Iodine in PDB 7ev5: Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase

The structure of Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase, PDB code: 7ev5 was solved by S.X.Au, N.D.Muhd Noor, H.Matsumura, R.N.Z.R.A.Rahman, Y.M.Normi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.26 / 1.44
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.356, 55.356, 143.094, 90, 90, 90
R / Rfree (%)	18.4 / 20.9

The structure of Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase (pdb code 7ev5). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase, PDB code: 7ev5:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase


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 Bleg-1 B3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:29.1 occ:0.48 O A:HOH626 3.2 25.4 1.0 O A:HOH591 3.8 30.7 1.0 O A:HOH617 3.9 32.5 1.0 O A:HOH498 4.1 31.2 1.0 O A:SER93 4.4 16.1 1.0 CG A:ARG94 4.5 17.1 1.0 C A:SER93 4.6 15.5 1.0 CA A:ARG94 4.6 14.5 1.0 CB A:SER93 4.6 15.5 1.0 N A:ARG94 4.7 14.4 1.0

Iodine binding site 2 out of 11 in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase


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 Bleg-1 B3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:19.5 occ:0.49 I A:IOD304 0.0 19.5 0.5 I A:IOD304 2.5 14.3 0.5 NH1 A:ARG163 3.2 3.3 0.5 O A:HOH481 3.5 14.4 1.0 O A:ALA88 3.6 19.7 1.0 NH2 A:ARG163 3.6 19.3 0.6 NE A:ARG163 3.7 17.2 0.6 CD A:ARG94 3.7 22.1 1.0 NE A:ARG94 3.9 18.5 1.0 CA A:GLY91 3.9 10.3 1.0 N A:GLY91 4.0 11.1 1.0 CD A:ARG163 4.0 20.3 0.5 O A:HOH516 4.1 15.3 1.0 O A:LEU89 4.1 11.8 1.0 CZ A:ARG163 4.1 18.5 0.6 CG A:ARG94 4.1 17.1 1.0 CZ A:ARG163 4.1 18.4 0.5 O A:HOH496 4.2 22.8 1.0 CB A:ARG94 4.3 17.7 1.0 CB A:ARG163 4.3 12.8 0.6 CB A:ARG163 4.3 12.8 0.5 NE A:ARG163 4.4 20.2 0.5 C A:LEU89 4.4 11.7 1.0 C A:ALA88 4.5 16.0 1.0 CG A:ARG163 4.7 14.7 0.5 CA A:LEU89 4.7 14.7 1.0 CD A:ARG163 4.8 11.3 0.6 CZ A:ARG94 4.9 15.4 1.0 C A:GLY91 5.0 12.6 1.0 N A:LEU89 5.0 13.6 1.0

Iodine binding site 3 out of 11 in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase


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 Bleg-1 B3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:14.3 occ:0.51 I A:IOD304 0.0 14.3 0.5 I A:IOD304 2.5 19.5 0.5 O A:HOH516 3.6 15.3 1.0 N A:ARG163 3.9 13.7 1.0 CA A:GLY91 3.9 10.3 1.0 CB A:LEU162 4.0 13.4 1.0 CD2 A:LEU162 4.1 14.7 1.0 CA A:LEU162 4.3 13.9 1.0 CB A:ARG163 4.4 12.8 0.5 CB A:ARG163 4.4 12.8 0.6 N A:GLY91 4.5 11.1 1.0 CG A:LEU162 4.5 14.1 1.0 C A:LEU162 4.6 14.2 1.0 CD A:ARG94 4.6 22.1 1.0 CD1 A:LEU95 4.7 14.8 1.0 CG A:LEU95 4.7 12.6 1.0 CA A:ARG163 4.7 12.8 0.5 CA A:ARG163 4.7 12.8 0.6 CB A:ARG94 4.7 17.7 1.0 CD1 A:LEU162 4.9 15.3 1.0 NH1 A:ARG163 5.0 3.3 0.5

Iodine binding site 4 out of 11 in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase


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 Bleg-1 B3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:19.9 occ:0.35 O A:HOH503 3.3 15.5 1.0 O A:HOH463 3.3 24.9 1.0 CB A:ASP107 4.0 13.2 0.5 OD1 A:ASP107 4.2 16.6 0.5 CA A:ASP107 4.2 13.2 0.5 CA A:ASP107 4.4 12.7 0.5 O A:ALA106 4.4 14.0 1.0 CB A:ASP107 5.0 15.3 0.5

Iodine binding site 5 out of 11 in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase


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 Bleg-1 B3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:17.6 occ:0.70 N A:HIS127 3.6 10.8 1.0 CE A:LYS177 3.8 14.8 1.0 NZ A:LYS177 3.9 16.8 1.0 CE A:LYS114 4.0 29.7 1.0 CD A:LYS177 4.0 12.7 1.0 CA A:PHE126 4.0 11.6 1.0 O A:HOH423 4.2 29.6 1.0 O A:HIS127 4.2 13.6 1.0 NZ A:LYS114 4.3 34.4 1.0 CD1 A:PHE126 4.3 16.8 1.0 C A:PHE126 4.3 12.9 1.0 CB A:PHE126 4.4 12.1 1.0 CA A:HIS127 4.5 11.2 1.0 CB A:HIS127 4.5 10.9 1.0 CD A:LYS114 4.5 24.2 1.0 O A:VAL125 4.7 14.1 1.0 CG A:LYS177 4.8 13.9 1.0 C A:HIS127 4.8 11.6 1.0 CG A:PHE126 4.8 13.3 1.0

Iodine binding site 6 out of 11 in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase


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 Bleg-1 B3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:24.1 occ:0.32 O A:HOH620 3.2 33.2 1.0 CD A:LYS41 3.6 32.4 1.0 CG2 A:THR38 3.7 19.4 1.0 O A:HOH632 3.8 23.6 1.0 CE A:LYS41 4.3 31.2 1.0 CG2 A:ILE37 4.4 19.2 1.0 CA A:THR38 4.6 15.1 1.0 CB A:THR38 4.6 16.4 1.0 CG A:LYS41 4.6 21.4 1.0 O A:HOH522 4.9 30.0 1.0 N A:THR38 4.9 14.2 1.0 CB A:LYS41 4.9 17.5 1.0

Iodine binding site 7 out of 11 in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase


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 Bleg-1 B3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:I308 b:20.6 occ:0.39 O A:HOH561 4.0 37.2 1.0 O A:HOH495 4.2 27.4 1.0 CB A:LYS41 4.3 17.5 1.0 CD A:LYS41 4.5 32.4 1.0 O A:LYS41 4.9 18.3 1.0 CG A:LYS41 4.9 21.4 1.0

Iodine binding site 8 out of 11 in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase


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 Bleg-1 B3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:I309 b:27.8 occ:0.51 O A:THR111 3.7 18.8 1.0 C A:THR111 3.7 17.6 1.0 NE2 A:HIS77 3.7 12.8 1.0 CE1 A:HIS77 3.8 12.0 1.0 CA A:THR111 3.9 14.8 1.0 CB A:THR111 4.1 17.1 1.0 CE A:LYS79 4.2 25.6 1.0 N A:ASN112 4.4 17.7 1.0 CG2 A:THR111 4.6 17.1 1.0 CB A:ASN112 4.8 25.6 1.0 NZ A:LYS79 4.9 28.2 1.0 CA A:ASN112 4.9 17.3 1.0

Iodine binding site 9 out of 11 in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase


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 Bleg-1 B3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:I310 b:21.3 occ:0.29 OD1 A:ASN112 3.1 42.2 1.0 CG A:GLU113 3.8 30.7 1.0 CG A:ASN112 3.8 31.8 1.0 OG1 A:THR111 3.9 17.5 1.0 CD A:GLU113 3.9 26.3 1.0 OE2 A:GLU113 3.9 32.3 1.0 N A:GLU113 4.0 15.8 1.0 ND2 A:ASN112 4.1 50.6 1.0 CA A:GLU113 4.4 17.2 1.0 C A:ASN112 4.4 20.1 1.0 OE1 A:GLU113 4.6 16.3 1.0 N A:ASN112 4.6 17.7 1.0 CB A:GLU113 4.7 25.2 1.0 O A:HOH401 4.7 17.0 1.0 CA A:ASN112 4.9 17.3 1.0 O A:ASN112 4.9 20.3 1.0 CB A:ASN112 4.9 25.6 1.0

Iodine binding site 10 out of 11 in the Crystal Structure of Bleg-1 B3 Metallo-Beta-Lactamase


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 Bleg-1 B3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:I311 b:31.5 occ:0.45 O A:HOH572 3.1 30.7 1.0 CA A:GLY164 3.9 15.8 1.0 O A:HOH457 4.0 29.3 1.0 CG A:PRO133 4.0 14.9 1.0 CG A:ARG163 4.1 12.3 0.6 N A:GLY164 4.1 12.0 1.0 O A:HOH623 4.6 32.6 1.0 CG A:ARG163 4.6 14.7 0.5 C A:ARG163 4.6 14.0 1.0 CZ2 A:TRP83 4.7 11.7 1.0 CB A:PRO133 4.7 12.2 1.0 CD A:PRO133 4.7 9.8 1.0 CD A:ARG163 4.7 11.3 0.6 O A:ARG163 4.8 11.9 1.0

S.X.Au, N.S.Dzulkifly, N.D.Muhd Noor, H.Matsumura, R.N.Z.R.A.Rahman, Y.M.Normi. Dual Activity Bleg-1 From Bacillus Lehensis G1 Revealed Structural Resemblance to B3 Metallo-Beta-Lactamase and Glyoxalase II: An Insight Into Its Enzyme Promiscuity and Evolutionary Divergence Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS22179377