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Iodine in PDB 6hks: Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide

Enzymatic activity of Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide

All present enzymatic activity of Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide:
3.1.3.48;

Protein crystallography data

The structure of Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide, PDB code: 6hks was solved by M.Genera, A.Haouz, C.Caillet-Saguy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.34 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.620, 77.430, 130.030, 90.00, 90.14, 90.00
R / Rfree (%) 19.4 / 24.7

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide (pdb code 6hks). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide, PDB code: 6hks:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 6hks

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Iodine binding site 1 out of 9 in the Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I601

b:41.2
occ:0.59
 I A:IOD601 0.0 41.2 0.6
I A:IOD601 1.5 60.1 0.4
O C:HOH702 3.3 35.4 1.0
N A:LYS552 3.8 46.2 1.0
CA A:PRO551 3.8 49.3 1.0
O A:HOH736 3.9 46.9 1.0
CD1 C:LEU510 4.0 49.2 1.0
CG2 C:VAL593 4.1 34.9 1.0
CB A:PRO551 4.2 46.8 1.0
CG A:LYS552 4.2 41.4 1.0
C A:PRO551 4.4 48.0 1.0
N C:GLY564 4.5 47.0 1.0
CA C:GLY564 4.6 39.6 1.0
CB C:ALA591 4.7 38.3 1.0
CE A:LYS552 4.7 35.8 1.0
CG2 A:ILE550 4.7 43.6 1.0
CD A:LYS552 4.7 38.4 1.0
CB A:LYS552 4.8 41.6 1.0
CD2 C:LEU510 4.8 43.6 1.0
CA A:LYS552 4.9 46.9 1.0
CD1 C:LEU561 5.0 40.4 1.0
N A:PRO551 5.0 58.4 1.0

Iodine binding site 2 out of 9 in 6hks

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Iodine binding site 2 out of 9 in the Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I601

b:60.1
occ:0.41
 I A:IOD601 0.0 60.1 0.4
I A:IOD601 1.5 41.2 0.6
O A:HOH736 2.5 46.9 1.0
O C:HOH702 3.0 35.4 1.0
N C:GLY564 3.6 47.0 1.0
CA C:GLY564 3.9 39.6 1.0
C C:ASN563 4.0 47.0 1.0
CG A:LYS552 4.0 41.4 1.0
CB C:ALA591 4.1 38.3 1.0
N A:LYS552 4.1 46.2 1.0
CE A:LYS552 4.3 35.8 1.0
NH1 A:ARG596 4.3 44.9 1.0
CA C:ASN563 4.4 45.1 1.0
O C:ASN563 4.5 41.6 1.0
CB A:PRO551 4.6 46.8 1.0
O A:LYS552 4.6 44.1 1.0
CD A:LYS552 4.6 38.4 1.0
CA A:PRO551 4.6 49.3 1.0
O C:ALA591 4.6 46.6 1.0
CD1 C:LEU510 4.9 49.2 1.0
C A:PRO551 4.9 48.0 1.0
CB A:LYS552 4.9 41.6 1.0
N C:ASN563 4.9 51.2 1.0
CA A:LYS552 5.0 46.9 1.0

Iodine binding site 3 out of 9 in 6hks

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Iodine binding site 3 out of 9 in the Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I601

