Magnesium 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:

Chlorine (Cl) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami, PDB code: 6sul:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6sul

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Magnesium binding site 1 out of 8 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg401

b:19.8
occ:1.00
 O1B A:ANP407 2.0 21.0 1.0
O1G A:ANP407 2.0 20.6 1.0
OD2 A:ASP219 2.1 18.9 1.0
O A:HOH523 2.1 21.6 1.0
O A:HOH545 2.1 20.3 1.0
OD1 A:ASP219 2.3 20.1 1.0
CG A:ASP219 2.5 18.4 1.0
PG A:ANP407 3.1 21.1 1.0
PB A:ANP407 3.2 19.9 1.0
N3B A:ANP407 3.5 20.6 1.0
MG A:MG402 3.6 18.3 0.2
O3G A:ANP407 3.7 20.6 1.0
OD2 A:ASP222 3.8 22.7 1.0
CB A:ASP219 4.0 18.5 1.0
OD2 A:ASP202 4.1 21.3 1.0
O3A A:ANP407 4.2 20.4 1.0
CB A:ASP221 4.3 21.7 1.0
NAD A:UAM406 4.3 22.0 1.0
O2B A:ANP407 4.3 22.6 1.0
NZ A:LYS52 4.3 23.0 1.0
ND2 A:ASN37 4.4 23.3 1.0
O2G A:ANP407 4.4 20.6 1.0
OD2 A:ASP221 4.5 23.6 1.0
CB A:GLU36 4.5 27.2 1.0
O1A A:ANP407 4.6 21.1 1.0
O2A A:ANP407 4.6 20.3 1.0
PA A:ANP407 4.6 20.1 1.0
OAI A:UAM406 4.7 21.3 1.0
CG A:GLU36 4.7 31.2 1.0
O A:ASP219 4.8 20.0 1.0
ND2 A:ASN207 4.9 18.2 1.0
CA A:ASP219 4.9 17.7 1.0
CG A:ASP222 5.0 21.3 1.0
CG A:ASP221 5.0 21.9 1.0

Magnesium binding site 2 out of 8 in 6sul

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Magnesium binding site 2 out of 8 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg402

b:18.3
occ:0.20
 O3G A:ANP407 1.9 20.6 1.0
O1A A:ANP407 1.9 21.1 1.0
OD2 A:ASP219 2.0 18.9 1.0
OD1 A:ASN207 2.0 18.6 1.0
PG A:ANP407 2.8 21.1 1.0
O A:HOH664 2.9 24.7 1.0
CG A:ASN207 2.9 17.6 1.0
CG A:ASP219 3.0 18.4 1.0
N3B A:ANP407 3.1 20.6 1.0
PA A:ANP407 3.1 20.1 1.0
ND2 A:ASN207 3.3 18.2 1.0
CB A:ASP219 3.4 18.5 1.0
O1G A:ANP407 3.5 20.6 1.0
MG A:MG401 3.6 19.8 1.0
O3A A:ANP407 3.7 20.4 1.0
PB A:ANP407 3.7 19.9 1.0
O2A A:ANP407 3.8 20.3 1.0
O1B A:ANP407 3.8 21.0 1.0
CE1 A:HIS204 3.9 18.9 1.0
NE2 A:HIS204 3.9 19.1 1.0
OD1 A:ASP219 4.0 20.1 1.0
O2G A:ANP407 4.2 20.6 1.0
CB A:ASN207 4.3 18.0 1.0
O5' A:ANP407 4.4 20.1 1.0
O A:GLY206 4.4 21.5 1.0
O A:HOH545 4.5 20.3 1.0
OD2 A:ASP202 4.6 21.3 1.0
CA A:ASN207 4.7 18.4 1.0
C A:GLY206 4.7 19.4 1.0
O A:HOH733 4.8 25.1 1.0
O3' A:ANP407 4.8 23.8 1.0
C5' A:ANP407 4.8 20.6 1.0
CA A:ASP219 4.9 17.7 1.0
N A:ASN207 4.9 17.6 1.0
O A:HOH530 5.0 23.6 1.0

