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Magnesium in PDB 7p84: Crystal Structure of L147A/I351A Variant of S-Adenosylmethionine Synthetase From Methanocaldococcus Jannaschii in Complex with Onb-Sam (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 Onb-Sam (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 Onb-Sam (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 Onb-Sam (2-Nitro Benzyme S-Adenosyl-Methionine), PDB code: 7p84 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) 48.04 / 2.05
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 76.104, 76.104, 280.674, 90, 90, 120
R / Rfree (%) 17.8 / 22.2

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 Onb-Sam (2-Nitro Benzyme S-Adenosyl-Methionine) (pdb code 7p84). 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 Onb-Sam (2-Nitro Benzyme S-Adenosyl-Methionine), PDB code: 7p84:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7p84

Go back to Magnesium Binding Sites List in 7p84
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 Onb-Sam (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 Onb-Sam (2-Nitro Benzyme S-Adenosyl-Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:32.2
occ:1.00
 O1G A:3PO501 2.1 36.6 1.0
O1A A:3PO501 2.1 30.6 1.0
O A:HOH628 2.2 29.7 1.0
O A:HOH634 2.2 29.0 1.0
O1B A:3PO501 2.2 38.1 1.0
OD2 A:ASP31 2.3 24.0 1.0
HZ3 A:LYS25 2.9 39.6 1.0
CG A:ASP31 3.1 31.3 1.0
PB A:3PO501 3.2 49.6 1.0
HE1 A:HIS29 3.3 34.9 1.0
PA A:3PO501 3.3 44.8 1.0
PG A:3PO501 3.4 42.5 1.0
OD1 A:ASP31 3.4 26.4 1.0
HZ1 A:LYS25 3.6 39.6 1.0
O3B A:3PO501 3.6 42.4 1.0
O3A A:3PO501 3.6 48.2 1.0
NZ A:LYS25 3.6 33.0 1.0
HH21 A:ARG291 3.8 34.6 1.0
HB3 A:ARG291 3.9 35.7 1.0
HE22 C:GLN63 3.9 29.8 1.0
HZ2 A:LYS25 3.9 39.6 1.0
O A:HOH703 4.0 38.1 1.0
HE A:ARG291 4.1 32.2 1.0
NH2 A:ARG291 4.2 28.9 1.0
O5' A:3PO501 4.2 48.8 1.0
CE1 A:HIS29 4.2 29.1 1.0
O2G A:3PO501 4.2 37.6 1.0
O C:HOH646 4.4 31.8 1.0
O3G A:3PO501 4.4 41.6 1.0
O2A A:3PO501 4.4 35.5 1.0
O A:ASP286 4.4 28.3 1.0
HE21 C:GLN63 4.5 29.8 1.0
HA2 A:GLY287 4.5 30.6 1.0
NE A:ARG291 4.5 26.8 1.0
NE2 C:GLN63 4.5 24.8 1.0
CB A:ASP31 4.5 25.6 1.0
CZ A:ARG291 4.5 31.2 1.0
HH22 A:ARG291 4.6 34.6 1.0
O2B A:3PO501 4.6 48.8 1.0
HB2 A:ASP31 4.6 30.8 1.0
HB2 A:ARG291 4.6 35.7 1.0
CB A:ARG291 4.7 29.7 1.0
HG3 A:ARG291 4.8 35.9 1.0
HE2 A:LYS25 4.8 38.2 1.0
CE A:LYS25 4.8 31.9 1.0
HD3 A:LYS25 4.9 33.6 1.0
HZ1 C:LYS313 5.0 34.6 1.0
NE2 A:HIS29 5.0 29.0 1.0

