Magnesium in PDB 7rkh: Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH

Enzymatic activity of Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH

All present enzymatic activity of Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH:
6.3.4.2;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH (pdb code 7rkh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH, PDB code: 7rkh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7rkh

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Magnesium binding site 1 out of 8 in the Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:30.0
occ:1.00
OD2 D:ASP70 1.9 31.5 1.0
OD1 D:ASP70 2.4 31.5 1.0
CG D:ASP70 2.4 31.5 1.0
O1B D:ATP602 2.9 43.5 1.0
O3G D:ATP602 3.0 43.5 1.0
HZ1 D:LYS16 3.1 26.8 1.0
OE2 D:GLU146 3.2 21.2 1.0
HA3 D:GLY17 3.3 37.3 1.0
HZ2 D:LYS16 3.4 26.8 1.0
H D:GLY17 3.4 37.3 1.0
HZ3 D:LYS16 3.4 26.8 1.0
HZ3 D:LYS38 3.5 19.4 1.0
OE1 D:GLU146 3.5 21.2 1.0
HE3 D:LYS38 3.5 19.4 1.0
NZ D:LYS16 3.6 26.8 1.0
CD D:GLU146 3.7 21.2 1.0
O3B D:ATP602 3.8 43.5 1.0
CB D:ASP70 3.9 31.5 1.0
N D:GLY17 3.9 37.3 1.0
HB2 D:LYS16 3.9 26.8 1.0
PB D:ATP602 3.9 43.5 1.0
CA D:GLY17 4.0 37.3 1.0
PG D:ATP602 4.0 43.5 1.0
O2A D:ATP602 4.0 43.5 1.0
HB3 D:ASP70 4.1 31.5 1.0
HA2 D:GLY17 4.1 37.3 1.0
NZ D:LYS38 4.2 19.4 1.0
HD3 D:LYS38 4.2 19.4 1.0
CE D:LYS38 4.3 19.4 1.0
HB2 D:ASP70 4.4 31.5 1.0
O4 D:UTP601 4.4 33.3 1.0
O1A D:ATP602 4.5 43.5 1.0
HZ1 D:LYS38 4.5 19.4 1.0
PA D:ATP602 4.5 43.5 1.0
O3A D:ATP602 4.6 43.5 1.0
OD2 D:ASP68 4.6 39.0 1.0
HH D:TYR74 4.6 28.7 1.0
HD13 D:LEU69 4.7 38.0 1.0
HA D:ASP70 4.7 37.3 1.0
CD D:LYS38 4.8 19.4 1.0
CA D:ASP70 4.9 37.3 1.0
O2G D:ATP602 4.9 43.5 1.0
C D:LYS16 4.9 37.3 1.0
CB D:LYS16 5.0 26.8 1.0
H D:ASP70 5.0 37.3 1.0

Magnesium binding site 2 out of 8 in 7rkh

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Magnesium binding site 2 out of 8 in the Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:30.0
occ:1.00
HZ3 D:LYS227 2.9 47.3 1.0
O1B C:UTP602 3.0 33.3 1.0
O2A C:UTP602 3.1 33.3 1.0
O3B C:UTP602 3.1 33.3 1.0
O3A C:UTP602 3.1 33.3 1.0
PB C:UTP602 3.3 33.3 1.0
HZ1 D:LYS227 3.6 47.3 1.0
NZ D:LYS227 3.7 47.3 1.0
PA C:UTP602 3.7 33.3 1.0
O3G C:UTP602 3.7 33.3 1.0
HZ3 D:LYS191 3.9 41.5 1.0
PG C:UTP602 3.9 33.3 1.0
HZ2 D:LYS227 3.9 47.3 1.0
HE2 C:HIS55 4.1 59.4 1.0
C5' C:UTP602 4.2 33.3 1.0
O1G C:UTP602 4.2 33.3 1.0
HZ2 D:LYS191 4.2 41.5 1.0
O5' C:UTP602 4.2 33.3 1.0
NZ D:LYS191 4.6 41.5 1.0
HG C:SER12 4.6 42.8 1.0
NE2 C:HIS55 4.8 59.4 1.0
O2B C:UTP602 4.8 33.3 1.0
HD2 C:HIS55 4.9 59.4 1.0
CE D:LYS227 4.9 47.3 1.0