Magnesium binding site 3 out of 8 in 6sul

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Magnesium binding site 3 out of 8 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg401

b:18.5
occ:1.00
 O3G B:ANP406 2.0 19.0 1.0
O B:HOH586 2.0 20.1 1.0
O2B B:ANP406 2.0 19.5 1.0
OD2 B:ASP219 2.1 19.6 1.0
O B:HOH527 2.1 19.3 1.0
OD1 B:ASP219 2.3 20.0 1.0
CG B:ASP219 2.5 18.3 1.0
PG B:ANP406 3.1 20.0 1.0
PB B:ANP406 3.2 19.1 1.0
N3B B:ANP406 3.5 19.2 1.0
MG B:MG402 3.6 16.8 0.2
O2G B:ANP406 3.7 20.3 1.0
OD2 B:ASP222 3.8 21.7 1.0
CB B:ASP219 4.0 19.1 1.0
OD2 B:ASP202 4.1 19.9 1.0
O3A B:ANP406 4.2 19.8 1.0
NAD B:UAM405 4.2 21.6 1.0
CB B:ASP221 4.3 20.7 1.0
NZ B:LYS52 4.3 22.5 1.0
O1B B:ANP406 4.4 21.1 1.0
O1G B:ANP406 4.4 21.1 1.0
ND2 B:ASN37 4.4 21.0 1.0
OD2 B:ASP221 4.4 21.9 1.0
O1A B:ANP406 4.5 20.3 1.0
CB B:GLU36 4.6 22.9 1.0
O2A B:ANP406 4.6 22.7 1.0
OAI B:UAM405 4.6 21.1 1.0
PA B:ANP406 4.6 20.1 1.0
CG B:GLU36 4.7 26.8 1.0
O B:ASP219 4.8 21.2 1.0
ND2 B:ASN207 4.9 19.9 1.0
CA B:ASP219 4.9 20.5 1.0
CG B:ASP221 5.0 21.1 1.0
CG B:ASP222 5.0 19.3 1.0

Magnesium binding site 4 out of 8 in 6sul

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Magnesium binding site 4 out of 8 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg402

b:16.8
occ:0.20
 O1A B:ANP406 1.9 20.3 1.0
OD2 B:ASP219 1.9 19.6 1.0
O2G B:ANP406 1.9 20.3 1.0
OD1 B:ASN207 2.0 19.6 1.0
PG B:ANP406 2.9 20.0 1.0
CG B:ASP219 2.9 18.3 1.0
O B:HOH663 2.9 24.1 1.0
CG B:ASN207 3.0 19.5 1.0
N3B B:ANP406 3.1 19.2 1.0
PA B:ANP406 3.1 20.1 1.0
ND2 B:ASN207 3.3 19.9 1.0
CB B:ASP219 3.4 19.1 1.0
O3G B:ANP406 3.5 19.0 1.0
MG B:MG401 3.6 18.5 1.0
O2A B:ANP406 3.7 22.7 1.0
O3A B:ANP406 3.7 19.8 1.0
PB B:ANP406 3.8 19.1 1.0
O2B B:ANP406 3.8 19.5 1.0
CE1 B:HIS204 3.8 20.9 1.0
NE2 B:HIS204 3.8 19.1 1.0
OD1 B:ASP219 4.0 20.0 1.0
O1G B:ANP406 4.2 21.1 1.0
CB B:ASN207 4.3 20.8 1.0
O5' B:ANP406 4.4 22.0 1.0
O B:GLY206 4.4 23.2 1.0
O B:HOH527 4.5 19.3 1.0
OD2 B:ASP202 4.6 19.9 1.0
CA B:ASN207 4.7 21.3 1.0
C B:GLY206 4.8 21.5 1.0
O3' B:ANP406 4.8 24.9 1.0
O B:HOH730 4.8 24.1 1.0
C5' B:ANP406 4.8 20.4 1.0
CA B:ASP219 4.9 20.5 1.0
O B:HOH540 5.0 22.2 1.0
N B:ASN207 5.0 20.1 1.0
ND1 B:HIS204 5.0 20.6 1.0

