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Chlorine in PDB 6ehi: Nuct From Helicobacter Pylori

Protein crystallography data

The structure of Nuct From Helicobacter Pylori, PDB code: 6ehi was solved by L.Celma, I.Li De La Sierra-Gallay, S.Quevillon-Cheruel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.41 / 1.58
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.350, 71.370, 110.470, 81.36, 74.30, 82.33
R / Rfree (%) 20.1 / 24.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Nuct From Helicobacter Pylori (pdb code 6ehi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Nuct From Helicobacter Pylori, PDB code: 6ehi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6ehi

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Chlorine binding site 1 out of 6 in the Nuct From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Nuct From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:19.1
occ:1.00
 NZ B:LYS102 3.2 15.9 1.0
NZ A:LYS102 3.2 14.1 1.0
O B:HOH347 3.3 31.5 1.0
O A:HOH364 3.4 25.4 1.0
CE A:LYS102 3.4 16.1 1.0
CE B:LYS102 3.5 15.4 1.0
ND2 B:ASN100 3.6 16.1 1.0
O A:HOH304 3.7 22.8 1.0
ND2 A:ASN100 3.7 12.3 1.0
O B:HOH325 3.7 26.5 1.0
OD1 B:ASN100 3.8 15.7 1.0
OD1 A:ASN100 3.8 13.0 1.0
CG B:ASN100 4.1 16.1 1.0
CG A:ASN100 4.2 11.4 1.0
ND2 A:ASN117 4.2 18.4 1.0
O B:HOH332 4.3 25.5 1.0
ND2 B:ASN117 4.3 23.3 1.0
O A:SER115 4.4 16.2 1.0
O B:SER115 4.4 17.0 1.0
O A:HOH352 4.5 25.0 1.0
CD A:LYS102 4.9 13.7 1.0
CG A:ASN117 4.9 15.6 1.0
OD1 A:ASN117 4.9 17.0 1.0
CD B:LYS102 5.0 13.6 1.0

Chlorine binding site 2 out of 6 in 6ehi

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Chlorine binding site 2 out of 6 in the Nuct From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Nuct From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl203

b:19.0
occ:1.00
 NZ D:LYS102 3.2 18.8 1.0
NZ C:LYS102 3.3 15.9 1.0
O C:HOH353 3.4 26.2 1.0
CE C:LYS102 3.5 16.4 1.0
CE D:LYS102 3.5 16.4 1.0
ND2 C:ASN100 3.5 15.5 1.0
ND2 D:ASN100 3.6 18.2 1.0
O D:HOH310 3.7 33.8 1.0
O C:HOH319 3.8 26.7 1.0
OD1 C:ASN100 3.8 15.3 1.0
OD1 D:ASN100 3.8 19.2 1.0
CG C:ASN100 4.1 14.2 1.0
CG D:ASN100 4.2 20.7 1.0
O D:SER115 4.2 16.9 1.0
O D:HOH337 4.3 29.1 1.0
ND2 D:ASN117 4.4 25.1 1.0
O C:SER115 4.4 18.1 1.0
ND2 C:ASN117 4.5 18.2 1.0
O1 C:GOL202 4.6 29.9 1.0
CD D:LYS102 4.9 15.7 1.0
OD1 D:ASN117 4.9 21.0 1.0

Chlorine binding site 3 out of 6 in 6ehi

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Chlorine binding site 3 out of 6 in the Nuct From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Nuct From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl203

b:20.4
occ:1.00
 O G:HOH352 3.2 33.9 1.0
NZ E:LYS102 3.2 20.5 1.0
NZ G:LYS102 3.2 16.9 1.0
ND2 E:ASN100 3.5 16.1 1.0
CE G:LYS102 3.5 18.5 1.0
CE E:LYS102 3.5 18.2 1.0
O E:HOH361 3.5 24.8 1.0
ND2 G:ASN100 3.6 17.8 1.0
O E:HOH306 3.7 29.8 1.0
OD1 G:ASN100 3.8 18.6 1.0
OD1 E:ASN100 3.8 18.9 1.0
O G:HOH331 3.8 28.5 1.0
CG E:ASN100 4.1 18.0 1.0
CG G:ASN100 4.1 15.8 1.0
O G:SER115 4.3 16.3 1.0
O G:HOH359 4.4 27.8 1.0
O E:SER115 4.4 21.6 1.0
ND2 E:ASN117 4.5 24.0 1.0
ND2 G:ASN117 4.6 22.7 1.0
OD1 E:ASN117 4.9 19.3 1.0
OD1 G:ASN117 5.0 19.6 1.0
CD E:LYS102 5.0 17.3 1.0

