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Iodine in PDB 4zv0: Structure of TSE6 in Complex with TSI6

Protein crystallography data

The structure of Structure of TSE6 in Complex with TSI6, PDB code: 4zv0 was solved by J.C.Whitney, S.Sawai, C.Ralston, J.D.Mougous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.26 / 1.40
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 83.209, 83.209, 83.758, 90.00, 90.00, 120.00
R / Rfree (%) 14.7 / 16.4

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of TSE6 in Complex with TSI6 (pdb code 4zv0). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Structure of TSE6 in Complex with TSI6, PDB code: 4zv0:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 4zv0

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Iodine binding site 1 out of 10 in the Structure of TSE6 in Complex with TSI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of TSE6 in Complex with TSI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:10.4
occ:0.62
 HD21 A:ASN289 2.8 12.3 1.0
HB3 A:ASN285 3.1 12.1 1.0
HH22 A:ARG321 3.1 15.3 1.0
HG3 A:PRO319 3.2 14.4 1.0
HA A:PRO319 3.3 13.2 1.0
HH12 A:ARG321 3.6 14.2 1.0
ND2 A:ASN289 3.7 10.2 1.0
NH2 A:ARG321 3.9 12.8 1.0
CB A:ASN285 4.0 10.1 1.0
O A:HOH718 4.0 21.1 1.0
CG A:PRO319 4.1 12.0 1.0
CA A:PRO319 4.1 11.0 1.0
CG A:ASN285 4.1 10.9 1.0
OD1 A:ASN289 4.2 10.1 1.0
HB3 A:PRO319 4.2 14.0 1.0
HD22 A:ASN289 4.2 12.3 1.0
HD3 A:PRO319 4.3 13.9 1.0
NH1 A:ARG321 4.3 11.8 1.0
N A:PRO319 4.3 10.9 1.0
CG A:ASN289 4.4 9.3 1.0
CB A:PRO319 4.4 11.7 1.0
OD1 A:ASN285 4.4 11.6 1.0
HH21 A:ARG321 4.5 15.3 1.0
CD A:PRO319 4.5 11.6 1.0
HB2 A:ASN285 4.5 12.1 1.0
ND2 A:ASN285 4.6 11.6 1.0
CZ A:ARG321 4.6 12.4 1.0
HD22 A:ASN285 4.7 13.9 1.0
HA A:ASN285 4.8 13.7 1.0
C A:HIS318 4.8 10.5 1.0
HG2 A:PRO319 4.8 14.4 1.0
CA A:ASN285 4.9 11.4 1.0
O A:ASN285 4.9 11.0 1.0
HD21 A:ASN285 5.0 13.9 1.0

Iodine binding site 2 out of 10 in 4zv0

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Iodine binding site 2 out of 10 in the Structure of TSE6 in Complex with TSI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of TSE6 in Complex with TSI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:29.6
occ:0.44
 O A:HOH820 3.1 43.4 1.0
HA A:PHE296 3.2 12.8 1.0
O A:HOH680 3.2 15.5 1.0
HG2 A:LYS295 3.3 23.4 1.0
HG21 A:VAL322 3.4 18.8 1.0
HD2 A:PHE296 3.5 13.3 1.0
HG11 A:VAL322 4.0 18.8 1.0
O A:HOH604 4.0 47.6 1.0
CA A:PHE296 4.0 10.7 1.0
HB2 A:PHE296 4.0 12.8 1.0
HD3 A:LYS295 4.0 29.9 1.0
HE2 A:LYS295 4.0 38.8 1.0
CG A:LYS295 4.2 19.5 1.0
OG A:SER299 4.2 16.1 1.0
CD2 A:PHE296 4.2 11.1 1.0
N A:PHE296 4.3 11.0 1.0
HG A:SER299 4.3 19.3 1.0
HB3 A:SER299 4.3 20.4 1.0
CG2 A:VAL322 4.4 15.6 1.0
CB A:PHE296 4.4 10.7 1.0
CD A:LYS295 4.5 24.9 1.0
O A:LYS295 4.5 13.6 1.0
C A:LYS295 4.5 12.9 1.0
H A:PHE296 4.6 13.2 1.0
HG22 A:VAL322 4.7 18.8 1.0
HZ2 A:LYS300 4.7 37.4 1.0
HB3 A:LYS295 4.7 16.6 1.0
CB A:SER299 4.7 17.0 1.0
HG3 A:LYS295 4.7 23.4 1.0
CE A:LYS295 4.7 32.3 1.0
O A:HOH793 4.8 22.5 1.0
CG A:PHE296 4.8 9.9 1.0
CG1 A:VAL322 4.8 15.6 1.0
HZ3 A:LYS300 4.9 37.4 1.0
HG23 A:VAL322 4.9 18.8 1.0
HB2 A:SER299 4.9 20.4 1.0
CB A:LYS295 5.0 13.8 1.0

