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Magnesium in PDB 1p7l: S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.

Enzymatic activity of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.

All present enzymatic activity of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.:
2.5.1.6;

Protein crystallography data

The structure of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met., PDB code: 1p7l was solved by F.Takusagawa, J.Komoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 225.820, 69.130, 118.230, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24.2

Other elements in 1p7l:

The structure of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met. also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met. (pdb code 1p7l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met., PDB code: 1p7l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1p7l

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Magnesium binding site 1 out of 8 in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg387

b:22.3
occ:1.00
 O1G A:ANP384 2.4 18.6 1.0
O1A A:ANP384 2.4 14.4 1.0
NZ A:LYS245 3.6 4.6 1.0
PG A:ANP384 3.6 17.4 1.0
OE2 A:GLU8 3.7 5.2 1.0
PA A:ANP384 3.8 4.4 1.0
N3B A:ANP384 3.9 11.0 1.0
NZ A:LYS165 4.0 2.0 1.0
OE1 A:GLU8 4.2 2.0 1.0
O B:GLN119 4.3 15.5 1.0
OD2 B:ASP271 4.3 11.9 1.0
O2A A:ANP384 4.3 12.3 1.0
OD1 B:ASP271 4.4 8.1 1.0
CD A:GLU8 4.4 2.0 1.0
O2G A:ANP384 4.4 21.5 1.0
OD2 B:ASP118 4.4 29.1 1.0
CE A:LYS245 4.6 2.0 1.0
O3A A:ANP384 4.6 11.9 1.0
O3G A:ANP384 4.7 21.0 1.0
O B:GLY259 4.7 12.5 1.0
CG B:ASP271 4.8 10.6 1.0
O5' A:ANP384 5.0 12.3 1.0
PB A:ANP384 5.0 4.8 1.0

Magnesium binding site 2 out of 8 in 1p7l

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Magnesium binding site 2 out of 8 in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg388

b:15.6
occ:1.00
 O2B A:ANP384 2.2 18.2 1.0
OD2 A:ASP16 2.2 22.0 1.0
O2G A:ANP384 2.4 21.5 1.0
O2A A:ANP384 2.4 12.3 1.0
CG A:ASP16 3.1 15.2 1.0
OD1 A:ASP16 3.2 20.9 1.0
PB A:ANP384 3.3 4.8 1.0
PG A:ANP384 3.3 17.4 1.0
N3B A:ANP384 3.5 11.0 1.0
PA A:ANP384 3.6 4.4 1.0
O3A A:ANP384 3.7 11.9 1.0
NZ A:LYS245 4.0 4.6 1.0
K A:K386 4.0 2.0 1.0
NH2 A:ARG244 4.1 2.0 1.0
O3G A:ANP384 4.3 21.0 1.0
O1G A:ANP384 4.3 18.6 1.0
O A:CYS239 4.4 5.8 1.0
OD2 A:ASP238 4.4 10.4 1.0
O1A A:ANP384 4.4 14.4 1.0
CE1 A:HIS14 4.4 4.7 1.0
CB A:ASP16 4.5 15.7 1.0
CZ A:ARG244 4.5 8.1 1.0
CB A:ARG244 4.5 6.3 1.0
O5' A:ANP384 4.5 12.3 1.0
O1B A:ANP384 4.6 17.3 1.0
NE A:ARG244 4.6 14.1 1.0
OE2 B:GLU42 4.9 22.3 1.0
NE2 A:HIS14 4.9 7.7 1.0
O A:ARG244 5.0 2.0 1.0

Magnesium binding site 3 out of 8 in 1p7l

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Magnesium binding site 3 out of 8 in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg487

b:25.0
occ:1.00
 O1G B:ANP484 2.3 13.6 1.0
O1A B:ANP484 2.4 9.4 1.0
NZ B:LYS245 3.4 14.4 1.0
PG B:ANP484 3.5 20.6 1.0
OE2 B:GLU8 3.7 13.4 1.0
PA B:ANP484 3.8 2.0 1.0
N3B B:ANP484 3.9 16.4 1.0
NZ B:LYS165 4.1 2.0 1.0
O2G B:ANP484 4.3 24.5 1.0
O2A B:ANP484 4.3 3.4 1.0
OD1 A:ASP271 4.3 9.7 1.0
OD2 A:ASP271 4.3 15.6 1.0
OE1 B:GLU8 4.4 2.0 1.0
O A:GLN119 4.4 15.3 1.0
CD B:GLU8 4.5 4.5 1.0
CE B:LYS245 4.5 3.9 1.0
OD2 A:ASP118 4.5 2.0 1.0
O3G B:ANP484 4.6 22.5 1.0
O A:GLY259 4.6 19.3 1.0
O3A B:ANP484 4.6 9.2 1.0
CG A:ASP271 4.7 15.7 1.0
PB B:ANP484 4.9 2.0 1.0
O5' B:ANP484 5.0 24.6 1.0
CA A:GLY260 5.0 2.4 1.0

