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Chlorine in PDB 2ntt: Crystal Structure of Sek

Protein crystallography data

The structure of Crystal Structure of Sek, PDB code: 2ntt was solved by S.Gunther, A.K.Varma, B.Moza, E.J.Sundberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.67 / 1.56
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.774, 45.790, 90.696, 90.00, 90.02, 90.00
R / Rfree (%) 16.3 / 20.2

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Sek (pdb code 2ntt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 13 binding sites of Chlorine where determined in the Crystal Structure of Sek, PDB code: 2ntt:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 13 in 2ntt

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Chlorine binding site 1 out of 13 in the Crystal Structure of Sek


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 Sek within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl5002

b:12.1
occ:1.00
 O A:HOH7223 3.2 17.7 1.0
N A:LYS156 3.2 9.0 1.0
ND2 A:ASN162 3.3 9.9 1.0
CA A:SER155 3.7 8.5 1.0
CG A:LYS156 3.7 12.5 1.0
CB A:ASN162 3.7 8.6 1.0
CB A:LYS156 3.9 10.6 1.0
C A:SER155 3.9 8.5 1.0
CB A:SER155 4.0 8.7 1.0
CG A:ASN162 4.0 8.9 1.0
CA A:LYS156 4.2 9.9 1.0
CD A:LYS156 4.2 15.4 1.0
CE2 A:TYR215 4.4 13.2 1.0
O A:LYS154 4.9 9.4 1.0
OG A:SER155 5.0 8.5 1.0
O A:HOH7135 5.0 22.6 1.0

Chlorine binding site 2 out of 13 in 2ntt

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Chlorine binding site 2 out of 13 in the Crystal Structure of Sek


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 Sek within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl5004

b:10.4
occ:1.00
 O B:HOH7034 3.1 12.6 1.0
O A:HOH7014 3.1 9.9 1.0
O B:HOH7050 3.3 7.8 1.0
N A:HIS153 3.3 8.0 1.0
CA A:GLY152 3.5 9.3 1.0
CD B:PRO189 3.6 6.5 1.0
N A:LYS154 3.7 7.0 1.0
CG B:PRO189 3.7 6.4 1.0
C A:GLY152 3.9 8.9 1.0
CB A:LYS154 3.9 7.3 1.0
CG A:LYS154 4.2 8.3 1.0
O B:HOH7047 4.2 9.7 1.0
CD A:LYS154 4.2 8.0 1.0
CA A:LYS154 4.3 7.9 1.0
CD2 B:LEU188 4.3 6.4 1.0
CA A:HIS153 4.4 7.7 1.0
C A:HIS153 4.4 7.5 1.0
O A:TYR151 4.5 9.9 1.0
N A:GLY152 4.7 9.6 1.0
CB B:LEU188 4.8 5.6 1.0
CZ B:PHE12 4.8 5.0 1.0
N B:PRO189 4.8 6.4 1.0
ND2 B:ASN8 4.9 7.2 1.0
CE A:LYS154 5.0 8.6 1.0
O B:HOH7049 5.0 7.7 1.0

Chlorine binding site 3 out of 13 in 2ntt

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Chlorine binding site 3 out of 13 in the Crystal Structure of Sek


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 Sek within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl5007

b:12.5
occ:1.00
 NE2 A:HIS142 3.1 12.6 1.0
N B:SER73 3.2 11.2 1.0
O A:HOH7158 3.2 16.1 1.0
O B:HOH7128 3.4 17.0 1.0
O A:HOH7157 3.5 15.8 1.0
CB A:TYR158 3.6 8.0 1.0
CA B:GLN72 3.9 9.9 1.0
CD2 A:HIS142 4.0 11.2 1.0
C B:GLN72 4.0 10.4 1.0
CA B:SER73 4.0 12.4 1.0
CG A:TYR158 4.1 8.2 1.0
CE1 A:HIS142 4.1 13.0 1.0
CB B:GLN72 4.3 9.6 1.0
CD1 A:TYR158 4.4 8.3 1.0
CG B:GLN72 4.5 10.3 1.0
O B:HOH7196 4.7 16.8 1.0
O A:HOH7164 4.7 18.6 1.0
CA A:TYR158 4.8 7.7 1.0
O A:HOH7178 4.9 26.2 1.0
N A:TYR158 4.9 8.1 1.0
CD2 A:TYR158 4.9 8.7 1.0
CB B:SER73 4.9 13.0 1.0
O A:PHE157 4.9 8.8 1.0
O B:GLY71 5.0 8.6 1.0
O B:HOH7195 5.0 11.0 1.0

