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Calcium in PDB 2r8y: Crystal Structure of Yrbi Phosphatase From Escherichia Coli in A Complex with Ca

Protein crystallography data

The structure of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in A Complex with Ca, PDB code: 2r8y 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) 36.61 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.578, 156.947, 113.991, 90.00, 96.72, 90.00
R / Rfree (%) 21.3 / 24.4

Other elements in 2r8y:

The structure of Crystal Structure of Yrbi Phosphatase From Escherichia Coli in A Complex with Ca also contains other interesting chemical elements:

Chlorine (Cl) 16 atoms

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 A Complex with Ca (pdb code 2r8y). 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 A Complex with Ca, PDB code: 2r8y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 2r8y

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


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 A Complex with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:19.4
occ:1.00
 OD2 A:ASP125 2.2 16.3 1.0
OD1 A:ASP32 2.2 19.5 1.0
O A:ASP34 2.3 14.4 1.0
O B:HOH359 2.4 20.6 1.0
O B:HOH383 2.4 24.2 1.0
O A:HOH311 2.4 16.5 1.0
CG A:ASP125 3.2 18.8 1.0
CG A:ASP32 3.3 18.6 1.0
C A:ASP34 3.5 14.0 1.0
OD1 A:ASP125 3.5 20.6 1.0
OD2 A:ASP32 3.8 20.4 1.0
O A:HOH304 4.1 13.3 1.0
OG B:SER187 4.2 25.8 1.0
OD2 A:ASP129 4.2 16.2 1.0
CA A:ASP34 4.3 14.1 1.0
CB A:ASP34 4.4 14.3 1.0
N A:ASP34 4.4 13.8 1.0
CB A:ASP125 4.5 16.4 1.0
CL A:CL301 4.5 22.9 1.0
N A:GLY35 4.5 13.8 1.0
CB A:ASP32 4.5 16.3 1.0
CG2 B:VAL56 4.5 15.7 1.0
CB B:SER187 4.6 23.4 1.0
CA A:GLY35 4.6 14.0 1.0
CB A:ASP126 4.7 15.3 1.0
N A:ASP126 4.8 15.7 1.0
N A:ASP125 4.8 16.0 1.0

Calcium binding site 2 out of 16 in 2r8y

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


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 A Complex with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:20.7
occ:1.00
 OD2 B:ASP125 2.2 15.1 1.0
OD1 B:ASP32 2.2 16.5 1.0
O B:ASP34 2.3 14.6 1.0
O C:HOH305 2.4 21.1 1.0
O C:HOH340 2.4 16.7 1.0
O B:HOH332 2.4 17.4 1.0
CG B:ASP125 3.2 16.9 1.0
CG B:ASP32 3.3 18.0 1.0
C B:ASP34 3.5 13.6 1.0
OD1 B:ASP125 3.6 19.8 1.0
OD2 B:ASP32 3.8 18.9 1.0
OD2 B:ASP129 4.2 17.4 1.0
O B:HOH308 4.3 16.0 1.0
CA B:ASP34 4.3 14.0 1.0
OG C:SER187 4.3 26.6 1.0
N B:ASP34 4.4 13.8 1.0
CB B:ASP34 4.4 13.8 1.0
N B:GLY35 4.5 13.5 1.0
CL B:CL302 4.5 23.9 1.0
CB B:ASP32 4.5 16.7 1.0
CB B:ASP125 4.6 15.2 1.0
CG2 C:VAL56 4.6 14.4 1.0
CA B:GLY35 4.6 13.4 1.0
CB C:SER187 4.6 23.8 1.0
CB B:ASP126 4.7 15.7 1.0
N B:ASP126 4.8 15.6 1.0
N B:ASP125 4.9 14.0 1.0

