
O1 F:PO4207 4.3 38.6 1.0
N F:ASP34 4.4 30.0 1.0
CB F:ASP125 4.5 28.3 1.0
O2 F:PO4207 4.5 37.7 1.0
O3 F:PO4207 4.5 37.0 1.0
O F:HOH374 4.6 36.9 1.0
N F:GLY35 4.6 28.7 1.0
N F:ASP125 4.6 27.8 1.0
OD2 F:ASP32 4.7 35.6 1.0
CB F:ASP126 4.8 28.4 1.0
OD1 F:ASP129 4.8 33.9 1.0
N F:ASP126 4.9 28.1 1.0
CG2 F:VAL36 4.9 28.3 1.0
CA F:GLY35 4.9 28.3 1.0
CA F:ASP125 4.9 28.1 1.0
CG F:ASP129 4.9 31.6 1.0

Calcium binding site 7 out of 16 in 2r8z

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Calcium binding site 7 out of 16 in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca207

b:20.4
occ:1.00
 OD1 G:ASP32 2.2 34.6 1.0
OD2 G:ASP125 2.2 30.1 1.0
O G:HOH400 2.2 35.4 1.0
O G:ASP34 2.3 28.8 1.0
O G:HOH210 2.3 18.8 1.0
O4 G:PO4208 2.4 43.6 1.0
CG G:ASP32 3.0 32.9 1.0
OD2 G:ASP32 3.3 36.0 1.0
CG G:ASP125 3.3 29.7 1.0
C G:ASP34 3.5 28.4 1.0
P G:PO4208 3.8 43.4 1.0
OD1 G:ASP125 3.8 30.9 1.0
OD2 G:ASP129 4.0 30.2 1.0
CA G:ASP34 4.2 28.7 1.0
O3 G:PO4208 4.2 41.7 1.0
N G:ASP34 4.3 28.6 1.0
CB G:ASP34 4.3 28.5 1.0
O2 G:PO4208 4.3 43.4 1.0
CB G:ASP32 4.4 31.0 1.0
O G:HOH211 4.5 26.1 1.0
CB G:ASP125 4.5 29.0 1.0
N G:GLY35 4.5 28.2 1.0
OG F:SER187 4.5 47.5 1.0
N G:ASP125 4.7 28.5 1.0
CA G:GLY35 4.7 27.8 1.0
CB G:ASP126 4.8 28.8 1.0
N G:ASP126 4.8 29.1 1.0
O1 G:PO4208 4.8 42.4 1.0
CG2 F:VAL56 4.9 31.4 1.0
CG G:ASP129 4.9 30.2 1.0
CA G:ASP125 5.0 28.8 1.0
CB F:SER187 5.0 47.1 1.0

Calcium binding site 8 out of 16 in 2r8z

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Calcium binding site 8 out of 16 in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca208

b:19.6
occ:1.00
 OD1 H:ASP32 2.1 37.8 1.0
OD2 H:ASP125 2.2 28.4 1.0
O G:HOH212 2.2 28.6 1.0
O H:ASP34 2.3 29.2 1.0
O4 H:PO4209 2.3 41.7 1.0
O H:HOH211 2.5 23.6 1.0
CG H:ASP32 3.1 35.3 1.0
CG H:ASP125 3.3 27.2 1.0
C H:ASP34 3.5 29.5 1.0
OD2 H:ASP32 3.5 39.2 1.0
O H:HOH369 3.7 43.5 1.0
P H:PO4209 3.8 40.7 1.0
OD1 H:ASP125 3.8 27.1 1.0
OD2 H:ASP129 4.2 27.1 1.0
CA H:ASP34 4.2 29.9 1.0
CB H:ASP34 4.2 30.0 1.0
O2 H:PO4209 4.2 39.0 1.0
N H:ASP34 4.3 29.9 1.0
CB H:ASP32 4.3 32.8 1.0
O3 H:PO4209 4.4 39.1 1.0
OG G:SER187 4.4 42.9 1.0
O H:HOH212 4.4 24.2 1.0
CB H:ASP125 4.5 26.8 1.0
N H:GLY35 4.5 29.0 1.0
O1 H:PO4209 4.7 39.7 1.0
N H:ASP125 4.7 26.9 1.0
CA H:GLY35 4.7 28.7 1.0
CB H:ASP126 4.8 27.1 1.0
N H:ASP126 4.9 27.0 1.0
CG2 G:VAL56 4.9 30.9 1.0
CA H:ASP125 5.0 26.8 1.0

