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Chlorine in PDB 6h1j: Tarp Native

Protein crystallography data

The structure of Tarp Native, PDB code: 6h1j was solved by Y.Guo, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.49 / 1.86
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.370, 95.250, 125.470, 90.00, 96.57, 90.00
R / Rfree (%) 17 / 21.6

Other elements in 6h1j:

The structure of Tarp Native also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Tarp Native (pdb code 6h1j). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Tarp Native, PDB code: 6h1j:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 6h1j

Go back to Chlorine Binding Sites List in 6h1j
Chlorine binding site 1 out of 10 in the Tarp Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Tarp Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:29.2
occ:1.00
 OG A:SER155 3.0 26.8 1.0
N A:SER155 3.3 25.5 1.0
C A:ALA153 3.3 25.9 1.0
CB A:SER155 3.3 25.5 1.0
NZ A:LYS158 3.4 26.1 1.0
CA A:ALA153 3.4 27.3 1.0
CG A:PRO131 3.5 52.4 1.0
O A:ALA153 3.5 24.6 1.0
CB A:ALA153 3.7 28.4 1.0
CE2 A:TYR121 3.7 27.3 1.0
N A:LEU154 3.8 24.1 1.0
OH A:TYR121 3.8 26.3 1.0
CD A:PRO131 3.8 52.4 1.0
CA A:SER155 3.8 26.2 1.0
CZ A:TYR121 4.1 26.3 1.0
C A:LEU154 4.3 24.3 1.0
CA A:LEU154 4.6 25.5 1.0
O A:HOH700 4.6 53.0 1.0
CD2 A:TYR121 4.6 25.4 1.0
O A:SER155 4.6 25.1 1.0
C A:SER155 4.7 25.6 1.0
CE A:LYS158 4.7 24.3 1.0
N A:ALA153 4.8 27.5 1.0
CB A:PRO131 4.9 48.6 1.0

Chlorine binding site 2 out of 10 in 6h1j

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Chlorine binding site 2 out of 10 in the Tarp Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Tarp Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:42.7
occ:1.00
 O A:HOH633 2.9 30.1 1.0
NE A:ARG259 3.2 32.8 1.0
NH1 A:ARG259 3.3 37.6 1.0
CB A:HIS263 3.7 33.4 1.0
CZ A:ARG259 3.7 33.9 1.0
O A:HOH549 3.7 42.0 1.0
CA A:TYR152 3.8 25.9 1.0
O A:TYR152 3.8 24.8 1.0
C A:TYR152 4.0 26.3 1.0
CG A:HIS263 4.1 40.4 1.0
O A:PHE151 4.2 24.2 1.0
CG A:ARG259 4.2 26.2 1.0
CD A:ARG259 4.3 30.4 1.0
CD2 A:HIS263 4.3 48.3 1.0
CD2 A:TYR152 4.5 27.6 1.0
CB A:TYR152 4.5 26.0 1.0
N A:TYR152 4.9 24.6 1.0
CG A:TYR152 4.9 26.1 1.0
N A:ALA153 4.9 27.5 1.0
C A:PHE151 5.0 23.8 1.0

Chlorine binding site 3 out of 10 in 6h1j

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Chlorine binding site 3 out of 10 in the Tarp Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Tarp Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:48.1
occ:1.00
 N A:LYS244 3.2 27.2 1.0
O A:ILE242 3.5 28.2 1.0
N A:ASN245 3.7 29.3 1.0
CB A:LYS244 3.8 34.6 1.0
CA A:LYS244 3.9 29.8 1.0
C A:TYR243 4.2 26.0 1.0
CA A:TYR243 4.2 26.7 1.0
C A:LYS244 4.2 30.4 1.0
CE A:LYS244 4.3 45.7 1.0
C A:ILE242 4.5 28.2 1.0
CG A:LYS244 4.5 38.2 1.0
CB A:ASN245 4.6 30.4 1.0
CA A:ASN245 4.7 30.5 1.0
N A:TYR243 4.8 25.2 1.0
CD A:LYS244 5.0 43.8 1.0