Calcium binding site 3 out of 16 in 2r8y

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


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 A Complex with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:21.9
occ:1.00
 OD1 C:ASP32 2.1 18.4 1.0
O D:HOH347 2.2 19.1 1.0
OD2 C:ASP125 2.3 17.6 1.0
O C:ASP34 2.3 14.8 1.0
O C:HOH348 2.4 19.1 1.0
CG C:ASP32 3.3 18.1 1.0
CG C:ASP125 3.3 18.2 1.0
C C:ASP34 3.5 14.9 1.0
OD1 C:ASP125 3.7 20.7 1.0
OD2 C:ASP32 3.8 18.9 1.0
OG D:SER187 3.9 30.5 1.0
O C:HOH310 4.2 20.0 1.0
OD2 C:ASP129 4.2 17.4 1.0
CA C:ASP34 4.3 14.9 1.0
CL C:CL303 4.4 24.8 1.0
N C:ASP34 4.4 14.6 1.0
CB C:ASP34 4.4 14.7 1.0
CB C:ASP32 4.5 16.6 1.0
N C:GLY35 4.5 14.4 1.0
CB C:ASP125 4.6 16.5 1.0
CA C:GLY35 4.6 14.4 1.0
CG2 D:VAL56 4.6 18.0 1.0
CB D:SER187 4.7 28.4 1.0
CB C:ASP126 4.7 16.5 1.0
N C:ASP126 4.9 15.8 1.0
N C:ASP125 4.9 16.0 1.0

Calcium binding site 4 out of 16 in 2r8y

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


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 A Complex with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca204

b:23.4
occ:1.00
 OD1 D:ASP32 2.2 22.0 1.0
O D:ASP34 2.2 17.7 1.0
OD2 D:ASP125 2.2 19.4 1.0
O D:HOH373 2.4 23.9 1.0
O D:HOH334 2.4 20.0 1.0
CG D:ASP32 3.3 20.7 1.0
CG D:ASP125 3.3 19.1 1.0
C D:ASP34 3.4 17.2 1.0
OD1 D:ASP125 3.7 20.7 1.0
OD2 D:ASP32 3.8 21.4 1.0
CA D:ASP34 4.2 17.3 1.0
O D:HOH311 4.2 18.1 1.0
OG A:SER187 4.3 31.6 1.0
OD2 D:ASP129 4.3 20.0 1.0
CB D:ASP34 4.4 17.5 1.0
N D:ASP34 4.4 17.5 1.0
N D:GLY35 4.4 16.1 1.0
CL D:CL304 4.4 27.5 1.0
CB D:ASP32 4.5 18.3 1.0
CG2 A:VAL56 4.5 18.3 1.0
CB D:ASP125 4.6 17.3 1.0
CA D:GLY35 4.6 16.0 1.0
CB A:SER187 4.7 30.5 1.0
CB D:ASP126 4.7 17.8 1.0
N D:ASP125 4.9 17.4 1.0
N D:ASP126 4.9 17.6 1.0

Calcium binding site 5 out of 16 in 2r8y

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Calcium binding site 5 out of 16 in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in A Complex with Ca


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 A Complex with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca205

b:26.7
occ:1.00
 OD1 E:ASP32 1.9 30.3 1.0
OD2 E:ASP125 2.2 16.7 1.0
O E:HOH334 2.3 19.4 1.0
O E:ASP34 2.4 14.8 1.0
CG E:ASP32 3.1 26.2 1.0
CG E:ASP125 3.2 18.2 1.0
C E:ASP34 3.5 15.9 1.0
OD2 E:ASP32 3.6 29.4 1.0
O E:HOH310 3.7 17.6 1.0
OD1 E:ASP125 3.7 17.0 1.0
CB E:ASP34 4.0 17.4 1.0
CA E:ASP34 4.2 16.4 1.0
OD2 E:ASP129 4.3 19.6 1.0
CB E:ASP32 4.3 22.0 1.0
N E:ASP34 4.4 16.6 1.0
CB E:ASP125 4.4 16.1 1.0
N E:GLY35 4.6 15.2 1.0
N E:ASP125 4.7 16.1 1.0
CG2 E:VAL36 4.9 14.8 1.0
CA E:GLY35 4.9 14.9 1.0
CB E:ASP126 4.9 15.8 1.0
CA E:ASP125 4.9 16.4 1.0
OD1 E:ASP129 4.9 19.1 1.0
N E:ASP126 4.9 15.5 1.0

