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Magnesium in PDB 7p8m: Crystal Structure of L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Dmnb- Sam (4,5-Dimethoxy-2-Nitro Benzyme S-Adenosyl-Methionine)

Enzymatic activity of Crystal Structure of L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Dmnb- Sam (4,5-Dimethoxy-2-Nitro Benzyme S-Adenosyl-Methionine)

All present enzymatic activity of Crystal Structure of L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Dmnb- Sam (4,5-Dimethoxy-2-Nitro Benzyme S-Adenosyl-Methionine):
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Dmnb- Sam (4,5-Dimethoxy-2-Nitro Benzyme S-Adenosyl-Methionine), PDB code: 7p8m was solved by E.Herrmann, A.Peters, N.V.Cornelissen, A.Rentmeister, D.Kuemmel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.85 / 1.71
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 76.49, 76.49, 280.99, 90, 90, 120
R / Rfree (%) 19.1 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Dmnb- Sam (4,5-Dimethoxy-2-Nitro Benzyme S-Adenosyl-Methionine) (pdb code 7p8m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Dmnb- Sam (4,5-Dimethoxy-2-Nitro Benzyme S-Adenosyl-Methionine), PDB code: 7p8m:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7p8m

Go back to Magnesium Binding Sites List in 7p8m
Magnesium binding site 1 out of 3 in the Crystal Structure of L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Dmnb- Sam (4,5-Dimethoxy-2-Nitro Benzyme S-Adenosyl-Methionine)


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 L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Dmnb- Sam (4,5-Dimethoxy-2-Nitro Benzyme S-Adenosyl-Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:28.0
occ:1.00
 O1A A:3PO501 2.0 30.6 1.0
O1G A:3PO501 2.1 29.2 1.0
O1B A:3PO501 2.1 28.4 1.0
OD2 A:ASP31 2.2 21.3 1.0
O A:HOH617 2.2 29.0 1.0
O C:HOH641 2.2 25.3 1.0
HZ3 A:LYS25 3.1 31.6 1.0
PB A:3PO501 3.1 32.5 1.0
CG A:ASP31 3.1 26.2 1.0
HE1 A:HIS29 3.2 28.9 1.0
PA A:3PO501 3.3 34.3 1.0
PG A:3PO501 3.3 29.9 1.0
OD1 A:ASP31 3.4 24.6 1.0
O3A A:3PO501 3.5 35.7 1.0
O3B A:3PO501 3.5 33.2 1.0
HZ1 A:LYS25 3.7 31.6 1.0
NZ A:LYS25 3.8 26.3 1.0
HB3 A:ARG291 3.9 31.9 1.0
HE22 C:GLN63 3.9 27.9 1.0
HH21 A:ARG291 4.1 28.1 1.0
O C:HOH662 4.1 28.7 1.0
CE1 A:HIS29 4.2 24.1 1.0
O A:HOH686 4.2 31.4 1.0
O5' A:3PO501 4.2 34.8 1.0
O2G A:3PO501 4.2 30.5 1.0
HE A:ARG291 4.2 36.1 1.0
HZ2 A:LYS25 4.3 31.6 1.0
O2A A:3PO501 4.3 30.0 1.0
NH2 A:ARG291 4.4 23.4 1.0
O3G A:3PO501 4.4 26.5 1.0
O A:ASP286 4.4 23.3 1.0
HE2 A:LYS25 4.4 31.8 1.0
O2B A:3PO501 4.5 30.2 1.0
HE21 C:GLN63 4.5 27.9 1.0
CB A:ASP31 4.5 22.3 1.0
HA2 A:GLY287 4.5 26.0 1.0
HG3 A:ARG291 4.5 36.9 1.0
NE A:ARG291 4.5 30.1 1.0
NE2 C:GLN63 4.6 23.3 1.0
HB2 A:ASP31 4.6 26.8 1.0
HB2 A:ARG291 4.6 31.9 1.0
CZ A:ARG291 4.6 28.2 1.0
CB A:ARG291 4.7 26.6 1.0
CE A:LYS25 4.7 26.5 1.0
HH22 A:ARG291 4.7 28.1 1.0
NE2 A:HIS29 4.9 25.3 1.0
HD3 A:LYS25 4.9 32.1 1.0
HB3 A:ASP31 5.0 26.8 1.0

Magnesium binding site 2 out of 3 in 7p8m

Go back to Magnesium Binding Sites List in 7p8m
Magnesium binding site 2 out of 3 in the Crystal Structure of L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Dmnb- Sam (4,5-Dimethoxy-2-Nitro Benzyme S-Adenosyl-Methionine)