b:42.7
occ:0.46
 I B:IOD601 0.0 42.7 0.5
I B:IOD601 1.2 52.2 0.6
NH1 B:ARG596 3.5 41.9 1.0
O D:HOH611 3.6 49.0 1.0
N D:GLY564 3.6 46.6 1.0
N B:LYS552 3.9 45.1 1.0
CG B:LYS552 3.9 54.3 1.0
C D:ASN563 4.0 48.6 1.0
CA D:GLY564 4.0 40.4 1.0
O B:LYS552 4.1 38.9 1.0
CB D:ALA591 4.3 54.5 1.0
CA D:ASN563 4.3 45.1 1.0
CB B:PRO551 4.3 41.1 1.0
CZ B:ARG596 4.4 42.8 1.0
OD1 B:ASN554 4.4 70.9 1.0
NZ B:LYS552 4.5 50.9 1.0
CD1 D:LEU510 4.5 52.4 1.0
O D:ASN563 4.5 47.2 1.0
NH2 B:ARG596 4.6 50.6 1.0
CA B:PRO551 4.6 39.8 1.0
C B:PRO551 4.7 42.3 1.0
CA B:LYS552 4.7 48.5 1.0
ND2 B:ASN554 4.8 66.3 1.0
CD B:LYS552 4.8 42.2 1.0
C B:LYS552 4.8 42.8 1.0
CB B:LYS552 4.9 45.8 1.0
CG2 D:VAL593 4.9 35.2 1.0

Iodine binding site 4 out of 9 in 6hks

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Iodine binding site 4 out of 9 in the Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I601

b:52.2
occ:0.55
 I B:IOD601 0.0 52.2 0.6
I B:IOD601 1.2 42.7 0.5
O D:HOH611 3.3 49.0 1.0
N B:LYS552 3.5 45.1 1.0
CB B:PRO551 3.6 41.1 1.0
CA B:PRO551 3.7 39.8 1.0
CD1 D:LEU510 3.7 52.4 1.0
CG2 D:VAL593 3.9 35.2 1.0
N D:GLY564 4.0 46.6 1.0
CG B:LYS552 4.1 54.3 1.0
C B:PRO551 4.1 42.3 1.0
CA D:GLY564 4.2 40.4 1.0
NH1 B:ARG596 4.3 41.9 1.0
O B:LYS552 4.4 38.9 1.0
CA B:LYS552 4.6 48.5 1.0
C D:ASN563 4.6 48.6 1.0
CB D:ALA591 4.7 54.5 1.0
CG D:LEU510 4.7 50.1 1.0
CB B:LYS552 4.8 45.8 1.0
CD1 D:LEU561 4.9 44.1 1.0
CD B:LYS552 4.9 42.2 1.0
C B:LYS552 5.0 42.8 1.0

Iodine binding site 5 out of 9 in 6hks

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Iodine binding site 5 out of 9 in the Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I601

b:57.5
occ:1.00
 N C:LYS552 3.8 43.3 1.0
CG C:LYS552 3.9 49.8 1.0
CB C:PRO551 4.0 44.5 1.0
NH1 C:ARG596 4.0 36.5 1.0
CA C:PRO551 4.1 54.7 1.0
C C:PRO551 4.5 56.8 1.0
CD C:LYS552 4.5 42.5 1.0
O C:LYS552 4.6 37.6 1.0
CA C:LYS552 4.8 44.9 1.0
CE C:LYS552 4.8 38.4 1.0
CB C:LYS552 4.8 46.1 1.0
NH2 C:ARG596 4.9 39.8 1.0
CZ C:ARG596 4.9 46.9 1.0

Iodine binding site 6 out of 9 in 6hks

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Iodine binding site 6 out of 9 in the Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I601

b:54.2
occ:1.00
 O E:HOH710 2.8 71.6 1.0
O A:HOH704 3.4 42.3 1.0
N E:LYS552 3.7 45.1 1.0
N A:GLY564 3.7 44.3 1.0
CB E:PRO551 3.9 32.3 1.0
NH1 E:ARG596 3.9 42.0 1.0
CD1 A:LEU510 4.0 58.4 1.0
CA A:GLY564 4.0 40.4 1.0
CA E:PRO551 4.1 40.1 1.0
CG E:LYS552 4.2 45.5 1.0
C A:ASN563 4.2 49.1 1.0
O E:LYS552 4.3 43.8 1.0
CB A:ALA591 4.3 38.2 1.0
C E:PRO551 4.4 47.4 1.0
CA A:ASN563 4.6 45.3 1.0
CA E:LYS552 4.7 47.1 1.0
CG2 A:VAL593 4.7 36.2 1.0
CB E:LYS552 4.8 44.5 1.0
CE E:LYS552 4.8 42.5 1.0
ND2 E:ASN554 4.8 61.5 1.0
CZ E:ARG596 4.8 42.8 1.0
O A:ASN563 4.9 39.4 1.0
NH2 E:ARG596 4.9 45.8 1.0
CD E:LYS552 4.9 40.9 1.0
C E:LYS552 4.9 44.2 1.0