Calcium binding site 6 out of 16 in 2r8y

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


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 A Complex with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca206

b:19.6
occ:1.00
 OD2 F:ASP125 2.2 19.3 1.0
O F:ASP34 2.2 15.1 1.0
OD1 F:ASP32 2.2 18.4 1.0
O G:HOH388 2.4 21.3 1.0
O F:HOH325 2.4 18.1 1.0
O F:HOH344 2.5 26.2 1.0
CG F:ASP125 3.2 17.9 1.0
CG F:ASP32 3.3 18.2 1.0
C F:ASP34 3.4 14.0 1.0
OD1 F:ASP125 3.6 21.1 1.0
OD2 F:ASP32 3.8 19.1 1.0
OG G:SER187 4.1 25.3 1.0
OD2 F:ASP129 4.2 16.9 1.0
CA F:ASP34 4.3 14.7 1.0
N F:ASP34 4.3 14.5 1.0
O G:HOH363 4.4 26.5 1.0
O F:HOH315 4.4 17.0 1.0
N F:GLY35 4.4 14.0 1.0
CB F:ASP34 4.4 14.4 1.0
CB F:ASP125 4.5 15.9 1.0
CG2 G:VAL56 4.5 17.5 1.0
CA F:GLY35 4.5 13.4 1.0
CL F:CL306 4.5 21.3 1.0
CB F:ASP32 4.5 17.0 1.0
CB F:ASP126 4.7 16.4 1.0
CB G:SER187 4.9 22.7 1.0
N F:ASP126 4.9 16.1 1.0
C F:GLY35 4.9 13.8 1.0
N F:ASP125 5.0 16.1 1.0

Calcium binding site 7 out of 16 in 2r8y

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


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 A Complex with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca207

b:19.8
occ:1.00
 OD1 G:ASP32 2.2 18.8 1.0
OD2 G:ASP125 2.2 17.5 1.0
O G:ASP34 2.3 13.7 1.0
O H:HOH309 2.3 21.6 1.0
O H:HOH337 2.4 18.8 1.0
O G:HOH330 2.5 15.5 1.0
CG G:ASP125 3.2 16.1 1.0
CG G:ASP32 3.3 17.6 1.0
C G:ASP34 3.5 12.8 1.0
OD1 G:ASP125 3.6 18.3 1.0
OD2 G:ASP32 3.8 18.0 1.0
OG H:SER187 4.1 24.4 1.0
O G:HOH317 4.2 16.6 1.0
OD2 G:ASP129 4.3 14.4 1.0
CA G:ASP34 4.3 13.1 1.0
N G:GLY35 4.4 12.9 1.0
CB G:ASP34 4.5 13.5 1.0
N G:ASP34 4.5 13.2 1.0
CL G:CL307 4.5 20.5 1.0
O H:HOH361 4.5 33.0 1.0
CB G:ASP32 4.5 15.6 1.0
CB G:ASP125 4.6 14.6 1.0
CA G:GLY35 4.6 12.6 1.0
CG2 H:VAL56 4.6 15.1 1.0
CB G:ASP126 4.7 15.2 1.0
CB H:SER187 4.8 23.0 1.0
N G:ASP126 4.8 14.8 1.0
N G:ASP125 4.9 13.9 1.0
C G:GLY35 5.0 12.7 1.0

