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Chlorine in PDB 6sul: Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami

Enzymatic activity of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami

All present enzymatic activity of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami:
2.7.1.230;

Protein crystallography data

The structure of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami, PDB code: 6sul was solved by G.P.Bourenkov, Y.A.Mokrushina, S.S.Terekhov, I.V.Smirnov, A.G.Gabibov, S.Altman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 99.78 / 1.35
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.340, 76.770, 101.200, 89.95, 99.62, 91.44
R / Rfree (%) 14.9 / 18.8

Other elements in 6sul:

The structure of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami (pdb code 6sul). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami, PDB code: 6sul:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 6sul

Go back to Chlorine Binding Sites List in 6sul
Chlorine binding site 1 out of 10 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:42.1
occ:1.00
 N A:PHE31 3.2 26.4 1.0
NH2 A:ARG26 3.2 31.4 1.0
NH1 A:ARG26 3.6 30.7 1.0
CB A:PHE31 3.7 25.4 1.0
O A:ILE29 3.8 31.6 1.0
CA A:HIS30 3.9 27.0 1.0
CZ A:ARG26 3.9 32.3 1.0
C A:HIS30 4.0 25.5 1.0
CA A:PHE31 4.1 26.3 1.0
O A:HOH662 4.5 45.3 1.0
C A:ILE29 4.5 28.4 1.0
N A:HIS30 4.6 26.5 1.0
O A:HOH610 4.8 45.2 1.0
CD2 A:TYR40 4.9 27.3 1.0
CE2 A:TYR40 5.0 26.2 1.0

Chlorine binding site 2 out of 10 in 6sul

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Chlorine binding site 2 out of 10 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:40.9
occ:1.00
 N A:ASP124 3.2 23.5 1.0
O A:HOH744 3.3 40.9 1.0
CB A:ASN123 3.5 25.0 1.0
CG A:ASP124 3.5 27.3 1.0
O A:HOH574 3.6 33.6 1.0
CB A:ASP124 3.6 24.8 1.0
OD2 A:ASP124 3.8 34.0 1.0
OD1 A:ASP124 3.9 29.5 1.0
CA A:ASN123 4.0 23.0 1.0
CA A:ASP124 4.0 25.2 1.0
C A:ASN123 4.1 22.2 1.0
CG A:ASN123 4.5 28.3 1.0

Chlorine binding site 3 out of 10 in 6sul

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Chlorine binding site 3 out of 10 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:49.1
occ:1.00
 O A:HOH762 3.0 41.5 1.0
N A:ILE93 3.2 27.6 1.0
N A:ASP92 3.3 35.4 1.0
O A:HOH569 3.6 34.2 1.0
CB A:ASP92 3.7 41.3 1.0
CA A:ASP92 3.8 35.5 1.0
O A:ILE93 3.9 29.2 1.0
C A:ASP92 4.0 29.8 1.0
CD2 A:LEU65 4.0 28.9 1.0
CB A:ILE93 4.0 29.5 1.0
CA A:ILE93 4.1 27.6 1.0
CG1 A:ILE93 4.2 29.7 1.0
C A:ARG91 4.2 35.0 1.0
CB A:ARG91 4.3 37.2 0.5
CB A:ARG91 4.3 35.9 0.5
CA A:ARG91 4.3 35.6 0.5
CA A:ARG91 4.3 36.0 0.5
C A:ILE93 4.5 28.5 1.0
CD1 A:ILE93 4.6 31.4 1.0
CD1 A:LEU65 4.8 27.1 1.0
CG A:LEU65 4.9 27.3 1.0
CG A:ASP92 4.9 52.9 1.0
CG A:ARG91 5.0 38.3 0.5

