Magnesium in PDB 7loo: S-Adenosyl Methionine Transferase Cocrystallized with Atp

Enzymatic activity of S-Adenosyl Methionine Transferase Cocrystallized with Atp

All present enzymatic activity of S-Adenosyl Methionine Transferase Cocrystallized with Atp:
2.5.1.6;

Protein crystallography data

The structure of S-Adenosyl Methionine Transferase Cocrystallized with Atp, PDB code: 7loo was solved by C.J.Jackson, L.L.Tan, P.Laurino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.99 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.922, 117.78, 113.21, 90, 107.52, 90
R / Rfree (%) 17 / 20.7

Other elements in 7loo:

The structure of S-Adenosyl Methionine Transferase Cocrystallized with Atp also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S-Adenosyl Methionine Transferase Cocrystallized with Atp (pdb code 7loo). 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-Adenosyl Methionine Transferase Cocrystallized with Atp, PDB code: 7loo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7loo

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Magnesium binding site 1 out of 8 in the S-Adenosyl Methionine Transferase Cocrystallized with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S-Adenosyl Methionine Transferase Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:20.8
occ:1.00
 O1 A:PO4402 1.9 27.1 1.0
O1 A:POP401 2.0 18.1 1.0
O6 A:POP401 2.1 24.6 1.0
OD2 A:ASP16 2.1 21.4 1.0
O A:HOH547 2.1 21.2 1.0
O A:HOH515 2.2 20.6 1.0
CG A:ASP16 3.0 21.3 1.0
P1 A:POP401 3.2 21.1 1.0
P2 A:POP401 3.3 26.4 1.0
P A:PO4402 3.3 49.2 1.0
OD1 A:ASP16 3.4 23.1 1.0
O A:POP401 3.4 28.1 1.0
NZ A:LYS245 3.5 21.9 1.0
O2 A:PO4402 3.7 44.9 1.0
K A:K404 3.8 85.7 1.0
O Q:HOH503 3.9 53.4 1.0
O5 A:POP401 4.0 27.9 1.0
O4 A:PO4402 4.0 29.1 1.0
O3 A:POP401 4.1 19.7 1.0
CE1 A:HIS14 4.1 20.9 1.0
OD2 A:ASP238 4.3 39.2 1.0
NH2 A:ARG244 4.3 24.8 1.0
O2 A:POP401 4.3 27.3 1.0
CB A:ARG244 4.4 22.1 1.0
CB A:ASP16 4.4 23.5 1.0
O4 A:POP401 4.4 31.6 1.0
O3 A:PO4402 4.4 51.6 1.0
O A:CYS239 4.5 26.2 0.6
O A:ARG244 4.5 20.3 1.0
O A:CYS239 4.6 25.4 0.4
CE A:LYS245 4.6 19.9 1.0
NE A:ARG244 4.7 26.0 1.0
NE2 A:HIS14 4.7 21.7 1.0
CZ A:ARG244 4.7 25.5 1.0
MG Q:MG404 4.8 32.0 1.0

Magnesium binding site 2 out of 8 in 7loo

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Magnesium binding site 2 out of 8 in the S-Adenosyl Methionine Transferase Cocrystallized with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S-Adenosyl Methionine Transferase Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:28.3
occ:1.00
 O A:HOH623 2.0 23.3 1.0
O A:HOH563 2.1 26.5 1.0
O3 Q:PO4402 2.1 29.7 1.0
O6 Q:POP401 2.1 25.9 1.0
O2 Q:POP401 2.1 18.1 1.0
OD2 A:ASP271 2.3 27.7 1.0
P1 Q:POP401 3.1 20.7 1.0
CG A:ASP271 3.2 29.7 1.0
P2 Q:POP401 3.2 25.9 1.0
O Q:POP401 3.3 26.6 1.0
P Q:PO4402 3.3 50.2 1.0
OD1 A:ASP271 3.5 30.1 1.0
O2 Q:PO4402 3.7 48.6 1.0
O Q:HOH534 3.7 29.8 1.0
O Q:HOH630 3.9 32.6 1.0
O1 Q:POP401 4.0 20.4 1.0
O Q:HOH514 4.0 37.1 1.0
O1 Q:PO4402 4.0 29.1 1.0
NZ A:LYS265 4.1 21.1 1.0
O5 Q:POP401 4.1 23.1 1.0
OD2 A:ASP118 4.1 31.8 1.0
O A:HOH516 4.3 25.1 1.0
CA A:GLY260 4.3 22.4 1.0
O3 Q:POP401 4.3 25.8 1.0
O4 Q:POP401 4.4 31.6 1.0
O4 Q:PO4402 4.5 45.2 1.0
CB A:ASP271 4.6 32.4 1.0
O Q:HOH561 4.6 32.9 1.0
NZ Q:LYS245 4.7 22.5 1.0
NZ Q:LYS165 4.8 22.6 1.0
MG Q:MG412 4.8 22.6 1.0
O A:HOH636 4.9 28.7 1.0

