Iodine in PDB 3q5m: Crystal Structure of Escherichia Coli Bamd

The structure of Crystal Structure of Escherichia Coli Bamd, PDB code: 3q5m was solved by C.Dong, H.Hou, X.Yang, Y.Dong, Y.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.60 / 2.60
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	106.549, 106.549, 65.070, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 26.1

The binding sites of Iodine atom in the Crystal Structure of Escherichia Coli Bamd (pdb code 3q5m). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure of Escherichia Coli Bamd, PDB code: 3q5m:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Crystal Structure of Escherichia Coli Bamd


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 Escherichia Coli Bamd within 5.0Å range: probe atom residue distance (Å) B Occ A:I224 b:0.7 occ:1.00 CD A:PRO64 3.5 41.0 1.0 CG A:PRO64 3.6 32.6 1.0 N A:LEU65 3.7 40.3 1.0 CB A:PRO64 3.8 32.0 1.0 CG A:LEU65 4.0 46.0 1.0 CD1 A:LEU65 4.1 39.2 1.0 CB A:ASP62 4.2 47.6 1.0 CB A:LEU65 4.2 40.2 1.0 CA A:ASP62 4.3 43.4 1.0 N A:PRO64 4.3 40.9 1.0 C A:ASP62 4.4 44.1 1.0 OD1 A:ASP62 4.5 58.0 1.0 CA A:PRO64 4.5 38.9 1.0 CA A:LEU65 4.5 40.9 1.0 C A:PRO64 4.6 43.1 1.0 CG A:ASP62 4.7 55.2 1.0 O A:ASP62 4.7 45.2 1.0 N A:LEU63 4.8 43.7 1.0

Iodine binding site 2 out of 7 in the Crystal Structure of Escherichia Coli Bamd


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 Escherichia Coli Bamd within 5.0Å range:

Iodine binding site 3 out of 7 in the Crystal Structure of Escherichia Coli Bamd


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 Escherichia Coli Bamd within 5.0Å range: probe atom residue distance (Å) B Occ A:I226 b:0.5 occ:1.00 ND2 A:ASN8 3.4 60.8 1.0 OG1 A:THR16 3.5 46.5 1.0 CG1 A:ILE13 3.6 57.7 1.0 NE2 A:GLN32 3.9 52.5 1.0 CA A:ILE13 3.9 57.1 1.0 CG A:PRO6 4.1 60.7 1.0 N A:ILE13 4.3 59.8 1.0 CB A:ILE13 4.3 56.0 1.0 CB A:THR16 4.3 48.0 1.0 CG A:ASN8 4.4 62.1 1.0 O A:GLU12 4.5 66.7 1.0 CB A:ASN8 4.6 61.4 1.0 CD A:PRO6 4.6 63.2 1.0 C A:GLU12 4.6 64.5 1.0 CG2 A:THR16 4.8 44.8 1.0 CD1 A:ILE13 4.8 58.2 1.0 CG2 A:ILE13 4.8 54.1 1.0 CG2 A:VAL5 4.8 47.1 1.0 CD A:GLN32 4.9 56.9 1.0 O A:PRO6 5.0 61.6 1.0

Iodine binding site 4 out of 7 in the Crystal Structure of Escherichia Coli Bamd


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 Escherichia Coli Bamd within 5.0Å range: probe atom residue distance (Å) B Occ A:I227 b:61.0 occ:1.00 NE A:ARG39 3.4 57.2 1.0 ND2 A:ASN38 3.6 58.0 1.0 OE1 A:GLU3 3.7 79.1 1.0 CB A:GLU3 3.7 79.7 1.0 O A:GLU3 3.7 76.8 1.0 NH2 A:ARG39 3.9 60.8 1.0 CG A:ARG39 4.0 59.8 1.0 CZ A:ARG39 4.1 58.6 1.0 CD A:GLU3 4.2 78.6 1.0 CG A:GLU3 4.2 73.4 1.0 CB A:ASN38 4.2 53.9 1.0 CD A:ARG39 4.3 56.2 1.0 CA A:GLU3 4.4 81.6 1.0 CG A:ASN38 4.4 56.8 1.0 C A:GLU3 4.4 82.1 1.0 CA A:ALA35 4.6 50.5 1.0 O A:ALA35 4.7 51.7 1.0 CB A:ALA35 5.0 53.4 1.0 N A:ARG39 5.0 59.0 1.0