Chlorine binding site 4 out of 10 in 6sul

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Chlorine binding site 4 out of 10 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:34.1
occ:1.00
 NH1 B:ARG165 3.2 29.5 1.0
N B:ARG165 3.3 23.3 1.0
O B:HOH679 3.4 38.0 1.0
N B:LEU164 3.4 21.2 1.0
CG B:ARG165 3.6 30.3 1.0
CB B:ARG165 3.7 27.6 1.0
C B:LYS163 3.9 22.2 1.0
CD B:ARG165 4.0 31.3 1.0
CA B:LYS163 4.1 21.9 1.0
CA B:ARG165 4.1 25.5 1.0
CA B:LEU164 4.2 20.7 1.0
C B:LEU164 4.2 21.5 1.0
O B:LEU162 4.2 24.6 1.0
CZ B:ARG165 4.3 31.6 1.0
CB B:LEU164 4.4 21.4 1.0
O B:HOH525 4.4 42.1 1.0
O B:HOH729 4.4 38.0 1.0
NE B:ARG165 4.6 32.0 1.0
O B:LYS163 4.6 22.7 1.0
OD1 B:ASP180 4.7 28.5 1.0
CB B:LYS163 5.0 26.3 1.0
O B:HOH609 5.0 40.6 1.0

Chlorine binding site 5 out of 10 in 6sul

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Chlorine binding site 5 out of 10 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:50.0
occ:1.00
 N B:ILE93 3.3 26.2 1.0
N B:ASP92 3.3 28.1 1.0
O B:ILE93 3.9 30.1 1.0
O B:HOH509 3.9 46.1 1.0
CA B:ASP92 3.9 32.8 1.0
CB B:ASP92 4.0 34.4 1.0
C B:ASP92 4.0 26.6 1.0
C B:ARG91 4.1 27.4 1.0
CB B:ARG91 4.1 33.8 1.0
CA B:ILE93 4.2 27.1 1.0
CB B:ILE93 4.2 27.7 1.0
CD2 B:LEU65 4.2 34.6 1.0
CA B:ARG91 4.2 29.4 1.0
C B:ILE93 4.5 26.8 1.0
CG1 B:ILE93 4.5 29.8 1.0
CG B:ARG91 4.7 37.9 1.0
CD1 B:LEU65 4.8 35.5 1.0
CD B:ARG91 4.8 45.3 1.0
CD1 B:ILE93 4.9 32.8 1.0
CG B:LEU65 5.0 32.9 1.0

Chlorine binding site 6 out of 10 in 6sul

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Chlorine binding site 6 out of 10 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:38.4
occ:1.00
 N C:PHE31 3.1 20.2 1.0
NH2 C:ARG26 3.2 30.9 1.0
NH1 C:ARG26 3.6 29.5 1.0
CB C:PHE31 3.8 22.5 1.0
CA C:HIS30 3.8 21.5 1.0
O C:ILE29 3.8 26.3 1.0
CZ C:ARG26 3.8 28.9 1.0
C C:HIS30 3.9 20.4 1.0
CA C:PHE31 4.1 20.9 1.0
O C:HOH688 4.4 58.7 1.0
C C:ILE29 4.5 23.8 1.0
N C:HIS30 4.5 20.6 1.0
CD2 C:TYR40 4.8 21.3 1.0
CE2 C:TYR40 4.9 20.4 1.0
CB C:HIS30 5.0 26.6 1.0

Chlorine binding site 7 out of 10 in 6sul

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Chlorine binding site 7 out of 10 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:31.5
occ:1.00
 O C:HOH569 2.7 27.8 1.0
NH1 C:ARG136 3.0 28.0 1.0
N C:SER80 3.1 17.8 1.0
NH2 C:ARG136 3.2 22.5 1.0
CZ C:ARG136 3.6 24.0 1.0
NZ C:LYS214 3.6 41.4 1.0
CB C:SER80 3.6 19.1 1.0
O C:GLY78 3.6 20.7 1.0
CA C:LEU79 3.8 17.5 1.0
C C:LEU79 3.9 18.9 1.0
O C:HOH765 3.9 42.3 1.0
CA C:SER80 3.9 17.7 1.0
CE2 C:TYR133 4.1 17.4 1.0
CD1 C:LEU79 4.3 21.7 1.0
CD2 C:TYR133 4.4 17.7 1.0
O C:ILE215 4.5 20.0 1.0
C C:GLY78 4.6 19.1 1.0
CG C:LEU79 4.6 18.6 1.0
N C:LEU79 4.7 18.0 1.0
CB C:LEU79 4.7 17.4 1.0
CE C:LYS214 4.8 37.6 1.0
NE C:ARG136 4.9 25.8 1.0
O C:HOH643 4.9 34.0 1.0
OG C:SER80 5.0 22.2 1.0

