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Magnesium in PDB 7xmv: E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P

Enzymatic activity of E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P

All present enzymatic activity of E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P:
2.7.6.1;

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P (pdb code 7xmv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P, PDB code: 7xmv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 7xmv

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Magnesium binding site 1 out of 12 in the E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:68.2
occ:1.00
 O A:HOH2601 1.9 61.8 1.0
O1 A:HSX401 2.0 64.0 1.0
OD2 A:ASP170 2.0 63.6 1.0
O A:HOH2611 2.1 60.7 1.0
O2 A:HSX401 2.2 64.0 1.0
O3 A:HSX401 2.7 64.0 1.0
CG A:ASP170 2.9 63.6 1.0
C2 A:HSX401 3.0 64.0 1.0
C1 A:HSX401 3.0 64.0 1.0
OD1 A:ASP170 3.1 63.6 1.0
C3 A:HSX401 3.4 64.0 1.0
OD1 A:ASP220 3.8 61.3 1.0
OD2 A:ASP220 4.0 61.3 1.0
C4 A:HSX401 4.1 64.0 1.0
O4 A:HSX401 4.1 64.0 1.0
O A:HOH2687 4.3 61.3 1.0
CB A:ASP170 4.3 63.6 1.0
CG A:ASP220 4.3 61.3 1.0
O1A A:ADP404 4.4 53.5 1.0
O A:HOH2685 4.5 57.7 1.0
OD1 A:ASP221 4.7 58.0 1.0
N A:GLY173 4.9 61.7 1.0

Magnesium binding site 2 out of 12 in 7xmv

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Magnesium binding site 2 out of 12 in the E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:56.9
occ:1.00
 O A:HOH2606 1.9 50.5 1.0
O3B A:ADP404 1.9 53.5 1.0
O A:HOH2618 2.0 50.1 1.0
O A:HOH2616 2.0 54.3 1.0
O2A A:ADP404 2.0 53.5 1.0
NE2 A:HIS131 2.2 47.8 1.0
CE1 A:HIS131 2.9 47.8 1.0
PA A:ADP404 3.1 53.5 1.0
PB A:ADP404 3.2 53.5 1.0
O3A A:ADP404 3.2 53.5 1.0
CD2 A:HIS131 3.3 47.8 1.0
ND1 A:HIS131 4.1 47.8 1.0
O1B A:ADP404 4.1 53.5 1.0
O1A A:ADP404 4.1 53.5 1.0
O2B A:ADP404 4.2 53.5 1.0
O5' A:ADP404 4.3 53.5 1.0
O A:HOH2611 4.3 60.7 1.0
CG A:HIS131 4.3 47.8 1.0
C5' A:ADP404 4.5 53.5 1.0
NH1 A:ARG99 4.5 45.9 1.0
O A:HOH2682 4.5 50.8 1.0
O A:HOH2668 4.9 57.5 1.0
OD2 A:ASP98 5.0 45.5 1.0

Magnesium binding site 3 out of 12 in 7xmv

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Magnesium binding site 3 out of 12 in the E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:67.1
occ:1.00
 O E:HOH2601 1.9 62.3 1.0
O1 E:HSX401 2.0 64.2 1.0
OD2 E:ASP170 2.0 63.5 1.0
O E:HOH2610 2.0 60.5 1.0
O2 E:HSX401 2.2 64.2 1.0
O3 E:HSX401 2.7 64.2 1.0
CG E:ASP170 2.9 63.5 1.0
C2 E:HSX401 3.0 64.2 1.0
C1 E:HSX401 3.0 64.2 1.0
OD1 E:ASP170 3.1 63.5 1.0
C3 E:HSX401 3.4 64.2 1.0
OD1 E:ASP220 3.8 61.3 1.0
OD2 E:ASP220 4.0 61.3 1.0
C4 E:HSX401 4.1 64.2 1.0
O4 E:HSX401 4.1 64.2 1.0
CB E:ASP170 4.3 63.5 1.0
CG E:ASP220 4.3 61.3 1.0
O E:HOH2692 4.3 62.4 1.0
O1A E:ADP404 4.4 52.9 1.0
O E:HOH2683 4.5 57.1 1.0
OD1 E:ASP221 4.7 58.0 1.0
N E:GLY173 4.9 60.5 1.0

