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Calcium in PDB 3toy: Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound

Enzymatic activity of Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound

All present enzymatic activity of Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound:
5.1.2.2; 5.5.1.1;

Protein crystallography data

The structure of Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound, PDB code: 3toy was solved by Y.Patskovsky, J.Kim, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammond, W.D.Zencheck, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative(Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 118.389, 131.838, 108.825, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 19.9

Other elements in 3toy:

The structure of Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound also contains other interesting chemical elements:

Nickel (Ni) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound (pdb code 3toy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound, PDB code: 3toy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3toy

Go back to Calcium Binding Sites List in 3toy
Calcium binding site 1 out of 8 in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound


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 Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca361

b:26.6
occ:1.00
 O A:HOH1177 2.3 26.2 1.0
OE2 A:GLU222 2.3 29.2 1.0
OD2 A:ASP196 2.4 30.0 1.0
OE1 A:GLU248 2.4 31.7 1.0
O A:HOH1176 2.5 27.2 1.0
OXT A:ACT362 2.5 32.0 1.0
OE2 A:GLU248 2.6 31.1 1.0
CD A:GLU248 2.9 32.9 1.0
CG A:ASP196 3.4 31.7 1.0
C A:ACT362 3.5 40.3 1.0
CD A:GLU222 3.5 27.0 1.0
OD1 A:ASP196 3.7 28.9 1.0
O A:ACT362 3.8 33.8 1.0
NZ A:LYS165 4.0 26.1 1.0
ND2 A:ASN198 4.0 28.9 1.0
NZ A:LYS167 4.1 33.6 1.0
CG A:GLU222 4.2 23.7 1.0
NE2 A:HIS298 4.2 29.1 1.0
CD2 A:HIS298 4.3 25.2 1.0
CG A:GLU248 4.4 21.7 1.0
OE1 A:GLU223 4.5 29.2 1.0
CE A:MET269 4.5 28.8 1.0
OE1 A:GLU222 4.5 27.7 1.0
O A:HOH411 4.6 25.9 1.0
CB A:ASP196 4.6 24.9 1.0
CH3 A:ACT362 4.7 39.6 1.0
O A:HOH438 4.8 34.7 1.0
CE A:LYS165 4.8 24.8 1.0
CG A:ASN198 4.8 29.5 1.0
O A:HOH430 4.8 29.1 1.0
OD1 A:ASN198 4.9 33.6 1.0

Calcium binding site 2 out of 8 in 3toy

Go back to Calcium Binding Sites List in 3toy
Calcium binding site 2 out of 8 in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound


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 Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca365

b:30.5
occ:0.50
 O C:HOH1249 2.2 44.9 1.0
O A:HOH1247 2.4 24.4 1.0
O A:ARG237 2.4 21.5 1.0
O A:HOH1248 2.5 28.6 1.0
O A:SER240 2.6 26.2 1.0
NH1 C:ARG239 3.1 34.2 0.5
C A:ARG237 3.6 23.0 1.0
O C:HOH566 3.6 49.3 1.0
C A:SER240 3.7 27.6 1.0
O A:HOH951 3.8 48.2 1.0
CZ C:ARG239 4.0 44.5 0.5
N A:SER240 4.0 21.2 1.0
CA A:SER240 4.2 24.8 1.0
CG A:ARG237 4.3 22.1 1.0
CB A:SER240 4.3 22.8 1.0
O A:GLU238 4.4 25.4 1.0
C A:GLU238 4.4 24.4 1.0
OD2 A:ASP266 4.4 22.1 1.0
CA A:ARG237 4.4 19.8 1.0
N A:GLU238 4.5 21.9 1.0
CD C:ARG239 4.6 38.2 0.5
CA A:GLU238 4.6 22.8 1.0
NE C:ARG239 4.6 50.4 0.5
OD1 A:ASP266 4.7 20.4 1.0
NH2 C:ARG239 4.8 37.6 0.5
N A:GLU241 4.8 26.3 1.0
C A:ARG239 4.9 29.2 1.0
N A:ARG239 4.9 23.1 1.0
CG A:ASP266 5.0 21.8 1.0

Calcium binding site 3 out of 8 in 3toy

Go back to Calcium Binding Sites List in 3toy
Calcium binding site 3 out of 8 in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound


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 Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca361