Chlorine binding site 4 out of 6 in 6ehi

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Chlorine binding site 4 out of 6 in the Nuct From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Nuct From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl203

b:18.1
occ:1.00
 NZ H:LYS102 3.1 15.2 1.0
O F:HOH351 3.2 31.7 1.0
NZ F:LYS102 3.3 15.2 1.0
O H:HOH353 3.4 21.6 1.0
CE H:LYS102 3.4 15.7 1.0
CE F:LYS102 3.5 16.2 1.0
ND2 H:ASN100 3.6 14.1 1.0
ND2 F:ASN100 3.6 12.4 1.0
O F:HOH345 3.7 22.6 1.0
OD1 H:ASN100 3.7 13.9 1.0
O H:HOH326 3.8 24.0 1.0
OD1 F:ASN100 3.8 14.3 1.0
CG H:ASN100 4.1 13.2 1.0
O F:HOH360 4.1 30.7 1.0
CG F:ASN100 4.1 15.2 1.0
ND2 H:ASN117 4.3 20.8 1.0
O H:SER115 4.4 17.4 1.0
O H:HOH346 4.4 25.6 1.0
O F:SER115 4.4 14.9 1.0
ND2 F:ASN117 4.6 22.1 1.0
OD1 H:ASN117 4.9 14.5 1.0
CD H:LYS102 4.9 13.3 1.0
CG H:ASN117 5.0 17.1 1.0
CD F:LYS102 5.0 14.2 1.0
OD1 F:ASN117 5.0 19.3 1.0

Chlorine binding site 5 out of 6 in 6ehi

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Chlorine binding site 5 out of 6 in the Nuct From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Nuct From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl203

b:18.3
occ:1.00
 O I:HOH353 2.6 20.5 0.5
NZ I:LYS102 3.2 16.2 1.0
NZ J:LYS102 3.3 13.1 1.0
O I:HOH353 3.4 13.0 0.5
CE I:LYS102 3.5 15.0 1.0
CE J:LYS102 3.5 15.4 1.0
ND2 J:ASN100 3.6 14.3 1.0
ND2 I:ASN100 3.6 14.4 1.0
O J:HOH328 3.7 20.6 1.0
OD1 I:ASN100 3.7 17.4 1.0
O I:HOH320 3.8 25.9 1.0
OD1 J:ASN100 3.8 15.7 1.0
O J:HOH351 4.0 29.0 1.0
CG I:ASN100 4.1 13.1 1.0
CG J:ASN100 4.1 13.5 1.0
ND2 I:ASN117 4.2 18.6 1.0
O I:SER115 4.3 17.2 1.0
O I:HOH340 4.3 29.5 1.0
O J:SER115 4.4 16.7 1.0
ND2 J:ASN117 4.5 20.8 1.0
OD1 I:ASN117 4.8 16.4 1.0
CG I:ASN117 4.9 17.0 1.0
OD1 J:ASN117 5.0 16.7 1.0
CD J:LYS102 5.0 12.8 1.0

Chlorine binding site 6 out of 6 in 6ehi

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Chlorine binding site 6 out of 6 in the Nuct From Helicobacter Pylori


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Nuct From Helicobacter Pylori within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl203

b:20.0
occ:1.00
 O K:HOH333 3.1 37.6 1.0
NZ K:LYS102 3.2 17.4 1.0
NZ L:LYS102 3.3 20.0 1.0
O L:HOH349 3.3 24.3 1.0
CE L:LYS102 3.5 18.9 1.0
CE K:LYS102 3.5 19.7 1.0
ND2 L:ASN100 3.5 18.5 1.0
ND2 K:ASN100 3.6 18.0 1.0
OD1 K:ASN100 3.7 19.2 1.0
O K:HOH318 3.8 24.6 1.0
O L:HOH306 3.8 29.1 1.0
OD1 L:ASN100 3.9 18.4 1.0
CG K:ASN100 4.1 15.6 1.0
CG L:ASN100 4.1 16.0 1.0
O K:SER115 4.3 18.9 1.0
O L:SER115 4.4 19.3 1.0
O3 K:GOL202 4.5 32.8 1.0
ND2 L:ASN117 4.5 23.7 1.0
O L:HOH351 4.5 31.3 1.0
ND2 K:ASN117 4.6 21.9 1.0
OD1 K:ASN117 4.9 18.4 1.0
CD K:LYS102 4.9 17.1 1.0

Reference:

L.Celma, C.Corbinais, J.Vercruyssen, X.Veaute, I.L.De La Sierra-Gallay, R.Guerois, D.Busso, A.Mathieu, S.Marsin, S.Quevillon-Cheruel, J.P.Radicella. Structural Basis For the Substrate Selectivity of Helicobacter Pylori Nuct Nuclease Activity. Plos One V. 12 89049 2017.
ISSN: ESSN 1932-6203
PubMed: 29206236
DOI: 10.1371/JOURNAL.PONE.0189049
Page generated: Sat Jul 27 22:22:21 2024

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