Magnesium in PDB 4q85: Ycao with Non-Hydrolyzable Atp (Ampcpp) Bound

The structure of Ycao with Non-Hydrolyzable Atp (Ampcpp) Bound, PDB code: 4q85 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)	125.20 / 3.29
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	110.282, 112.402, 130.683, 89.40, 73.63, 77.62
R / Rfree (%)	19 / 23.9

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Ycao with Non-Hydrolyzable Atp (Ampcpp) Bound (pdb code 4q85). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 19 binding sites of Magnesium where determined in the Ycao with Non-Hydrolyzable Atp (Ampcpp) Bound, PDB code: 4q85:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 19 in the Ycao with Non-Hydrolyzable Atp (Ampcpp) 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 Non-Hydrolyzable Atp (Ampcpp) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:6.5 occ:1.00 O A:LYS336 2.4 71.7 1.0 O A:LEU216 2.5 63.7 1.0 O A:LEU334 2.7 41.9 1.0 OG A:SER215 2.7 45.6 1.0 OH A:TYR247 3.4 50.5 1.0 CE1 A:TYR247 3.5 47.9 1.0 C A:LYS336 3.6 71.4 1.0 C A:LEU216 3.7 56.3 1.0 N A:LYS336 3.7 64.9 1.0 N A:LEU216 3.7 55.5 1.0 C A:LEU334 3.7 47.1 1.0 C A:PHE335 3.8 59.0 1.0 CZ A:TYR247 3.8 48.4 1.0 CA A:PHE335 4.0 56.5 1.0 CB A:SER215 4.0 52.8 1.0 C A:SER215 4.2 54.6 1.0 CA A:LYS336 4.2 70.7 1.0 N A:PHE335 4.2 54.8 1.0 CA A:SER215 4.2 56.8 1.0 O A:PHE335 4.3 67.4 1.0 CA A:LEU216 4.3 54.6 1.0 O A:GLN337 4.4 65.8 1.0 CD1 A:TYR247 4.5 48.2 1.0 N A:GLN337 4.7 67.8 1.0 O A:ASP333 4.7 57.5 1.0 C A:GLN337 4.8 68.6 1.0 CB A:LYS336 4.8 72.8 1.0 N A:PRO217 4.8 49.6 1.0 CB A:ALA339 4.8 65.6 1.0 CA A:ALA339 4.9 67.4 1.0 O A:SER215 4.9 47.2 1.0 CE2 A:TYR247 5.0 47.0 1.0 CA A:LEU334 5.0 47.6 1.0

Magnesium binding site 2 out of 19 in the Ycao with Non-Hydrolyzable Atp (Ampcpp) 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 Non-Hydrolyzable Atp (Ampcpp) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:24.8 occ:1.00 O1B A:APC601 2.1 73.6 1.0 OE2 A:GLU199 2.4 72.2 1.0 OE2 A:GLU78 2.9 52.4 1.0 O1G A:APC601 2.9 100.0 1.0 OE1 A:GLU199 3.1 66.3 1.0 CD A:GLU199 3.1 70.8 1.0 OE1 A:GLU78 3.3 78.3 1.0 PB A:APC601 3.4 79.2 1.0 CD A:GLU78 3.4 63.0 1.0 O A:MET183 3.6 44.8 1.0 O3B A:APC601 3.8 99.0 1.0 OE1 A:GLN195 3.9 56.3 1.0 O2B A:APC601 4.0 84.2 1.0 PG A:APC601 4.0 0.5 1.0 NH2 A:ARG79 4.2 58.0 1.0 OE1 A:GLU75 4.2 73.5 1.0 O5' A:APC601 4.4 69.6 1.0 O3' A:APC601 4.5 72.8 1.0 CG A:GLU199 4.6 66.0 1.0 C A:MET183 4.7 47.4 1.0 O2G A:APC601 4.8 95.8 1.0 CD A:GLN195 4.8 56.1 1.0 C3' A:APC601 4.8 77.5 1.0 CG A:GLU75 4.9 62.0 1.0 NE2 A:GLN195 4.9 58.2 1.0 C3A A:APC601 5.0 70.6 1.0 CG A:GLU78 5.0 59.7 1.0 CD A:GLU75 5.0 68.6 1.0

