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Chlorine in PDB 5c6m: Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis

Enzymatic activity of Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis

All present enzymatic activity of Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis:
4.1.2.4;

Protein crystallography data

The structure of Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis, PDB code: 5c6m was solved by O.H.Weiergraeber, M.Dick, J.Bramski, J.Pietruszka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.70 / 1.76
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.030, 52.510, 143.210, 90.00, 122.34, 90.00
R / Rfree (%) 16.8 / 19.8

Other elements in 5c6m:

The structure of Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis (pdb code 5c6m). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis, PDB code: 5c6m:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5c6m

Go back to Chlorine Binding Sites List in 5c6m
Chlorine binding site 1 out of 4 in the Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis


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 Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:23.7
occ:1.00
 O A:HOH688 3.0 15.9 1.0
O A:HOH482 3.0 18.6 1.0
NH1 A:ARG51 3.1 20.2 1.0
N A:ARG51 3.2 16.8 1.0
CG A:ARG51 3.5 17.8 1.0
CB A:ARG51 3.5 16.4 1.0
CD A:PRO50 3.6 18.6 1.0
CD A:ARG51 3.6 21.7 1.0
CD B:ARG51 3.7 23.8 1.0
N A:PRO50 3.8 17.7 1.0
CB A:PRO50 3.9 16.6 1.0
CA A:ARG51 4.0 15.8 1.0
CB A:TYR49 4.0 16.6 1.0
CG A:PRO50 4.0 19.1 1.0
CB B:ARG51 4.1 19.0 1.0
CZ A:ARG51 4.1 18.4 1.0
C A:PRO50 4.2 15.3 1.0
CA A:PRO50 4.2 15.4 1.0
CL B:CL302 4.2 24.2 1.0
C A:TYR49 4.3 16.9 1.0
NE A:ARG51 4.3 21.2 1.0
OH B:TYR96 4.4 17.6 1.0
O B:HOH460 4.5 24.3 1.0
CG B:ARG51 4.6 16.3 1.0
CA A:TYR49 4.7 16.2 1.0
CG A:TYR49 4.8 18.6 1.0
NE B:ARG51 4.8 21.3 1.0
O A:HOH570 4.8 32.5 1.0
O A:TYR49 5.0 16.6 1.0

Chlorine binding site 2 out of 4 in 5c6m

Go back to Chlorine Binding Sites List in 5c6m
Chlorine binding site 2 out of 4 in the Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis


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 Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:24.2
occ:1.00
 O A:HOH482 3.0 18.6 1.0
O B:HOH668 3.1 13.2 1.0
NH1 B:ARG51 3.1 19.6 1.0
N B:ARG51 3.2 13.9 1.0
CG B:ARG51 3.5 16.3 1.0
CB B:ARG51 3.5 19.0 1.0
CD B:PRO50 3.6 16.8 1.0
CD B:ARG51 3.6 23.8 1.0
N B:PRO50 3.7 16.4 1.0
CD A:ARG51 3.8 21.7 1.0
CB B:PRO50 3.8 16.5 1.0
CA B:ARG51 3.9 15.1 1.0
CG B:PRO50 4.0 18.1 1.0
CB B:TYR49 4.0 18.6 1.0
C B:PRO50 4.1 16.0 1.0
CB A:ARG51 4.1 16.4 1.0
CA B:PRO50 4.1 14.4 1.0
CZ B:ARG51 4.2 18.4 1.0
CL A:CL302 4.2 23.7 1.0
C B:TYR49 4.3 16.6 1.0
NE B:ARG51 4.3 21.3 1.0
OH A:TYR96 4.4 19.1 1.0
O B:HOH542 4.6 35.0 1.0
CG A:ARG51 4.6 17.8 1.0
CA B:TYR49 4.7 15.4 1.0
O A:HOH473 4.7 24.3 1.0
CG B:TYR49 4.8 16.2 1.0
NE A:ARG51 4.9 21.2 1.0
O B:TYR49 4.9 14.4 1.0

Chlorine binding site 3 out of 4 in 5c6m

Go back to Chlorine Binding Sites List in 5c6m
Chlorine binding site 3 out of 4 in the Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis


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 Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:43.1
occ:1.00
 O C:HOH569 2.8 39.3 1.0
NH1 C:ARG51 3.2 45.9 1.0
O C:HOH432 3.2 32.8 1.0
N C:ARG51 3.3 38.7 1.0
CD C:PRO50 3.6 38.5 1.0
CG C:ARG51 3.6 49.6 1.0
CB C:ARG51 3.6 49.3 1.0
CD D:ARG51 3.6 44.6 1.0
N C:PRO50 3.8 34.9 1.0
CD C:ARG51 3.8 51.5 1.0
CB C:PRO50 3.9 37.3 1.0
CB D:ARG51 4.0 40.8 1.0
CG C:PRO50 4.1 35.1 1.0
CA C:ARG51 4.1 46.5 1.0
O D:HOH451 4.2 40.6 1.0
CB C:TYR49 4.2 38.2 1.0
CA C:PRO50 4.2 37.2 1.0
C C:PRO50 4.2 38.9 1.0
CZ C:ARG51 4.3 51.2 1.0
OH D:TYR96 4.3 42.9 1.0
CL D:CL301 4.3 41.9 1.0
CG D:ARG51 4.4 40.8 1.0
C C:TYR49 4.4 38.7 1.0
NE C:ARG51 4.5 51.5 1.0
NE D:ARG51 4.7 44.0 1.0
CA C:TYR49 4.9 36.3 1.0
CG C:TYR49 5.0 39.8 1.0

Chlorine binding site 4 out of 4 in 5c6m

Go back to Chlorine Binding Sites List in 5c6m
Chlorine binding site 4 out of 4 in the Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis


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 Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl301

b:41.9
occ:1.00
 O C:HOH432 3.0 32.8 1.0
O D:HOH493 3.0 39.7 1.0
NH1 D:ARG51 3.0 46.0 1.0
N D:ARG51 3.3 41.3 1.0
CG D:ARG51 3.4 40.8 1.0
CD D:PRO50 3.5 44.2 1.0
CB D:ARG51 3.6 40.8 1.0
CD D:ARG51 3.7 44.6 1.0
CB D:PRO50 3.7 44.0 1.0
N D:PRO50 3.8 42.8 1.0
CG D:PRO50 3.9 45.1 1.0
CA D:ARG51 4.1 40.5 1.0
CD C:ARG51 4.1 51.5 1.0
CA D:PRO50 4.1 42.6 1.0
CZ D:ARG51 4.1 44.2 1.0
C D:PRO50 4.2 41.5 1.0
CB D:TYR49 4.2 42.4 1.0
CB C:ARG51 4.3 49.3 1.0
CL C:CL301 4.3 43.1 1.0
NE D:ARG51 4.3 44.0 1.0
C D:TYR49 4.4 41.9 1.0
OH C:TYR96 4.4 42.8 1.0
CG C:ARG51 4.8 49.6 1.0
CA D:TYR49 4.8 42.4 1.0
CG D:TYR49 4.9 44.2 1.0

Reference:

M.Dick, O.H.Weiergraber, T.Classen, C.Bisterfeld, J.Bramski, H.Gohlke, J.Pietruszka. Trading Off Stability Against Activity in Extremophilic Aldolases. Sci Rep V. 6 17908 2016.
ISSN: ESSN 2045-2322
PubMed: 26783049
DOI: 10.1038/SREP17908
Page generated: Sat Dec 12 11:34:29 2020

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