Iodine binding site 3 out of 10 in 4zv0

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Iodine binding site 3 out of 10 in the Structure of TSE6 in Complex with TSI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of TSE6 in Complex with TSI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:29.1
occ:0.56
 HD3 A:LYS329 3.0 36.9 1.0
H A:ALA326 3.3 27.5 1.0
HB2 A:LYS329 3.4 23.1 1.0
HD22 A:LEU325 3.5 28.0 1.0
HA A:LEU325 3.6 22.6 1.0
HZ3 A:LYS329 3.7 43.0 1.0
CD A:LYS329 3.9 30.7 1.0
HG2 A:LYS329 3.9 26.0 1.0
N A:ALA326 4.1 22.9 1.0
HD23 A:LEU325 4.1 28.0 1.0
HE2 A:LYS329 4.1 35.3 1.0
HB3 A:LEU325 4.1 21.0 1.0
HB3 A:ALA326 4.2 34.5 1.0
CB A:LYS329 4.2 19.2 1.0
CG A:LYS329 4.2 21.7 1.0
CD2 A:LEU325 4.3 23.3 1.0
CE A:LYS329 4.4 29.4 1.0
CA A:LEU325 4.4 18.8 1.0
NZ A:LYS329 4.5 35.9 1.0
HD2 A:LYS329 4.6 36.9 1.0
CB A:LEU325 4.7 17.5 1.0
HB3 A:LYS329 4.7 23.1 1.0
O A:HOH705 4.8 39.4 1.0
C A:LEU325 4.8 17.8 1.0
O A:HOH723 4.9 48.4 1.0
O A:ALA326 4.9 21.8 1.0
CB A:ALA326 4.9 28.8 1.0
HZ2 A:LYS329 4.9 43.0 1.0
HD21 A:LEU325 5.0 28.0 1.0

Iodine binding site 4 out of 10 in 4zv0

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Iodine binding site 4 out of 10 in the Structure of TSE6 in Complex with TSI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of TSE6 in Complex with TSI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:18.4
occ:0.52
 H A:GLN412 2.7 12.9 1.0
HB2 A:GLN412 3.2 13.2 1.0
HB1 A:ALA411 3.5 23.8 1.0
HG3 A:GLN412 3.5 14.0 1.0
N A:GLN412 3.5 10.8 1.0
HG21 A:VAL351 3.6 22.4 1.0
HA A:ALA411 3.7 23.2 1.0
O A:HOH620 3.7 16.7 1.0
HG22 A:VAL351 3.8 22.4 1.0
O A:HOH776 3.8 18.8 1.0
CB A:GLN412 3.9 11.0 1.0
CG A:GLN412 4.1 11.7 1.0
CG2 A:VAL351 4.1 18.6 1.0
CB A:ALA411 4.2 19.8 1.0
CA A:ALA411 4.3 19.4 1.0
CA A:GLN412 4.3 10.5 1.0
C A:ALA411 4.4 17.2 1.0
HE21 A:GLN412 4.4 15.9 1.0
HB2 A:ALA411 4.5 23.8 1.0
HD12 A:LEU347 4.5 21.3 1.0
O A:GLN412 4.6 12.2 1.0
CD A:GLN412 4.6 12.7 1.0
HG23 A:VAL351 4.7 22.4 1.0
HG11 A:VAL351 4.7 22.0 1.0
NE2 A:GLN412 4.7 13.2 1.0
HB3 A:GLN412 4.7 13.2 1.0
HB2 A:LEU347 4.8 22.2 1.0
HG13 A:VAL351 4.9 22.0 1.0
C A:GLN412 4.9 9.6 1.0
HG2 A:GLN412 5.0 14.0 1.0

Iodine binding site 5 out of 10 in 4zv0

Go back to Iodine Binding Sites List in 4zv0
Iodine binding site 5 out of 10 in the Structure of TSE6 in Complex with TSI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of TSE6 in Complex with TSI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:25.6
occ:0.52
 O A:HOH796 4.8 29.9 1.0

