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Magnesium in PDB 5t8s: Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium

Enzymatic activity of Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium

All present enzymatic activity of Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium:
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium, PDB code: 5t8s was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.28 / 1.70
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 115.710, 115.710, 146.240, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 17.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium (pdb code 5t8s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium, PDB code: 5t8s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5t8s

Go back to Magnesium Binding Sites List in 5t8s
Magnesium binding site 1 out of 4 in the Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:21.1
occ:1.00
 O A:HOH535 2.0 21.5 1.0
O1A B:3PO404 2.0 13.5 0.9
O B:HOH557 2.1 20.1 1.0
O A:HOH543 2.3 18.9 1.0
O B:HOH578 2.3 14.4 1.0
O1G B:3PO404 2.3 18.6 0.9
PA B:3PO404 3.4 12.7 0.9
PG B:3PO404 3.6 20.5 0.9
OD2 A:ASP276 3.7 21.9 1.0
O3B B:3PO404 3.7 13.8 0.9
OE2 B:GLU9 3.9 16.3 1.0
NZ B:LYS250 4.0 14.3 1.0
O3A B:3PO404 4.0 15.7 0.9
OD1 A:ASP276 4.1 17.8 1.0
O A:HOH629 4.1 20.3 1.0
O B:HOH587 4.1 14.8 1.0
NZ B:LYS168 4.1 13.5 1.0
OD2 A:ASP121 4.2 16.9 1.0
O2A B:3PO404 4.2 11.6 0.9
CG A:ASP276 4.3 20.4 1.0
O5' B:3PO404 4.3 13.4 0.9
O2G B:3PO404 4.5 13.6 0.9
PB B:3PO404 4.6 12.6 0.9
OE1 B:GLU9 4.6 16.9 1.0
CE B:LYS250 4.6 14.1 1.0
O A:GLN122 4.6 18.0 1.0
O A:HOH623 4.6 15.6 1.0
CA A:GLY265 4.6 14.2 1.0
O3G B:3PO404 4.7 24.6 0.9
CD B:GLU9 4.7 18.5 1.0
N A:GLY265 5.0 16.9 1.0

Magnesium binding site 2 out of 4 in 5t8s

Go back to Magnesium Binding Sites List in 5t8s
Magnesium binding site 2 out of 4 in the Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:12.5
occ:0.83
 OD2 A:ASP17 1.9 12.5 1.0
O4 A:PO4405 2.0 12.6 0.8
O6 A:POP404 2.1 14.8 0.7
O3 A:POP404 2.1 15.4 0.7
O A:HOH656 2.2 17.7 1.0
O A:HOH524 2.2 17.5 1.0
CG A:ASP17 2.9 11.6 1.0
OD1 A:ASP17 3.2 11.3 1.0
P1 A:POP404 3.3 16.3 0.7
P2 A:POP404 3.3 13.5 0.7
P A:PO4405 3.4 16.9 0.8
NZ A:LYS250 3.5 14.9 1.0
O A:POP404 3.6 15.3 0.7
O1 A:POP404 3.8 16.1 0.7
O B:HOH595 3.9 22.6 1.0
O3 A:PO4405 4.0 16.3 0.8
CE1 A:HIS15 4.0 12.3 1.0
O4 A:POP404 4.0 14.7 0.7
O A:HOH502 4.0 21.4 1.0
O2 A:PO4405 4.2 14.8 0.8
CB A:ASP17 4.2 9.6 1.0
NH2 A:ARG249 4.4 15.4 1.0
O1 A:PO4405 4.4 14.7 0.8
O5 A:POP404 4.4 13.5 0.7
O2 A:POP404 4.5 17.4 0.7
O A:CYS244 4.5 13.2 0.5
O A:CYS244 4.6 13.4 0.5
CE A:LYS250 4.6 14.7 1.0
CB A:ARG249 4.6 10.3 1.0
NE2 A:HIS15 4.7 12.2 1.0
MG B:MG403 4.7 16.2 0.7
O A:ARG249 4.9 10.9 1.0
NE A:ARG249 4.9 13.0 1.0
CZ A:ARG249 4.9 14.0 1.0