Magnesium binding site 3 out of 8 in 7loo

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Magnesium binding site 3 out of 8 in the S-Adenosyl Methionine Transferase Cocrystallized with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S-Adenosyl Methionine Transferase Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:47.7
occ:1.00
 O6 B:POP401 1.9 52.5 1.0
OD2 B:ASP16 2.1 71.1 1.0
O2 B:POP401 2.1 53.5 1.0
O B:HOH506 2.2 43.6 1.0
O B:HOH515 2.3 49.9 1.0
O B:HOH518 2.4 54.3 1.0
CG B:ASP16 3.1 59.6 1.0
P2 B:POP401 3.2 59.8 1.0
P1 B:POP401 3.3 60.4 1.0
OD1 B:ASP16 3.4 56.9 1.0
O R:HOH527 3.5 57.2 1.0
O B:POP401 3.6 61.9 1.0
NZ B:LYS245 3.6 56.5 1.0
O4 B:POP401 4.0 67.0 1.0
OD2 B:ASP238 4.1 76.5 1.0
NH2 B:ARG244 4.1 55.2 1.0
O1 B:POP401 4.1 69.1 1.0
CE1 B:HIS14 4.2 59.0 1.0
MG R:MG402 4.3 81.2 1.0
O5 B:POP401 4.3 61.4 1.0
O3 B:POP401 4.4 60.8 1.0
CB B:ASP16 4.4 55.6 1.0
CB B:ARG244 4.6 52.5 1.0
O B:CYS239 4.6 47.6 1.0
O B:ARG244 4.6 55.9 1.0
NE B:ARG244 4.6 53.1 1.0
CZ B:ARG244 4.6 58.2 1.0
CE B:LYS245 4.7 57.4 1.0
NE2 B:HIS14 4.8 62.5 1.0

Magnesium binding site 4 out of 8 in 7loo

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Magnesium binding site 4 out of 8 in the S-Adenosyl Methionine Transferase Cocrystallized with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S-Adenosyl Methionine Transferase Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:81.9
occ:1.00
 O R:HOH524 2.5 62.7 1.0
O R:HOH513 2.7 52.0 1.0
O1 R:POP401 2.8 65.7 1.0
O4 R:POP401 2.9 68.0 1.0
OD2 B:ASP271 2.9 69.2 1.0
O B:HOH502 2.9 61.3 1.0
CA B:GLY260 3.6 68.1 1.0
P1 R:POP401 3.7 56.3 1.0
O3 R:POP401 3.9 51.6 1.0
P2 R:POP401 3.9 60.9 1.0
O B:GLY259 3.9 62.8 1.0
CG B:ASP271 3.9 73.3 1.0
NZ R:LYS245 3.9 62.2 1.0
NZ B:LYS265 4.0 64.0 1.0
O R:POP401 4.1 61.7 1.0
O6 R:POP401 4.1 54.0 1.0
N B:GLY260 4.3 65.0 1.0
C B:GLY259 4.4 65.8 1.0
MG R:MG403 4.4 45.7 1.0
N B:ALA261 4.4 60.0 1.0
OD1 B:ASP271 4.4 70.8 1.0
C B:GLY260 4.6 62.2 1.0
O R:ARG244 4.7 60.6 1.0
O B:HOH508 4.8 53.8 1.0
CE R:LYS245 4.9 62.4 1.0

Magnesium binding site 5 out of 8 in 7loo

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Magnesium binding site 5 out of 8 in the S-Adenosyl Methionine Transferase Cocrystallized with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of S-Adenosyl Methionine Transferase Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg404

b:32.0
occ:1.00
 O Q:HOH642 2.0 24.9 1.0
O Q:HOH553 2.0 27.1 1.0
O4 A:PO4402 2.1 29.1 1.0
O5 A:POP401 2.1 27.9 1.0
O3 A:POP401 2.1 19.7 1.0
OD2 Q:ASP271 2.3 27.6 1.0
P1 A:POP401 3.2 21.1 1.0
CG Q:ASP271 3.2 30.9 1.0
P2 A:POP401 3.3 26.4 1.0
P A:PO4402 3.3 49.2 1.0
O A:POP401 3.4 28.1 1.0
OD1 Q:ASP271 3.5 30.3 1.0
O A:HOH540 3.7 25.5 1.0
O2 A:PO4402 3.7 44.9 1.0
O A:HOH510 3.9 45.6 1.0
O1 A:POP401 4.0 18.1 1.0
O1 A:PO4402 4.0 27.1 1.0
O6 A:POP401 4.0 24.6 1.0
O A:HOH639 4.1 32.5 1.0
NZ Q:LYS265 4.1 20.5 1.0
OD2 Q:ASP118 4.1 30.3 1.0
O Q:HOH535 4.2 22.6 1.0
CA Q:GLY260 4.3 24.9 1.0
O2 A:POP401 4.4 27.3 1.0
O4 A:POP401 4.5 31.6 1.0
O3 A:PO4402 4.5 51.6 1.0
CB Q:ASP271 4.6 28.8 1.0
NZ A:LYS245 4.6 21.9 1.0
O A:HOH549 4.7 30.1 1.0
NZ A:LYS165 4.8 28.0 1.0
MG A:MG403 4.8 20.8 1.0

