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Calcium in PDB 3r4i: Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution

Enzymatic activity of Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution

All present enzymatic activity of Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution:
4.1.3.6;

Protein crystallography data

The structure of Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution, PDB code: 3r4i was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.60 / 2.24
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 148.468, 148.468, 79.570, 90.00, 90.00, 120.00
R / Rfree (%) 15.1 / 17.4

Other elements in 3r4i:

The structure of Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution (pdb code 3r4i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution, PDB code: 3r4i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in 3r4i

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Calcium binding site 1 out of 13 in the Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution


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 A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca341

b:35.0
occ:1.00
 OE1 A:GLU151 2.5 33.6 1.0
OD2 A:ASP177 2.6 33.6 1.0
O A:HOH427 2.6 24.4 1.0
O A:HOH381 2.7 9.5 1.0
O A:HOH372 2.8 13.6 1.0
CD A:GLU151 3.4 34.9 1.0
CG A:ASP177 3.7 27.8 1.0
OE2 A:GLU151 3.7 30.5 1.0
NH1 A:ARG86 4.0 36.3 1.0
CB A:ASP177 4.1 24.9 1.0
CA A:GLY174 4.3 21.3 1.0
OD2 A:ASP55 4.3 37.0 1.0
NZ A:LYS117 4.4 26.5 1.0
CG A:GLU151 4.6 28.3 1.0
CD1 A:LEU149 4.7 23.7 1.0
OD1 A:ASP177 4.7 28.9 1.0
CG A:LEU149 4.8 30.1 1.0
CB A:GLU151 4.8 32.7 1.0
N A:ASP177 4.9 31.8 1.0
OE1 A:GLU54 4.9 32.4 1.0
C A:GLY174 5.0 24.7 1.0

Calcium binding site 2 out of 13 in 3r4i

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Calcium binding site 2 out of 13 in the Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution


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 A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca346

b:31.2
occ:1.00
 OD1 A:ASP230 2.5 33.7 1.0
O A:HOH390 2.5 20.7 1.0
O A:HOH391 2.6 17.7 1.0
O B:HOH408 2.6 11.6 1.0
OD2 A:ASP230 2.7 45.6 1.0
O A:HOH550 2.9 35.4 1.0
CG A:ASP230 2.9 38.9 1.0
OG1 B:THR274 4.4 32.2 1.0
CB A:ASP230 4.4 36.1 1.0
O A:HOH475 4.5 15.9 1.0
OE2 B:GLU270 4.5 37.4 1.0
CG A:ARG229 4.8 31.4 1.0
CG B:GLU270 4.9 31.3 1.0
O B:GLU270 4.9 38.2 1.0
CB B:THR274 5.0 33.8 1.0

Calcium binding site 3 out of 13 in 3r4i

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Calcium binding site 3 out of 13 in the Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution


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 A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca339

b:22.8
occ:1.00
 OE1 B:GLU151 2.4 34.1 1.0
OD2 B:ASP177 2.5 39.4 1.0
O B:HOH395 2.5 38.4 1.0
O B:HOH397 2.6 14.9 1.0
O B:HOH432 2.6 19.2 1.0
CL B:CL354 2.6 38.4 1.0
CD B:GLU151 3.3 36.7 1.0
CG B:ASP177 3.5 29.5 1.0
OE2 B:GLU151 3.6 31.6 1.0
CB B:ASP177 4.0 23.1 1.0
NH1 B:ARG86 4.1 33.9 1.0
NZ B:LYS117 4.3 27.9 1.0
OD2 B:ASP55 4.3 33.5 1.0
CA B:GLY174 4.3 21.2 1.0
O B:HOH642 4.3 26.0 1.0
CG B:GLU151 4.5 25.9 1.0
OD1 B:ASP177 4.6 31.9 1.0
CB B:GLU151 4.8 23.2 1.0
CG B:LEU149 4.8 32.2 1.0
N B:ASP177 4.8 33.1 1.0
CD1 B:LEU149 4.9 23.8 1.0
OE1 B:GLU54 4.9 37.5 1.0
C B:GLY174 5.0 24.4 1.0

Calcium binding site 4 out of 13 in 3r4i

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Calcium binding site 4 out of 13 in the Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution


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 A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca340

b:35.8
occ:1.00
 O A:HOH385 2.4 41.1 1.0
OD1 B:ASP230 2.6 32.7 1.0
OD2 B:ASP230 2.7 46.0 1.0
CG B:ASP230 3.0 42.9 1.0
O B:HOH458 3.3 28.5 1.0
OE2 A:GLU270 4.4 36.0 1.0
CB B:ASP230 4.5 31.7 1.0
OG1 A:THR274 4.6 35.4 1.0
O B:HOH487 4.7 18.1 1.0
CG A:GLU270 4.8 29.8 1.0
CD A:GLU271 4.9 40.3 1.0
O A:GLU270 5.0 35.1 1.0

Calcium binding site 5 out of 13 in 3r4i

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Calcium binding site 5 out of 13 in the Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution


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 A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca343

b:43.5
occ:1.00
 O C:HOH442 2.5 24.2 1.0
OE1 C:GLU151 2.6 37.4 1.0
O C:HOH407 2.7 34.5 1.0
OD2 C:ASP177 2.8 32.5 1.0
CL C:CL353 3.0 29.4 1.0
CD C:GLU151 3.5 34.7 1.0
NH1 C:ARG86 3.5 25.8 1.0
OE2 C:GLU151 3.7 28.6 1.0
CG C:ASP177 4.0 27.1 1.0
O C:ACT357 4.2 15.7 1.0
OD2 C:ASP55 4.2 34.7 1.0
NZ C:LYS117 4.4 30.9 1.0
OXT C:ACT357 4.5 19.9 1.0
CB C:ASP177 4.5 18.9 1.0
OE1 C:GLU54 4.5 33.8 1.0
CG C:LEU149 4.6 33.6 1.0
CZ C:ARG86 4.6 36.2 1.0
CA C:GLY174 4.6 17.1 1.0
CD1 C:LEU149 4.7 31.4 1.0
CG C:GLU151 4.8 25.1 1.0
C C:ACT357 4.8 23.4 1.0
NH2 C:ARG86 4.9 24.1 1.0
OD1 C:ASP177 5.0 29.9 1.0

Calcium binding site 6 out of 13 in 3r4i

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Calcium binding site 6 out of 13 in the Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution


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 A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca344

b:37.0
occ:1.00
 O C:HOH426 2.5 15.1 1.0
OD1 C:ASP230 2.6 39.6 1.0
O C:HOH402 2.7 9.2 1.0
OD2 C:ASP230 2.8 50.3 1.0
CG C:ASP230 3.1 43.6 1.0
CB C:ASP230 4.6 31.0 1.0
O C:HOH532 4.8 29.7 1.0

Calcium binding site 7 out of 13 in 3r4i

Go back to Calcium Binding Sites List in 3r4i
Calcium binding site 7 out of 13 in the Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution


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 A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca342

b:29.0
occ:1.00
 OD2 D:ASP177 2.5 35.1 1.0
O D:HOH430 2.5 27.8 1.0
OE1 D:GLU151 2.5 34.6 1.0
O D:HOH364 2.5 7.9 1.0
CL D:CL352 2.9 25.7 1.0
CD D:GLU151 3.3 35.4 1.0
OE2 D:GLU151 3.5 30.5 1.0
CG D:ASP177 3.6 30.2 1.0
NH1 D:ARG86 3.9 28.7 1.0
CB D:ASP177 4.1 18.1 1.0
NZ D:LYS117 4.1 24.3 1.0
OD2 D:ASP55 4.1 36.6 1.0
OXT D:ACT358 4.3 21.8 1.0
O D:ACT358 4.4 18.7 1.0
CA D:GLY174 4.5 23.2 1.0
CG D:GLU151 4.6 25.0 1.0
OD1 D:ASP177 4.6 30.9 1.0
OE1 D:GLU54 4.6 35.7 1.0
CG D:LEU149 4.8 30.8 1.0
C D:ACT358 4.8 16.4 1.0
CD1 D:LEU149 4.9 28.3 1.0
CB D:GLU151 4.9 28.2 1.0
N D:ASP177 5.0 34.0 1.0
O D:HOH551 5.0 26.3 1.0
CZ D:ARG86 5.0 34.1 1.0

Calcium binding site 8 out of 13 in 3r4i

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Calcium binding site 8 out of 13 in the Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution


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 A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca345

b:39.5
occ:1.00
 O D:HOH549 2.5 26.6 1.0
OD1 D:ASP230 2.6 40.4 1.0
OD2 D:ASP230 3.0 49.9 1.0
CG D:ASP230 3.2 45.8 1.0
O D:HOH464 4.4 15.5 1.0
CB D:ASP230 4.7 36.7 1.0
CG D:ARG229 4.9 36.4 1.0

Calcium binding site 9 out of 13 in 3r4i

Go back to Calcium Binding Sites List in 3r4i
Calcium binding site 9 out of 13 in the Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution


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 A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca350

b:57.9
occ:1.00
 OE1 D:GLU126 3.1 67.5 1.0
OE2 D:GLU126 3.5 50.3 1.0
CD D:GLU126 3.7 65.2 1.0
CZ D:PHE90 4.5 50.5 1.0
CE2 D:PHE90 5.0 37.4 1.0

Calcium binding site 10 out of 13 in 3r4i

Go back to Calcium Binding Sites List in 3r4i
Calcium binding site 10 out of 13 in the Crystal Structure of A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution


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 A Citrate Lyase (BXE_B2899) From Burkholderia Xenovorans LB400 at 2.24 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca347

b:51.1
occ:1.00
 OD1 E:ASP230 2.7 39.3 1.0
OD2 E:ASP230 3.0 43.8 1.0
CG E:ASP230 3.3 39.8 1.0
CB E:ASP230 4.8 33.0 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Sat Dec 12 04:27:40 2020

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