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Iodine in PDB 4gog: Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex

Protein crystallography data

The structure of Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex, PDB code: 4gog was solved by C.A.Smith, S.B.Vakulenko, J.Munoz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.31 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.950, 81.220, 72.120, 90.00, 102.29, 90.00
R / Rfree (%) 14.9 / 16.8

Other elements in 4gog:

The structure of Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex (pdb code 4gog). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 19 binding sites of Iodine where determined in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex, PDB code: 4gog:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 19 in 4gog

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Iodine binding site 1 out of 19 in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex


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 the Ges-1 Imipenem Acyl-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:19.8
occ:0.40
O A:HOH654 4.0 16.4 1.0
CA A:LEU22 4.0 11.0 0.9
CA A:LEU22 4.0 10.9 0.1
N A:LEU22 4.1 10.8 0.9
N A:LEU22 4.1 10.7 0.1
C A:LYS21 4.3 10.4 1.0
O A:LYS21 4.3 10.0 1.0
CD1 A:LEU22 4.4 14.9 0.9
CB A:LEU22 4.4 12.8 0.9
CD A:LYS25 4.4 15.1 1.0
CG A:LEU22 4.4 11.7 0.1
CB A:LEU22 4.4 11.4 0.1
CB A:LYS21 4.6 10.8 1.0
CB A:LYS25 4.9 9.9 1.0

Iodine binding site 2 out of 19 in 4gog

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Iodine binding site 2 out of 19 in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex


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 the Ges-1 Imipenem Acyl-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:13.3
occ:0.39
O A:HOH658 3.4 23.7 1.0
CE A:MET56 3.6 16.3 0.6
N A:ARG55 3.8 8.1 1.0
CE A:MET56 3.8 14.2 0.5
N A:MET56 3.9 8.6 1.0
CG A:MET56 3.9 12.1 0.5
CG A:MET56 4.0 11.5 0.6
CA A:HIS54 4.0 8.2 1.0
CB A:MET56 4.1 10.3 0.5
O A:HOH803 4.1 29.5 1.0
O A:GLY53 4.2 10.4 1.0
C A:HIS54 4.2 8.1 1.0
N A:HIS54 4.2 8.3 1.0
C A:GLY53 4.3 9.1 1.0
CB A:MET56 4.4 10.3 0.6
CA A:ARG55 4.5 8.4 1.0
CA A:MET56 4.6 9.0 0.5
SD A:MET56 4.6 15.0 0.6
SD A:MET56 4.6 13.8 0.5
C A:ARG55 4.7 7.9 1.0
CA A:MET56 4.7 9.0 0.6

Iodine binding site 3 out of 19 in 4gog

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Iodine binding site 3 out of 19 in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex


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 the Ges-1 Imipenem Acyl-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:13.3
occ:0.42
O B:HOH841 3.2 37.3 1.0
O B:HOH812 3.3 38.5 1.0
O B:HOH810 3.3 34.0 1.0
NH1 A:ARG204 3.6 8.6 1.0
CD1 A:ILE207 4.1 8.8 1.0
CD A:ARG204 4.1 8.5 1.0
CB B:SER109 4.1 8.4 1.0
CE1 A:HIS200 4.2 17.1 1.0
OE1 A:GLU203 4.2 14.6 0.2
CD A:GLU203 4.4 14.4 0.2
CE1 B:HIS111 4.5 12.6 1.0
CZ A:ARG204 4.6 8.1 1.0
OE2 A:GLU203 4.7 15.3 0.2
ND1 A:HIS200 4.8 17.1 1.0
CG1 A:VAL225 4.8 10.6 1.0
OG B:SER109 4.8 8.6 1.0
NE A:ARG204 4.9 8.1 1.0
CG A:GLU203 4.9 12.8 0.2

Iodine binding site 4 out of 19 in 4gog

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Iodine binding site 4 out of 19 in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex


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 the Ges-1 Imipenem Acyl-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:30.1
occ:0.84
O A:HOH720 3.2 22.0 1.0
O A:HOH657 3.4 24.0 1.0
O A:LEU134 3.8 13.0 0.6
CA A:GLY139 4.0 18.5 0.7
C A:LEU134 4.0 13.8 0.6
CA A:GLY139 4.0 18.7 0.3
N A:ARG135 4.0 15.7 0.5
CD A:PRO140 4.1 17.9 1.0
CB A:LEU134 4.1 12.8 0.6
CA A:ARG135 4.1 16.3 0.5
N A:ARG135 4.2 14.1 0.6
CB A:LEU134 4.2 14.3 0.5
CA A:ARG135 4.2 15.0 0.6
C A:LEU134 4.4 14.9 0.5
CB A:ARG135 4.5 16.8 0.5
CA A:LEU134 4.7 13.5 0.6
O A:LEU134 4.7 14.9 0.5
CD A:LYS160 4.7 20.1 1.0
N A:GLY139 4.8 18.9 0.7
N A:GLY139 4.9 19.4 0.3
CB A:LYS160 4.9 15.5 1.0
CD1 A:LEU134 5.0 13.9 0.5
CA A:LEU134 5.0 14.2 0.5
N A:PRO140 5.0 17.5 1.0

Iodine binding site 5 out of 19 in 4gog

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Iodine binding site 5 out of 19 in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex


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 the Ges-1 Imipenem Acyl-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I506

b:13.4
occ:0.19
I B:IOD511 2.8 13.9 0.3
O A:HOH702 3.2 26.3 1.0
O A:LYS222 3.3 13.0 1.0
C A:LYS222 3.9 10.6 1.0
CA A:ASP223 4.0 10.6 1.0
CD2 B:LEU107 4.1 13.9 1.0
N A:ASP223 4.2 9.9 1.0
CG B:LEU107 4.2 11.0 1.0
CB A:ASP223 4.2 13.8 1.0
CB A:LYS222 4.6 12.5 1.0
CA B:ALA108 4.6 8.7 1.0
O A:HOH730 4.7 20.1 1.0
N B:ALA108 4.9 8.0 1.0
CA A:LYS222 4.9 10.0 1.0
O A:HOH649 4.9 14.0 1.0
CB B:ALA108 5.0 9.5 1.0

