Magnesium in PDB 4q86: Ycao with Amp Bound

Protein crystallography data

The structure of Ycao with Amp Bound, PDB code: 4q86 was solved by J.R.Chekan, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 127.14 / 2.25
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 111.254, 112.949, 132.886, 89.94, 73.51, 77.23
R / Rfree (%) 21.8 / 25

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Magnesium atom in the Ycao with Amp Bound (pdb code 4q86). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the Ycao with Amp Bound, PDB code: 4q86:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in 4q86

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Magnesium binding site 1 out of 21 in the Ycao with Amp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ycao with Amp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:14.2
occ:1.00
O A:LEU216 2.5 28.4 1.0
OG A:SER215 2.5 25.5 1.0
O A:LYS336 2.7 35.8 1.0
O A:LEU334 2.8 30.2 1.0
O A:HOH784 3.5 31.9 1.0
N A:LEU216 3.5 28.0 1.0
C A:LEU216 3.6 31.2 1.0
CE1 A:TYR247 3.6 37.8 1.0
OH A:TYR247 3.7 40.1 1.0
C A:LYS336 3.8 32.8 1.0
CB A:SER215 3.8 28.5 1.0
N A:LYS336 3.8 29.4 1.0
C A:LEU334 3.8 26.9 1.0
CZ A:TYR247 3.9 37.7 1.0
C A:SER215 3.9 28.8 1.0
C A:PHE335 3.9 27.4 1.0
CA A:SER215 4.0 28.6 1.0
CA A:PHE335 4.1 27.2 1.0
CA A:LEU216 4.2 27.7 1.0
CA A:LYS336 4.3 34.4 1.0
N A:PHE335 4.3 25.6 1.0
O A:PHE335 4.5 33.3 1.0
CD1 A:TYR247 4.5 35.5 1.0
O A:ASP333 4.6 33.0 1.0
CA A:ALA339 4.7 35.1 1.0
O A:ASP338 4.7 32.2 1.0
O A:SER215 4.7 28.4 1.0
CB A:LYS336 4.7 34.1 1.0
N A:PRO217 4.8 32.2 1.0
CB A:ALA339 4.8 36.3 1.0
N A:ALA339 4.9 32.5 1.0
C A:ASP338 4.9 32.6 1.0
O A:GLN337 4.9 30.2 1.0
O A:HOH794 4.9 28.9 1.0
N A:GLN337 5.0 33.2 1.0
CA A:LEU334 5.0 25.0 1.0
CB A:LEU216 5.0 29.7 1.0
CE2 A:TYR247 5.0 38.4 1.0

Magnesium binding site 2 out of 21 in 4q86

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Magnesium binding site 2 out of 21 in the Ycao with Amp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ycao with Amp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:18.1
occ:1.00
OE2 A:GLU199 1.9 17.9 1.0
O A:HOH1032 1.9 25.7 1.0
O A:HOH1024 2.0 28.4 1.0
O A:HOH1031 2.0 30.7 1.0
O A:HOH796 2.0 13.4 1.0
O A:HOH1016 2.1 19.0 1.0
CD A:GLU199 2.9 21.4 1.0
OE1 A:GLU199 3.3 22.8 1.0
OE2 A:GLU78 3.8 21.0 1.0
O A:HOH741 4.1 22.8 1.0
OE1 A:GLN195 4.1 32.0 1.0
OE1 A:GLU78 4.1 32.3 1.0
O A:HOH1007 4.2 21.9 1.0
O A:HOH773 4.2 23.4 1.0
O A:MET183 4.3 22.5 1.0
CG A:GLU199 4.3 21.6 1.0
O A:HOH863 4.3 18.7 1.0
O3P A:AMP601 4.3 19.7 1.0
CD A:GLU78 4.4 24.0 1.0
NE2 A:GLN195 4.5 33.5 1.0
OE1 A:GLU75 4.5 27.1 1.0
NH2 A:ARG79 4.5 19.9 1.0
O A:HOH872 4.5 33.0 1.0
NH2 A:ARG203 4.6 25.2 1.0
CD A:GLN195 4.7 27.8 1.0
CB A:GLU199 5.0 20.3 1.0

