Iodine in PDB 4l85: Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli

The structure of Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli, PDB code: 4l85 was solved by S.Kumar, D.A.Yernool, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.21 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.918, 108.918, 74.408, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 21.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli (pdb code 4l85). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 35 binding sites of Iodine where determined in the Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli, PDB code: 4l85:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 35 in the Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli


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 Receiver Domain of Kdpe D52A Mutant From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:78.6 occ:0.45 OE1 A:GLU30 3.4 91.7 1.0 NE A:ARG18 3.6 84.8 1.0 CG A:ARG15 3.6 0.9 1.0 CA A:ARG15 3.8 75.1 1.0 CD A:ARG18 3.9 83.9 1.0 N A:ARG15 4.1 73.0 1.0 CB A:ARG15 4.2 81.0 1.0 O A:ARG14 4.3 69.3 1.0 C A:ARG14 4.4 74.9 1.0 CD A:ARG15 4.4 0.1 1.0 CD A:GLU30 4.4 91.3 1.0 CB A:ARG18 4.5 71.8 1.0 O B:HOH313 4.6 78.3 1.0 OE2 A:GLU30 4.6 96.1 1.0 CZ A:ARG18 4.6 82.5 1.0 CG A:ARG18 4.8 72.8 1.0 NH2 A:ARG18 4.9 78.2 1.0

Iodine binding site 2 out of 35 in the Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli


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 Receiver Domain of Kdpe D52A Mutant From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:92.3 occ:0.33 CA A:ARG36 4.0 81.8 1.0 N A:ARG36 4.0 79.6 1.0 CB A:ARG36 4.1 86.5 1.0 CD A:ARG36 4.1 94.3 1.0 C A:GLN35 4.5 82.5 1.0 NE A:ARG36 4.6 0.5 1.0 CB A:GLN35 4.7 97.4 1.0 CG A:ARG36 4.7 85.5 1.0 CD2 A:LEU39 4.7 91.3 1.0 O A:GLN35 4.9 79.6 1.0

Iodine binding site 3 out of 35 in the Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli


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 Receiver Domain of Kdpe D52A Mutant From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:0.3 occ:0.48 OE1 A:GLU107 3.4 50.1 1.0 O A:HOH314 3.4 64.3 1.0 CA A:PHE103 3.4 65.1 1.0 CD2 A:LEU99 3.4 70.8 1.0 N A:GLY104 3.5 66.2 1.0 O A:PRO102 3.6 63.4 1.0 O A:HOH301 3.6 60.2 1.0 C A:PHE103 3.9 66.8 1.0 O A:SER100 4.0 57.4 1.0 CD A:GLU107 4.0 54.9 1.0 O A:HOH303 4.0 55.7 1.0 O A:HOH311 4.1 60.0 1.0 CG A:LEU99 4.1 64.4 1.0 CB A:LEU99 4.2 56.9 1.0 OE2 A:GLU107 4.2 52.9 1.0 N A:PHE103 4.2 63.5 1.0 CB A:PHE103 4.3 58.8 1.0 C A:PRO102 4.3 61.0 1.0 CA A:GLY104 4.8 50.0 1.0 N A:SER100 4.9 53.4 1.0 CD1 A:PHE103 4.9 54.1 1.0 CA A:LEU99 4.9 53.9 1.0

Iodine binding site 4 out of 35 in the Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli


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 Receiver Domain of Kdpe D52A Mutant From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:0.4 occ:0.51 O A:HOH328 3.8 75.7 1.0 CD1 B:LEU39 4.0 86.8 1.0 CG2 B:THR43 4.1 86.0 1.0 CA A:ALA20 4.3 58.9 1.0 I B:IOD205 4.5 90.4 0.3 O A:THR19 4.5 64.3 1.0 CB B:THR43 4.7 95.4 1.0 O A:ALA20 4.8 65.8 1.0 CB A:ALA20 4.8 57.7 1.0 CG B:LEU39 4.9 85.9 1.0 OG1 B:THR43 4.9 97.6 1.0 N A:ALA20 5.0 61.6 1.0

Iodine binding site 5 out of 35 in the Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli


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 Receiver Domain of Kdpe D52A Mutant From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:72.9 occ:0.17 CD1 A:LEU53 2.5 98.9 1.0 CD1 A:ILE61 3.3 87.7 1.0 N A:ILE61 3.7 85.5 1.0 CG A:LEU53 3.8 95.7 1.0 CB A:ALA90 3.8 61.3 1.0 C A:GLY60 3.9 64.7 1.0 CG1 A:ILE61 3.9 95.6 1.0 CD1 A:ILE64 4.2 59.3 1.0 CD2 A:LEU53 4.2 95.8 1.0 CA A:ILE61 4.2 87.8 1.0 O A:GLY60 4.3 65.2 1.0 CA A:GLY60 4.3 69.6 1.0 I A:IOD206 4.4 0.8 0.6 CA A:ALA90 4.6 60.6 1.0 CG1 A:VAL77 4.7 56.2 1.0 CG2 A:VAL77 4.7 54.7 1.0 CB A:ILE61 4.7 96.9 1.0 CD2 A:LEU51 4.9 58.4 1.0

Iodine binding site 6 out of 35 in the Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli


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 Receiver Domain of Kdpe D52A Mutant From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:I206 b:0.8 occ:0.62 NH1 A:ARG81 3.3 0.3 1.0 O A:HOH347 3.9 0.1 1.0 N A:ILE61 4.0 85.5 1.0 O A:HOH331 4.0 80.7 1.0 CA A:GLY60 4.1 69.6 1.0 N A:GLY60 4.1 66.9 1.0 CG1 A:ILE61 4.1 95.6 1.0 CZ A:ARG81 4.3 0.5 1.0 NH2 A:ARG81 4.4 0.4 1.0 I A:IOD205 4.4 72.9 0.2 CD1 A:LEU53 4.5 98.9 1.0 C A:GLY60 4.6 64.7 1.0 O A:HOH346 4.6 89.6 1.0 CB A:ILE61 4.9 96.9 1.0 CD1 A:ILE61 5.0 87.7 1.0

Iodine binding site 7 out of 35 in the Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli


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 Receiver Domain of Kdpe D52A Mutant From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:I207 b:0.2 occ:0.47 N A:GLU30 3.7 61.3 1.0 CA A:PHE29 3.8 60.3 1.0 NH2 A:ARG18 4.0 78.2 1.0 CD1 A:PHE29 4.1 76.6 1.0 CG A:GLU30 4.1 80.0 1.0 O A:VAL28 4.2 54.9 1.0 CB A:PHE29 4.2 65.5 1.0 C A:PHE29 4.3 58.6 1.0 NH2 A:ARG44 4.4 68.4 1.0 O A:GLU30 4.6 57.8 1.0 CG A:PHE29 4.7 73.4 1.0 O A:HOH334 4.7 84.2 1.0 CA A:GLU30 4.8 61.8 1.0 CZ A:ARG44 4.8 61.1 1.0 CB A:GLU30 4.9 64.8 1.0 N A:PHE29 4.9 52.8 1.0 CD A:GLU30 5.0 91.3 1.0

Iodine binding site 8 out of 35 in the Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli


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 Receiver Domain of Kdpe D52A Mutant From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:I208 b:0.4 occ:0.47 O A:HOH328 3.1 75.7 1.0 O B:HOH304 3.1 56.9 1.0 OE1 A:GLN109 3.2 70.8 1.0 CA A:GLY106 4.1 43.2 1.0 N A:GLY106 4.3 47.7 1.0 CG2 A:ILE105 4.3 57.0 1.0 CD A:GLN109 4.3 64.5 1.0 O A:HOH304 4.7 54.1 1.0 C A:ILE105 4.8 51.1 1.0 NE2 A:GLN109 4.8 59.0 1.0 O B:THR43 4.8 87.4 1.0 CG2 B:THR43 4.9 86.0 1.0 CB B:THR43 5.0 95.4 1.0 CG1 A:ILE105 5.0 56.7 1.0

Iodine binding site 9 out of 35 in the Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli


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 Receiver Domain of Kdpe D52A Mutant From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:I209 b:0.5 occ:0.46 O A:HOH317 3.3 67.6 1.0 CB A:ALA80 3.5 0.9 1.0 CD B:GLN69 3.6 91.4 1.0 CG B:GLN69 3.7 84.8 1.0 CA A:ALA80 3.8 99.9 1.0 N A:ALA80 3.9 0.3 1.0 NE2 B:GLN69 3.9 93.6 1.0 OE1 B:GLN69 4.0 92.8 1.0 CZ A:PHE103 4.3 64.2 1.0 C A:SER79 4.5 64.0 1.0 CE2 A:PHE103 4.7 62.7 1.0 CD A:LYS101 4.8 98.2 1.0 O A:SER79 4.8 67.0 1.0 CB A:LYS101 4.9 75.5 1.0 CB B:GLN69 4.9 67.7 1.0

Iodine binding site 10 out of 35 in the Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Receiver Domain of Kdpe D52A Mutant From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:59.1 occ:0.30 I B:IOD212 1.7 73.7 0.2 NZ B:LYS101 3.0 0.6 1.0 N B:GLY54 3.4 0.5 1.0 CA B:GLY54 3.4 0.8 1.0 CA B:SER79 3.7 74.9 1.0 O B:LEU78 3.7 66.5 1.0 C B:SER79 3.8 77.2 1.0 N B:ALA80 3.9 84.2 1.0 C B:LEU78 3.9 66.8 1.0 N B:SER79 3.9 70.8 1.0 O B:GLY54 4.3 0.9 1.0 CB B:LEU78 4.3 70.8 1.0 C B:GLY54 4.4 0.5 1.0 CE B:LYS101 4.4 0.5 1.0 N B:LEU53 4.5 80.5 1.0 CB B:ALA52 4.5 73.3 1.0 O B:SER79 4.5 74.4 1.0 C B:ALA52 4.6 74.4 1.0 C B:LEU53 4.6 0.7 1.0 CA B:ALA80 4.6 87.5 1.0 CA B:ALA52 4.6 72.8 1.0 CA B:LEU78 4.8 65.6 1.0 CB B:ALA80 4.9 93.1 1.0

A.Narayanan, S.Kumar, A.N.Evrard, L.N.Paul, D.A.Yernool. An Asymmetric Heterodomain Interface Stabilizes A Response Regulator-Dna Complex. Nat Commun V. 5 3282 2014.
ISSN: ESSN 2041-1723
PubMed: 24526190
DOI: 10.1038/NCOMMS4282