Iodine binding site 6 out of 19 in 4gog

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Iodine binding site 6 out of 19 in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex


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 the Ges-1 Imipenem Acyl-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I507

b:20.8
occ:0.28
O A:HOH894 3.3 31.6 1.0
NH2 A:ARG105 3.5 13.7 1.0
NH1 A:ARG105 3.6 13.0 1.0
OE1 B:GLN210 3.6 13.2 1.0
CB A:PRO101 4.0 12.7 1.0
CZ A:ARG105 4.0 12.7 1.0
CD2 A:LEU124 4.2 15.6 1.0
CD B:GLN210 4.3 10.0 1.0
CG A:PRO101 4.4 12.1 1.0
O A:HOH854 4.5 27.4 1.0
CB B:GLN210 4.5 8.4 1.0
CH2 A:TRP99 4.6 16.8 0.5
CG B:GLN210 4.6 8.7 1.0
CD1 A:LEU124 4.7 13.5 1.0
CZ2 A:TRP99 4.9 16.0 0.7

Iodine binding site 7 out of 19 in 4gog

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Iodine binding site 7 out of 19 in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex


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 the Ges-1 Imipenem Acyl-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I508

b:24.0
occ:0.21
NA A:NA510 3.6 8.1 1.0
N A:ASP94 4.1 13.5 1.0
CG A:PRO93 4.2 14.7 1.0
CB A:ASP94 4.3 17.0 1.0
CA A:ASP94 4.4 15.8 1.0
CB A:PRO93 4.7 14.4 1.0
C A:PRO93 4.7 13.1 1.0

Iodine binding site 8 out of 19 in 4gog

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Iodine binding site 8 out of 19 in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex


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 the Ges-1 Imipenem Acyl-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I509

b:40.4
occ:0.23
O A:HOH882 3.3 40.9 1.0
O A:HOH647 3.7 19.8 1.0
CG2 A:ILE150 3.8 20.7 1.0
OE2 A:GLU76 3.9 19.9 0.5
O A:HOH874 4.0 35.9 1.0
NZ A:LYS187 4.1 19.9 0.5
CA A:ALA193 4.3 12.9 1.0
CB A:ALA193 4.3 14.0 1.0
CE A:LYS187 4.5 18.8 0.5
NZ A:LYS149 4.5 29.4 1.0
CB A:ILE150 4.6 20.2 1.0
CA A:ILE150 4.6 19.2 1.0
O A:ALA193 4.8 13.2 1.0
O A:LYS149 4.8 20.2 1.0

Iodine binding site 9 out of 19 in 4gog

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Iodine binding site 9 out of 19 in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex


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 the Ges-1 Imipenem Acyl-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I502

b:12.9
occ:0.42
O B:HOH808 3.2 46.1 1.0
O A:HOH672 3.3 22.6 1.0
O B:HOH798 3.4 21.3 0.5
NH1 B:ARG204 3.6 9.0 1.0
CD1 B:ILE207 4.0 8.9 1.0
CD B:ARG204 4.1 9.6 1.0
OE1 B:GLU203 4.2 22.9 1.0
CB A:SER109 4.2 9.3 1.0
CE1 B:HIS200 4.3 18.1 1.0
CD B:GLU203 4.3 20.5 1.0
CE1 A:HIS111 4.4 12.1 1.0
OE2 B:GLU203 4.6 22.2 1.0
CZ B:ARG204 4.6 8.2 1.0
NE B:ARG204 4.8 8.7 1.0
O B:HOH798 4.8 20.7 0.5
OG A:SER109 4.8 8.7 1.0
NZ B:LYS245 4.9 23.3 1.0
ND1 B:HIS200 4.9 18.2 1.0
CG B:GLU203 4.9 16.0 1.0

Iodine binding site 10 out of 19 in 4gog

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Iodine binding site 10 out of 19 in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex


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 the Ges-1 Imipenem Acyl-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I503

b:17.5
occ:0.53
O B:HOH671 3.0 23.7 1.0
CA B:GLY139 4.1 12.6 1.0
CE B:LYS160 4.1 17.5 0.4
CD B:PRO140 4.1 11.5 1.0
CB B:LEU134 4.1 10.5 1.0
N B:ARG135 4.2 11.1 1.0
C B:LEU134 4.3 11.6 1.0
CA B:ARG135 4.4 11.8 0.8
O B:LEU134 4.4 12.8 1.0
CD B:LYS160 4.4 14.2 0.6
CA B:ARG135 4.4 12.3 0.2
CB B:LYS160 4.7 11.8 0.6
NZ B:LYS160 4.7 17.8 0.4
CG B:ARG135 4.8 14.8 0.2
CB B:LYS160 4.8 12.6 0.4
N B:GLY139 4.9 13.3 1.0
CA B:LEU134 4.9 10.4 1.0
CB B:ARG135 5.0 12.1 0.8

Reference:

C.A.Smith, H.Frase, M.Toth, M.Kumarasiri, K.Wiafe, J.Munoz, S.Mobashery, S.B.Vakulenko. Structural Basis For Progression Toward the Carbapenemase Activity in the Ges Family of Beta-Lactamases. J.Am.Chem.Soc. V. 134 19512 2012.
ISSN: ISSN 0002-7863
PubMed: 23148776
DOI: 10.1021/JA308197J
Page generated: Sun Dec 13 19:32:50 2020

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