Chlorine binding site 4 out of 10 in 6h1j

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Chlorine binding site 4 out of 10 in the Tarp Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Tarp Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:43.3
occ:1.00
 OH A:TYR226 2.9 29.7 1.0
NH2 A:ARG259 3.1 32.4 1.0
NE2 A:GLN182 3.2 34.0 1.0
NH1 A:ARG259 3.4 37.6 1.0
N A:GLN265 3.6 31.6 1.0
CA A:GLY264 3.7 31.4 1.0
CZ A:ARG259 3.7 33.9 1.0
CE1 A:TYR226 3.8 27.9 1.0
CZ A:TYR226 3.8 29.0 1.0
C A:GLY264 4.1 31.2 1.0
CD A:GLN182 4.1 39.0 1.0
OE1 A:GLN182 4.3 40.5 1.0
O A:HIS263 4.3 32.2 1.0
CB A:GLN265 4.5 38.8 1.0
CD1 A:LEU260 4.5 27.0 1.0
CA A:GLN265 4.7 34.5 1.0
N A:GLY264 4.7 30.8 1.0
OH A:TYR256 4.8 29.2 1.0
C A:HIS263 4.9 32.1 1.0
CD1 A:ILE230 4.9 29.4 1.0

Chlorine binding site 5 out of 10 in 6h1j

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Chlorine binding site 5 out of 10 in the Tarp Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Tarp Native within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:37.7
occ:1.00
 O A:HOH591 2.9 21.4 1.0
O A:HOH510 3.0 23.6 1.0
CB A:LYS255 3.8 27.2 1.0
CE1 A:TYR152 3.9 25.7 1.0
O A:ILE146 4.0 33.6 1.0
CD A:LYS255 4.0 34.3 1.0
CG A:LYS255 4.1 29.4 1.0
O A:HOH684 4.1 34.2 1.0
CG2 A:ILE146 4.1 31.6 1.0
CA A:ILE146 4.2 30.8 1.0
CD2 A:PHE151 4.4 26.7 1.0
CG1 A:ILE146 4.4 33.4 1.0
CB A:ILE146 4.5 30.4 1.0
C A:ILE146 4.5 32.7 1.0
CD1 A:TYR152 4.6 25.3 1.0
O A:LYS255 4.6 23.8 1.0
CA A:LYS255 4.7 25.3 1.0
CZ A:TYR152 4.8 26.9 1.0
OH A:TYR152 4.9 25.9 1.0
O A:ILE145 4.9 27.3 1.0
CB A:PHE151 4.9 26.9 1.0
C A:LYS255 4.9 24.5 1.0
CE A:LYS255 4.9 36.1 1.0

Chlorine binding site 6 out of 10 in 6h1j

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Chlorine binding site 6 out of 10 in the Tarp Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Tarp Native within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:33.7
occ:1.00
 OG B:SER155 2.8 30.2 1.0
O B:HOH698 2.8 39.0 1.0
C B:ALA153 3.3 18.9 1.0
O B:ALA153 3.4 22.6 1.0
N B:SER155 3.4 25.8 1.0
CB B:SER155 3.4 26.4 1.0
CA B:ALA153 3.5 18.9 1.0
CE2 B:TYR121 3.5 31.7 1.0
NZ B:LYS158 3.5 24.3 1.0
CG B:PRO131 3.8 42.1 1.0
CB B:ALA153 3.8 19.2 1.0
N B:LEU154 3.9 19.6 1.0
OH B:TYR121 3.9 30.5 1.0
CA B:SER155 4.0 26.1 1.0
CZ B:TYR121 4.0 31.9 1.0
CD B:PRO131 4.2 40.6 1.0
CD2 B:TYR121 4.4 32.6 1.0
C B:LEU154 4.4 22.1 1.0
O B:SER155 4.7 29.1 1.0
CA B:LEU154 4.7 21.1 1.0
C B:SER155 4.8 28.3 1.0
N B:ALA153 4.9 18.0 1.0
CE B:LYS158 4.9 23.7 1.0
CB B:PRO131 4.9 36.3 1.0

Chlorine binding site 7 out of 10 in 6h1j

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Chlorine binding site 7 out of 10 in the Tarp Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Tarp Native within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:23.1
occ:1.00
 NZ B:LYS248 3.0 20.2 1.0
O B:HOH592 3.0 18.9 1.0
O B:HOH628 3.1 25.9 1.0
N B:ILE146 3.3 19.0 1.0
N B:ILE145 3.6 18.4 1.0
CE B:LYS248 3.8 20.0 1.0
CG1 B:ILE146 3.8 22.2 1.0
CB B:ILE146 3.8 20.3 1.0
CD1 B:ILE146 3.9 24.6 1.0
CB B:ILE145 4.0 19.5 1.0
CA B:ILE145 4.1 18.9 1.0
CB B:ASP144 4.2 24.6 1.0
CA B:ILE146 4.2 19.0 1.0
C B:ILE145 4.2 18.8 1.0
C B:ASP144 4.2 21.3 1.0
CD2 B:LEU252 4.2 18.6 1.0
CA B:ASP144 4.5 22.1 1.0
CG1 B:ILE145 4.8 20.1 1.0
N B:ASP147 4.9 20.8 1.0
CG2 B:ILE145 5.0 21.0 1.0