Magnesium binding site 3 out of 4 in 5t8s

Go back to Magnesium Binding Sites List in 5t8s
Magnesium binding site 3 out of 4 in the Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:10.3
occ:1.00
 O2B B:3PO404 2.0 12.3 0.9
OD2 B:ASP17 2.1 11.2 1.0
O2A B:3PO404 2.1 11.6 0.9
O2G B:3PO404 2.1 13.6 0.9
O B:HOH583 2.1 12.1 1.0
O B:HOH528 2.2 12.3 1.0
CG B:ASP17 3.0 12.7 1.0
PB B:3PO404 3.1 12.6 0.9
PG B:3PO404 3.3 20.5 0.9
PA B:3PO404 3.3 12.7 0.9
OD1 B:ASP17 3.3 11.8 1.0
O3B B:3PO404 3.5 13.8 0.9
O3A B:3PO404 3.5 15.7 0.9
NZ B:LYS250 3.6 14.3 1.0
O B:HOH618 3.8 14.7 1.0
NH2 B:ARG249 4.1 13.5 1.0
O1A B:3PO404 4.2 13.5 0.9
OD2 B:ASP243 4.2 17.7 1.0
O1G B:3PO404 4.2 18.6 0.9
CE1 B:HIS15 4.2 12.2 1.0
O3G B:3PO404 4.3 24.6 0.9
CB B:ASP17 4.3 9.9 1.0
O5' B:3PO404 4.4 13.4 0.9
O1B B:3PO404 4.4 14.2 0.9
O B:CYS244 4.5 12.8 1.0
CB B:ARG249 4.5 12.2 1.0
CZ B:ARG249 4.6 13.5 1.0
NE B:ARG249 4.6 14.4 1.0
CE B:LYS250 4.7 14.1 1.0
OE2 A:GLU43 4.8 15.5 1.0
NE2 B:HIS15 4.8 13.7 1.0
O B:ARG249 4.8 12.5 1.0
OD1 B:ASP243 5.0 16.9 1.0
O B:HOH523 5.0 23.0 1.0
CG B:ASP243 5.0 16.8 1.0

Magnesium binding site 4 out of 4 in 5t8s

Go back to Magnesium Binding Sites List in 5t8s
Magnesium binding site 4 out of 4 in the Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:16.2
occ:0.74
 O3 A:PO4405 2.1 16.3 0.8
O1 A:POP404 2.1 16.1 0.7
O B:HOH600 2.1 22.8 1.0
O4 A:POP404 2.1 14.7 0.7
O A:HOH736 2.2 21.4 1.0
OD2 B:ASP276 2.2 22.6 1.0
P2 A:POP404 3.2 13.5 0.7
P1 A:POP404 3.2 16.3 0.7
CG B:ASP276 3.3 20.2 1.0
O A:POP404 3.3 15.3 0.7
P A:PO4405 3.3 16.9 0.8
OD1 B:ASP276 3.6 20.0 1.0
O2 A:PO4405 3.7 14.8 0.8
O A:HOH692 3.9 23.7 1.0
O4 A:PO4405 3.9 12.6 0.8
O6 A:POP404 3.9 14.8 0.7
NZ B:LYS270 4.0 16.9 1.0
O A:HOH659 4.1 23.7 1.0
O3 A:POP404 4.1 15.4 0.7
O A:HOH556 4.1 19.6 1.0
O A:HOH652 4.2 30.7 1.0
O B:HOH572 4.2 22.8 1.0
O2 A:POP404 4.3 17.4 0.7
OD2 B:ASP121 4.4 19.5 1.0
O5 A:POP404 4.4 13.5 0.7
CA B:GLY265 4.4 15.8 1.0
NZ A:LYS250 4.5 14.9 1.0
CB B:ASP276 4.6 17.2 1.0
O1 A:PO4405 4.6 14.7 0.8
MG A:MG403 4.7 12.5 0.8
O B:HOH697 4.8 19.7 1.0

Reference:

D.M.Dranow, S.L.Delker, D.D.Lorimer, T.E.Edwards. Crystal Structure of A S-Adenosylmethionine Synthase From Neisseria Gonorrhoeae with Bound S-Adenosylmethionine, Amp, Pyrophosphate, Phosphate, and Magnesium To Be Published.
Page generated: Mon Sep 30 04:46:29 2024

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