b:23.8
occ:1.00
 OE2 B:GLU222 2.3 24.9 1.0
O B:HOH1180 2.3 25.1 1.0
OD2 B:ASP196 2.3 23.8 1.0
OE1 B:GLU248 2.4 25.5 1.0
O B:HOH1181 2.4 24.2 1.0
OXT B:ACT362 2.5 29.9 1.0
OE2 B:GLU248 2.6 26.1 1.0
CD B:GLU248 2.9 26.1 1.0
CG B:ASP196 3.3 25.3 1.0
CD B:GLU222 3.4 26.8 1.0
C B:ACT362 3.5 39.4 1.0
OD1 B:ASP196 3.7 22.6 1.0
O B:ACT362 3.8 32.5 1.0
ND2 B:ASN198 4.0 23.2 1.0
NZ B:LYS165 4.1 23.3 1.0
CG B:GLU222 4.1 24.1 1.0
NZ B:LYS167 4.1 30.1 1.0
NE2 B:HIS298 4.3 24.6 1.0
CD2 B:HIS298 4.3 21.3 1.0
CG B:GLU248 4.4 18.8 1.0
OE1 B:GLU222 4.4 23.9 1.0
CB B:ASP196 4.5 24.2 1.0
OE1 B:GLU223 4.5 24.8 1.0
CE B:MET269 4.6 25.8 1.0
O B:HOH390 4.7 24.2 1.0
O B:HOH1284 4.7 55.4 1.0
CE B:LYS165 4.7 21.5 1.0
CG B:ASN198 4.7 20.9 1.0
CH3 B:ACT362 4.8 38.1 1.0
OD1 B:ASN198 4.9 27.1 1.0
O B:HOH403 4.9 25.3 1.0
O B:HOH418 4.9 30.9 1.0

Calcium binding site 4 out of 8 in 3toy

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Calcium binding site 4 out of 8 in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound


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 Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca366

b:27.8
occ:0.50
 O B:HOH411 2.2 25.4 1.0
O B:HOH701 2.3 38.7 1.0
O B:ARG237 2.3 21.7 1.0
O B:SER240 2.4 25.7 1.0
O B:HOH460 2.6 30.1 1.0
O B:HOH723 3.5 48.5 1.0
C B:SER240 3.5 26.9 1.0
C B:ARG237 3.6 24.9 1.0
N B:SER240 3.9 20.3 1.0
CA B:SER240 4.0 22.1 1.0
CB B:SER240 4.2 23.4 1.0
O B:GLU238 4.3 26.1 1.0
CG B:ARG237 4.3 19.4 1.0
C B:GLU238 4.3 23.4 1.0
CA B:ARG237 4.4 19.8 1.0
OD2 B:ASP266 4.5 21.1 1.0
N B:GLU238 4.5 18.4 1.0
CA B:GLU238 4.5 24.1 0.5
CA B:GLU238 4.6 24.8 0.5
N B:GLU241 4.7 21.7 1.0
OD1 B:ASP266 4.7 23.4 1.0
C B:ARG239 4.8 25.1 1.0
N B:ARG239 4.8 20.4 1.0
OG B:SER240 4.9 22.9 1.0
O B:ILE242 5.0 22.2 1.0

Calcium binding site 5 out of 8 in 3toy

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Calcium binding site 5 out of 8 in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound


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 Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca361

b:22.5
occ:1.00
 O C:HOH1188 2.3 23.5 1.0
OE2 C:GLU222 2.3 22.7 1.0
OE1 C:GLU248 2.4 23.3 1.0
OD2 C:ASP196 2.4 22.2 1.0
OXT C:ACT362 2.5 26.1 1.0
O C:HOH1189 2.6 25.5 1.0
OE2 C:GLU248 2.6 26.8 1.0
CD C:GLU248 2.8 25.9 1.0
CG C:ASP196 3.3 22.9 1.0
CD C:GLU222 3.4 22.2 1.0
C C:ACT362 3.5 34.1 1.0
OD1 C:ASP196 3.7 22.5 1.0
O C:ACT362 3.8 28.0 1.0
ND2 C:ASN198 4.0 23.2 1.0
NZ C:LYS165 4.1 22.9 1.0
CG C:GLU222 4.1 19.9 1.0
NZ C:LYS167 4.2 29.1 1.0
NE2 C:HIS298 4.3 21.9 1.0
CG C:GLU248 4.3 19.8 1.0
CD2 C:HIS298 4.3 19.4 1.0
OE1 C:GLU222 4.5 21.6 1.0
OE1 C:GLU223 4.5 24.5 1.0
CB C:ASP196 4.6 19.2 1.0
CE C:MET269 4.6 16.9 1.0
O C:HOH447 4.7 21.2 1.0
CE C:LYS165 4.7 20.7 1.0
CG C:ASN198 4.8 26.4 1.0
CH3 C:ACT362 4.8 29.1 1.0
O C:HOH438 4.9 26.9 1.0
O C:HOH446 4.9 24.5 1.0
O C:HOH1352 4.9 58.7 1.0

Calcium binding site 6 out of 8 in 3toy

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Calcium binding site 6 out of 8 in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound


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 Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca365

b:25.2
occ:0.50
 O C:HOH1347 2.1 45.0 1.0
O C:HOH419 2.2 25.0 1.0
O C:ARG237 2.3 19.6 1.0
O C:SER240 2.4 22.2 1.0
O C:HOH382 2.8 30.4 1.0
O C:HOH1349 3.5 42.6 1.0
C C:SER240 3.5 23.1 1.0
C C:ARG237 3.5 18.1 1.0
N C:SER240 3.9 20.6 1.0
CA C:SER240 4.0 18.4 1.0
O C:GLU238 4.0 20.7 0.5
CB C:SER240 4.2 22.5 1.0
C C:GLU238 4.3 23.6 0.5
CG C:ARG237 4.4 20.1 1.0
CA C:ARG237 4.4 16.4 1.0
OD2 C:ASP266 4.5 19.8 1.0
N C:GLU238 4.5 20.0 0.5
N C:GLU238 4.5 19.4 0.5
C C:GLU238 4.5 21.6 0.5
CA C:GLU238 4.5 22.1 0.5
CA C:GLU238 4.6 21.4 0.5
N C:GLU241 4.6 21.3 1.0
O C:GLU238 4.7 21.2 0.5
OD1 C:ASP266 4.7 19.9 1.0
C C:ARG239 4.8 25.4 1.0
N C:ARG239 4.8 19.4 1.0
OG C:SER240 4.9 21.4 1.0
O C:ILE242 4.9 19.1 1.0
O C:HOH1348 5.0 48.6 1.0

Calcium binding site 7 out of 8 in 3toy

Go back to Calcium Binding Sites List in 3toy
Calcium binding site 7 out of 8 in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound


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 Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca361

b:21.5
occ:1.00
 OE2 D:GLU222 2.2 22.9 1.0
O D:HOH1195 2.3 19.8 1.0
OD2 D:ASP196 2.4 21.3 1.0
O D:HOH1194 2.4 21.7 1.0
OE1 D:GLU248 2.4 22.4 1.0
O D:ACT362 2.5 28.9 1.0
OE2 D:GLU248 2.6 24.6 1.0
CD D:GLU248 2.8 22.3 1.0
CG D:ASP196 3.3 24.2 1.0
CD D:GLU222 3.4 19.0 1.0
C D:ACT362 3.5 33.5 1.0
OD1 D:ASP196 3.6 20.8 1.0
OXT D:ACT362 3.8 31.3 1.0
NZ D:LYS165 4.0 21.9 1.0
ND2 D:ASN198 4.0 21.7 1.0
CG D:GLU222 4.0 18.5 1.0
NZ D:LYS167 4.1 29.3 1.0
NE2 D:HIS298 4.3 19.8 1.0
CG D:GLU248 4.4 17.9 1.0
CD2 D:HIS298 4.4 19.7 1.0
OE1 D:GLU222 4.4 19.4 1.0
OE1 D:GLU223 4.5 25.0 1.0
CE D:MET269 4.5 19.4 1.0
CB D:ASP196 4.5 20.1 1.0
O D:HOH413 4.7 21.6 1.0
CE D:LYS165 4.7 19.9 1.0
CH3 D:ACT362 4.8 33.3 1.0
O D:HOH870 4.8 46.3 1.0
O D:HOH392 4.8 29.5 1.0
CG D:ASN198 4.8 25.0 1.0
O D:HOH418 4.9 22.0 1.0

Calcium binding site 8 out of 8 in 3toy

Go back to Calcium Binding Sites List in 3toy
Calcium binding site 8 out of 8 in the Crystal Structure of Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound


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 Enolase BRADO_4202 (Target Efi-501651) From Bradyrhizobium Sp. ORS278 with Calcium and Acetate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca365

b:30.3
occ:0.50
 O D:HOH1519 2.0 29.8 0.5
O D:HOH1519 2.1 27.5 0.5
O D:HOH1197 2.2 25.6 1.0
O D:ARG237 2.4 20.3 1.0
O D:SER240 2.4 24.4 1.0
O D:HOH685 2.7 30.3 1.0
NH1 B:ARG239 2.9 72.1 1.0
C D:SER240 3.5 21.5 1.0
O B:HOH1293 3.5 41.9 1.0
C D:ARG237 3.6 20.7 1.0
O D:HOH1198 3.8 45.7 1.0
N D:SER240 3.9 18.7 1.0
CZ B:ARG239 4.0 74.2 1.0
CA D:SER240 4.0 18.8 1.0
CB D:SER240 4.2 19.9 1.0
O D:GLU238 4.2 25.8 1.0
C D:GLU238 4.3 23.9 1.0
CA D:GLU238 4.5 23.1 0.5
CA D:ARG237 4.5 18.9 1.0
CA D:GLU238 4.5 22.0 0.5
CG D:ARG237 4.5 21.5 1.0
N D:GLU238 4.5 19.6 1.0
OD2 D:ASP266 4.5 18.8 1.0
CD B:ARG239 4.6 54.4 1.0
NE B:ARG239 4.6 68.7 1.0
N D:GLU241 4.7 21.5 1.0
C D:ARG239 4.7 26.6 1.0
NH2 B:ARG239 4.7 73.8 1.0
N D:ARG239 4.8 21.9 1.0
OD1 D:ASP266 4.8 19.7 1.0
OG D:SER240 5.0 19.6 1.0
CA D:GLU241 5.0 23.9 1.0

Reference:

Y.Patskovsky, J.Kim, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammond, W.D.Zencheck, H.J.Imker, J.A.Gerlt, S.C.Almo. Crystal Structure of Mandelate Racemase From Bradyrhizobium Sp. ORS278 To Be Published.
Page generated: Sat Jul 13 19:50:48 2024

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