Magnesium binding site 5 out of 8 in 6sul

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Magnesium binding site 5 out of 8 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
C:Mg401

b:15.7
occ:1.00
 O1G C:ANP406 1.9 16.7 1.0
O1B C:ANP406 2.0 17.8 1.0
O C:HOH551 2.1 18.0 1.0
O C:HOH540 2.1 16.4 1.0
OD2 C:ASP219 2.1 14.6 1.0
OD1 C:ASP219 2.3 16.6 1.0
CG C:ASP219 2.5 15.3 1.0
PG C:ANP406 3.1 17.2 1.0
PB C:ANP406 3.2 16.7 1.0
N3B C:ANP406 3.5 17.0 1.0
MG C:MG402 3.7 13.0 0.2
O3G C:ANP406 3.7 18.3 1.0
OD2 C:ASP222 3.8 19.1 1.0
CB C:ASP219 4.0 14.8 1.0
OD2 C:ASP202 4.1 16.8 1.0
O3A C:ANP406 4.2 16.1 1.0
NAD C:UAM405 4.3 20.4 1.0
CB C:ASP221 4.3 17.8 1.0
NZ C:LYS52 4.3 18.5 0.5
NZ C:LYS52 4.3 19.8 0.5
O2B C:ANP406 4.4 17.7 1.0
O2G C:ANP406 4.4 17.5 1.0
ND2 C:ASN37 4.5 18.9 1.0
OD2 C:ASP221 4.5 18.6 1.0
O1A C:ANP406 4.5 16.6 1.0
CB C:GLU36 4.5 23.1 1.0
PA C:ANP406 4.6 16.6 1.0
OAI C:UAM405 4.6 19.9 1.0
O2A C:ANP406 4.6 16.5 1.0
CG C:GLU36 4.7 26.4 1.0
O C:ASP219 4.8 16.0 1.0
ND2 C:ASN207 4.9 15.2 1.0
CA C:ASP219 4.9 14.1 1.0
CG C:ASP221 4.9 16.7 1.0
CG C:ASP222 4.9 18.6 1.0

Magnesium binding site 6 out of 8 in 6sul

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Magnesium binding site 6 out of 8 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg402

b:13.0
occ:0.20
 O1A C:ANP406 1.8 16.6 1.0
O3G C:ANP406 1.9 18.3 1.0
OD1 C:ASN207 2.0 15.5 1.0
OD2 C:ASP219 2.1 14.6 1.0
O C:HOH717 2.8 21.0 1.0
PG C:ANP406 2.9 17.2 1.0
CG C:ASN207 3.0 13.7 1.0
PA C:ANP406 3.0 16.6 1.0
CG C:ASP219 3.0 15.3 1.0
N3B C:ANP406 3.1 17.0 1.0
ND2 C:ASN207 3.3 15.2 1.0
CB C:ASP219 3.5 14.8 1.0
O1G C:ANP406 3.6 16.7 1.0
O3A C:ANP406 3.7 16.1 1.0
MG C:MG401 3.7 15.7 1.0
O2A C:ANP406 3.7 16.5 1.0
PB C:ANP406 3.8 16.7 1.0
CE1 C:HIS204 3.9 17.1 1.0
NE2 C:HIS204 3.9 16.6 1.0
O1B C:ANP406 3.9 17.8 1.0
OD1 C:ASP219 4.1 16.6 1.0
O2G C:ANP406 4.2 17.5 1.0
O5' C:ANP406 4.3 16.5 1.0
O C:GLY206 4.3 16.8 1.0
CB C:ASN207 4.3 14.5 1.0
O C:HOH540 4.6 16.4 1.0
OD2 C:ASP202 4.7 16.8 1.0
C C:GLY206 4.7 14.9 1.0
CA C:ASN207 4.7 13.8 1.0
O3' C:ANP406 4.7 19.4 1.0
C5' C:ANP406 4.7 18.0 1.0
O C:HOH783 4.7 21.6 1.0
N C:ASN207 4.9 14.4 1.0
O C:HOH544 4.9 19.9 1.0
C3' C:ANP406 4.9 18.2 1.0
CA C:ASP219 5.0 14.1 1.0