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 L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Dmnb- Sam (4,5-Dimethoxy-2-Nitro Benzyme S-Adenosyl-Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:53.1
occ:1.00
 O3G C:3PO501 2.0 26.9 1.0
OE1 A:GLU308 2.1 31.1 1.0
OE2 A:GLU308 2.1 26.3 1.0
O5' C:3PO501 2.2 30.5 1.0
O3A C:3PO501 2.2 34.6 1.0
O A:HOH655 2.2 35.5 1.0
CD A:GLU308 2.3 27.8 1.0
PA C:3PO501 2.7 37.5 1.0
PG C:3PO501 3.0 26.7 1.0
O3B C:3PO501 3.2 28.0 1.0
PB C:3PO501 3.3 31.9 1.0
O2A C:3PO501 3.6 31.1 1.0
HZ1 C:LYS25 3.6 30.1 1.0
O1G C:3PO501 3.7 26.5 1.0
O C:HOH646 3.7 28.2 1.0
CG A:GLU308 3.7 27.6 1.0
HA A:GLU308 3.7 32.8 1.0
HE1 A:HIS318 3.8 33.0 1.0
O C:HOH742 3.8 35.0 1.0
HE2 A:LYS313 3.9 32.6 1.0
O1A C:3PO501 3.9 36.8 1.0
HG2 A:GLU308 4.0 33.1 1.0
HB3 A:GLU308 4.1 30.3 1.0
O2B C:3PO501 4.2 30.7 1.0
HG A:SER165 4.2 38.0 1.0
HB3 A:SER165 4.2 36.1 1.0
O2G C:3PO501 4.3 22.7 1.0
CB A:GLU308 4.3 25.3 1.0
HE3 A:LYS313 4.3 32.6 1.0
HG3 A:GLU308 4.3 33.1 1.0
OG A:SER165 4.3 31.7 1.0
O1B C:3PO501 4.4 28.6 1.0
NZ C:LYS25 4.5 25.1 1.0
HZ1 A:LYS313 4.5 33.1 1.0
CA A:GLU308 4.5 27.4 1.0
HE2 C:LYS25 4.5 26.8 1.0
CE A:LYS313 4.5 27.2 1.0
CE1 A:HIS318 4.6 27.5 1.0
HA3 A:GLY320 4.6 32.8 1.0
HE3 C:LYS25 4.7 26.8 1.0
MG C:MG502 4.8 27.6 1.0
H A:ALA309 4.8 32.7 1.0
CB A:SER165 4.8 30.1 1.0
HZ3 C:LYS25 4.8 30.1 1.0
HZ1 C:LYS204 4.8 35.9 1.0
CE C:LYS25 4.8 22.3 1.0
O C:HOH703 4.9 28.0 1.0
HZ2 C:LYS204 4.9 35.9 1.0
HZ2 C:LYS25 5.0 30.1 1.0
NZ A:LYS313 5.0 27.6 1.0

Magnesium binding site 3 out of 3 in 7p8m

Go back to Magnesium Binding Sites List in 7p8m
Magnesium binding site 3 out of 3 in the Crystal Structure of L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Dmnb- Sam (4,5-Dimethoxy-2-Nitro Benzyme S-Adenosyl-Methionine)


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 L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Dmnb- Sam (4,5-Dimethoxy-2-Nitro Benzyme S-Adenosyl-Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:27.6
occ:1.00
 O1A C:3PO501 1.9 36.8 1.0
O1B C:3PO501 2.0 28.6 1.0
O1G C:3PO501 2.1 26.5 1.0
O C:HOH619 2.2 23.9 1.0
OD2 C:ASP31 2.2 21.9 1.0
O C:HOH634 2.2 25.0 1.0
PB C:3PO501 3.1 31.9 1.0
HZ3 C:LYS25 3.1 30.1 1.0
HE1 C:HIS29 3.1 24.2 1.0
CG C:ASP31 3.1 24.0 1.0
PA C:3PO501 3.1 37.5 1.0
PG C:3PO501 3.3 26.7 1.0
OD1 C:ASP31 3.4 27.6 1.0
O3A C:3PO501 3.5 34.6 1.0
O3B C:3PO501 3.5 28.0 1.0
HZ1 C:LYS25 3.6 30.1 1.0
NZ C:LYS25 3.8 25.1 1.0
O5' C:3PO501 3.8 30.5 1.0
HH21 C:ARG291 3.8 31.7 1.0
HE C:ARG291 3.8 37.0 1.0
HE21 A:GLN63 4.0 29.9 1.0
CE1 C:HIS29 4.0 20.2 1.0
O C:HOH701 4.1 30.5 1.0
O3G C:3PO501 4.2 26.9 1.0
NE C:ARG291 4.3 30.9 1.0
NH2 C:ARG291 4.3 26.4 1.0
O C:ASP286 4.3 21.9 1.0
O2A C:3PO501 4.3 31.1 1.0
HZ2 C:LYS25 4.3 30.1 1.0
O2G C:3PO501 4.4 22.7 1.0
OD2 C:ASP285 4.4 30.6 1.0
HE2 C:LYS25 4.4 26.8 1.0
O2B C:3PO501 4.4 30.7 1.0
HA2 C:GLY287 4.5 26.7 1.0
CB C:ASP31 4.5 22.9 1.0
HB2 C:ASP31 4.5 27.5 1.0
HB3 C:ARG291 4.5 44.2 1.0
HE22 A:GLN63 4.6 29.9 1.0
CZ C:ARG291 4.6 24.0 1.0
NE2 C:HIS29 4.6 22.8 1.0
NE2 A:GLN63 4.6 24.9 1.0
HZ1 A:LYS313 4.7 33.1 1.0
CE C:LYS25 4.7 22.3 1.0
MG A:MG503 4.8 53.1 1.0
HH22 C:ARG291 4.8 31.7 1.0
HD3 C:ARG291 4.9 38.5 1.0
HB2 C:ARG291 4.9 44.2 1.0
H C:ASP31 4.9 27.4 1.0
OD1 C:ASP285 5.0 24.5 1.0
HB3 C:ASP31 5.0 27.5 1.0

Reference:

A.Peters, E.Herrmann, N.V.Cornelissen, N.Klocker, D.Kummel, A.Rentmeister. Visible-Light Removable Photocaging Groups Accepted By Mjmat Variant: Structural Basis and Compatibility with Dna and Rna Methyltransferases. Chembiochem 2021.
ISSN: ESSN 1439-7633
PubMed: 34606675
DOI: 10.1002/CBIC.202100437
Page generated: Thu Oct 3 04:02:33 2024

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