Iodine binding site 7 out of 9 in 6hks

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Iodine binding site 7 out of 9 in the Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I601

b:55.0
occ:1.00
 O B:HOH702 3.3 53.6 1.0
N F:LYS552 3.7 41.0 1.0
CG F:LYS552 3.7 45.4 1.0
N B:GLY564 3.8 45.5 1.0
NH1 F:ARG596 4.0 45.8 1.0
CA B:GLY564 4.0 36.7 1.0
CA F:PRO551 4.1 44.2 1.0
CB F:PRO551 4.1 40.3 1.0
CB B:ALA591 4.3 45.1 1.0
C B:ASN563 4.3 44.0 1.0
NZ F:LYS552 4.3 67.3 1.0
CD1 B:LEU510 4.4 52.3 1.0
C F:PRO551 4.4 48.7 1.0
CD F:LYS552 4.5 48.4 1.0
O F:LYS552 4.5 45.7 1.0
CG2 B:VAL593 4.6 37.8 1.0
CA B:ASN563 4.6 35.8 1.0
CA F:LYS552 4.7 44.8 1.0
CB F:LYS552 4.7 35.0 1.0
CZ F:ARG596 4.9 47.1 1.0
CG B:LEU510 4.9 44.0 1.0
NH2 F:ARG596 5.0 44.7 1.0
O B:ALA591 5.0 49.5 1.0
C F:LYS552 5.0 45.5 1.0

Iodine binding site 8 out of 9 in 6hks

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Iodine binding site 8 out of 9 in the Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I602

b:39.7
occ:0.54
 I F:IOD602 0.0 39.7 0.5
I F:IOD602 1.5 59.8 0.5
O F:HOH739 3.6 53.5 1.0
CD1 F:LEU510 3.8 50.1 1.0
CG2 F:VAL593 4.1 33.2 1.0
O F:HOH738 4.2 53.4 1.0
N F:GLY564 4.4 43.4 1.0
CA F:GLY564 4.7 42.3 1.0
CB F:ALA591 4.7 33.9 1.0

Iodine binding site 9 out of 9 in 6hks

Go back to Iodine Binding Sites List in 6hks
Iodine binding site 9 out of 9 in the Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of the PTPN3 Pdz Domain Bound to the HPV16 E6 Oncoprotein C-Terminal Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I602

b:59.8
occ:0.46
 I F:IOD602 0.0 59.8 0.5
I F:IOD602 1.5 39.7 0.5
O F:HOH738 2.7 53.4 1.0
O F:HOH739 3.1 53.5 1.0
N F:GLY564 3.8 43.4 1.0
CB F:ALA591 4.0 33.9 1.0
C F:ASN563 4.2 50.5 1.0
CA F:GLY564 4.3 42.3 1.0
CA F:ASN563 4.4 51.7 1.0
CD1 F:LEU510 4.5 50.1 1.0
O F:ASN563 4.9 52.9 1.0

Reference:

M.Genera, D.Samson, B.Raynal, A.Haouz, B.Baron, C.Simenel, R.Guerois, N.Wolff, C.Caillet-Saguy. Structural and Functional Characterization of the Pdz Domain of the Human Phosphatase PTPN3 and Its Interaction with the Human Papillomavirus E6 Oncoprotein. Sci Rep V. 9 7438 2019.
ISSN: ESSN 2045-2322
PubMed: 31092861
DOI: 10.1038/S41598-019-43932-X
Page generated: Sun Aug 11 23:15:38 2024

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