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Chlorine 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:

Calcium (Ca) 16 atoms

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 16 binding sites of Chlorine where determined in the Crystal Structure of Yrbi Phosphatase From Escherichia Coli in A Complex with Ca, PDB code: 2r8y:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 16 in 2r8y

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl301

b:22.9
occ:1.00
 O B:HOH359 2.9 20.6 1.0
NZ A:LYS102 3.0 18.4 1.0
O B:HOH361 3.0 24.4 1.0
N A:GLY77 3.2 18.4 1.0
CE A:LYS102 3.2 18.9 1.0
OD2 A:ASP32 3.4 20.4 1.0
O A:HOH311 3.4 16.5 1.0
O A:HOH304 3.4 13.3 1.0
O A:HOH327 3.6 22.0 1.0
CA A:GLY77 3.8 19.2 1.0
CG2 A:ILE128 4.0 18.9 1.0
O B:SER187 4.0 23.7 1.0
CB B:SER187 4.1 23.4 1.0
C A:THR76 4.2 18.5 1.0
CG A:ASP32 4.3 18.6 1.0
CA A:THR76 4.4 17.8 1.0
CA A:CA201 4.5 19.4 1.0
OD1 A:ASP32 4.6 19.5 1.0
OG1 A:THR76 4.6 18.8 1.0
CD A:LYS102 4.7 18.9 1.0
C B:SER187 4.8 22.9 1.0
CA B:SER187 4.9 23.1 1.0
N B:SER187 4.9 22.0 1.0
OD1 A:ASP129 4.9 16.9 1.0
C A:GLY77 5.0 18.9 1.0

Chlorine binding site 2 out of 16 in 2r8y

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl302

b:23.9
occ:1.00
 O C:HOH340 3.1 16.7 1.0
NZ B:LYS102 3.1 14.9 1.0
N B:GLY77 3.2 17.3 1.0
O C:HOH349 3.3 22.9 1.0
CE B:LYS102 3.3 17.7 1.0
OD2 B:ASP32 3.4 18.9 1.0
O B:HOH332 3.4 17.4 1.0
O B:HOH308 3.5 16.0 1.0
O B:HOH316 3.6 17.3 1.0
CA B:GLY77 3.8 17.4 1.0
CG2 B:ILE128 3.9 18.5 1.0
O C:SER187 4.0 23.4 1.0
CB C:SER187 4.1 23.8 1.0
C B:THR76 4.2 17.1 1.0
CG B:ASP32 4.3 18.0 1.0
CA B:THR76 4.4 17.2 1.0
CA B:CA202 4.5 20.7 1.0
OD1 B:ASP32 4.6 16.5 1.0
OG1 B:THR76 4.7 18.5 1.0
CD B:LYS102 4.8 18.0 1.0
C C:SER187 4.8 22.6 1.0
OD1 B:ASP129 4.9 19.0 1.0
CA C:SER187 4.9 23.2 1.0
C B:GLY77 4.9 17.6 1.0
N C:SER187 5.0 22.0 1.0

Chlorine binding site 3 out of 16 in 2r8y

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl303

b:24.8
occ:1.00
 O D:HOH347 2.9 19.1 1.0
N C:GLY77 3.2 20.4 1.0
NZ C:LYS102 3.3 21.8 1.0
OD2 C:ASP32 3.4 18.9 1.0
O C:HOH356 3.4 22.2 1.0
CE C:LYS102 3.4 21.4 1.0
O C:HOH348 3.4 19.1 1.0
O C:HOH310 3.5 20.0 1.0
CA C:GLY77 3.8 21.0 1.0
CB D:SER187 3.8 28.4 1.0
CG2 C:ILE128 4.0 21.0 1.0
O D:SER187 4.1 28.5 1.0
C C:THR76 4.2 19.8 1.0
CG C:ASP32 4.2 18.1 1.0
OG D:SER187 4.4 30.5 1.0
CA C:THR76 4.4 19.6 1.0
CA C:CA203 4.4 21.9 1.0
OD1 C:ASP32 4.4 18.4 1.0
OG1 C:THR76 4.6 20.0 1.0
CA D:SER187 4.8 28.2 1.0
CD C:LYS102 4.9 24.0 1.0
C D:SER187 4.9 28.0 1.0
OD1 C:ASP129 4.9 15.2 1.0
C C:GLY77 5.0 20.8 1.0
O C:GLN99 5.0 30.7 1.0