Iodine binding site 6 out of 10 in 4zv0

Go back to Iodine Binding Sites List in 4zv0
Iodine binding site 6 out of 10 in the Structure of TSE6 in Complex with TSI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of TSE6 in Complex with TSI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I101

b:15.5
occ:0.88
 HH22 B:ARG20 2.8 17.2 0.7
HH12 B:ARG20 2.9 14.9 0.7
NH2 B:ARG20 3.6 14.3 0.7
NH1 B:ARG20 3.7 12.4 0.7
HB3 A:ARG365 4.0 13.3 1.0
CZ B:ARG20 4.1 11.3 0.7
HH21 B:ARG20 4.2 17.2 0.7
HD2 A:ARG365 4.3 13.2 1.0
HH11 B:ARG20 4.4 14.9 0.7
O B:HOH229 4.7 46.3 1.0
CB A:ARG365 4.9 11.1 1.0

Iodine binding site 7 out of 10 in 4zv0

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Iodine binding site 7 out of 10 in the Structure of TSE6 in Complex with TSI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of TSE6 in Complex with TSI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I102

b:56.4
occ:0.23
 O B:HOH271 3.1 18.4 1.0
HB3 B:PRO22 3.2 19.2 1.0
CB B:PRO22 3.9 16.0 1.0
HB2 B:PRO22 4.0 19.2 1.0
H B:GLY23 4.0 14.1 1.0
O B:HOH276 4.2 20.0 1.0
N B:GLY23 4.2 11.8 1.0
HA B:PRO22 4.4 14.2 1.0
HA2 B:GLY23 4.5 16.8 1.0
CA B:PRO22 4.5 11.9 1.0
C B:PRO22 4.5 13.2 1.0
HA3 B:GLY23 4.7 16.8 1.0
CA B:GLY23 4.7 14.0 1.0
O B:HOH329 4.9 39.0 1.0

Iodine binding site 8 out of 10 in 4zv0

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Iodine binding site 8 out of 10 in the Structure of TSE6 in Complex with TSI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of TSE6 in Complex with TSI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I103

b:28.1
occ:0.45
 O B:HOH320 2.5 36.2 1.0
O A:HOH655 2.6 32.5 1.0
H B:GLU25 2.6 10.9 1.0
HD1 B:TYR24 2.9 12.4 1.0
HA B:TYR24 3.1 11.0 1.0
N B:GLU25 3.5 9.1 1.0
HG21 A:ILE370 3.6 16.9 1.0
O A:HOH824 3.7 32.7 1.0
CD1 B:TYR24 3.8 10.3 1.0
HD13 A:ILE370 3.8 23.3 1.0
HG3 A:MSE361 3.8 15.9 1.0
CA B:TYR24 4.0 9.1 1.0
O B:GLY23 4.1 14.8 1.0
HB2 A:MSE361 4.1 18.4 1.0
CB B:GLU25 4.1 14.4 1.0
HE1 B:TYR24 4.2 12.1 1.0
C B:TYR24 4.3 10.5 1.0
CA B:GLU25 4.4 9.5 1.0
CE1 B:TYR24 4.5 10.1 1.0
CG2 A:ILE370 4.5 14.1 1.0
CG A:MSE361 4.6 13.3 1.0
HD21 A:ASN359 4.6 23.7 1.0
O A:HOH813 4.6 43.0 1.0
O B:HOH266 4.6 26.0 1.0
CB A:MSE361 4.7 15.3 1.0
O A:HOH710 4.8 35.0 1.0
HG23 A:ILE370 4.8 16.9 1.0
CD1 A:ILE370 4.8 19.4 1.0
C B:GLY23 4.8 11.8 1.0
CG B:TYR24 4.8 7.6 1.0
HB3 A:MSE361 4.8 18.4 1.0
OD1 A:ASN359 4.8 16.3 1.0
HG22 A:ILE370 4.9 16.9 1.0
HG2 A:MSE361 4.9 15.9 1.0
N B:TYR24 4.9 9.9 1.0
HA B:GLU25 4.9 11.4 1.0
CB B:TYR24 4.9 9.2 1.0