Chlorine binding site 8 out of 10 in 6sul

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Chlorine binding site 8 out of 10 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:34.4
occ:1.00
 N D:ARG165 3.2 20.7 1.0
NH1 D:ARG165 3.2 26.8 1.0
O D:HOH1436 3.3 37.0 1.0
N D:LEU164 3.4 18.6 1.0
CG D:ARG165 3.5 26.4 1.0
CB D:ARG165 3.7 24.8 1.0
CD D:ARG165 3.8 29.2 1.0
C D:LYS163 3.9 18.7 1.0
CA D:ARG165 4.1 20.9 1.0
CA D:LYS163 4.1 19.8 1.0
CA D:LEU164 4.1 20.1 1.0
C D:LEU164 4.2 20.2 1.0
O D:LEU162 4.2 21.6 1.0
CZ D:ARG165 4.3 26.3 1.0
O D:HOH1243 4.3 41.6 1.0
CB D:LEU164 4.3 20.5 1.0
NE D:ARG165 4.5 29.5 1.0
O D:HOH1453 4.6 34.2 1.0
O D:LYS163 4.6 21.9 1.0
OD1 D:ASP180 4.8 26.8 1.0

Chlorine binding site 9 out of 10 in 6sul

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Chlorine binding site 9 out of 10 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl404

b:53.3
occ:1.00
 N D:GLU274 3.6 23.5 1.0
CA D:GLU274 3.9 23.3 1.0
CB D:GLU274 4.0 24.5 1.0
O D:HOH1381 4.0 45.2 1.0
CB D:ASP273 4.1 28.2 1.0
C D:ASP273 4.1 21.6 1.0
OE1 D:GLU274 4.4 29.9 1.0
CA D:ASP273 4.6 24.9 1.0
O D:ASP273 4.7 22.5 1.0
O D:HOH1231 4.8 35.7 1.0
O D:HOH1489 4.8 34.1 1.0

Chlorine binding site 10 out of 10 in 6sul

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Chlorine binding site 10 out of 10 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl405

b:24.7
occ:1.00
 O D:HOH1475 3.2 31.4 1.0
N D:GLN193 3.3 22.3 1.0
NE2 D:GLN193 3.3 25.7 1.0
CB D:ASN192 3.7 22.9 1.0
CG D:GLN193 3.8 26.5 1.0
CA D:ASN192 3.9 22.0 1.0
CB D:GLN193 4.0 24.8 1.0
C D:ASN192 4.0 22.4 1.0
CD D:GLN193 4.1 27.9 1.0
CA D:GLN193 4.2 23.9 1.0
CG D:ASN192 4.8 23.6 1.0

Reference:

S.S.Terekhov, Y.A.Mokrushina, A.S.Nazarov, A.Zlobin, A.Zalevsky, G.Bourenkov, A.Golovin, A.Belogurov Jr., I.A.Osterman, A.A.Kulikova, V.A.Mitkevich, H.J.Lou, B.E.Turk, M.Wilmanns, I.V.Smirnov, S.Altman, A.G.Gabibov. A Kinase Bioscavenger Provides Antibiotic Resistance By Extremely Tight Substrate Binding. Sci Adv V. 6 Z9861 2020.
ISSN: ESSN 2375-2548
PubMed: 32637600
DOI: 10.1126/SCIADV.AAZ9861
Page generated: Mon Jul 29 15:10:29 2024

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