Atomistry » Magnesium » PDB 5t3k-5tfc » 5t8s
Atomistry »
  Magnesium »
    PDB 5t3k-5tfc »
      5t8s »

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

Last articles

Mg in 1RTD
Mg in 1RTK
Mg in 1RRP
Mg in 1RS0
Mg in 1RRG
Mg in 1RRF
Mg in 1RQJ
Mg in 1RQY
Mg in 1RQN
Mg in 1RQI
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy