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Chlorine in PDB 5qfj: Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B:
3.1.3.48;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B, PDB code: 5qfj was solved by D.A.Keedy, Z.B.Hill, J.T.Biel, E.Kang, T.J.Rettenmaier, J.Brandao-Neto, F.Von Delft, J.A.Wells, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.27 / 1.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.451, 90.451, 107.302, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 23.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B (pdb code 5qfj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B, PDB code: 5qfj:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5qfj

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Chlorine binding site 1 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:39.2
occ:0.19
CL09 A:JOJ402 0.0 39.2 0.2
CL09 A:JOJ402 0.0 39.2 0.2
C08 A:JOJ402 1.7 46.8 0.2
C08 A:JOJ402 1.7 46.8 0.2
C10 A:JOJ402 2.7 51.8 0.2
C10 A:JOJ402 2.7 51.8 0.2
HG2 A:GLU252 2.8 87.2 1.0
N07 A:JOJ402 2.8 36.4 0.2
N07 A:JOJ402 2.8 36.5 0.2
HA A:VAL249 3.0 43.2 1.0
HE2 A:MET74 3.0 43.3 1.0
HE3 A:MET74 3.1 43.3 1.0
HG21 A:VAL249 3.2 42.5 1.0
HB3 A:GLU252 3.2 47.2 1.0
CL11 A:JOJ402 3.3 65.7 0.2
CL11 A:JOJ402 3.3 65.7 0.2
HG13 A:VAL249 3.3 49.2 1.0
O A:HOH718 3.3 58.1 0.3
O A:HOH718 3.3 58.0 0.3
CE A:MET74 3.4 36.1 1.0
O A:HOH667 3.5 35.4 0.3
O A:HOH667 3.5 35.5 0.3
O A:HOH678 3.5 50.7 0.3
HB2 A:GLU252 3.6 47.2 1.0
O A:HOH667 3.6 36.7 0.2
O A:HOH667 3.6 36.7 0.2
CG A:GLU252 3.6 72.7 1.0
CB A:GLU252 3.7 39.3 1.0
O A:HOH678 3.8 65.3 0.2
O A:HOH678 3.8 65.3 0.2
HE1 A:MET74 3.8 43.3 1.0
N05 A:JOJ402 3.8 51.1 0.2
N05 A:JOJ402 3.8 51.1 0.2
C06 A:JOJ402 3.9 43.1 0.2
C06 A:JOJ402 3.9 43.0 0.2
O A:HOH678 3.9 27.4 0.3
CA A:VAL249 3.9 36.0 1.0
HD12 A:LEU234 4.0 47.0 1.0
CG2 A:VAL249 4.0 35.4 1.0
CG1 A:VAL249 4.1 41.0 1.0
HG3 A:GLU252 4.1 87.2 1.0
CB A:VAL249 4.2 33.8 1.0
O A:VAL249 4.5 36.3 1.0
HG23 A:VAL249 4.6 42.5 1.0
O A:HOH545 4.6 62.0 0.3
O A:HOH545 4.6 62.1 0.3
HG22 A:VAL249 4.6 42.5 1.0
HG22 A:THR230 4.6 47.7 1.0
HG11 A:VAL249 4.6 49.2 1.0
HG12 A:VAL249 4.7 49.2 1.0
CD A:GLU252 4.7 67.6 1.0
HD13 A:LEU234 4.8 47.0 1.0
C A:VAL249 4.8 26.2 1.0
CD1 A:LEU234 4.8 39.1 1.0
O A:LYS248 4.8 35.3 0.3
O A:LYS248 4.8 35.5 0.3
N A:VAL249 4.8 37.5 1.0
O A:LYS248 4.9 36.0 0.2
O A:LYS248 4.9 36.0 0.2
H061 A:JOJ402 4.9 51.7 0.2
H061 A:JOJ402 4.9 51.7 0.2
C04 A:JOJ402 5.0 46.9 0.2
C04 A:JOJ402 5.0 46.9 0.2

Chlorine binding site 2 out of 4 in 5qfj

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Chlorine binding site 2 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:39.2
occ:0.19
CL09 A:JOJ402 0.0 39.2 0.2
CL09 A:JOJ402 0.0 39.2 0.2
C08 A:JOJ402 1.7 46.8 0.2
C08 A:JOJ402 1.7 46.8 0.2
C10 A:JOJ402 2.7 51.8 0.2
C10 A:JOJ402 2.7 51.8 0.2
HG2 A:GLU252 2.8 87.2 1.0
N07 A:JOJ402 2.8 36.4 0.2
N07 A:JOJ402 2.8 36.5 0.2
HA A:VAL249 3.0 43.2 1.0
HE2 A:MET74 3.0 43.3 1.0
HE3 A:MET74 3.1 43.3 1.0
HG21 A:VAL249 3.2 42.5 1.0
HB3 A:GLU252 3.2 47.2 1.0
CL11 A:JOJ402 3.3 65.7 0.2
CL11 A:JOJ402 3.3 65.7 0.2
HG13 A:VAL249 3.3 49.2 1.0
O A:HOH718 3.3 58.1 0.3
O A:HOH718 3.3 58.0 0.3
CE A:MET74 3.4 36.1 1.0
O A:HOH667 3.5 35.4 0.3
O A:HOH667 3.5 35.5 0.3
O A:HOH678 3.5 50.7 0.3
HB2 A:GLU252 3.6 47.2 1.0
O A:HOH667 3.6 36.7 0.2
O A:HOH667 3.6 36.7 0.2
CG A:GLU252 3.6 72.7 1.0
CB A:GLU252 3.7 39.3 1.0
O A:HOH678 3.8 65.3 0.2
O A:HOH678 3.8 65.3 0.2
HE1 A:MET74 3.8 43.3 1.0
N05 A:JOJ402 3.8 51.1 0.2
N05 A:JOJ402 3.8 51.1 0.2
C06 A:JOJ402 3.9 43.1 0.2
C06 A:JOJ402 3.9 43.0 0.2
O A:HOH678 3.9 27.4 0.3
CA A:VAL249 3.9 36.0 1.0
HD12 A:LEU234 4.0 47.0 1.0
CG2 A:VAL249 4.0 35.4 1.0
CG1 A:VAL249 4.1 41.0 1.0
HG3 A:GLU252 4.1 87.2 1.0
CB A:VAL249 4.2 33.8 1.0
O A:VAL249 4.5 36.3 1.0
HG23 A:VAL249 4.6 42.5 1.0
O A:HOH545 4.6 62.0 0.3
O A:HOH545 4.6 62.1 0.3
HG22 A:VAL249 4.6 42.5 1.0
HG22 A:THR230 4.6 47.7 1.0
HG11 A:VAL249 4.6 49.2 1.0
HG12 A:VAL249 4.7 49.2 1.0
CD A:GLU252 4.7 67.6 1.0
HD13 A:LEU234 4.8 47.0 1.0
C A:VAL249 4.8 26.2 1.0
CD1 A:LEU234 4.8 39.1 1.0
O A:LYS248 4.8 35.3 0.3
O A:LYS248 4.8 35.5 0.3
N A:VAL249 4.8 37.5 1.0
O A:LYS248 4.9 36.0 0.2
O A:LYS248 4.9 36.0 0.2
H061 A:JOJ402 4.9 51.7 0.2
H061 A:JOJ402 4.9 51.7 0.2
C04 A:JOJ402 5.0 46.9 0.2
C04 A:JOJ402 5.0 46.9 0.2

Chlorine binding site 3 out of 4 in 5qfj

Go back to Chlorine Binding Sites List in 5qfj
Chlorine binding site 3 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:65.7
occ:0.19
CL11 A:JOJ402 0.0 65.7 0.2
CL11 A:JOJ402 0.0 65.7 0.2
C10 A:JOJ402 1.4 51.8 0.2
C10 A:JOJ402 1.4 51.8 0.2
H041 A:JOJ402 2.2 56.2 0.2
H041 A:JOJ402 2.2 56.2 0.2
N05 A:JOJ402 2.3 51.1 0.2
N05 A:JOJ402 2.3 51.1 0.2
O A:HOH718 2.3 58.1 0.3
O A:HOH718 2.3 58.0 0.3
C08 A:JOJ402 2.4 46.8 0.2
C08 A:JOJ402 2.4 46.8 0.2
OE1 A:GLU76 2.6 47.6 0.3
OE1 A:GLU76 2.6 47.6 0.3
HH21 A:ARG238 2.6 54.1 0.3
HH21 A:ARG238 2.6 54.2 0.3
C04 A:JOJ402 2.7 46.9 0.2
C04 A:JOJ402 2.7 46.9 0.2
HH22 A:ARG238 2.8 54.2 0.3
HH22 A:ARG238 2.8 54.1 0.3
NH2 A:ARG238 3.0 45.1 0.3
NH2 A:ARG238 3.0 45.1 0.3
OE1 A:GLU76 3.1 52.5 0.2
OE1 A:GLU76 3.1 52.5 0.2
CL09 A:JOJ402 3.3 39.2 0.2
CL09 A:JOJ402 3.3 39.2 0.2
HD13 A:LEU234 3.3 47.0 1.0
C06 A:JOJ402 3.4 43.1 0.2
C06 A:JOJ402 3.4 43.0 0.2
C02 A:JOJ402 3.5 59.1 0.2
C02 A:JOJ402 3.5 59.1 0.2
HD12 A:LEU234 3.5 47.0 1.0
HB3 A:GLU76 3.5 47.2 0.3
HB3 A:GLU76 3.5 47.2 0.3
N07 A:JOJ402 3.5 36.4 0.2
N07 A:JOJ402 3.5 36.5 0.2
H042 A:JOJ402 3.6 56.2 0.2
H042 A:JOJ402 3.6 56.2 0.2
S03 A:JOJ402 3.6 75.7 0.2
S03 A:JOJ402 3.6 75.8 0.2
HB3 A:GLU76 3.6 47.1 0.2
HB3 A:GLU76 3.6 47.1 0.2
CD A:GLU76 3.8 52.9 0.3
CD A:GLU76 3.8 52.9 0.3
CD1 A:LEU234 3.8 39.1 1.0
HD21 A:LEU234 3.9 48.2 1.0
O A:HOH678 3.9 50.7 0.3
CD A:GLU76 4.0 52.5 0.2
CD A:GLU76 4.0 52.5 0.2
HH21 A:ARG238 4.0 74.6 0.2
HH21 A:ARG238 4.0 74.6 0.2
O A:HOH656 4.0 43.9 0.3
O A:HOH656 4.0 43.9 0.3
HG21 A:VAL249 4.0 42.5 1.0
HD22 A:LEU234 4.0 48.2 1.0
O A:HOH667 4.0 35.4 0.3
O A:HOH667 4.0 35.5 0.3
HB2 A:GLU76 4.1 47.2 0.3
HB2 A:GLU76 4.1 47.2 0.3
O A:HOH667 4.1 36.7 0.2
O A:HOH667 4.1 36.7 0.2
CB A:GLU76 4.2 39.4 0.3
CB A:GLU76 4.2 39.3 0.3
CZ A:ARG238 4.3 45.0 0.3
CZ A:ARG238 4.3 44.9 0.3
O A:HOH678 4.3 65.3 0.2
O A:HOH678 4.3 65.3 0.2
HB2 A:GLU76 4.3 47.1 0.2
HB2 A:GLU76 4.3 47.1 0.2
CD2 A:LEU234 4.4 40.2 1.0
CB A:GLU76 4.4 39.3 0.2
CB A:GLU76 4.4 39.3 0.2
H061 A:JOJ402 4.4 51.7 0.2
H061 A:JOJ402 4.4 51.7 0.2
NH2 A:ARG238 4.4 62.1 0.2
NH2 A:ARG238 4.4 62.2 0.2
HD11 A:LEU234 4.5 47.0 1.0
CG A:GLU76 4.6 50.5 0.3
CG A:GLU76 4.6 50.5 0.3
O A:HOH678 4.6 27.4 0.3
OE2 A:GLU76 4.6 52.6 0.2
OE2 A:GLU76 4.6 52.6 0.2
OE2 A:GLU76 4.6 51.7 0.3
OE2 A:GLU76 4.6 51.7 0.3
HH22 A:ARG238 4.6 74.6 0.2
HH22 A:ARG238 4.6 74.6 0.2
N01 A:JOJ402 4.7 57.8 0.2
N01 A:JOJ402 4.7 57.8 0.2
HE A:ARG238 4.7 63.1 0.3
HE A:ARG238 4.7 63.1 0.3
CG A:GLU76 4.7 50.2 0.2
CG A:GLU76 4.7 50.3 0.2
HE A:ARG238 4.7 62.8 0.2
HE A:ARG238 4.7 62.8 0.2
CG A:LEU234 4.8 34.8 1.0
CG2 A:VAL249 4.9 35.4 1.0
H011 A:JOJ402 5.0 69.3 0.2
H011 A:JOJ402 5.0 69.3 0.2
NE A:ARG238 5.0 52.6 0.3
NE A:ARG238 5.0 52.6 0.3

Chlorine binding site 4 out of 4 in 5qfj

Go back to Chlorine Binding Sites List in 5qfj
Chlorine binding site 4 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of PTP1B in Complex with COMPOUND_FMSOA000814B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:65.7
occ:0.19
CL11 A:JOJ402 0.0 65.7 0.2
CL11 A:JOJ402 0.0 65.7 0.2
C10 A:JOJ402 1.4 51.8 0.2
C10 A:JOJ402 1.4 51.8 0.2
H041 A:JOJ402 2.2 56.2 0.2
H041 A:JOJ402 2.2 56.2 0.2
N05 A:JOJ402 2.3 51.1 0.2
N05 A:JOJ402 2.3 51.1 0.2
O A:HOH718 2.3 58.1 0.3
O A:HOH718 2.3 58.0 0.3
C08 A:JOJ402 2.4 46.8 0.2
C08 A:JOJ402 2.4 46.8 0.2
OE1 A:GLU76 2.6 47.6 0.3
OE1 A:GLU76 2.6 47.6 0.3
HH21 A:ARG238 2.6 54.1 0.3
HH21 A:ARG238 2.6 54.2 0.3
C04 A:JOJ402 2.7 46.9 0.2
C04 A:JOJ402 2.7 46.9 0.2
HH22 A:ARG238 2.8 54.2 0.3
HH22 A:ARG238 2.8 54.1 0.3
NH2 A:ARG238 3.0 45.1 0.3
NH2 A:ARG238 3.0 45.1 0.3
OE1 A:GLU76 3.1 52.5 0.2
OE1 A:GLU76 3.1 52.5 0.2
CL09 A:JOJ402 3.3 39.2 0.2
CL09 A:JOJ402 3.3 39.2 0.2
HD13 A:LEU234 3.3 47.0 1.0
C06 A:JOJ402 3.4 43.1 0.2
C06 A:JOJ402 3.4 43.0 0.2
C02 A:JOJ402 3.5 59.1 0.2
C02 A:JOJ402 3.5 59.1 0.2
HD12 A:LEU234 3.5 47.0 1.0
HB3 A:GLU76 3.5 47.2 0.3
HB3 A:GLU76 3.5 47.2 0.3
N07 A:JOJ402 3.5 36.4 0.2
N07 A:JOJ402 3.5 36.5 0.2
H042 A:JOJ402 3.6 56.2 0.2
H042 A:JOJ402 3.6 56.2 0.2
S03 A:JOJ402 3.6 75.7 0.2
S03 A:JOJ402 3.6 75.8 0.2
HB3 A:GLU76 3.6 47.1 0.2
HB3 A:GLU76 3.6 47.1 0.2
CD A:GLU76 3.8 52.9 0.3
CD A:GLU76 3.8 52.9 0.3
CD1 A:LEU234 3.8 39.1 1.0
HD21 A:LEU234 3.9 48.2 1.0
O A:HOH678 3.9 50.7 0.3
CD A:GLU76 4.0 52.5 0.2
CD A:GLU76 4.0 52.5 0.2
HH21 A:ARG238 4.0 74.6 0.2
HH21 A:ARG238 4.0 74.6 0.2
O A:HOH656 4.0 43.9 0.3