Magnesium binding site 3 out of 21 in 4q86

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Magnesium binding site 3 out of 21 in the Ycao with Amp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ycao with Amp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:31.2
occ:1.00
O A:HOH872 2.0 33.0 1.0
O A:HOH717 2.1 18.0 1.0
O A:HOH991 2.1 35.4 1.0
O A:HOH1007 2.2 21.9 1.0
OE1 A:GLU75 2.3 27.1 1.0
O A:HOH725 2.3 24.8 1.0
CD A:GLU75 3.3 25.7 1.0
O A:HOH764 3.3 25.5 1.0
OE2 A:GLU75 3.6 24.9 1.0
O A:HOH741 3.7 22.8 1.0
NE2 A:GLN293 3.9 31.1 1.0
O A:HOH1031 4.0 30.7 1.0
O A:HOH1016 4.2 19.0 1.0
O A:ASN59 4.2 25.7 1.0
OE1 A:GLN293 4.2 32.5 1.0
O2P A:AMP601 4.3 24.8 1.0
OE1 A:GLU290 4.4 42.9 1.0
CD A:GLN293 4.5 32.5 1.0
O3P A:AMP601 4.6 19.7 1.0
O A:HOH778 4.6 31.6 1.0
CG A:GLU75 4.7 21.9 1.0
CE A:LYS61 4.9 30.7 1.0
O A:HOH1032 4.9 25.7 1.0
O A:HOH843 5.0 35.0 1.0

Magnesium binding site 4 out of 21 in 4q86

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Magnesium binding site 4 out of 21 in the Ycao with Amp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ycao with Amp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:7.4
occ:1.00
O B:LEU216 2.5 20.3 1.0
OG B:SER215 2.6 22.1 1.0
O B:LEU334 2.7 18.0 1.0
O B:LYS336 2.7 26.3 1.0
O B:HOH862 2.9 45.4 1.0
O B:HOH824 3.0 24.5 1.0
N B:LEU216 3.5 22.9 1.0
CE1 B:TYR247 3.6 29.0 1.0
C B:LEU216 3.6 22.9 1.0
OH B:TYR247 3.6 32.2 1.0
C B:LEU334 3.6 17.9 1.0
N B:LYS336 3.7 24.1 1.0
C B:LYS336 3.8 26.5 1.0
CB B:SER215 3.8 22.5 1.0
CZ B:TYR247 3.9 27.8 1.0
C B:PHE335 3.9 22.8 1.0
C B:SER215 3.9 20.7 1.0
CA B:PHE335 4.0 21.2 1.0
CA B:SER215 4.0 19.1 1.0
CA B:LEU216 4.2 21.8 1.0
N B:PHE335 4.2 17.9 1.0
CA B:LYS336 4.2 25.8 1.0
O B:PHE335 4.5 24.0 1.0
CD1 B:TYR247 4.5 25.0 1.0
O B:ASP333 4.6 23.9 1.0
CB B:LYS336 4.7 24.9 1.0
O B:SER215 4.7 21.6 1.0
O B:ASP338 4.7 23.6 1.0
CA B:ALA339 4.8 27.2 1.0
N B:PRO217 4.8 22.9 1.0
CA B:LEU334 4.8 17.7 1.0
CE2 B:TYR247 4.9 26.3 1.0
CB B:LEU216 4.9 21.1 1.0
N B:GLN337 4.9 28.9 1.0
CB B:ALA339 5.0 27.5 1.0
O B:GLN337 5.0 23.0 1.0

Magnesium binding site 5 out of 21 in 4q86

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Magnesium binding site 5 out of 21 in the Ycao with Amp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ycao with Amp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:18.0
occ:1.00
O B:HOH975 1.9 26.4 1.0
OE2 B:GLU199 2.0 15.6 1.0
O B:HOH756 2.1 17.9 1.0
O B:HOH1019 2.1 18.6 1.0
O B:HOH1025 2.2 13.6 1.0
O B:HOH943 2.2 23.6 1.0
CD B:GLU199 3.0 16.0 1.0
OE1 B:GLU199 3.4 17.5 1.0
OE2 B:GLU78 3.7 21.4 1.0
O B:HOH1031 3.8 27.5 1.0
O B:HOH769 3.9 32.7 1.0
OE1 B:GLU78 4.0 23.8 1.0
NE2 B:GLN195 4.1 23.7 1.0
CD B:GLU78 4.3 23.2 1.0
O B:MET183 4.3 26.1 1.0
O3P B:AMP601 4.4 17.4 1.0
CG B:GLU199 4.4 15.8 1.0
O B:HOH715 4.4 17.4 1.0
OE1 B:GLN195 4.4 25.5 1.0
OE1 B:GLU75 4.6 26.7 1.0
O B:HOH757 4.6 16.2 1.0
NH2 B:ARG79 4.6 21.4 1.0
NH2 B:ARG203 4.7 25.5 1.0
CD B:GLN195 4.7 22.4 1.0
O B:HOH1026 4.7 26.2 1.0
MG B:MG604 4.7 24.8 1.0
C5' B:AMP601 5.0 20.0 1.0
CB B:GLU199 5.0 16.5 1.0

