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Iodine in PDB 4bh5: Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli

Protein crystallography data

The structure of Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli, PDB code: 4bh5 was solved by C.Morlot, N.T.Peters, D.C.Yang, T.Uehara, T.Vernet, T.G.Bernhardt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.40 / 1.57
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 57.404, 57.404, 129.320, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 20.7

Other elements in 4bh5:

The structure of Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 4 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Iodine atom in the Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli (pdb code 4bh5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 23 binding sites of Iodine where determined in the Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli, PDB code: 4bh5:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 23 in 4bh5

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Iodine binding site 1 out of 23 in the Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1420

b:11.7
occ:0.90
 N A:ALA410 3.6 8.9 1.0
CB A:ALA410 3.9 5.7 1.0
NZ A:LYS321 3.9 10.6 1.0
CD A:LYS321 4.1 9.2 1.0
CA A:ALA410 4.4 8.3 1.0
NE A:ARG405 4.4 8.2 1.0
CE A:LYS321 4.4 9.9 1.0
CZ A:ARG405 4.4 7.5 1.0
CA A:GLN409 4.4 9.5 1.0
C A:GLN409 4.5 9.3 1.0
CD A:ARG405 4.6 7.6 1.0
NH1 A:ARG405 4.7 5.6 1.0
O A:GLY408 4.7 11.1 1.0
NH2 A:ARG405 4.8 8.7 1.0

Iodine binding site 2 out of 23 in 4bh5

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Iodine binding site 2 out of 23 in the Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1421

b:18.2
occ:0.40
 I B:IOD1421 1.2 12.9 0.5
N A:SER392 3.8 14.3 1.0
NH1 B:ARG406 3.9 10.1 1.0
CA A:GLN370 3.9 11.7 1.0
CB A:SER392 3.9 12.4 1.0
CA A:SER392 4.0 13.9 1.0
CB A:GLN370 4.0 10.8 1.0
N A:SER391 4.1 12.6 1.0
C A:SER391 4.2 15.6 1.0
O A:ASN369 4.4 9.6 1.0
CA A:SER391 4.7 14.5 1.0
O A:SER391 4.7 16.9 1.0
N A:GLN370 4.7 7.8 1.0
CA B:ALA293 4.7 15.1 1.0
O A:GLN370 4.8 10.5 1.0
CD B:PRO294 4.8 15.2 1.0
C A:GLN370 4.9 8.6 1.0
OG A:SER392 4.9 8.8 1.0
CA A:GLY390 4.9 11.5 1.0
C A:ASN369 4.9 8.4 1.0
CZ B:ARG406 5.0 13.6 1.0

Iodine binding site 3 out of 23 in 4bh5

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Iodine binding site 3 out of 23 in the Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1422

b:34.7
occ:0.40
 N A:GLN348 3.2 11.3 1.0
CB A:GLN348 3.6 12.9 1.0
CA A:GLN348 4.0 13.1 1.0
CA A:LEU347 4.0 11.4 1.0
CD1 A:LEU347 4.1 13.5 1.0
C A:LEU347 4.1 11.5 1.0
O A:HOH2067 4.3 35.8 1.0
O A:HOH2066 4.5 13.8 1.0
CD1 A:TRP346 4.6 14.3 1.0
O A:TRP346 4.6 11.6 1.0
NE1 A:TRP346 4.9 16.5 1.0
N A:LEU347 5.0 10.6 1.0
CB A:LEU347 5.0 11.5 1.0
CG A:LEU347 5.0 14.2 1.0
CG A:GLN348 5.0 16.4 1.0

Iodine binding site 4 out of 23 in 4bh5

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Iodine binding site 4 out of 23 in the Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1423

b:59.6
occ:0.60
 O A:HOH2061 3.2 24.3 1.0
O A:HOH2071 3.3 20.2 1.0
CG A:ARG340 3.4 7.7 0.5
O A:GLY339 3.5 10.0 1.0
C A:GLY339 3.7 9.2 1.0
NE2 A:GLN379 3.8 21.2 1.0
CG A:GLN379 3.9 14.7 1.0
CA A:GLY339 4.1 8.7 1.0
N A:ARG340 4.2 8.2 1.0
NH2 A:ARG340 4.2 13.8 0.5
CD A:ARG340 4.3 9.3 0.5
CB A:GLN379 4.3 12.1 1.0
CD A:GLN379 4.4 18.5 1.0
N A:GLY339 4.4 10.5 1.0
CB A:ARG340 4.4 9.4 0.5
NH1 A:ARG340 4.5 14.2 0.5
CB A:ARG340 4.5 8.8 0.5
CA A:ARG340 4.6 8.5 0.5
CA A:ARG340 4.6 8.6 0.5
CZ A:ARG340 4.7 16.9 0.5
NE A:ARG340 4.8 15.2 0.5
CA A:GLN379 4.8 8.9 1.0

Iodine binding site 5 out of 23 in 4bh5

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Iodine binding site 5 out of 23 in the Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1420

b:17.0
occ:0.40
 I B:IOD1500 1.1 13.8 0.5
CB B:SER392 3.8 12.7 1.0
N B:SER392 3.8 14.1 1.0
CA B:SER392 3.9 13.8 1.0
CA B:GLN370 4.0 10.3 1.0
CB B:GLN370 4.1 13.3 1.0
N B:SER391 4.2 12.3 1.0
C B:SER391 4.3 15.2 1.0
O B:ASN369 4.5 8.5 1.0
O B:SER391 4.8 17.3 1.0
N B:GLN370 4.8 8.6 1.0
O B:GLN370 4.8 9.2 1.0
CA B:SER391 4.8 14.6 1.0
OG B:SER392 4.8 11.0 1.0
C B:GLN370 4.9 9.4 1.0
C B:ASN369 5.0 8.8 1.0