O A:HOH656 4.0 43.9 0.3
HG21 A:VAL249 4.0 42.5 1.0
HD22 A:LEU234 4.0 48.2 1.0
O A:HOH667 4.0 35.4 0.3
O A:HOH667 4.0 35.5 0.3
HB2 A:GLU76 4.1 47.2 0.3
HB2 A:GLU76 4.1 47.2 0.3
O A:HOH667 4.1 36.7 0.2
O A:HOH667 4.1 36.7 0.2
CB A:GLU76 4.2 39.4 0.3
CB A:GLU76 4.2 39.3 0.3
CZ A:ARG238 4.3 45.0 0.3
CZ A:ARG238 4.3 44.9 0.3
O A:HOH678 4.3 65.3 0.2
O A:HOH678 4.3 65.3 0.2
HB2 A:GLU76 4.3 47.1 0.2
HB2 A:GLU76 4.3 47.1 0.2
CD2 A:LEU234 4.4 40.2 1.0
CB A:GLU76 4.4 39.3 0.2
CB A:GLU76 4.4 39.3 0.2
H061 A:JOJ402 4.4 51.7 0.2
H061 A:JOJ402 4.4 51.7 0.2
NH2 A:ARG238 4.4 62.1 0.2
NH2 A:ARG238 4.4 62.2 0.2
HD11 A:LEU234 4.5 47.0 1.0
CG A:GLU76 4.6 50.5 0.3
CG A:GLU76 4.6 50.5 0.3
O A:HOH678 4.6 27.4 0.3
OE2 A:GLU76 4.6 52.6 0.2
OE2 A:GLU76 4.6 52.6 0.2
OE2 A:GLU76 4.6 51.7 0.3
OE2 A:GLU76 4.6 51.7 0.3
HH22 A:ARG238 4.6 74.6 0.2
HH22 A:ARG238 4.6 74.6 0.2
N01 A:JOJ402 4.7 57.8 0.2
N01 A:JOJ402 4.7 57.8 0.2
HE A:ARG238 4.7 63.1 0.3
HE A:ARG238 4.7 63.1 0.3
CG A:GLU76 4.7 50.2 0.2
CG A:GLU76 4.7 50.3 0.2
HE A:ARG238 4.7 62.8 0.2
HE A:ARG238 4.7 62.8 0.2
CG A:LEU234 4.8 34.8 1.0
CG2 A:VAL249 4.9 35.4 1.0
H011 A:JOJ402 5.0 69.3 0.2
H011 A:JOJ402 5.0 69.3 0.2
NE A:ARG238 5.0 52.6 0.3
NE A:ARG238 5.0 52.6 0.3

Reference:

D.A.Keedy, Z.B.Hill, J.T.Biel, E.Kang, T.J.Rettenmaier, J.Brandao-Neto, N.M.Pearce, F.Von Delft, J.A.Wells, J.S.Fraser. An Expanded Allosteric Network in PTP1B By Multitemperature Crystallography, Fragment Screening, and Covalent Tethering. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29877794
DOI: 10.7554/ELIFE.36307
Page generated: Fri Jul 26 15:35:17 2024

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