Magnesium binding site 3 out of 8 in 7rkh

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Magnesium binding site 3 out of 8 in the Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:30.0
occ:1.00
OD2 A:ASP70 1.9 31.5 1.0
OD1 A:ASP70 2.4 31.5 1.0
CG A:ASP70 2.4 31.5 1.0
O1B A:ATP602 2.9 43.5 1.0
O3G A:ATP602 3.0 43.5 1.0
HZ1 A:LYS16 3.1 26.8 1.0
OE2 A:GLU146 3.2 21.2 1.0
HA3 A:GLY17 3.3 37.3 1.0
HZ2 A:LYS16 3.4 26.8 1.0
H A:GLY17 3.4 37.3 1.0
HZ3 A:LYS16 3.4 26.8 1.0
HZ3 A:LYS38 3.5 19.4 1.0
OE1 A:GLU146 3.5 21.2 1.0
HE3 A:LYS38 3.5 19.4 1.0
NZ A:LYS16 3.6 26.8 1.0
CD A:GLU146 3.7 21.2 1.0
O3B A:ATP602 3.8 43.5 1.0
CB A:ASP70 3.9 31.5 1.0
N A:GLY17 3.9 37.3 1.0
HB2 A:LYS16 3.9 26.8 1.0
PB A:ATP602 3.9 43.5 1.0
CA A:GLY17 4.0 37.3 1.0
PG A:ATP602 4.0 43.5 1.0
O2A A:ATP602 4.0 43.5 1.0
HB3 A:ASP70 4.1 31.5 1.0
HA2 A:GLY17 4.1 37.3 1.0
NZ A:LYS38 4.2 19.4 1.0
HD3 A:LYS38 4.2 19.4 1.0
CE A:LYS38 4.3 19.4 1.0
HB2 A:ASP70 4.4 31.5 1.0
O4 A:UTP601 4.4 33.3 1.0
O1A A:ATP602 4.5 43.5 1.0
HZ1 A:LYS38 4.5 19.4 1.0
PA A:ATP602 4.5 43.5 1.0
O3A A:ATP602 4.6 43.5 1.0
OD2 A:ASP68 4.6 39.0 1.0
HH A:TYR74 4.6 28.7 1.0
HD13 A:LEU69 4.7 38.0 1.0
HA A:ASP70 4.7 37.3 1.0
CD A:LYS38 4.8 19.4 1.0
CA A:ASP70 4.9 37.3 1.0
O2G A:ATP602 4.9 43.5 1.0
C A:LYS16 4.9 37.3 1.0
CB A:LYS16 5.0 26.8 1.0
H A:ASP70 5.0 37.3 1.0

Magnesium binding site 4 out of 8 in 7rkh

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Magnesium binding site 4 out of 8 in the Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:30.0
occ:1.00
HZ3 A:LYS227 2.9 47.3 1.0
O2B B:UTP602 3.0 33.3 1.0
O1A B:UTP602 3.1 33.3 1.0
O3B B:UTP602 3.1 33.3 1.0
O3A B:UTP602 3.1 33.3 1.0
PB B:UTP602 3.3 33.3 1.0
HZ1 A:LYS227 3.6 47.3 1.0
NZ A:LYS227 3.7 47.3 1.0
PA B:UTP602 3.7 33.3 1.0
O2G B:UTP602 3.7 33.3 1.0
HZ3 A:LYS191 3.9 41.5 1.0
PG B:UTP602 3.9 33.3 1.0
HZ2 A:LYS227 3.9 47.3 1.0
HE2 B:HIS55 4.1 59.4 1.0
C5' B:UTP602 4.2 33.3 1.0
O1G B:UTP602 4.2 33.3 1.0
HZ2 A:LYS191 4.2 41.5 1.0
O5' B:UTP602 4.2 33.3 1.0
NZ A:LYS191 4.6 41.5 1.0
HG B:SER12 4.6 42.8 1.0
NE2 B:HIS55 4.8 59.4 1.0
O1B B:UTP602 4.8 33.3 1.0
HD2 B:HIS55 4.9 59.4 1.0
CE A:LYS227 4.9 47.3 1.0
HD2 A:LYS227 5.0 47.3 1.0