Magnesium binding site 3 out of 19 in the Ycao with Non-Hydrolyzable Atp (Ampcpp) 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 Non-Hydrolyzable Atp (Ampcpp) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:31.6 occ:1.00 O2B A:APC601 2.3 84.2 1.0 OE1 A:GLU290 2.8 93.0 1.0 OE2 A:GLU290 2.8 89.3 1.0 OE2 A:GLU202 3.1 75.7 1.0 CD A:GLU290 3.1 88.4 1.0 O3G A:APC601 3.2 92.6 1.0 OE1 A:GLU202 3.3 74.5 1.0 NZ A:LYS61 3.4 0.7 1.0 NH1 A:ARG286 3.4 88.9 1.0 NH2 A:ARG203 3.5 0.6 1.0 CD A:GLU202 3.6 72.2 1.0 PB A:APC601 3.7 79.2 1.0 O3B A:APC601 4.0 99.0 1.0 PG A:APC601 4.1 0.5 1.0 C3A A:APC601 4.3 70.6 1.0 O1G A:APC601 4.5 100.0 1.0 CG A:GLU290 4.5 79.0 1.0 CZ A:ARG286 4.6 97.7 1.0 CZ A:ARG203 4.7 0.9 1.0 CE A:LYS61 4.8 95.5 1.0 O1B A:APC601 4.8 73.6 1.0 NH2 A:ARG286 4.9 0.3 1.0 O A:PHE274 4.9 44.1 1.0

Magnesium binding site 4 out of 19 in the Ycao with Non-Hydrolyzable Atp (Ampcpp) 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 Non-Hydrolyzable Atp (Ampcpp) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:24.6 occ:1.00 O B:LEU216 2.4 42.6 1.0 O B:LYS336 2.5 56.8 1.0 O B:LEU334 2.9 48.3 1.0 OG B:SER215 2.9 37.2 1.0 CE1 B:TYR247 3.3 51.4 1.0 OH B:TYR247 3.3 56.2 1.0 C B:LEU216 3.6 43.0 1.0 CZ B:TYR247 3.7 53.2 1.0 C B:LYS336 3.7 56.2 1.0 N B:LEU216 3.7 44.0 1.0 C B:PHE335 3.9 47.8 1.0 N B:LYS336 3.9 49.9 1.0 C B:LEU334 4.0 45.2 1.0 CA B:PHE335 4.1 46.2 1.0 CB B:SER215 4.2 40.9 1.0 O B:GLN337 4.2 51.5 1.0 C B:SER215 4.2 45.9 1.0 CA B:LEU216 4.3 42.2 1.0 CD1 B:TYR247 4.3 46.2 1.0 O B:PHE335 4.4 44.6 1.0 CA B:LYS336 4.4 52.7 1.0 CA B:SER215 4.4 46.5 1.0 N B:PHE335 4.5 45.4 1.0 N B:PRO217 4.6 41.9 1.0 C B:GLN337 4.7 51.1 1.0 N B:GLN337 4.7 58.2 1.0 CB B:ALA339 4.8 40.6 1.0 CA B:ALA339 4.9 43.4 1.0 CE2 B:TYR247 4.9 52.2 1.0 CA B:PRO217 4.9 40.2 1.0 CA B:GLN337 5.0 53.3 1.0 N B:ALA339 5.0 45.4 1.0 O B:ASP333 5.0 45.8 1.0 CB B:LYS336 5.0 56.7 1.0 O B:SER215 5.0 45.1 1.0

Magnesium binding site 5 out of 19 in the Ycao with Non-Hydrolyzable Atp (Ampcpp) 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 Non-Hydrolyzable Atp (Ampcpp) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:9.0 occ:1.00 OE2 B:GLU199 2.3 39.9 1.0 O2B B:APC601 2.4 55.1 1.0 OE1 B:GLU199 2.8 51.3 1.0 O2G B:APC601 2.8 55.9 1.0 CD B:GLU199 2.9 45.6 1.0 OE2 B:GLU78 2.9 53.4 1.0 OE1 B:GLU78 3.5 63.5 1.0 PB B:APC601 3.6 57.4 1.0 CD B:GLU78 3.6 57.9 1.0 O B:MET183 3.6 46.7 1.0 O1B B:APC601 3.7 60.6 1.0 PG B:APC601 3.9 59.1 1.0 OE1 B:GLN195 4.0 51.9 1.0 NH2 B:ARG79 4.1 62.6 1.0 O3G B:APC601 4.2 55.5 1.0 O3B B:APC601 4.3 55.0 1.0 OE1 B:GLU75 4.3 36.9 1.0 CG B:GLU199 4.4 42.6 1.0 C B:MET183 4.7 45.8 1.0 O5' B:APC601 4.7 48.0 1.0 O B:SER180 4.7 62.5 1.0 C5' B:APC601 4.8 45.4 1.0 NH2 B:ARG203 4.9 0.1 1.0 CD B:GLN195 4.9 50.2 1.0 NE2 B:GLN195 5.0 54.7 1.0