Magnesium binding site 4 out of 12 in 7xmv

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Magnesium binding site 4 out of 12 in the E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg403

b:55.1
occ:1.00
 O E:HOH2605 1.9 49.3 1.0
O3B E:ADP404 1.9 52.9 1.0
O E:HOH2615 1.9 50.2 1.0
O E:HOH2618 2.0 53.8 1.0
O2A E:ADP404 2.0 52.9 1.0
NE2 E:HIS131 2.2 48.0 1.0
CE1 E:HIS131 2.9 48.0 1.0
PA E:ADP404 3.1 52.9 1.0
PB E:ADP404 3.2 52.9 1.0
O3A E:ADP404 3.2 52.9 1.0
CD2 E:HIS131 3.3 48.0 1.0
ND1 E:HIS131 4.1 48.0 1.0
O1A E:ADP404 4.1 52.9 1.0
O1B E:ADP404 4.1 52.9 1.0
O2B E:ADP404 4.2 52.9 1.0
O5' E:ADP404 4.3 52.9 1.0
O E:HOH2610 4.3 60.5 1.0
CG E:HIS131 4.3 48.0 1.0
O E:HOH2678 4.4 49.6 1.0
C5' E:ADP404 4.5 52.9 1.0
NH1 E:ARG99 4.5 45.4 1.0
O E:HOH2673 4.9 54.1 1.0
OD2 E:ASP98 5.0 44.9 1.0

Magnesium binding site 5 out of 12 in 7xmv

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Magnesium binding site 5 out of 12 in the E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:68.4
occ:1.00
 O C:HOH2601 1.9 61.9 1.0
O1 C:HSX401 2.0 63.9 1.0
O C:HOH2610 2.0 61.0 1.0
OD2 C:ASP170 2.0 64.4 1.0
O2 C:HSX401 2.2 63.9 1.0
O3 C:HSX401 2.7 63.9 1.0
CG C:ASP170 2.9 64.4 1.0
C2 C:HSX401 3.0 63.9 1.0
C1 C:HSX401 3.0 63.9 1.0
OD1 C:ASP170 3.1 64.4 1.0
C3 C:HSX401 3.4 63.9 1.0
OD1 C:ASP220 3.8 61.4 1.0
OD2 C:ASP220 4.0 61.4 1.0
C4 C:HSX401 4.1 63.9 1.0
O4 C:HSX401 4.1 63.9 1.0
O C:HOH2684 4.3 62.7 1.0
CB C:ASP170 4.3 64.4 1.0
CG C:ASP220 4.3 61.4 1.0
O2A C:ADP404 4.4 53.9 1.0
O C:HOH2683 4.4 58.1 1.0
OD1 C:ASP221 4.7 58.1 1.0
N C:GLY173 4.9 62.2 1.0

Magnesium binding site 6 out of 12 in 7xmv

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Magnesium binding site 6 out of 12 in the E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:57.2
occ:1.00
 O C:HOH2604 1.9 50.6 1.0
O1B C:ADP404 1.9 53.9 1.0
O C:HOH2617 1.9 50.1 1.0
O C:HOH2618 2.0 54.2 1.0
O1A C:ADP404 2.0 53.9 1.0
NE2 C:HIS131 2.2 48.3 1.0
CE1 C:HIS131 2.9 48.3 1.0
PA C:ADP404 3.1 53.9 1.0
PB C:ADP404 3.2 53.9 1.0
O3A C:ADP404 3.2 53.9 1.0
CD2 C:HIS131 3.3 48.3 1.0
ND1 C:HIS131 4.1 48.3 1.0
O2A C:ADP404 4.1 53.9 1.0
O3B C:ADP404 4.1 53.9 1.0
O2B C:ADP404 4.2 53.9 1.0
O5' C:ADP404 4.3 53.9 1.0
O C:HOH2610 4.3 61.0 1.0
CG C:HIS131 4.3 48.3 1.0
C5' C:ADP404 4.5 53.9 1.0
O C:HOH2677 4.5 50.7 1.0
NH1 C:ARG99 4.5 45.7 1.0
O C:HOH2668 4.9 57.8 1.0
OD2 C:ASP98 5.0 45.5 1.0

Magnesium binding site 7 out of 12 in 7xmv

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Magnesium binding site 7 out of 12 in the E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:66.9
occ:1.00
 O D:HOH2601 1.9 62.3 1.0
O1 D:HSX401 2.0 63.2 1.0
OD2 D:ASP170 2.0 63.9 1.0
O D:HOH2611 2.1 60.0 1.0
O2 D:HSX401 2.2 63.2 1.0
O3 D:HSX401 2.7 63.2 1.0
CG D:ASP170 2.9 63.9 1.0
C2 D:HSX401 3.0 63.2 1.0
C1 D:HSX401 3.0 63.2 1.0
OD1 D:ASP170 3.1 63.9 1.0
C3 D:HSX401 3.4 63.2 1.0
OD1 D:ASP220 3.8 60.4 1.0
OD2 D:ASP220 4.0 60.4 1.0
C4 D:HSX401 4.1 63.2 1.0
O4 D:HSX401 4.1 63.2 1.0
CB D:ASP170 4.3 63.9 1.0
O D:HOH2688 4.3 63.6 1.0
CG D:ASP220 4.3 60.4 1.0
O1A D:ADP404 4.4 52.9 1.0
O D:HOH2682 4.4 57.9 1.0
OD1 D:ASP221 4.7 57.3 1.0
N D:GLY173 4.9 60.6 1.0