Iodine binding site 9 out of 10 in 4zv0

Go back to Iodine Binding Sites List in 4zv0
Iodine binding site 9 out of 10 in the Structure of TSE6 in Complex with TSI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of TSE6 in Complex with TSI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I104

b:25.5
occ:0.55
 HA3 B:GLY86 3.0 15.6 1.0
HB3 B:HIS52 3.3 34.0 1.0
HA B:ILE83 3.5 14.2 1.0
HG3 B:ARG87 3.5 20.0 1.0
HA B:HIS52 3.5 22.8 1.0
HB3 B:LEU51 3.7 18.1 1.0
HG22 B:ILE83 3.8 20.4 1.0
HB2 B:LEU51 3.8 18.1 1.0
CA B:GLY86 3.9 13.0 1.0
HE B:ARG87 4.0 35.3 1.0
N B:HIS52 4.0 20.4 1.0
CA B:HIS52 4.1 19.0 1.0
CB B:HIS52 4.1 28.4 1.0
C B:GLY86 4.1 14.5 1.0
C B:LEU51 4.1 21.4 1.0
HB B:ILE83 4.2 13.9 1.0
O B:ILE83 4.2 11.4 1.0
CB B:LEU51 4.2 15.1 1.0
H B:HIS52 4.3 24.5 1.0
O B:LEU51 4.3 20.4 1.0
CA B:ILE83 4.4 11.9 1.0
CG B:ARG87 4.4 16.7 1.0
N B:ARG87 4.4 14.1 1.0
HG2 B:ARG87 4.5 20.0 1.0
HA2 B:GLY86 4.5 15.6 1.0
H B:ARG87 4.5 16.9 1.0
HB2 B:HIS52 4.5 34.0 1.0
H B:GLY86 4.5 14.3 1.0
CG2 B:ILE83 4.6 17.0 1.0
O B:GLY86 4.6 18.0 1.0
CB B:ILE83 4.6 11.6 1.0
NE B:ARG87 4.7 29.4 1.0
N B:GLY86 4.8 11.9 1.0
C B:ILE83 4.8 10.7 1.0
CA B:LEU51 4.8 16.9 1.0
O B:GLY82 4.9 10.1 1.0

Iodine binding site 10 out of 10 in 4zv0

Go back to Iodine Binding Sites List in 4zv0
Iodine binding site 10 out of 10 in the Structure of TSE6 in Complex with TSI6


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of TSE6 in Complex with TSI6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I105

b:22.3
occ:0.43
 HZ3 B:LYS76 2.5 13.5 1.0
O B:HOH247 3.1 23.2 1.0
HB2 B:ARG73 3.1 8.7 1.0
NZ B:LYS76 3.3 11.2 1.0
HH21 B:ARG73 3.4 15.1 1.0
HZ1 B:LYS76 3.5 13.5 1.0
HE B:ARG73 3.5 12.1 1.0
HB3 B:SER72 3.7 8.3 1.0
HD2 B:LYS76 3.7 12.7 1.0
HA B:ARG73 3.7 7.7 1.0
HZ2 B:LYS76 3.7 13.5 1.0
O B:HOH316 3.8 44.7 1.0
O B:PRO69 3.8 8.4 1.0
O B:HOH278 3.8 24.6 1.0
H B:ARG73 3.8 8.9 1.0
NH2 B:ARG73 3.9 12.6 1.0
HB3 B:PRO69 4.0 12.6 1.0
N B:ARG73 4.0 7.4 1.0
CB B:ARG73 4.0 7.3 1.0
CA B:ARG73 4.1 6.4 1.0
NE B:ARG73 4.1 10.1 1.0
HA B:PRO69 4.1 10.2 1.0
OG B:SER72 4.3 9.6 1.0
CZ B:ARG73 4.3 10.4 1.0
CE B:LYS76 4.4 10.8 1.0
HH22 B:ARG73 4.4 15.1 1.0
CB B:SER72 4.4 6.9 1.0
CD B:LYS76 4.4 10.6 1.0
OD1 B:ASP65 4.4 15.2 1.0
HB3 B:ARG73 4.5 8.7 1.0
HE3 B:LYS76 4.6 13.0 1.0
C B:SER72 4.6 7.3 1.0
C B:PRO69 4.6 7.4 1.0
CA B:PRO69 4.6 8.5 1.0
CB B:PRO69 4.7 10.5 1.0
HD3 B:LYS76 4.7 12.7 1.0
O B:HOH262 4.8 15.6 1.0
HB2 B:PRO69 5.0 12.6 1.0

Reference:

J.C.Whitney, D.Quentin, S.Sawai, M.Leroux, B.N.Harding, H.E.Ledvina, B.Q.Tran, H.Robinson, Y.A.Goo, D.R.Goodlett, S.Raunser, J.D.Mougous. An Interbacterial Nad(P)(+) Glycohydrolase Toxin Requires Elongation Factor Tu For Delivery to Target Cells. Cell V. 163 607 2015.
ISSN: ISSN 1097-4172
PubMed: 26456113
DOI: 10.1016/J.CELL.2015.09.027
Page generated: Sun Aug 11 20:29:36 2024

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