Calcium binding site 8 out of 16 in 2r8y

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


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 A Complex with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca208

b:19.8
occ:1.00
 OD1 H:ASP32 2.2 21.7 1.0
OD2 H:ASP125 2.2 19.2 1.0
O H:ASP34 2.3 15.3 1.0
O E:HOH329 2.3 17.3 1.0
O E:HOH372 2.3 27.0 1.0
O H:HOH317 2.5 19.0 1.0
CG H:ASP125 3.2 19.6 1.0
CG H:ASP32 3.3 19.0 1.0
C H:ASP34 3.5 15.3 1.0
OD1 H:ASP125 3.6 21.3 1.0
OD2 H:ASP32 3.8 19.6 1.0
O H:HOH326 4.2 15.4 1.0
OD2 H:ASP129 4.3 17.9 1.0
OG E:SER187 4.3 26.3 1.0
CA H:ASP34 4.3 15.6 1.0
N H:ASP34 4.4 15.4 1.0
CB H:ASP34 4.4 15.6 1.0
N H:GLY35 4.4 14.6 1.0
CB H:ASP32 4.5 17.6 1.0
CL H:CL308 4.6 24.8 1.0
CG2 E:VAL56 4.6 16.4 1.0
CB H:ASP125 4.6 18.0 1.0
CA H:GLY35 4.6 14.8 1.0
CB E:SER187 4.7 25.6 1.0
CB H:ASP126 4.7 17.9 1.0
N H:ASP126 4.8 17.9 1.0
N H:ASP125 4.9 17.4 1.0
C H:GLY35 5.0 14.2 1.0

Calcium binding site 9 out of 16 in 2r8y

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


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 A Complex with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca209

b:36.8
occ:1.00
 O I:ASP34 2.3 30.2 1.0
OD2 I:ASP125 2.3 31.8 1.0
OD1 I:ASP32 2.3 31.6 1.0
O I:HOH861 2.5 33.8 1.0
CG I:ASP32 3.3 31.2 1.0
CG I:ASP125 3.3 31.8 1.0
C I:ASP34 3.5 30.0 1.0
OD1 I:ASP125 3.6 31.4 1.0
OD2 I:ASP32 3.7 32.0 1.0
O I:HOH590 4.1 30.4 1.0
OD2 I:ASP129 4.2 36.6 1.0
CA I:ASP34 4.3 30.2 1.0
OG L:SER187 4.3 51.5 1.0
CB I:ASP34 4.4 30.5 1.0
N I:ASP34 4.4 30.2 1.0
N I:GLY35 4.4 29.8 1.0
CL I:CL309 4.5 48.1 1.0
CB I:ASP32 4.5 30.4 1.0
CA I:GLY35 4.6 29.8 1.0
CB I:ASP125 4.6 31.3 1.0
CG2 L:VAL56 4.7 35.4 1.0
CB L:SER187 4.8 51.3 1.0
CB I:ASP126 4.8 32.6 1.0
N I:ASP125 5.0 30.7 1.0
N I:ASP126 5.0 32.1 1.0

Calcium binding site 10 out of 16 in 2r8y

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


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 A Complex with Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca210

b:34.7
occ:1.00
 OD2 J:ASP125 2.2 27.5 1.0
OD1 J:ASP32 2.3 33.6 1.0
O J:ASP34 2.3 28.9 1.0
O J:HOH417 2.4 28.3 1.0
CG J:ASP125 3.3 29.3 1.0
CG J:ASP32 3.4 31.7 1.0
C J:ASP34 3.5 28.9 1.0
OD1 J:ASP125 3.7 30.2 1.0
OD2 J:ASP32 3.9 32.8 1.0
OG I:SER187 3.9 45.3 1.0
O J:HOH428 4.0 32.4 1.0
OD2 J:ASP129 4.1 32.8 1.0
CA J:ASP34 4.3 29.0 1.0
CL J:CL310 4.4 46.1 1.0
CB J:ASP34 4.4 29.2 1.0
O J:HOH902 4.4 34.6 1.0
N J:ASP34 4.4 29.0 1.0
N J:GLY35 4.5 28.8 1.0
CB J:ASP125 4.6 28.6 1.0
CB J:ASP32 4.6 30.6 1.0
CG2 I:VAL56 4.6 30.7 1.0
CB J:ASP126 4.7 29.0 1.0
CA J:GLY35 4.7 28.4 1.0
CB I:SER187 4.8 44.1 1.0
N J:ASP126 4.8 29.1 1.0
N J:ASP125 4.9 28.4 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: Tue Jul 8 08:08:01 2025

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