Iodine binding site 5 out of 7 in the Crystal Structure of Escherichia Coli Bamd


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 Escherichia Coli Bamd within 5.0Å range: probe atom residue distance (Å) B Occ A:I228 b:78.8 occ:1.00 N A:TYR45 3.7 69.8 1.0 CD A:PRO44 3.7 75.2 1.0 CA A:GLY43 3.7 65.9 1.0 CB A:TYR45 3.9 70.0 1.0 N A:SER46 3.9 55.7 1.0 C A:TYR45 3.9 58.3 1.0 CD2 A:LEU36 3.9 53.2 1.0 N A:PRO44 4.0 75.6 1.0 CA A:TYR45 4.0 65.8 1.0 O A:TYR40 4.1 49.6 1.0 CD2 A:TYR45 4.1 77.3 1.0 C A:GLY43 4.1 69.9 1.0 CA A:SER46 4.2 54.5 1.0 CB A:PRO10 4.2 60.5 1.0 CG2 A:VAL49 4.3 42.3 1.0 CB A:TYR40 4.3 50.4 1.0 O A:TYR45 4.4 55.0 1.0 CG A:TYR45 4.5 74.9 1.0 N A:GLY43 4.5 64.1 1.0 CB A:LEU36 4.5 55.8 1.0 CG A:LEU36 4.6 54.4 1.0 CD1 A:LEU36 4.6 52.1 1.0 CG A:PRO44 4.6 77.5 1.0 CB A:SER46 4.7 53.6 1.0 C A:PRO44 4.8 76.1 1.0 O A:GLY43 4.9 67.8 1.0

Iodine binding site 6 out of 7 in the Crystal Structure of Escherichia Coli Bamd


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 Escherichia Coli Bamd within 5.0Å range: probe atom residue distance (Å) B Occ A:I229 b:0.1 occ:1.00 CG A:PRO44 3.6 77.5 1.0 CB A:ASN11 4.3 67.1 1.0 CB A:PRO44 4.4 77.6 1.0 N A:ASN11 4.5 65.1 1.0 CB A:PRO10 4.6 60.5 1.0 CD A:PRO44 4.6 75.2 1.0 CE2 A:TYR45 4.7 80.3 1.0 CG A:PRO10 4.7 62.2 1.0 ND2 A:ASN11 4.7 69.5 1.0 OH A:TYR45 4.7 85.8 1.0 CD A:PRO10 4.8 63.1 1.0 CG A:ASN11 4.8 68.7 1.0 CA A:ASN11 4.9 66.6 1.0

Iodine binding site 7 out of 7 in the Crystal Structure of Escherichia Coli Bamd


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 Escherichia Coli Bamd within 5.0Å range: probe atom residue distance (Å) B Occ A:I230 b:0.2 occ:1.00 ND2 A:ASN77 3.7 57.5 1.0 OD1 A:ASN77 4.1 59.1 1.0 CG A:GLN47 4.2 61.3 1.0 CG A:GLN50 4.3 38.3 1.0 CD2 A:PHE73 4.3 40.2 1.0 CG A:ASN77 4.3 56.0 1.0 CE2 A:PHE73 4.4 40.3 1.0 CA A:GLN47 4.5 55.7 1.0 CD1 A:LEU76 4.5 47.1 1.0 O A:SER46 4.8 56.4 1.0 CB A:GLN47 4.8 56.0 1.0 NE2 A:GLN47 4.9 71.8 1.0 CB A:LEU76 4.9 53.7 1.0 N A:GLN47 5.0 57.2 1.0 CB A:GLN50 5.0 40.0 1.0

C.Dong, H.F.Hou, X.Yang, Y.Q.Shen, Y.H.Dong. Structure of Escherichia Coli Bamd and Its Functional Implications in Outer Membrane Protein Assembly Acta Crystallogr.,Sect.D V. 68 95 2012.
ISSN: ISSN 0907-4449
PubMed: 22281737
DOI: 10.1107/S0907444911051031