Calcium binding site 9 out of 16 in 2r8z

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Calcium binding site 9 out of 16 in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca209

b:39.9
occ:1.00
 O I:HOH270 2.0 33.2 1.0
OD1 I:ASP32 2.1 40.9 1.0
OD2 I:ASP125 2.2 35.5 1.0
O I:ASP34 2.4 36.8 1.0
O I:HOH211 2.4 32.0 1.0
O4 I:PO4210 2.4 68.1 1.0
CG I:ASP32 3.2 39.5 1.0
CG I:ASP125 3.2 36.3 1.0
C I:ASP34 3.6 36.6 1.0
OD1 I:ASP125 3.7 36.4 1.0
OD2 I:ASP32 3.7 41.3 1.0
P I:PO4210 3.8 67.5 1.0
OD2 I:ASP129 4.0 36.3 1.0
O2 I:PO4210 4.3 67.3 1.0
O3 I:PO4210 4.3 67.1 1.0
CA I:ASP34 4.4 36.8 1.0
CB I:ASP32 4.4 38.2 1.0
OG L:SER187 4.4 51.9 1.0
CB I:ASP34 4.4 36.8 1.0
N I:ASP34 4.5 36.6 1.0
CB I:ASP125 4.5 36.4 1.0
N I:ASP125 4.6 36.7 1.0
CB I:ASP126 4.6 36.5 1.0
N I:GLY35 4.6 36.5 1.0
N I:ASP126 4.6 36.5 1.0
CA I:GLY35 4.8 36.2 1.0
CG I:ASP129 4.8 36.3 1.0
O1 I:PO4210 4.9 67.2 1.0
OD1 I:ASP129 4.9 36.5 1.0
CA I:ASP125 4.9 36.6 1.0
C I:ASP125 4.9 36.6 1.0

Calcium binding site 10 out of 16 in 2r8z

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Calcium binding site 10 out of 16 in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in Complex with A Phosphate and A Calcium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca210

b:37.4
occ:1.00
 OD1 J:ASP32 2.2 42.2 1.0
OD2 J:ASP125 2.2 38.1 1.0
O J:HOH309 2.4 43.0 1.0
O4 J:PO4211 2.4 89.6 1.0
O J:ASP34 2.4 37.6 1.0
CG J:ASP32 3.3 40.0 1.0
CG J:ASP125 3.4 37.5 1.0
C J:ASP34 3.6 37.6 1.0
P J:PO4211 3.8 89.5 1.0
OD2 J:ASP32 3.8 42.0 1.0
OD1 J:ASP125 4.0 38.3 1.0
O J:HOH244 4.0 53.3 1.0
OD2 J:ASP129 4.1 37.3 1.0
OG I:SER187 4.1 58.4 1.0
CB J:ASP34 4.3 37.7 1.0
O3 J:PO4211 4.3 89.1 1.0
CA J:ASP34 4.3 37.8 1.0
O2 J:PO4211 4.4 89.2 1.0
CB J:ASP125 4.5 36.9 1.0
CB J:ASP126 4.5 36.8 1.0
N J:ASP34 4.5 37.7 1.0
CB J:ASP32 4.5 38.3 1.0
O J:HOH212 4.5 41.1 1.0
N J:ASP126 4.6 36.7 1.0
N J:GLY35 4.6 37.6 1.0
N J:ASP125 4.7 36.7 1.0
CA J:GLY35 4.8 37.5 1.0
O1 J:PO4211 4.8 89.5 1.0
CA J:ASP125 4.9 36.9 1.0
C J:ASP125 5.0 36.7 1.0
CG J:ASP129 5.0 36.9 1.0
CB I:SER187 5.0 58.1 1.0
OD1 J:ASP129 5.0 37.2 1.0

Reference:

T.Biswas, L.Yi, P.Aggarwal, J.Wu, J.R.Rubin, J.A.Stuckey, R.W.Woodard, O.V.Tsodikov. The Tail of Kdsc: Conformational Changes Control the Activity of A Haloacid Dehalogenase Superfamily Phosphatase. J.Biol.Chem. V. 284 30594 2009.
ISSN: ISSN 0021-9258
PubMed: 19726684
DOI: 10.1074/JBC.M109.012278
Page generated: Fri Jul 12 15:48:39 2024

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