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Chlorine in PDB 4ebk: Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound

Protein crystallography data

The structure of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound, PDB code: 4ebk was solved by P.J.Stogios, A.Dong, G.Minasov, E.Evdokimova, O.Egorova, V.Yim, M.Kudritska, P.Courvalin, A.Savchenko, W.F.Anderson, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.89 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.906, 84.451, 98.762, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 22.1

Other elements in 4ebk:

The structure of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound also contains other interesting chemical elements:

Iodine (I) 14 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound (pdb code 4ebk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 17 binding sites of Chlorine where determined in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound, PDB code: 4ebk:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 17 in 4ebk

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Chlorine binding site 1 out of 17 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:47.3
occ:1.00
OE1 A:GLU179 2.8 50.4 1.0
O B:HOH631 3.1 53.1 1.0
O A:HOH511 3.2 48.5 1.0
CA A:GLN176 3.7 25.2 1.0
CD A:GLU179 3.8 43.3 1.0
N A:GLN176 4.0 29.1 1.0
CG A:ARG175 4.0 25.8 1.0
CB A:GLN176 4.0 28.6 1.0
O A:ARG175 4.1 21.4 1.0
CB A:GLU179 4.1 28.0 1.0
C A:ARG175 4.1 27.5 1.0
NE2 A:HIS173 4.4 29.6 1.0
CG A:GLN176 4.4 30.9 1.0
OE2 A:GLU179 4.6 46.9 1.0
CG A:GLU179 4.6 35.1 1.0
CB A:ARG175 4.6 25.6 1.0
NH1 A:ARG175 4.7 26.9 1.0
O B:HOH630 4.9 58.5 1.0
C A:GLN176 5.0 23.1 1.0

Chlorine binding site 2 out of 17 in 4ebk

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Chlorine binding site 2 out of 17 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl310

b:66.6
occ:1.00
NZ A:LYS156 2.2 55.4 1.0
CL A:CL319 3.0 56.4 1.0
CD A:GLN152 3.4 32.0 1.0
O A:HOH457 3.4 46.6 1.0
NE2 A:GLN152 3.5 29.9 1.0
NE2 B:GLN152 3.6 25.9 1.0
OE1 B:GLN152 3.7 30.0 1.0
CE A:LYS156 3.7 50.4 1.0
OE1 A:GLN152 3.7 29.2 1.0
CG A:GLN152 3.7 27.1 1.0
CB A:GLN152 3.8 24.2 1.0
O A:LEU199 3.9 24.7 1.0
CD B:GLN152 3.9 31.0 1.0
CD2 A:LEU199 4.0 39.6 1.0
CD A:LYS156 4.2 43.6 1.0
CG A:LYS156 4.3 38.5 1.0
CA A:GLN152 4.7 21.6 1.0
CA A:LEU199 4.7 25.8 1.0
C A:LEU199 4.7 25.6 1.0
O A:GLN152 4.8 20.8 1.0
CB A:LEU199 5.0 24.8 1.0

Chlorine binding site 3 out of 17 in 4ebk

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Chlorine binding site 3 out of 17 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl311

b:62.8
occ:1.00
O A:HOH524 3.1 35.1 1.0
CD2 A:LEU157 3.9 37.9 1.0
O A:HOH627 4.1 32.5 1.0
CG2 A:THR153 4.1 25.7 1.0
CG A:LEU157 4.1 32.6 1.0
CB A:LYS156 4.2 31.5 1.0
CD A:LYS156 4.3 43.6 1.0
O B:HOH583 4.5 59.4 1.0
O A:THR153 4.6 29.8 1.0
CD1 A:LEU157 4.6 22.7 1.0
O A:HOH575 4.7 53.8 1.0
CA A:THR153 4.8 22.4 1.0
CB A:THR153 4.9 25.9 1.0
CG A:LYS156 4.9 38.5 1.0
O A:HOH479 5.0 35.0 1.0

Chlorine binding site 4 out of 17 in 4ebk

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Chlorine binding site 4 out of 17 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl319

b:56.4
occ:1.00
CL A:CL310 3.0 66.6 1.0
O B:HOH401 3.3 34.1 1.0
CD B:LYS156 3.4 41.8 1.0
NZ A:LYS156 3.5 55.4 1.0
CD B:GLN152 3.7 31.0 1.0
OE1 A:GLN152 3.8 29.2 1.0
OE1 B:GLN152 3.9 30.0 1.0
NE2 B:GLN152 3.9 25.9 1.0
CE B:LYS156 3.9 51.4 1.0
CB B:GLN152 4.0 27.6 1.0
NZ B:LYS156 4.0 55.4 1.0
CG B:LYS156 4.0 32.6 1.0
CG B:GLN152 4.1 26.7 1.0
NE2 A:GLN152 4.1 29.9 1.0
CD2 B:LEU199 4.2 33.9 1.0
CD A:GLN152 4.2 32.0 1.0
O B:LEU199 4.5 26.1 1.0
CE A:LYS156 4.7 50.4 1.0
O B:GLN152 4.8 24.4 1.0
CA B:GLN152 4.9 24.8 1.0
O A:HOH457 4.9 46.6 1.0

Chlorine binding site 5 out of 17 in 4ebk

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Chlorine binding site 5 out of 17 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl312

b:67.8
occ:1.00
O A:HOH627 3.9 32.5 1.0
I A:IOD306 3.9 42.8 0.5
N A:ALA131 3.9 24.5 1.0
CA A:ALA131 4.0 27.2 1.0
CB A:ALA131 4.1 23.0 1.0
CB A:GLU130 4.1 34.4 1.0
O A:ASP127 4.2 31.1 1.0
OE2 A:GLU130 4.2 44.9 1.0
C A:GLU130 4.3 27.6 1.0
CG2 A:THR153 4.3 25.7 1.0
CG A:LYS134 4.4 36.5 1.0
C61 A:TOY301 4.5 43.5 1.0
N61 A:TOY301 4.6 46.9 1.0
O A:HOH617 4.6 66.0 1.0
O A:GLU130 4.7 28.7 1.0
CA A:GLU130 4.9 28.6 1.0