Magnesium binding site 4 out of 8 in 1p7l

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Magnesium binding site 4 out of 8 in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg488

b:10.1
occ:1.00
 O2B B:ANP484 2.3 19.9 1.0
OD2 B:ASP16 2.3 15.6 1.0
O2G B:ANP484 2.4 24.5 1.0
O2A B:ANP484 2.5 3.4 1.0
CG B:ASP16 3.1 9.2 1.0
OD1 B:ASP16 3.2 14.1 1.0
PB B:ANP484 3.3 2.0 1.0
PG B:ANP484 3.4 20.6 1.0
N3B B:ANP484 3.6 16.4 1.0
PA B:ANP484 3.8 2.0 1.0
O3A B:ANP484 3.8 9.2 1.0
NH2 B:ARG244 4.0 4.4 1.0
K B:K486 4.1 2.0 1.0
NZ B:LYS245 4.2 14.4 1.0
O3G B:ANP484 4.3 22.5 1.0
O B:CYS239 4.3 14.2 1.0
CZ B:ARG244 4.4 5.2 1.0
O1G B:ANP484 4.4 13.6 1.0
OD2 B:ASP238 4.4 12.1 1.0
CB B:ASP16 4.5 11.2 1.0
CB B:ARG244 4.5 8.0 1.0
CE1 B:HIS14 4.5 8.2 1.0
NE B:ARG244 4.5 12.4 1.0
O1A B:ANP484 4.5 9.4 1.0
O1B B:ANP484 4.6 17.3 1.0
O5' B:ANP484 4.7 24.6 1.0
OE2 A:GLU42 4.8 9.6 1.0
O B:ARG244 5.0 7.7 1.0

Magnesium binding site 5 out of 8 in 1p7l

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Magnesium binding site 5 out of 8 in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg688

b:47.9
occ:1.00
 OD2 C:ASP16 2.1 4.6 1.0
O2B C:PPK684 2.2 27.2 1.0
O2A C:PPK684 2.7 16.2 1.0
OD1 C:ASP16 2.8 5.2 1.0
CG C:ASP16 2.8 3.3 1.0
O2G C:PPK684 3.0 11.1 1.0
PB C:PPK684 3.6 24.8 1.0
PG C:PPK684 3.9 21.8 1.0
N3B C:PPK684 3.9 18.8 1.0
K C:K686 4.0 17.8 1.0
NH2 C:ARG244 4.0 23.1 1.0
PA C:PPK684 4.0 16.4 1.0
O C:CYS239 4.0 19.2 1.0
O3A C:PPK684 4.1 19.4 1.0
CZ C:ARG244 4.2 16.1 1.0
CB C:ARG244 4.2 19.5 1.0
CB C:ASP16 4.2 6.8 1.0
NE C:ARG244 4.3 17.8 1.0
NZ C:LYS245 4.5 32.4 1.0
OE2 D:GLU42 4.5 9.5 1.0
OD2 C:ASP238 4.5 5.6 1.0
CE1 C:HIS14 4.6 2.0 1.0
O1B C:PPK684 4.7 14.5 1.0
O3G C:PPK684 4.7 6.4 1.0
CG C:ARG244 4.8 19.2 1.0
O1A C:PPK684 4.9 29.3 1.0
NH1 C:ARG244 4.9 15.1 1.0
O4A C:PPK684 5.0 19.2 1.0

Magnesium binding site 6 out of 8 in 1p7l

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Magnesium binding site 6 out of 8 in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg887

b:38.2
occ:1.00
 O1G D:PPK884 2.4 20.7 1.0
O1A D:PPK884 2.5 18.6 1.0
OD1 C:ASP271 3.0 11.2 1.0
OD2 C:ASP271 3.2 23.9 1.0
CG C:ASP271 3.5 25.3 1.0
PG D:PPK884 3.5 11.5 1.0
N3B D:PPK884 3.7 8.6 1.0
PA D:PPK884 3.8 17.8 1.0
O3A D:PPK884 3.8 11.6 1.0
OD2 C:ASP118 3.8 16.9 1.0
O C:GLN119 4.0 19.6 1.0
NZ D:LYS165 4.1 17.8 1.0
PB D:PPK884 4.4 5.8 1.0
O3G D:PPK884 4.4 12.5 1.0
O2G D:PPK884 4.5 2.8 1.0
CG C:ASP118 4.6 17.3 1.0
O4A D:PPK884 4.7 9.6 1.0
OE2 D:GLU8 4.7 22.6 1.0
CA C:GLY260 4.8 18.6 1.0
O2A D:PPK884 4.8 23.1 1.0
NZ D:LYS245 4.8 22.9 1.0
CB C:ASP271 5.0 21.6 1.0