Magnesium binding site 5 out of 8 in 7rkh

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Magnesium binding site 5 out of 8 in the Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:30.0
occ:1.00
HZ3 B:LYS227 2.9 47.3 1.0
O1B A:UTP601 3.0 33.3 1.0
O2A A:UTP601 3.1 33.3 1.0
O3B A:UTP601 3.1 33.3 1.0
O3A A:UTP601 3.1 33.3 1.0
PB A:UTP601 3.3 33.3 1.0
HZ1 B:LYS227 3.7 47.3 1.0
PA A:UTP601 3.7 33.3 1.0
NZ B:LYS227 3.7 47.3 1.0
O3G A:UTP601 3.7 33.3 1.0
HZ3 B:LYS191 3.8 41.5 1.0
PG A:UTP601 3.9 33.3 1.0
HZ2 B:LYS227 4.0 47.3 1.0
HE2 A:HIS55 4.1 59.4 1.0
C5' A:UTP601 4.2 33.3 1.0
HZ2 B:LYS191 4.2 41.5 1.0
O1G A:UTP601 4.2 33.3 1.0
O5' A:UTP601 4.2 33.3 1.0
NZ B:LYS191 4.5 41.5 1.0
HG A:SER12 4.6 42.8 1.0
NE2 A:HIS55 4.8 59.4 1.0
O2B A:UTP601 4.8 33.3 1.0
HD2 A:HIS55 4.9 59.4 1.0
CE B:LYS227 5.0 47.3 1.0

Magnesium binding site 6 out of 8 in 7rkh

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Magnesium binding site 6 out of 8 in the Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:30.0
occ:1.00
OD2 B:ASP70 1.9 31.5 1.0
OD1 B:ASP70 2.4 31.5 1.0
CG B:ASP70 2.4 31.5 1.0
O1B B:ATP603 2.9 43.5 1.0
O3G B:ATP603 3.0 43.5 1.0
HZ1 B:LYS16 3.1 26.8 1.0
OE2 B:GLU146 3.2 21.2 1.0
HA3 B:GLY17 3.3 37.3 1.0
HZ2 B:LYS16 3.3 26.8 1.0
H B:GLY17 3.4 37.3 1.0
HZ3 B:LYS16 3.4 26.8 1.0
HZ3 B:LYS38 3.5 19.4 1.0
OE1 B:GLU146 3.5 21.2 1.0
HE3 B:LYS38 3.5 19.4 1.0
NZ B:LYS16 3.6 26.8 1.0
CD B:GLU146 3.7 21.2 1.0
O3B B:ATP603 3.8 43.5 1.0
CB B:ASP70 3.9 31.5 1.0
N B:GLY17 3.9 37.3 1.0
HB2 B:LYS16 3.9 26.8 1.0
PB B:ATP603 3.9 43.5 1.0
CA B:GLY17 4.0 37.3 1.0
PG B:ATP603 4.0 43.5 1.0
O2A B:ATP603 4.0 43.5 1.0
HB3 B:ASP70 4.1 31.5 1.0
HA2 B:GLY17 4.1 37.3 1.0
NZ B:LYS38 4.2 19.4 1.0
HD3 B:LYS38 4.2 19.4 1.0
CE B:LYS38 4.3 19.4 1.0
HB2 B:ASP70 4.4 31.5 1.0
O4 B:UTP602 4.4 33.3 1.0
O1A B:ATP603 4.5 43.5 1.0
HZ1 B:LYS38 4.5 19.4 1.0
PA B:ATP603 4.5 43.5 1.0
O3A B:ATP603 4.5 43.5 1.0
OD2 B:ASP68 4.6 39.0 1.0
HH B:TYR74 4.6 28.7 1.0
HD13 B:LEU69 4.7 38.0 1.0
HA B:ASP70 4.7 37.3 1.0
CD B:LYS38 4.8 19.4 1.0
CA B:ASP70 4.9 37.3 1.0
O2G B:ATP603 4.9 43.5 1.0
C B:LYS16 4.9 37.3 1.0
CB B:LYS16 5.0 26.8 1.0
H B:ASP70 5.0 37.3 1.0