Chlorine binding site 4 out of 16 in 2r8y

Go back to Chlorine Binding Sites List in 2r8y
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl304

b:27.5
occ:1.00
 O D:HOH373 2.9 23.9 1.0
NZ D:LYS102 3.2 22.4 1.0
N D:GLY77 3.3 24.3 1.0
CE D:LYS102 3.4 24.7 1.0
OD2 D:ASP32 3.4 21.4 1.0
O D:HOH311 3.5 18.1 1.0
O D:HOH368 3.5 24.5 1.0
O D:HOH334 3.6 20.0 1.0
CA D:GLY77 3.8 24.6 1.0
CG2 D:ILE128 3.9 22.7 1.0
O A:SER187 4.0 30.4 1.0
CB A:SER187 4.1 30.5 1.0
C D:THR76 4.3 23.9 1.0
CG D:ASP32 4.3 20.7 1.0
CA D:CA204 4.4 23.4 1.0
CA D:THR76 4.4 23.5 1.0
OD1 D:ASP32 4.6 22.0 1.0
OG1 D:THR76 4.6 23.7 1.0
C A:SER187 4.8 30.2 1.0
CA A:SER187 4.9 30.3 1.0
CD D:LYS102 4.9 26.9 1.0
OD1 D:ASP129 4.9 20.5 1.0
OG A:SER187 5.0 31.6 1.0
N A:SER187 5.0 30.3 1.0

Chlorine binding site 5 out of 16 in 2r8y

Go back to Chlorine Binding Sites List in 2r8y
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl305

b:84.1
occ:1.00
 NZ E:LYS102 3.6 35.5 1.0
CE E:LYS102 3.6 35.1 1.0
N E:GLY77 3.8 26.6 1.0
OD2 E:ASP32 3.9 29.4 1.0
O E:HOH374 3.9 29.0 1.0
CA E:GLY77 4.4 28.1 1.0
C E:THR76 4.5 25.8 1.0
CA E:THR76 4.6 25.5 1.0
OG1 E:THR76 4.8 30.8 1.0
O E:ILE75 4.9 23.1 1.0
OD2 E:ASP34 4.9 21.7 1.0
CG E:ASP32 5.0 26.2 1.0

Chlorine binding site 6 out of 16 in 2r8y

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl306

b:21.3
occ:1.00
 O G:HOH388 2.9 21.3 1.0
NZ F:LYS102 3.2 18.1 1.0
O F:HOH325 3.3 18.1 1.0
N F:GLY77 3.3 17.6 1.0
CE F:LYS102 3.4 16.9 1.0
OD2 F:ASP32 3.5 19.1 1.0
O F:HOH319 3.6 18.5 1.0
O F:HOH315 3.7 17.0 1.0
CB G:SER187 3.8 22.7 1.0
CA F:GLY77 3.8 18.2 1.0
CG2 F:ILE128 3.8 21.1 1.0
O G:SER187 4.0 22.6 1.0
C F:THR76 4.3 18.1 1.0
CG F:ASP32 4.4 18.2 1.0
OG G:SER187 4.4 25.3 1.0
CA F:THR76 4.5 18.2 1.0
CA F:CA206 4.5 19.6 1.0
OD1 F:ASP32 4.6 18.4 1.0
CA G:SER187 4.7 22.7 1.0
OG1 F:THR76 4.8 19.9 1.0
C G:SER187 4.8 22.4 1.0
CD F:LYS102 4.8 17.1 1.0
OD1 F:ASP129 4.9 16.9 1.0
N G:SER187 4.9 22.6 1.0
CG1 F:ILE128 5.0 22.0 1.0
C F:GLY77 5.0 17.9 1.0

Chlorine binding site 7 out of 16 in 2r8y

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl307

b:20.5
occ:1.00
 O H:HOH337 2.9 18.8 1.0
NZ G:LYS102 3.1 12.2 1.0
O G:HOH394 3.1 23.5 1.0
N G:GLY77 3.2 17.9 1.0
CE G:LYS102 3.4 14.3 1.0
O G:HOH330 3.4 15.5 1.0
O G:HOH317 3.4 16.6 1.0
OD2 G:ASP32 3.5 18.0 1.0
O G:HOH351 3.5 22.6 1.0
CA G:GLY77 3.7 18.4 1.0
CG2 G:ILE128 3.9 18.4 1.0
O H:SER187 3.9 23.1 1.0
CB H:SER187 4.0 23.0 1.0
C G:THR76 4.3 18.1 1.0
CG G:ASP32 4.3 17.6 1.0
CA G:THR76 4.4 17.7 1.0
CA G:CA207 4.5 19.8 1.0
OD1 G:ASP32 4.6 18.8 1.0
OG H:SER187 4.7 24.4 1.0
OG1 G:THR76 4.7 19.1 1.0
CA H:SER187 4.8 22.4 1.0
C H:SER187 4.8 22.1 1.0
N H:SER187 4.9 21.5 1.0
CD G:LYS102 4.9 14.7 1.0
C G:GLY77 4.9 18.3 1.0