Magnesium binding site 7 out of 8 in 1p7l

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Magnesium binding site 7 out of 8 in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg687

b:19.8
occ:1.00
 O1A C:PPK684 2.4 29.3 1.0
O1G C:PPK684 2.5 20.1 1.0
OD1 D:ASP271 3.2 18.5 1.0
OD2 D:ASP271 3.3 13.9 1.0
PA C:PPK684 3.7 16.4 1.0
OD2 D:ASP118 3.7 20.6 1.0
CG D:ASP271 3.7 20.6 1.0
PG C:PPK684 3.7 21.8 1.0
O D:GLN119 3.7 8.5 1.0
O3A C:PPK684 3.9 19.4 1.0
NZ C:LYS165 3.9 23.1 1.0
N3B C:PPK684 3.9 18.8 1.0
O4A C:PPK684 4.5 19.2 1.0
CG D:ASP118 4.5 21.7 1.0
O2G C:PPK684 4.5 11.1 1.0
PB C:PPK684 4.5 24.8 1.0
OE2 C:GLU8 4.7 11.7 1.0
O2A C:PPK684 4.7 16.2 1.0
NZ C:LYS245 4.7 32.4 1.0
O3G C:PPK684 4.7 6.4 1.0
OE1 C:GLU8 4.8 7.3 1.0
CA D:GLY260 4.9 2.0 1.0
C D:GLN119 4.9 3.8 1.0
CA D:GLY120 4.9 2.0 1.0
CB D:ASP118 5.0 14.2 1.0

Magnesium binding site 8 out of 8 in 1p7l

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Magnesium binding site 8 out of 8 in the S-Adenosylmethionine Synthetase Complexed with Amppnp and Met.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of S-Adenosylmethionine Synthetase Complexed with Amppnp and Met. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg888

b:25.3
occ:1.00
 O2B D:PPK884 2.1 2.0 1.0
OD2 D:ASP16 2.1 7.4 1.0
O2A D:PPK884 2.8 23.1 1.0
O2G D:PPK884 2.8 2.8 1.0
CG D:ASP16 2.8 5.5 1.0
OD1 D:ASP16 2.9 10.1 1.0
PB D:PPK884 3.5 5.8 1.0
PG D:PPK884 3.8 11.5 1.0
N3B D:PPK884 3.8 8.6 1.0
NH2 D:ARG244 3.9 28.4 1.0
PA D:PPK884 4.0 17.8 1.0
K D:K886 4.0 42.0 1.0
O3A D:PPK884 4.1 11.6 1.0
CB D:ARG244 4.1 29.9 1.0
CZ D:ARG244 4.2 27.2 1.0
O D:CYS239 4.2 23.1 1.0
NE D:ARG244 4.3 26.0 1.0
CB D:ASP16 4.3 6.1 1.0
NZ D:LYS245 4.3 22.9 1.0
OE2 C:GLU42 4.5 10.4 1.0
O3G D:PPK884 4.6 12.5 1.0
CE1 D:HIS14 4.6 16.7 1.0
O1B D:PPK884 4.6 2.0 1.0
OD2 D:ASP238 4.7 14.9 1.0
CG D:ARG244 4.7 27.6 1.0
NH1 D:ARG244 4.8 16.9 1.0
O1A D:PPK884 4.8 18.6 1.0
O1G D:PPK884 4.9 20.7 1.0
O D:ARG244 5.0 32.2 1.0

Reference:

J.Komoto, T.Yamada, Y.Takata, G.D.Markham, F.Takusagawa. Crystal Structure of the S-Adenosylmethionine Synthetase Ternary Complex: A Novel Catalytic Mechanism of S-Adenosylmethionine Synthesis From Atp and Met. Biochemistry V. 43 1821 2004.
ISSN: ISSN 0006-2960
PubMed: 14967023
DOI: 10.1021/BI035611T
Page generated: Tue Aug 13 10:49:34 2024

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