Chlorine in PDB 8db5: Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15

Enzymatic activity of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15

All present enzymatic activity of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15:
5.1.3.13;

Protein crystallography data

The structure of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15, PDB code: 8db5 was solved by J.B.Thoden, M.K.Ghosh, D.F.Xiang, F.M.Raushel, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.81 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.549, 154.525, 120.506, 90, 91.28, 90
R / Rfree (%) 18.9 / 23.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15 (pdb code 8db5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15, PDB code: 8db5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 8db5

Go back to Chlorine Binding Sites List in 8db5
Chlorine binding site 1 out of 7 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15


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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:16.4
occ:1.00
 NZ A:LYS74 3.0 12.6 1.0
O A:HOH373 3.0 34.2 1.0
O A:HOH375 3.2 21.7 1.0
ND2 A:ASN121 3.2 7.1 1.0
CB A:ASN121 3.7 7.8 1.0
O B:HOH307 3.9 23.9 1.0
CE A:LYS74 3.9 12.4 1.0
CG A:ASN121 4.0 7.7 1.0
O B:HOH326 4.0 18.4 1.0
CB A:HIS67 4.0 13.3 1.0
OH A:TYR134 4.1 6.4 0.5
CE2 A:TYR134 4.2 6.6 0.5
OH A:TYR134 4.2 7.2 0.5
CZ A:TYR134 4.2 6.5 0.5
CD A:LYS74 4.3 12.1 1.0
CE1 A:TYR134 4.3 7.2 0.5
O A:HOH333 4.3 12.4 1.0
CZ A:TYR134 4.4 7.1 0.5
O A:HOH310 4.4 17.8 1.0
O A:HIS67 4.5 10.6 1.0
O A:ASN121 4.7 8.1 1.0
O A:HOH360 4.8 5.8 1.0
C A:HIS67 4.9 12.1 1.0
ND1 A:HIS67 4.9 15.5 1.0
CG A:HIS67 4.9 14.4 1.0
CA A:ASN121 4.9 7.8 1.0
CD2 A:TYR134 5.0 6.5 0.5

Chlorine binding site 2 out of 7 in 8db5

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Chlorine binding site 2 out of 7 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15


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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:18.2
occ:1.00
 NZ B:LYS74 3.0 6.2 1.0
O B:HOH365 3.0 10.6 1.0
ND2 B:ASN121 3.0 5.5 1.0
CB B:ASN121 3.5 5.6 1.0
CE B:LYS74 3.6 6.5 1.0
CG B:ASN121 3.7 5.7 1.0
CD B:LYS74 3.9 6.7 1.0
OH B:TYR134 4.1 25.7 1.0
O A:HOH304 4.2 12.9 1.0
CE1 B:TYR134 4.3 17.5 1.0
O B:HIS67 4.3 6.2 1.0
CB B:HIS67 4.3 6.8 1.0
CZ B:TYR134 4.4 17.4 1.0
O B:HOH337 4.6 6.8 1.0
O B:HOH375 4.6 6.7 1.0
O B:HOH411 4.6 14.2 1.0
O B:ASN121 4.6 5.8 1.0
CA B:ASN121 4.7 5.6 1.0
C B:ASN121 4.8 5.5 1.0
C B:HIS67 4.9 6.5 1.0
OD1 B:ASN121 4.9 5.8 1.0

Chlorine binding site 3 out of 7 in 8db5

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Chlorine binding site 3 out of 7 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15


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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl202

b:22.4
occ:1.00
 O D:HOH339 2.9 20.1 1.0
NZ D:LYS74 2.9 11.2 1.0
ND2 D:ASN121 3.1 8.6 1.0
O D:HOH358 3.3 25.1 1.0
O D:HOH344 3.5 31.3 1.0
CB D:ASN121 3.6 8.6 1.0
CE D:LYS74 3.7 10.9 1.0
CG D:ASN121 3.8 9.3 1.0
CD D:LYS74 4.1 10.7 1.0
CE1 D:TYR134 4.2 14.5 1.0
CB D:HIS67 4.3 13.7 1.0
OH D:TYR134 4.3 19.1 1.0
O D:HOH394 4.3 13.6 1.0
CZ D:TYR134 4.5 15.1 1.0
O D:HIS67 4.5 9.9 1.0
O D:HOH348 4.6 12.3 1.0
O D:ASN121 4.7 7.6 1.0
O D:HOH332 4.8 7.4 1.0
O3B D:GDP201 4.8 55.4 1.0
CA D:ASN121 4.9 8.5 1.0
C D:HIS67 5.0 11.4 1.0
C D:ASN121 5.0 8.1 1.0

Chlorine binding site 4 out of 7 in 8db5

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Chlorine binding site 4 out of 7 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15