Magnesium binding site 6 out of 19 in the Ycao with Non-Hydrolyzable Atp (Ampcpp) 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 Non-Hydrolyzable Atp (Ampcpp) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:9.8 occ:1.00 O3B B:APC601 2.7 55.0 1.0 O1B B:APC601 2.8 60.6 1.0 OE1 B:GLU290 2.9 89.7 1.0 OE2 B:GLU290 2.9 0.4 1.0 CD B:GLU290 3.2 89.2 1.0 O1G B:APC601 3.2 56.0 1.0 OE2 B:GLU202 3.2 60.3 1.0 NZ B:LYS61 3.3 89.1 1.0 PB B:APC601 3.3 57.4 1.0 NH1 B:ARG286 3.4 87.0 1.0 NH2 B:ARG203 3.4 0.1 1.0 OE1 B:GLU202 3.4 61.7 1.0 PG B:APC601 3.4 59.1 1.0 CD B:GLU202 3.8 63.9 1.0 O2G B:APC601 3.8 55.9 1.0 NH2 B:ARG286 4.1 86.2 1.0 C3A B:APC601 4.1 49.2 1.0 CZ B:ARG286 4.2 85.9 1.0 CG B:GLU290 4.6 75.5 1.0 CZ B:ARG203 4.6 96.2 1.0 CE B:LYS61 4.7 78.8 1.0 O2B B:APC601 4.8 55.1 1.0 O3G B:APC601 4.8 55.5 1.0 OE2 B:GLU199 4.9 39.9 1.0

Magnesium binding site 7 out of 19 in the Ycao with Non-Hydrolyzable Atp (Ampcpp) 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 Non-Hydrolyzable Atp (Ampcpp) Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:39.4 occ:1.00 O C:LYS336 2.2 75.0 1.0 O C:LEU334 2.8 76.4 1.0 O C:LEU216 2.9 66.2 1.0 OH C:TYR247 3.0 61.3 1.0 OG C:SER215 3.1 69.8 1.0 C C:LYS336 3.4 78.9 1.0 CE1 C:TYR247 3.4 60.1 1.0 C C:PHE335 3.5 61.1 1.0 N C:LYS336 3.6 67.5 1.0 CZ C:TYR247 3.6 60.1 1.0 CA C:PHE335 3.7 59.1 1.0 C C:LEU334 3.8 61.9 1.0 O C:PHE335 3.9 63.7 1.0 CA C:LYS336 4.1 68.9 1.0 C C:LEU216 4.1 68.0 1.0 N C:PHE335 4.1 59.2 1.0 N C:LEU216 4.2 65.1 1.0 O C:GLN337 4.2 67.6 1.0 CB C:SER215 4.4 69.8 1.0 N C:GLN337 4.4 85.4 1.0 C C:GLN337 4.6 80.3 1.0 CD1 C:TYR247 4.6 58.8 1.0 C C:SER215 4.6 66.2 1.0 CA C:SER215 4.7 69.3 1.0 CA C:GLN337 4.7 81.3 1.0 CA C:LEU216 4.8 67.3 1.0 CB C:LYS336 4.8 63.7 1.0 O C:ASP333 4.9 66.2 1.0 CE2 C:TYR247 4.9 55.4 1.0