Chlorine binding site 6 out of 17 in 4ebk

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Chlorine binding site 6 out of 17 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl313

b:52.6
occ:1.00
O A:HOH633 2.5 45.4 1.0
O A:HOH426 3.0 36.8 1.0
O A:HOH510 3.2 42.4 0.5
O A:HOH510 3.3 44.0 0.5
CG A:MSE240 4.0 29.0 1.0
CB A:MSE240 4.1 29.3 1.0
N A:GLU246 4.2 36.5 1.0
CE A:MSE240 4.2 31.8 1.0
CB A:GLU246 4.2 46.9 1.0
CA A:MSE240 4.3 30.1 1.0
CB A:LEU245 4.4 31.2 1.0
O A:MSE240 4.5 33.0 1.0
CB A:LEU222 4.5 33.2 1.0
CD2 A:LEU245 4.5 35.0 1.0
CA A:GLU246 4.6 41.2 1.0
CG A:LEU245 4.8 36.1 1.0
O A:LEU222 4.8 35.6 1.0
C A:MSE240 4.9 31.7 1.0
C A:LEU245 4.9 34.8 1.0
O A:HOH445 5.0 24.6 1.0
SE A:MSE240 5.0 36.5 1.0

Chlorine binding site 7 out of 17 in 4ebk

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Chlorine binding site 7 out of 17 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl314

b:65.6
occ:1.00
O A:HOH564 3.4 49.0 1.0
N A:ALA120 3.5 26.2 1.0
CB A:ALA120 3.9 27.5 1.0
CA A:PRO119 4.1 33.4 1.0
C A:PRO119 4.3 27.9 1.0
CB A:PRO119 4.3 29.2 1.0
CA A:ALA120 4.3 27.5 1.0
CB A:PRO92 4.5 25.2 1.0
CG A:PRO92 4.7 27.7 1.0
O A:HOH626 4.7 41.1 1.0
O A:HOH551 4.8 61.7 1.0
O A:HOH557 4.8 49.0 1.0

Chlorine binding site 8 out of 17 in 4ebk

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Chlorine binding site 8 out of 17 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl315

b:66.8
occ:1.00
O B:HOH564 3.2 43.2 1.0
CD1 A:LEU244 3.8 43.9 1.0
CB A:ALA242 3.9 39.5 1.0
CG A:ARG238 3.9 62.6 1.0
CD2 A:LEU239 4.0 34.0 1.0
O A:ARG238 4.4 31.2 1.0
O B:HOH481 4.6 30.8 1.0
C A:ARG238 4.6 38.0 1.0
CA A:LEU239 4.7 32.2 1.0
CD A:ARG238 4.7 75.9 1.0
N A:LEU239 4.8 32.1 1.0
CG A:LEU239 4.8 36.5 1.0
CG A:LEU244 4.9 43.8 1.0
CB A:ARG238 4.9 49.4 1.0

Chlorine binding site 9 out of 17 in 4ebk

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Chlorine binding site 9 out of 17 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl316

b:38.4
occ:1.00
O B:HOH623 3.1 35.9 1.0
N A:ARG175 3.4 26.2 1.0
CE B:LYS134 3.6 47.1 1.0
CD B:LYS134 3.7 41.7 1.0
CB A:ARG175 3.8 25.6 1.0
CD2 A:HIS173 3.8 32.2 1.0
N A:ALA174 3.9 20.5 1.0
CB A:ALA174 4.0 20.3 1.0
O B:HOH573 4.1 23.5 1.0
CA A:ARG175 4.2 23.7 1.0
CB A:HIS173 4.2 27.5 1.0
CA A:ALA174 4.2 25.7 1.0
C A:ALA174 4.3 24.4 1.0
O A:HOH605 4.3 30.1 1.0
CG A:HIS173 4.4 31.3 1.0
O B:HOH410 4.4 33.1 1.0
NZ B:LYS134 4.5 46.6 1.0
C A:HIS173 4.6 28.7 1.0
CL A:CL318 4.8 60.4 1.0
OE1 B:GLN149 5.0 28.8 1.0
I B:IOD309 5.0 35.7 0.5

Chlorine binding site 10 out of 17 in 4ebk

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Chlorine binding site 10 out of 17 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl317

b:64.8
occ:1.00
O B:HOH621 3.1 42.5 1.0
NZ A:LYS134 3.3 51.8 1.0
NH2 B:ARG30 3.5 35.5 1.0
NH1 B:ARG30 3.8 36.3 1.0
OG B:SER27 4.0 50.4 1.0
CZ B:ARG30 4.1 37.0 1.0
CE A:LYS134 4.2 52.5 1.0
N B:SER27 4.3 40.6 1.0
O B:HOH577 4.4 31.8 1.0
O B:HOH587 4.4 53.4 1.0
CL B:CL301 4.5 45.2 1.0
CA B:GLY26 4.5 33.5 1.0
O B:HOH402 4.5 47.1 1.0
CB B:HIS173 4.6 33.0 1.0
C B:GLY26 4.7 36.2 1.0
O B:HOH584 4.9 45.3 1.0
CB B:SER27 5.0 44.8 1.0

Reference:

P.J.Stogios, A.Dong, G.Minasov, E.Evdokimova, O.Egorova, V.Yim, M.Kudritska, P.Courvalin, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')-Iib, Tobramycin-Bound To Be Published.
Page generated: Sat Dec 12 10:34:05 2020

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