Magnesium binding site 7 out of 8 in 7rkh

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Magnesium binding site 7 out of 8 in the Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:30.0
occ:1.00
HZ3 C:LYS227 2.9 47.3 1.0
O2B D:UTP601 3.0 33.3 1.0
O1A D:UTP601 3.1 33.3 1.0
O3B D:UTP601 3.1 33.3 1.0
O3A D:UTP601 3.1 33.3 1.0
PB D:UTP601 3.3 33.3 1.0
HZ1 C:LYS227 3.7 47.3 1.0
NZ C:LYS227 3.7 47.3 1.0
PA D:UTP601 3.7 33.3 1.0
O2G D:UTP601 3.7 33.3 1.0
HZ3 C:LYS191 3.9 41.5 1.0
PG D:UTP601 3.9 33.3 1.0
HZ2 C:LYS227 4.0 47.3 1.0
HE2 D:HIS55 4.1 59.4 1.0
C5' D:UTP601 4.2 33.3 1.0
O1G D:UTP601 4.2 33.3 1.0
O5' D:UTP601 4.2 33.3 1.0
HZ2 C:LYS191 4.2 41.5 1.0
NZ C:LYS191 4.6 41.5 1.0
HG D:SER12 4.6 42.8 1.0
NE2 D:HIS55 4.8 59.4 1.0
O1B D:UTP601 4.8 33.3 1.0
HD2 D:HIS55 4.9 59.4 1.0
CE C:LYS227 4.9 47.3 1.0
HD2 C:LYS227 5.0 47.3 1.0

Magnesium binding site 8 out of 8 in 7rkh

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Magnesium binding site 8 out of 8 in the Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast Ctp Synthase (URA8) Tetramer Bound to Atp/Utp at Neutral pH within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:30.0
occ:1.00
OD2 C:ASP70 1.9 31.5 1.0
OD1 C:ASP70 2.4 31.5 1.0
CG C:ASP70 2.4 31.5 1.0
O1B C:ATP603 2.9 43.5 1.0
O3G C:ATP603 3.0 43.5 1.0
HZ1 C:LYS16 3.1 26.8 1.0
OE2 C:GLU146 3.2 21.2 1.0
HA3 C:GLY17 3.3 37.3 1.0
HZ2 C:LYS16 3.4 26.8 1.0
H C:GLY17 3.4 37.3 1.0
HZ3 C:LYS16 3.4 26.8 1.0
HZ3 C:LYS38 3.5 19.4 1.0
OE1 C:GLU146 3.5 21.2 1.0
HE3 C:LYS38 3.5 19.4 1.0
NZ C:LYS16 3.6 26.8 1.0
CD C:GLU146 3.7 21.2 1.0
O3B C:ATP603 3.8 43.5 1.0
CB C:ASP70 3.9 31.5 1.0
N C:GLY17 3.9 37.3 1.0
HB2 C:LYS16 3.9 26.8 1.0
PB C:ATP603 3.9 43.5 1.0
CA C:GLY17 4.0 37.3 1.0
PG C:ATP603 4.0 43.5 1.0
O2A C:ATP603 4.0 43.5 1.0
HB3 C:ASP70 4.1 31.5 1.0
HA2 C:GLY17 4.1 37.3 1.0
NZ C:LYS38 4.2 19.4 1.0
HD3 C:LYS38 4.2 19.4 1.0
CE C:LYS38 4.3 19.4 1.0
HB2 C:ASP70 4.4 31.5 1.0
O4 C:UTP602 4.4 33.3 1.0
O1A C:ATP603 4.5 43.5 1.0
HZ1 C:LYS38 4.5 19.4 1.0
PA C:ATP603 4.5 43.5 1.0
O3A C:ATP603 4.6 43.5 1.0
OD2 C:ASP68 4.6 39.0 1.0
HH C:TYR74 4.6 28.7 1.0
HD13 C:LEU69 4.7 38.0 1.0
HA C:ASP70 4.7 37.3 1.0
CD C:LYS38 4.8 19.4 1.0
CA C:ASP70 4.9 37.3 1.0
O2G C:ATP603 4.9 43.5 1.0
C C:LYS16 4.9 37.3 1.0
CB C:LYS16 5.0 26.8 1.0
H C:ASP70 5.0 37.3 1.0

Reference:

J.M.Hansen, A.Horowitz, E.M.Lynch, D.P.Farrell, J.Quispe, F.Dimaio, J.M.Kollman. Cryo-Em Structures of Ctp Synthase Filaments Reveal Mechanism of pH-Sensitive Assembly During Budding Yeast Starvation. Elife V. 10 2021.
ISSN: ESSN 2050-084X
PubMed: 34734801
DOI: 10.7554/ELIFE.73368
Page generated: Thu Nov 25 10:09:30 2021

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