Magnesium binding site 6 out of 21 in 4q86

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Magnesium binding site 6 out of 21 in the Ycao with Amp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ycao with Amp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:24.8
occ:1.00
O B:HOH1031 1.9 27.5 1.0
OE1 B:GLU75 2.0 26.7 1.0
O B:HOH1026 2.0 26.2 1.0
O B:HOH776 2.1 27.2 1.0
O B:HOH745 2.1 22.2 1.0
O B:HOH739 2.2 20.7 1.0
CD B:GLU75 3.0 22.9 1.0
OE2 B:GLU75 3.5 24.6 1.0
O B:HOH1025 3.6 13.6 1.0
O B:HOH943 3.7 23.6 1.0
O2P B:AMP601 3.9 19.5 1.0
O B:HOH805 4.0 21.7 1.0
O B:HOH715 4.0 17.4 1.0
O B:HOH986 4.1 26.3 1.0
O B:ASN59 4.2 22.8 1.0
O3P B:AMP601 4.2 17.4 1.0
CG B:GLU75 4.3 21.0 1.0
NE2 B:GLN293 4.4 33.1 1.0
OE1 B:GLN293 4.5 34.5 1.0
O B:HOH756 4.5 17.9 1.0
C5' B:AMP601 4.6 20.0 1.0
P B:AMP601 4.6 18.3 1.0
OE1 B:GLU290 4.7 30.3 1.0
MG B:MG603 4.7 18.0 1.0
CE B:LYS61 4.8 25.6 1.0
CD B:GLN293 4.9 31.0 1.0
CB B:GLU75 5.0 20.8 1.0

Magnesium binding site 7 out of 21 in 4q86

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Magnesium binding site 7 out of 21 in the Ycao with Amp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ycao with Amp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:17.8
occ:1.00
OG C:SER215 2.5 53.8 1.0
O C:LEU216 2.6 41.1 1.0
O C:LYS336 2.6 40.3 1.0
O C:LEU334 2.8 37.5 1.0
O C:HOH820 3.3 44.5 1.0
N C:LEU216 3.6 36.2 1.0
CE1 C:TYR247 3.6 47.1 1.0
C C:LEU216 3.7 39.5 1.0
OH C:TYR247 3.7 53.6 1.0
N C:LYS336 3.7 37.4 1.0
C C:LYS336 3.7 40.3 1.0
C C:LEU334 3.7 36.5 1.0
CB C:SER215 3.8 45.8 1.0
C C:PHE335 3.9 37.5 1.0
CZ C:TYR247 3.9 47.4 1.0
C C:SER215 4.0 40.4 1.0
CA C:PHE335 4.1 36.5 1.0
CA C:SER215 4.1 42.5 1.0
CA C:LYS336 4.2 38.7 1.0
CA C:LEU216 4.2 35.8 1.0
N C:PHE335 4.2 38.3 1.0
O C:PHE335 4.4 44.8 1.0
CD1 C:TYR247 4.5 46.5 1.0
O C:ASP333 4.6 36.7 1.0
O C:ASP338 4.7 35.3 1.0
CB C:LYS336 4.7 41.2 1.0
CA C:ALA339 4.7 46.1 1.0
O C:SER215 4.8 36.6 1.0
N C:PRO217 4.8 43.8 1.0
O C:GLN337 4.9 35.5 1.0
N C:ALA339 4.9 41.6 1.0
C C:ASP338 4.9 40.9 1.0
N C:GLN337 4.9 42.3 1.0
CB C:ALA339 4.9 41.9 1.0
CA C:LEU334 4.9 35.0 1.0
CE2 C:TYR247 5.0 45.8 1.0

Magnesium binding site 8 out of 21 in 4q86

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Magnesium binding site 8 out of 21 in the Ycao with Amp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ycao with Amp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:26.1
occ:1.00
OE2 C:GLU199 1.8 30.7 1.0
O C:HOH928 1.9 26.7 1.0
O C:HOH735 2.1 26.2 1.0
O C:HOH803 2.1 33.3 1.0
O C:HOH886 2.2 32.4 1.0
O C:HOH931 2.5 33.3 1.0
CD C:GLU199 2.8 33.4 1.0
OE1 C:GLU199 3.2 36.0 1.0
OE1 C:GLN195 3.9 49.5 1.0
OE2 C:GLU78 4.0 46.3 1.0
CG C:GLU199 4.1 33.8 1.0
O C:HOH930 4.1 40.2 1.0
OE1 C:GLU78 4.2 51.0 1.0
O C:HOH772 4.2 33.5 1.0
O C:MET183 4.3 43.1 1.0
NE2 C:GLN195 4.4 39.9 1.0
O C:HOH901 4.4 26.1 1.0
O2P C:AMP601 4.5 32.2 1.0
CD C:GLU78 4.5 46.2 1.0
CD C:GLN195 4.5 41.1 1.0
NH2 C:ARG203 4.6 45.7 1.0
NH1 C:ARG79 4.7 59.2 1.0
CB C:GLU199 4.7 35.9 1.0
OE2 C:GLU75 4.8 34.5 1.0