Chlorine binding site 8 out of 10 in 6h1j

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Chlorine binding site 8 out of 10 in the Tarp Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Tarp Native within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:41.1
occ:1.00
 OG C:SER155 3.0 35.4 1.0
OH C:TYR121 3.2 35.2 1.0
CB C:SER155 3.4 29.3 1.0
C C:ALA153 3.4 25.3 1.0
CA C:ALA153 3.4 24.8 1.0
N C:SER155 3.6 33.1 1.0
O C:ALA153 3.6 28.2 1.0
CB C:ALA153 3.6 24.2 1.0
CE1 C:TYR121 3.8 29.0 1.0
NZ C:LYS132 3.8 44.6 1.0
CZ C:TYR121 3.8 31.0 1.0
NZ C:LYS158 3.9 27.5 1.0
N C:LEU154 3.9 22.9 1.0
CA C:SER155 4.0 31.6 1.0
C C:LEU154 4.6 26.1 1.0
O C:HOH641 4.6 36.7 1.0
N C:ALA153 4.8 24.8 1.0
CA C:LEU154 4.8 25.5 1.0
C C:SER155 4.9 35.1 1.0
O C:SER155 4.9 36.1 1.0
CE C:LYS132 4.9 38.7 1.0
CD C:LYS132 4.9 34.6 1.0
CD1 C:TYR121 5.0 29.5 1.0

Chlorine binding site 9 out of 10 in 6h1j

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Chlorine binding site 9 out of 10 in the Tarp Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Tarp Native within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:45.1
occ:1.00
 O C:HOH542 2.9 29.8 1.0
O C:HOH539 3.0 22.6 1.0
CB C:LYS255 3.7 31.2 1.0
CD C:LYS255 3.8 39.4 1.0
O C:HOH594 3.9 47.1 1.0
CE1 C:TYR152 3.9 27.6 1.0
O C:HOH686 4.0 52.2 1.0
CG C:LYS255 4.0 36.0 1.0
O C:ILE146 4.4 33.3 1.0
CA C:ILE146 4.4 30.7 1.0
CG2 C:ILE146 4.5 32.9 1.0
CA C:LYS255 4.6 25.3 1.0
CD1 C:TYR152 4.6 29.2 1.0
O C:LYS255 4.6 25.7 1.0
CE C:LYS255 4.8 46.4 1.0
CG1 C:ILE146 4.8 34.2 1.0
CD2 C:PHE151 4.8 33.3 1.0
CB C:ILE146 4.8 33.4 1.0
OH C:TYR152 4.9 28.9 1.0
O C:ILE145 4.9 29.3 1.0
CZ C:TYR152 4.9 27.4 1.0
C C:ILE146 4.9 30.9 1.0
C C:LYS255 4.9 23.1 1.0

Chlorine binding site 10 out of 10 in 6h1j

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Chlorine binding site 10 out of 10 in the Tarp Native


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Tarp Native within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:54.8
occ:1.00
 N C:TYR226 3.1 33.4 1.0
N C:GLN225 3.3 38.2 1.0
CA C:GLY223 3.3 39.1 1.0
C C:GLY223 3.3 37.7 1.0
O C:HOH699 3.4 52.4 1.0
N C:ASN224 3.5 36.7 1.0
CB C:GLN225 3.6 44.6 1.0
CB C:TYR226 3.7 29.8 1.0
N C:GLY223 3.7 41.5 1.0
CA C:GLN225 3.7 40.5 1.0
O C:GLY223 3.8 34.7 1.0
C C:GLN225 3.9 35.3 1.0
CA C:TYR226 4.0 30.4 1.0
OE1 C:GLN225 4.0 62.7 1.0
CG C:GLN225 4.1 52.3 1.0
C C:ASN224 4.2 39.5 1.0
CD C:GLN225 4.4 59.1 1.0
CA C:ASN224 4.4 39.5 1.0

Reference:

D.Gerlach, Y.Guo, C.De Castro, S.H.Kim, K.Schlatterer, F.F.Xu, C.Pereira, P.H.Seeberger, S.Ali, J.Codee, W.Sirisarn, B.Schulte, C.Wolz, J.Larsen, A.Molinaro, B.L.Lee, G.Xia, T.Stehle, A.Peschel. Methicillin-Resistant Staphylococcus Aureus Alters Cell Wall Glycosylation to Evade Immunity. Nature V. 563 705 2018.
ISSN: ESSN 1476-4687
PubMed: 30464342
DOI: 10.1038/S41586-018-0730-X
Page generated: Sun Jul 28 00:23:02 2024

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