Iodine binding site 6 out of 23 in 4bh5

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Iodine binding site 6 out of 23 in the Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1421

b:12.9
occ:0.50
 I A:IOD1421 1.2 18.2 0.4
NH1 B:ARG406 3.6 10.1 1.0
CA B:ALA293 3.7 15.1 1.0
N B:ALA293 4.0 14.9 1.0
CB A:SER392 4.1 12.4 1.0
CB B:ALA293 4.1 17.1 1.0
CA A:SER392 4.2 13.9 1.0
O B:GLY292 4.3 13.7 1.0
CD B:PRO294 4.3 15.2 1.0
C B:GLY292 4.3 15.1 1.0
N A:SER392 4.4 14.3 1.0
CZ B:ARG406 4.6 13.6 1.0
CA A:GLN370 4.6 11.7 1.0
NH2 B:ARG406 4.8 15.2 1.0
CB A:GLN370 4.8 10.8 1.0
C A:SER391 4.9 15.6 1.0
C B:ALA293 4.9 15.4 1.0
O A:ASN369 5.0 9.6 1.0

Iodine binding site 7 out of 23 in 4bh5

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Iodine binding site 7 out of 23 in the Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1422

b:9.9
occ:0.80
 NH1 C:ARG405 3.5 13.6 1.0
O B:HOH2023 3.6 24.1 1.0
N B:ALA410 3.7 8.2 1.0
SD C:MET363 3.7 7.5 0.5
NZ B:LYS321 3.9 11.7 1.0
CB B:ALA410 4.0 5.5 1.0
O C:HOH2061 4.0 18.1 1.0
CE C:MET363 4.1 5.1 0.5
CD B:LYS321 4.1 10.6 1.0
SD C:MET363 4.2 24.6 0.5
CD C:ARG405 4.2 12.7 1.0
CE B:LYS321 4.4 13.1 1.0
CA C:GLY408 4.4 14.1 1.0
CA B:GLN409 4.4 9.4 1.0
CA B:ALA410 4.5 8.3 1.0
CZ B:ARG405 4.5 7.8 1.0
NE B:ARG405 4.5 6.7 1.0
C B:GLN409 4.5 7.9 1.0
O B:HOH2102 4.6 36.4 1.0
CZ C:ARG405 4.6 14.8 1.0
O B:GLY408 4.7 9.7 1.0
NH1 B:ARG405 4.7 7.9 1.0
CD B:ARG405 4.8 7.4 1.0
NE C:ARG405 4.9 11.6 1.0
NH2 B:ARG405 4.9 8.0 1.0
O C:GLY408 4.9 15.0 1.0

Iodine binding site 8 out of 23 in 4bh5

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Iodine binding site 8 out of 23 in the Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1423

b:44.8
occ:0.40
 O B:HOH2064 3.3 21.3 1.0
O B:HOH2052 3.6 22.9 1.0
NE2 B:GLN379 3.6 22.8 1.0
O B:GLY339 3.7 10.0 1.0
C B:GLY339 3.8 10.3 1.0
CA B:GLY339 4.2 7.3 1.0
CG B:GLN379 4.2 16.7 1.0
N B:ARG340 4.2 9.0 1.0
NH2 B:ARG340 4.2 22.5 1.0
CD B:GLN379 4.4 20.3 1.0
CB B:ARG340 4.4 11.6 1.0
CB B:GLN379 4.6 11.3 1.0
O B:HOH2079 4.6 30.8 1.0
CA B:ARG340 4.6 10.2 1.0
N B:GLY339 4.6 9.5 1.0
NE B:ARG340 4.7 24.7 1.0
CZ B:ARG340 4.8 22.6 1.0

Iodine binding site 9 out of 23 in 4bh5

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Iodine binding site 9 out of 23 in the Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1500

b:13.8
occ:0.50
 I B:IOD1420 1.1 17.0 0.4
CB B:SER392 4.0 12.7 1.0
CA B:SER392 4.2 13.8 1.0
N B:SER392 4.5 14.1 1.0
CA B:GLN370 4.7 10.3 1.0
CB B:GLN370 4.9 13.3 1.0
C B:SER391 4.9 15.2 1.0

Iodine binding site 10 out of 23 in 4bh5

Go back to Iodine Binding Sites List in 4bh5
Iodine binding site 10 out of 23 in the Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Lytm Domain of Envc, An Activator of Cell Wall Amidases in Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1501

b:50.6
occ:0.50
 O B:HOH2069 3.7 27.1 1.0
O B:HOH2064 4.6 21.3 1.0
CA B:GLY359 4.8 15.9 1.0

Reference:

N.T.Peters, C.Morlot, D.C.Yang, T.Uehara, T.Vernet, T.G.Bernhardt. Structure-Function Analysis of the Lytm Domain of Envc, An Activator of Cell Wall Remodeling at the Escherichia Coli Division Site. Mol.Microbiol. V. 89 690 2013.
ISSN: ISSN 0950-382X
PubMed: 23796240
DOI: 10.1111/MMI.12304
Page generated: Sun Dec 13 19:32:03 2020

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