Magnesium binding site 8 out of 12 in 7xmv

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Magnesium binding site 8 out of 12 in the E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:54.7
occ:1.00
 O D:HOH2605 1.9 49.7 1.0
O3B D:ADP404 1.9 52.9 1.0
O D:HOH2615 1.9 49.9 1.0
O2A D:ADP404 2.0 52.9 1.0
O D:HOH2620 2.0 53.5 1.0
NE2 D:HIS131 2.2 48.2 1.0
CE1 D:HIS131 2.9 48.2 1.0
PA D:ADP404 3.1 52.9 1.0
PB D:ADP404 3.2 52.9 1.0
O3A D:ADP404 3.2 52.9 1.0
CD2 D:HIS131 3.3 48.2 1.0
ND1 D:HIS131 4.1 48.2 1.0
O1A D:ADP404 4.1 52.9 1.0
O1B D:ADP404 4.1 52.9 1.0
O2B D:ADP404 4.2 52.9 1.0
O D:HOH2611 4.2 60.0 1.0
O5' D:ADP404 4.3 52.9 1.0
CG D:HIS131 4.3 48.2 1.0
O D:HOH2673 4.4 51.8 1.0
C5' D:ADP404 4.5 52.9 1.0
NH1 D:ARG99 4.5 44.8 1.0
O D:HOH2669 4.9 54.9 1.0
OD2 D:ASP98 5.0 44.2 1.0

Magnesium binding site 9 out of 12 in 7xmv

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Magnesium binding site 9 out of 12 in the E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:67.3
occ:1.00
 O B:HOH2601 1.9 61.7 1.0
O1 B:HSX401 2.0 64.3 1.0
OD2 B:ASP170 2.0 63.7 1.0
O B:HOH2612 2.1 59.8 1.0
O2 B:HSX401 2.2 64.3 1.0
O3 B:HSX401 2.7 64.3 1.0
CG B:ASP170 2.9 63.7 1.0
C2 B:HSX401 3.0 64.3 1.0
C1 B:HSX401 3.0 64.3 1.0
OD1 B:ASP170 3.1 63.7 1.0
C3 B:HSX401 3.4 64.3 1.0
OD1 B:ASP220 3.8 61.2 1.0
OD2 B:ASP220 4.0 61.2 1.0
C4 B:HSX401 4.1 64.3 1.0
O4 B:HSX401 4.1 64.3 1.0
O B:HOH2688 4.3 62.7 1.0
CB B:ASP170 4.3 63.7 1.0
CG B:ASP220 4.3 61.2 1.0
O2A B:ADP404 4.4 53.1 1.0
O B:HOH2685 4.5 57.7 1.0
OD1 B:ASP221 4.7 58.0 1.0
N B:GLY173 4.9 60.7 1.0

Magnesium binding site 10 out of 12 in 7xmv

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Magnesium binding site 10 out of 12 in the E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of E.Coli Phosphoribosylpyrophosphate (Prpp) Synthetase Type A(Amp/Adp) Filament Bound with Adp, Amp and R5P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:55.5
occ:1.00
 O B:HOH2607 1.9 49.3 1.0
O1B B:ADP404 1.9 53.1 1.0
O B:HOH2614 1.9 50.4 1.0
O B:HOH2618 2.0 53.7 1.0
O1A B:ADP404 2.0 53.1 1.0
NE2 B:HIS131 2.2 48.0 1.0
CE1 B:HIS131 2.9 48.0 1.0
PA B:ADP404 3.1 53.1 1.0
PB B:ADP404 3.2 53.1 1.0
O3A B:ADP404 3.2 53.1 1.0
CD2 B:HIS131 3.3 48.0 1.0
ND1 B:HIS131 4.1 48.0 1.0
O3B B:ADP404 4.1 53.1 1.0
O2A B:ADP404 4.1 53.1 1.0
O2B B:ADP404 4.2 53.1 1.0
O B:HOH2612 4.3 59.8 1.0
O5' B:ADP404 4.3 53.1 1.0
CG B:HIS131 4.3 48.0 1.0
O B:HOH2677 4.4 50.2 1.0
C5' B:ADP404 4.5 53.1 1.0
NH1 B:ARG99 4.5 45.5 1.0
O B:HOH2672 5.0 54.1 1.0
OD2 B:ASP98 5.0 45.0 1.0

Reference:

H.H.Hu, G.M.Lu, C.C.Chang, Y.Li, J.Zhong, C.J.Guo, X.Zhou, B.Yin, T.Zhang, J.L.Liu. Filamentation Modulates Allosteric Regulation of Prps. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35736577
DOI: 10.7554/ELIFE.79552
Page generated: Thu Oct 3 12:31:12 2024

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