Magnesium binding site 2 out of 3 in 7p84

Go back to Magnesium Binding Sites List in 7p84
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 Onb-Sam (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 Onb-Sam (2-Nitro Benzyme S-Adenosyl-Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:57.3
occ:1.00
 O3G C:3PO501 2.0 35.7 1.0
OE2 A:GLU308 2.0 30.5 1.0
O5' C:3PO501 2.1 39.4 1.0
OE1 A:GLU308 2.2 35.4 1.0
CD A:GLU308 2.2 33.0 1.0
O3A C:3PO501 2.3 40.7 1.0
O A:HOH623 2.6 36.0 1.0
PA C:3PO501 2.7 43.5 1.0
PG C:3PO501 3.1 29.4 1.0
O3B C:3PO501 3.2 30.1 1.0
HZ1 C:LYS25 3.3 32.0 1.0
O C:HOH722 3.3 39.7 1.0
PB C:3PO501 3.3 36.0 1.0
HA A:GLU308 3.5 38.1 1.0
O C:HOH620 3.6 28.8 1.0
CG A:GLU308 3.6 30.0 1.0
O2A C:3PO501 3.8 32.2 1.0
HG2 A:GLU308 3.8 36.0 1.0
HG A:SER165 3.8 42.4 1.0
O1G C:3PO501 3.8 30.2 1.0
O1A C:3PO501 3.8 38.4 1.0
HE2 A:LYS313 4.1 34.5 1.0
NZ C:LYS25 4.1 26.7 1.0
HB3 A:GLU308 4.2 34.3 1.0
HE1 A:HIS318 4.2 39.5 1.0
HB3 A:SER165 4.2 37.0 1.0
OG A:SER165 4.2 35.3 1.0
CB A:GLU308 4.2 28.6 1.0
HG3 A:GLU308 4.3 36.0 1.0
O2G C:3PO501 4.3 25.9 1.0
HE2 C:LYS25 4.3 31.9 1.0
O2B C:3PO501 4.3 33.3 1.0
CA A:GLU308 4.3 31.7 1.0
HZ3 C:LYS25 4.4 32.0 1.0
O1B C:3PO501 4.4 36.8 1.0
HE3 A:LYS313 4.6 34.5 1.0
HZ1 A:LYS313 4.6 37.7 1.0
O A:HOH674 4.6 26.7 1.0
CE C:LYS25 4.6 26.6 1.0
HE3 C:LYS25 4.6 31.9 1.0
HZ2 C:LYS25 4.7 32.0 1.0
CE A:LYS313 4.7 28.8 1.0
HZ2 C:LYS204 4.8 34.7 1.0
CB A:SER165 4.8 30.8 1.0
H A:ALA309 4.8 34.8 1.0
HA3 A:GLY320 4.8 30.4 1.0
MG C:MG502 4.9 32.0 1.0
OD2 A:ASP163 4.9 35.0 1.0

Magnesium binding site 3 out of 3 in 7p84

Go back to Magnesium Binding Sites List in 7p84
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 Onb-Sam (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 Onb-Sam (2-Nitro Benzyme S-Adenosyl-Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:32.0
occ:1.00
 O1A C:3PO501 1.9 38.4 1.0
O1B C:3PO501 2.1 36.8 1.0
O C:HOH629 2.1 28.9 1.0
OD2 C:ASP31 2.1 26.6 1.0
O1G C:3PO501 2.2 30.2 1.0
O C:HOH608 2.3 29.7 1.0
CG C:ASP31 3.0 27.3 1.0
HZ3 C:LYS25 3.1 32.0 1.0
PB C:3PO501 3.2 36.0 1.0
PA C:3PO501 3.2 43.5 1.0
HE1 C:HIS29 3.2 29.3 1.0
OD1 C:ASP31 3.3 26.4 1.0
PG C:3PO501 3.4 29.4 1.0
O3A C:3PO501 3.6 40.7 1.0
O3B C:3PO501 3.6 30.1 1.0
HZ1 C:LYS25 3.8 32.0 1.0
NZ C:LYS25 3.8 26.7 1.0
O C:HOH691 3.9 27.7 1.0
HH21 C:ARG291 3.9 36.1 1.0
HE22 A:GLN63 3.9 30.8 1.0
O5' C:3PO501 4.0 39.4 1.0
HE C:ARG291 4.1 43.4 1.0
CE1 C:HIS29 4.1 24.4 1.0
O2A C:3PO501 4.2 32.2 1.0
HZ2 C:LYS25 4.2 32.0 1.0
NH2 C:ARG291 4.2 30.1 1.0
O3G C:3PO501 4.3 35.7 1.0
O C:ASP286 4.3 24.8 1.0
NE C:ARG291 4.3 36.1 1.0
HA2 C:GLY287 4.3 30.6 1.0
CB C:ASP31 4.4 23.7 1.0
OD2 C:ASP285 4.4 30.1 1.0
HB2 C:ASP31 4.4 28.4 1.0
HE21 A:GLN63 4.4 30.8 1.0
O2B C:3PO501 4.5 33.3 1.0
CZ C:ARG291 4.5 32.4 1.0
NE2 A:GLN63 4.5 25.7 1.0
O2G C:3PO501 4.5 25.9 1.0
HB3 C:ARG291 4.6 41.8 1.0
HB2 C:ARG291 4.6 41.8 1.0
HH22 C:ARG291 4.7 36.1 1.0
NE2 C:HIS29 4.8 24.4 1.0
HZ1 A:LYS313 4.8 37.7 1.0
HE2 C:LYS25 4.8 31.9 1.0
HD3 C:ARG291 4.8 43.6 1.0
MG A:MG503 4.9 57.3 1.0
H C:ASP31 4.9 32.6 1.0
CE C:LYS25 4.9 26.6 1.0
HB3 C:ASP31 4.9 28.4 1.0
HD3 C:LYS25 5.0 28.9 1.0
H16 C:EU9503 5.0 38.6 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 04:02:03 2024

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