Chlorine binding site 4 out of 13 in 2ntt

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Chlorine binding site 4 out of 13 in the Crystal Structure of Sek


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 Sek within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl5008

b:17.3
occ:1.00
 O A:HOH7315 3.1 32.6 1.0
O A:HOH7113 3.2 16.0 1.0
O A:HOH7144 3.3 17.1 1.0
N A:GLU203 3.3 8.5 1.0
CA A:VAL202 3.6 7.6 1.0
CD2 A:LEU170 4.0 12.7 1.0
C A:VAL202 4.0 8.1 1.0
CB A:VAL202 4.0 7.5 1.0
CD1 A:LEU170 4.2 14.7 1.0
CB A:GLU203 4.2 9.8 1.0
O A:HOH7190 4.2 25.1 1.0
CA A:GLU203 4.3 8.6 1.0
CG1 A:VAL202 4.4 8.7 1.0
CG A:LEU170 4.4 13.3 1.0
CB A:LEU170 4.5 14.2 1.0
O A:HOH7215 4.5 28.9 1.0
O A:THR201 4.6 7.7 1.0
N A:VAL202 4.9 7.2 1.0
O A:GLU203 4.9 8.4 1.0

Chlorine binding site 5 out of 13 in 2ntt

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Chlorine binding site 5 out of 13 in the Crystal Structure of Sek


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 Sek within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl5009

b:13.2
occ:1.00
 O A:HOH7264 3.0 34.0 1.0
O A:HOH7033 3.1 9.0 1.0
O A:HOH7109 3.2 19.9 1.0
N A:ALA84 3.3 6.4 1.0
CA A:THR83 3.8 5.3 1.0
CB A:THR83 3.8 5.3 1.0
CG2 A:THR83 4.0 5.3 1.0
CB A:ALA84 4.0 7.7 1.0
C A:THR83 4.0 5.6 1.0
CZ A:PHE57 4.1 10.8 1.0
O A:HOH7166 4.2 22.7 1.0
CA A:ALA84 4.3 7.6 1.0
CB A:PHE119 4.4 11.5 1.0
O A:HOH7263 4.4 42.0 1.0
CG2 A:THR201 4.7 7.3 1.0
CE1 A:PHE57 4.9 11.7 1.0
O A:VAL82 4.9 5.9 1.0
O A:PHE119 4.9 9.4 1.0

Chlorine binding site 6 out of 13 in 2ntt

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Chlorine binding site 6 out of 13 in the Crystal Structure of Sek


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 Sek within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl5010

b:18.5
occ:1.00
 N A:ASN94 3.2 8.2 1.0
O A:HOH7105 3.5 18.2 1.0
O A:HOH7134 3.5 17.5 1.0
CB A:ASN94 3.7 7.7 1.0
CG A:ASN94 3.9 7.9 1.0
CA A:ASN94 4.0 7.9 1.0
CA A:ARG93 4.0 10.0 1.0
C A:ARG93 4.1 9.1 1.0
O A:SER92 4.1 13.7 1.0
O A:HOH7250 4.2 54.0 1.0
ND2 A:ASN94 4.2 8.7 1.0
O A:ASN94 4.3 8.5 1.0
OD1 A:ASN94 4.3 7.5 1.0
C A:ASN94 4.6 7.9 1.0
CG A:ARG93 4.8 9.1 1.0
O A:HOH7104 4.8 17.5 1.0
C A:SER92 4.9 13.5 1.0
N A:ARG93 5.0 11.3 1.0
CB A:ARG93 5.0 9.9 1.0

Chlorine binding site 7 out of 13 in 2ntt

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Chlorine binding site 7 out of 13 in the Crystal Structure of Sek