Chlorine binding site 8 out of 16 in 2r8y

Go back to Chlorine Binding Sites List in 2r8y
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl308

b:24.8
occ:1.00
 O E:HOH329 3.1 17.3 1.0
NZ H:LYS102 3.2 23.1 1.0
N H:GLY77 3.2 21.2 1.0
O H:HOH317 3.4 19.0 1.0
CE H:LYS102 3.4 24.2 1.0
O H:HOH326 3.4 15.4 1.0
OD2 H:ASP32 3.4 19.6 1.0
O H:HOH329 3.5 23.2 1.0
CA H:GLY77 3.7 21.7 1.0
O E:SER187 3.9 25.0 1.0
CG2 H:ILE128 3.9 20.9 1.0
CB E:SER187 4.0 25.6 1.0
C H:THR76 4.2 21.4 1.0
CG H:ASP32 4.3 19.0 1.0
CA H:THR76 4.4 21.1 1.0
CA H:CA208 4.6 19.8 1.0
OD1 H:ASP32 4.6 21.7 1.0
OG1 H:THR76 4.7 20.6 1.0
C E:SER187 4.7 24.8 1.0
CA E:SER187 4.8 25.0 1.0
CD H:LYS102 4.8 25.5 1.0
OD1 H:ASP129 4.9 19.1 1.0
N E:SER187 4.9 25.1 1.0
C H:GLY77 4.9 21.9 1.0

Chlorine binding site 9 out of 16 in 2r8y

Go back to Chlorine Binding Sites List in 2r8y
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl309

b:48.1
occ:1.00
 NZ I:LYS102 3.1 39.4 1.0
O I:HOH861 3.2 33.8 1.0
CE I:LYS102 3.3 40.1 1.0
O I:HOH590 3.4 30.4 1.0
OD2 I:ASP32 3.4 32.0 1.0
N I:GLY77 3.5 36.9 1.0
CG2 I:ILE128 3.8 36.1 1.0
CA I:GLY77 3.9 37.4 1.0
CB L:SER187 3.9 51.3 1.0
O L:SER187 4.1 51.0 1.0
CG I:ASP32 4.4 31.2 1.0
C I:THR76 4.4 36.6 1.0
CA I:CA209 4.5 36.8 1.0
CA I:THR76 4.6 36.1 1.0
OD1 I:ASP129 4.7 36.0 1.0
OD1 I:ASP32 4.8 31.6 1.0
OG1 I:THR76 4.8 35.6 1.0
CD I:LYS102 4.8 41.0 1.0
CA L:SER187 4.9 51.2 1.0
OG L:SER187 4.9 51.5 1.0
C L:SER187 4.9 50.9 1.0

Chlorine binding site 10 out of 16 in 2r8y

Go back to Chlorine Binding Sites List in 2r8y
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl310

b:46.1
occ:1.00
 NZ J:LYS102 3.1 48.7 1.0
N J:GLY77 3.2 37.4 1.0
O J:HOH428 3.3 32.4 1.0
CE J:LYS102 3.5 48.9 1.0
OD2 J:ASP32 3.5 32.8 1.0
O J:HOH417 3.6 28.3 1.0
CA J:GLY77 3.7 37.9 1.0
CB I:SER187 3.7 44.1 1.0
CG2 J:ILE128 4.0 32.7 1.0
O I:SER187 4.0 44.0 1.0
OG I:SER187 4.0 45.3 1.0
C J:THR76 4.2 37.2 1.0
CA J:CA210 4.4 34.7 1.0
CG J:ASP32 4.4 31.7 1.0
CA J:THR76 4.4 37.0 1.0
OD1 J:ASP32 4.5 33.6 1.0
OG1 J:THR76 4.7 36.8 1.0
CA I:SER187 4.7 44.1 1.0
C I:SER187 4.8 43.8 1.0
C J:GLY77 4.9 38.1 1.0
CD J:LYS102 5.0 49.7 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: Sat Jul 20 11:10:17 2024

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