Magnesium binding site 8 out of 19 in the Ycao with Non-Hydrolyzable Atp (Ampcpp) 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 Non-Hydrolyzable Atp (Ampcpp) Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:28.4 occ:1.00 OE2 C:GLU199 2.3 60.9 1.0 OE1 C:GLU199 3.0 55.4 1.0 OE2 C:GLU78 3.0 75.1 1.0 CD C:GLU199 3.0 55.4 1.0 OE1 C:GLU78 3.7 65.2 1.0 CD C:GLU78 3.8 70.1 1.0 OE2 C:GLU75 3.8 97.4 1.0 NE2 C:GLN195 4.0 86.6 1.0 O C:MET183 4.0 74.7 1.0 NH1 C:ARG79 4.2 65.9 1.0 CG C:GLU199 4.5 54.5 1.0 NH2 C:ARG79 4.6 64.1 1.0 NH2 C:ARG203 4.7 81.2 1.0 CD C:GLU75 4.8 85.5 1.0 O C:SER180 4.9 72.2 1.0 CG C:GLU75 4.9 82.7 1.0 CZ C:ARG79 4.9 65.8 1.0 NH1 C:ARG203 5.0 73.5 1.0

Magnesium binding site 9 out of 19 in the Ycao with Non-Hydrolyzable Atp (Ampcpp) 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 Non-Hydrolyzable Atp (Ampcpp) Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:15.7 occ:1.00 O D:LYS336 2.3 57.7 1.0 O D:LEU216 2.5 43.7 1.0 OG D:SER215 2.8 35.7 1.0 O D:LEU334 3.0 54.5 1.0 OH D:TYR247 3.4 58.4 1.0 CE1 D:TYR247 3.4 56.1 1.0 C D:LYS336 3.5 51.1 1.0 C D:LEU216 3.7 41.8 1.0 CZ D:TYR247 3.8 55.5 1.0 N D:LYS336 3.9 46.4 1.0 C D:PHE335 3.9 43.6 1.0 N D:LEU216 3.9 41.1 1.0 O D:HOH709 3.9 31.9 1.0 C D:LEU334 4.0 53.8 1.0 O D:GLN337 4.0 59.1 1.0 CA D:PHE335 4.1 46.0 1.0 CB D:SER215 4.2 38.5 1.0 CA D:LYS336 4.3 49.0 1.0 O D:PHE335 4.3 41.2 1.0 C D:SER215 4.3 39.1 1.0 CA D:LEU216 4.4 41.2 1.0 CA D:SER215 4.5 40.8 1.0 C D:GLN337 4.5 59.1 1.0 N D:PHE335 4.5 49.2 1.0 CD1 D:TYR247 4.5 54.9 1.0 N D:GLN337 4.6 51.2 1.0 CA D:GLN337 4.8 56.0 1.0 N D:PRO217 4.8 44.1 1.0 CB D:ALA339 4.8 63.6 1.0 CA D:ALA339 4.8 60.6 1.0 N D:ALA339 4.9 58.6 1.0 CB D:LYS336 4.9 52.8 1.0 C D:ASP338 5.0 61.1 1.0 O D:ASP333 5.0 48.8 1.0

Magnesium binding site 10 out of 19 in the Ycao with Non-Hydrolyzable Atp (Ampcpp) 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 Non-Hydrolyzable Atp (Ampcpp) Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg603 b:24.6 occ:1.00 O1G D:APC601 2.1 57.9 1.0 O2B D:APC601 2.5 53.8 1.0 OE2 D:GLU290 2.5 83.5 1.0 OE1 D:GLU290 2.9 87.4 1.0 CD D:GLU290 3.0 71.4 1.0 NH2 D:ARG203 3.0 77.6 1.0 OE2 D:GLU202 3.1 67.1 1.0 NZ D:LYS61 3.3 73.5 1.0 O D:HOH708 3.4 23.3 1.0 PG D:APC601 3.6 60.0 1.0 OE1 D:GLU202 3.7 60.8 1.0 CD D:GLU202 3.8 64.6 1.0 PB D:APC601 3.9 50.3 1.0 NH1 D:ARG286 4.0 84.8 1.0 O3G D:APC601 4.2 54.1 1.0 CZ D:ARG203 4.3 75.3 1.0 O3B D:APC601 4.3 54.3 1.0 O1B D:APC601 4.4 54.2 1.0 CG D:GLU290 4.5 58.8 1.0 O2G D:APC601 4.5 59.6 1.0 NH2 D:ARG286 4.6 73.2 1.0 CE D:LYS61 4.7 74.3 1.0 NE D:ARG203 4.8 69.3 1.0 CZ D:ARG286 4.8 78.5 1.0

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