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 Sek within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl5012

b:34.4
occ:1.00
 O A:HOH7332 2.7 30.3 1.0
ND2 A:ASN11 3.2 13.7 1.0
O A:HOH7267 3.9 41.0 1.0
CD A:LYS16 4.0 8.2 1.0
CG A:ASN11 4.1 11.5 1.0
CE A:LYS16 4.1 9.0 1.0
OD1 A:ASN11 4.2 14.1 1.0
CG A:LYS16 4.4 8.6 1.0
CZ A:PHE12 4.6 5.7 1.0
CB A:LYS16 4.8 7.9 1.0
CE1 A:PHE12 4.8 5.5 1.0

Chlorine binding site 8 out of 13 in 2ntt

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Chlorine binding site 8 out of 13 in the Crystal Structure of Sek


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Sek within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl5001

b:10.2
occ:1.00
 O B:HOH7028 3.1 11.8 1.0
N B:HIS153 3.3 8.6 1.0
CA B:GLY152 3.5 9.3 1.0
N B:LYS154 3.7 7.9 1.0
C B:GLY152 3.9 9.3 1.0
CB B:LYS154 3.9 8.1 1.0
CD B:LYS154 4.2 9.1 1.0
O B:HOH7043 4.2 9.7 1.0
CG B:LYS154 4.2 9.2 1.0
CA B:LYS154 4.3 8.4 1.0
CA B:HIS153 4.4 8.5 1.0
C B:HIS153 4.4 8.4 1.0
O B:TYR151 4.5 9.9 1.0
N B:GLY152 4.7 9.3 1.0
CE B:LYS154 5.0 9.3 1.0

Chlorine binding site 9 out of 13 in 2ntt

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Chlorine binding site 9 out of 13 in the Crystal Structure of Sek


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Sek within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl5003

b:12.0
occ:1.00
 O B:HOH7226 3.1 18.6 1.0
N B:LYS156 3.2 9.5 1.0
O B:HOH7359 3.2 26.9 1.0
ND2 B:ASN162 3.3 9.4 1.0
CA B:SER155 3.7 8.6 1.0
CB B:ASN162 3.7 9.2 1.0
CG B:LYS156 3.7 12.8 1.0
CB B:LYS156 3.8 10.7 1.0
C B:SER155 3.9 8.6 1.0
CB B:SER155 4.0 8.3 1.0
CG B:ASN162 4.0 9.4 1.0
CA B:LYS156 4.1 10.3 1.0
CD B:LYS156 4.2 15.6 1.0
CE2 B:TYR215 4.5 13.9 1.0
O B:HOH7154 4.9 22.4 1.0
O B:LYS154 5.0 9.2 1.0

Chlorine binding site 10 out of 13 in 2ntt

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Chlorine binding site 10 out of 13 in the Crystal Structure of Sek


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Sek within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl5005

b:13.0
occ:1.00
 O B:HOH7346 3.0 31.0 1.0
O B:HOH7258 3.1 34.3 1.0
O B:HOH7091 3.1 21.4 1.0
O B:HOH7024 3.2 9.6 1.0
N B:ALA84 3.3 6.1 1.0
CA B:THR83 3.7 5.2 1.0
CB B:THR83 3.8 5.3 1.0
CB B:ALA84 4.0 7.0 1.0
CG2 B:THR83 4.0 5.0 1.0
C B:THR83 4.0 5.3 1.0
O B:HOH7180 4.1 25.1 1.0
CZ B:PHE57 4.2 9.7 1.0
CA B:ALA84 4.2 7.2 1.0
CB B:PHE119 4.4 11.7 1.0
O B:HOH7358 4.6 42.5 1.0
CG2 B:THR201 4.7 7.3 1.0
O B:VAL82 4.8 5.7 1.0
O B:PHE119 4.9 9.4 1.0
CE1 B:PHE57 4.9 10.4 1.0
O B:HOH7233 5.0 29.5 1.0

Reference:

S.Gunther, A.K.Varma, B.Moza, K.J.Kasper, A.W.Wyatt, P.Zhu, A.K.Rahman, Y.Li, R.A.Mariuzza, J.K.Mccormick, E.J.Sundberg. A Novel Loop Domain in Superantigens Extends Their T Cell Receptor Recognition Site J.Mol.Biol. V. 371 210 2007.
ISSN: ISSN 0022-2836
PubMed: 17560605
DOI: 10.1016/J.JMB.2007.05.038
Page generated: Thu Jul 10 23:20:10 2025

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