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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl203

b:22.8
occ:1.00
 O E:HOH407 2.7 24.4 1.0
NZ E:LYS74 2.8 19.1 1.0
O E:HOH381 3.0 13.6 1.0
ND2 E:ASN121 3.1 8.2 1.0
CB E:ASN121 3.6 8.9 1.0
O E:HOH343 3.8 20.3 1.0
CE E:LYS74 3.8 18.5 1.0
CG E:ASN121 3.9 9.1 1.0
OH E:TYR134 3.9 20.6 1.0
O E:HOH362 4.0 18.2 1.0
CD E:LYS74 4.1 18.1 1.0
CZ E:TYR134 4.1 17.3 1.0
CE1 E:TYR134 4.3 16.9 1.0
CB E:HIS67 4.3 11.5 1.0
O E:HOH387 4.5 15.0 1.0
O E:HIS67 4.5 11.7 1.0
O E:HOH359 4.7 11.8 1.0
O E:HOH327 4.8 11.3 1.0
O E:ASN121 4.8 8.6 1.0
CE2 E:TYR134 4.8 17.1 1.0
CA E:ASN121 4.9 9.4 1.0
C E:HIS67 5.0 11.6 1.0

Chlorine binding site 5 out of 7 in 8db5

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Chlorine binding site 5 out of 7 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15


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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl201

b:24.1
occ:1.00
 O F:HOH358 2.9 12.5 1.0
NZ F:LYS74 3.0 6.7 1.0
ND2 F:ASN121 3.3 5.5 1.0
O E:HOH348 3.5 22.3 1.0
O E:HOH385 3.6 30.0 1.0
CB F:ASN121 3.7 5.9 1.0
CE F:LYS74 3.8 6.8 1.0
CG F:ASN121 4.0 6.1 1.0
OH F:TYR134 4.0 21.0 1.0
CD F:LYS74 4.0 6.8 1.0
CB F:HIS67 4.2 9.0 1.0
CZ F:TYR134 4.3 17.2 1.0
CE1 F:TYR134 4.4 17.2 1.0
O F:HOH404 4.4 13.2 1.0
O F:HIS67 4.4 7.3 1.0
O F:HOH340 4.5 6.9 1.0
O F:HOH366 4.7 8.0 1.0
O F:ASN121 4.7 5.6 1.0
ND1 F:HIS67 4.8 10.7 1.0
O3B E:GDP202 4.8 31.2 1.0
CA F:ASN121 4.9 6.0 1.0
C F:HIS67 4.9 7.6 1.0
CG F:HIS67 5.0 9.8 1.0
C F:ASN121 5.0 5.9 1.0

Chlorine binding site 6 out of 7 in 8db5

Go back to Chlorine Binding Sites List in 8db5
Chlorine binding site 6 out of 7 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15


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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl202

b:24.3
occ:1.00
 NZ G:LYS74 2.9 12.3 1.0
O G:HOH335 3.1 19.9 1.0
ND2 G:ASN121 3.4 9.3 1.0
CE G:LYS74 3.7 12.0 1.0
CB G:ASN121 3.8 9.4 1.0
CD G:LYS74 4.1 11.8 1.0
CG G:ASN121 4.1 9.3 1.0
OH G:TYR134 4.1 23.0 1.0
CE1 G:TYR134 4.2 17.4 1.0
CB G:HIS67 4.3 13.7 1.0
O G:HOH363 4.3 18.3 1.0
CZ G:TYR134 4.4 18.1 1.0
O G:HIS67 4.5 11.9 1.0
O G:ASN121 4.7 9.6 1.0
O G:HOH347 4.7 16.3 1.0
O G:HOH327 4.8 11.0 1.0
C G:HIS67 4.9 13.1 1.0
ND1 G:HIS67 4.9 15.6 1.0
CA G:ASN121 5.0 9.8 1.0
O1B H:GDP201 5.0 53.1 1.0

Chlorine binding site 7 out of 7 in 8db5

Go back to Chlorine Binding Sites List in 8db5
Chlorine binding site 7 out of 7 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15


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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3,5- Epimerase From Campylobacter Jejuni, Serotype Hs:15 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl202

b:24.4
occ:1.00
 O H:HOH413 2.7 32.1 1.0
NZ H:LYS74 2.8 12.0 1.0
O H:HOH340 2.9 13.7 1.0
ND2 H:ASN121 3.1 8.4 1.0
CB H:ASN121 3.5 8.1 1.0
CG H:ASN121 3.8 8.3 1.0
CE H:LYS74 3.8 11.7 1.0
O G:HOH312 3.9 19.2 1.0
CD H:LYS74 3.9 11.7 1.0
OH H:TYR134 4.3 19.3 1.0
O H:HIS67 4.3 8.8 1.0
CB H:HIS67 4.3 9.9 1.0
CE1 H:TYR134 4.4 16.1 1.0
O H:HOH415 4.4 10.6 1.0
O H:HOH380 4.4 10.9 1.0
CZ H:TYR134 4.5 16.2 1.0
O H:ASN121 4.6 7.4 1.0
O H:HOH377 4.7 6.1 1.0
CA H:ASN121 4.7 8.2 1.0
C H:HIS67 4.9 9.6 1.0
C H:ASN121 4.9 7.3 1.0
OD1 H:ASN121 5.0 8.8 1.0

Reference:

M.K.Ghosh, D.F.Xiang, J.B.Thoden, H.M.Holden, F.M.Raushel. C3- and C3/C5-Epimerases Required For the Biosynthesis of the Capsular Polysaccharides From Campylobacter Jejuni . Biochemistry V. 61 2036 2022.
ISSN: ISSN 0006-2960
PubMed: 36093987
DOI: 10.1021/ACS.BIOCHEM.2C00364
Page generated: Tue Jul 30 08:40:51 2024

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