Magnesium binding site 7 out of 8 in 6sul

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Magnesium binding site 7 out of 8 in the Amicoumacin Kinase Amin in Complex with Amp-Pnp, MG2+ and Ami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
D:Mg401

b:19.2
occ:1.00
 O D:HOH1315 2.0 20.5 1.0
O3G D:ANP407 2.0 19.6 1.0
O2B D:ANP407 2.0 19.7 1.0
O D:HOH1261 2.1 19.5 1.0
OD2 D:ASP219 2.1 18.0 1.0
OD1 D:ASP219 2.3 19.5 1.0
CG D:ASP219 2.5 17.6 1.0
PG D:ANP407 3.1 20.7 1.0
PB D:ANP407 3.2 20.5 1.0
N3B D:ANP407 3.5 21.4 1.0
MG D:MG402 3.6 20.9 0.2
O2G D:ANP407 3.8 20.3 1.0
OD2 D:ASP222 3.8 22.0 1.0
CB D:ASP219 4.0 18.3 1.0
OD2 D:ASP202 4.1 19.1 1.0
O3A D:ANP407 4.2 21.0 1.0
NAD D:UAM406 4.2 20.4 1.0
CB D:ASP221 4.3 21.6 1.0
NZ D:LYS52 4.3 24.1 1.0
O1B D:ANP407 4.4 23.1 1.0
O1G D:ANP407 4.4 19.6 1.0
ND2 D:ASN37 4.5 23.9 1.0
O1A D:ANP407 4.5 20.8 1.0
OD2 D:ASP221 4.5 23.6 1.0
O2A D:ANP407 4.6 21.4 1.0
PA D:ANP407 4.6 20.6 1.0
OAI D:UAM406 4.7 20.8 1.0
CB D:GLU36 4.7 24.7 1.0
O D:ASP219 4.7 18.4 1.0
CG D:GLU36 4.8 31.6 1.0
ND2 D:ASN207 4.8 18.3 1.0
CA D:ASP219 4.9 18.6 1.0
CG D:ASP222 4.9 20.4 1.0
CG D:ASP221 5.0 22.8 1.0

Magnesium binding site 8 out of 8 in 6sul

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg402

b:20.9
occ:0.20
 O1A D:ANP407 1.8 20.8 1.0
O2G D:ANP407 1.9 20.3 1.0
OD2 D:ASP219 2.0 18.0 1.0
OD1 D:ASN207 2.0 18.4 1.0
PG D:ANP407 2.9 20.7 1.0
O D:HOH1371 2.9 25.7 1.0
CG D:ASN207 3.0 17.0 1.0
CG D:ASP219 3.0 17.6 1.0
N3B D:ANP407 3.0 21.4 1.0
PA D:ANP407 3.0 20.6 1.0
ND2 D:ASN207 3.3 18.3 1.0
CB D:ASP219 3.4 18.3 1.0
O3G D:ANP407 3.5 19.6 1.0
MG D:MG401 3.6 19.2 1.0
O3A D:ANP407 3.7 21.0 1.0
O2A D:ANP407 3.7 21.4 1.0
PB D:ANP407 3.8 20.5 1.0
O2B D:ANP407 3.8 19.7 1.0
NE2 D:HIS204 3.8 18.6 1.0
CE1 D:HIS204 3.9 18.7 1.0
OD1 D:ASP219 4.1 19.5 1.0
O1G D:ANP407 4.2 19.6 1.0
O5' D:ANP407 4.3 20.7 1.0
CB D:ASN207 4.4 16.8 1.0
O D:GLY206 4.4 21.3 1.0
O D:HOH1261 4.5 19.5 1.0
OD2 D:ASP202 4.7 19.1 1.0
O3' D:ANP407 4.7 23.7 1.0
CA D:ASN207 4.7 19.2 1.0
C D:GLY206 4.8 18.9 1.0
O D:HOH1449 4.8 27.7 1.0
C5' D:ANP407 4.8 20.2 1.0
CA D:ASP219 4.9 18.6 1.0
C3' D:ANP407 5.0 23.5 1.0
O D:HOH1274 5.0 21.9 1.0
N D:ASN207 5.0 17.3 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 Jan 25 15:12:21 2021

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