Magnesium binding site 9 out of 21 in 4q86

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Magnesium binding site 9 out of 21 in the Ycao with Amp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Ycao with Amp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:36.1
occ:1.00
O C:HOH836 2.0 29.2 1.0
O C:HOH929 2.0 32.8 1.0
O C:HOH732 2.1 19.8 1.0
O C:HOH930 2.1 40.2 1.0
O C:HOH922 2.2 31.7 1.0
OE2 C:GLU75 2.2 34.5 1.0
CD C:GLU75 3.2 34.8 1.0
OE1 C:GLU75 3.6 36.1 1.0
O C:HOH931 3.8 33.3 1.0
O1P C:AMP601 4.0 30.6 1.0
O C:HOH901 4.0 26.1 1.0
O C:HOH928 4.0 26.7 1.0
NE2 C:GLN293 4.1 43.8 1.0
O C:ASN59 4.1 34.8 1.0
O2P C:AMP601 4.2 32.2 1.0
OE1 C:GLN293 4.3 48.1 1.0
OE1 C:GLU290 4.5 47.7 1.0
CG C:GLU75 4.5 37.7 1.0
CE C:LYS61 4.6 47.0 1.0
P C:AMP601 4.6 31.7 1.0
CD C:GLN293 4.6 46.6 1.0
O C:HOH735 4.7 26.2 1.0
C5' C:AMP601 4.9 35.0 1.0

Magnesium binding site 10 out of 21 in 4q86

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Magnesium binding site 10 out of 21 in the Ycao with Amp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Ycao with Amp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:15.4
occ:1.00
OG D:SER215 2.6 30.1 1.0
O D:LYS336 2.6 24.5 1.0
O D:LEU216 2.7 29.5 1.0
O D:LEU334 2.7 28.5 1.0
O D:HOH816 3.2 21.5 1.0
OH D:TYR247 3.6 39.7 1.0
N D:LYS336 3.6 27.1 1.0
N D:LEU216 3.7 32.7 1.0
C D:LEU334 3.7 27.2 1.0
CE1 D:TYR247 3.7 37.4 1.0
C D:LYS336 3.7 27.1 1.0
C D:LEU216 3.8 29.3 1.0
C D:PHE335 3.8 27.6 1.0
CB D:SER215 3.8 29.6 1.0
CZ D:TYR247 3.9 39.0 1.0
CA D:PHE335 3.9 27.1 1.0
C D:SER215 4.0 31.2 1.0
CA D:SER215 4.1 29.5 1.0
CA D:LYS336 4.1 30.1 1.0
N D:PHE335 4.2 28.9 1.0
CA D:LEU216 4.3 29.8 1.0
O D:PHE335 4.4 27.9 1.0
O D:ASP333 4.5 29.2 1.0
CD1 D:TYR247 4.6 32.0 1.0
CB D:LYS336 4.6 29.7 1.0
O D:ASP338 4.7 31.5 1.0
CA D:ALA339 4.8 36.2 1.0
O D:SER215 4.8 30.7 1.0
CA D:LEU334 4.9 27.9 1.0
N D:GLN337 4.9 29.8 1.0
N D:PRO217 4.9 32.1 1.0
C D:ASP338 4.9 35.8 1.0
O D:GLN337 4.9 26.0 1.0
N D:ALA339 5.0 37.4 1.0
CE2 D:TYR247 5.0 38.4 1.0
CB D:ALA339 5.0 33.6 1.0

Reference:

K.L.Dunbar, J.R.Chekan, C.L.Cox, B.J.Burkhart, S.K.Nair, D.A.Mitchell. Discovery of A New Atp-Binding Motif Involved in Peptidic Azoline Biosynthesis. Nat.Chem.Biol. V. 10 823 2014.
ISSN: ISSN 1552-4450
PubMed: 25129028
DOI: 10.1038/NCHEMBIO.1608
Page generated: Mon Dec 14 19:22:01 2020

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