Magnesium binding site 6 out of 8 in 7loo

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Magnesium binding site 6 out of 8 in the S-Adenosyl Methionine Transferase Cocrystallized with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of S-Adenosyl Methionine Transferase Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg412

b:22.6
occ:1.00
 O1 Q:PO4402 2.0 29.1 1.0
O1 Q:POP401 2.1 20.4 1.0
OD2 Q:ASP16 2.1 22.3 1.0
O5 Q:POP401 2.1 23.1 1.0
O Q:HOH547 2.1 21.3 1.0
O Q:HOH530 2.2 21.4 1.0
CG Q:ASP16 3.0 22.9 1.0
P2 Q:POP401 3.3 25.9 1.0
P1 Q:POP401 3.3 20.7 1.0
OD1 Q:ASP16 3.3 23.0 1.0
P Q:PO4402 3.4 50.2 1.0
O Q:POP401 3.5 26.6 1.0
NZ Q:LYS245 3.6 22.5 1.0
O2 Q:PO4402 3.6 48.6 1.0
K Q:K405 3.7 76.4 1.0
O6 Q:POP401 4.0 25.9 1.0
O3 Q:PO4402 4.1 29.7 1.0
O2 Q:POP401 4.1 18.1 1.0
NH2 Q:ARG244 4.2 26.0 1.0
CE1 Q:HIS14 4.2 20.0 1.0
CB Q:ARG244 4.3 19.3 1.0
OD2 Q:ASP238 4.4 38.8 1.0
CB Q:ASP16 4.4 21.9 1.0
O4 Q:POP401 4.4 31.6 1.0
O3 Q:POP401 4.4 25.8 1.0
O4 Q:PO4402 4.5 45.2 1.0
O Q:CYS239 4.5 27.5 0.6
O Q:CYS239 4.5 27.5 0.4
NE Q:ARG244 4.5 26.2 1.0
O Q:ARG244 4.5 19.2 1.0
CZ Q:ARG244 4.6 26.4 1.0
CE Q:LYS245 4.7 22.7 1.0
NE2 Q:HIS14 4.8 19.9 1.0
MG A:MG410 4.8 28.3 1.0

Magnesium binding site 7 out of 8 in 7loo

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Magnesium binding site 7 out of 8 in the S-Adenosyl Methionine Transferase Cocrystallized with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of S-Adenosyl Methionine Transferase Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg402

b:81.2
occ:1.00
 O B:HOH504 2.3 51.3 1.0
O B:HOH518 2.6 54.3 1.0
O1 B:POP401 2.8 69.1 1.0
O4 B:POP401 2.8 67.0 1.0
OD2 R:ASP271 2.9 69.7 1.0
O R:HOH512 3.2 62.1 1.0
O R:HOH520 3.5 71.0 1.0
O B:HOH507 3.5 73.4 1.0
CA R:GLY260 3.7 68.9 1.0
P1 B:POP401 3.7 60.4 1.0
P2 B:POP401 3.8 59.8 1.0
O2 B:POP401 3.8 53.5 1.0
NZ B:LYS245 3.9 56.5 1.0
CG R:ASP271 3.9 70.8 1.0
O R:GLY259 3.9 65.7 1.0
O6 B:POP401 4.0 52.5 1.0
NZ R:LYS265 4.0 77.5 1.0
O B:POP401 4.0 61.9 1.0
MG B:MG403 4.3 47.7 1.0
OD1 R:ASP271 4.3 72.0 1.0
N R:GLY260 4.4 70.8 1.0
N R:ALA261 4.4 62.6 1.0
C R:GLY259 4.4 71.1 1.0
C R:GLY260 4.6 65.2 1.0
O B:ARG244 4.8 55.9 1.0
O R:HOH501 4.8 61.4 1.0
CE B:LYS245 4.9 57.4 1.0

Magnesium binding site 8 out of 8 in 7loo

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Magnesium binding site 8 out of 8 in the S-Adenosyl Methionine Transferase Cocrystallized with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of S-Adenosyl Methionine Transferase Cocrystallized with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg403

b:45.7
occ:1.00
 O6 R:POP401 2.0 54.0 1.0
O3 R:POP401 2.0 51.6 1.0
OD2 R:ASP16 2.0 68.3 1.0
O R:HOH513 2.2 52.0 1.0
O R:HOH505 2.2 42.3 1.0
O R:HOH530 2.4 53.0 1.0
CG R:ASP16 3.0 59.3 1.0
P2 R:POP401 3.3 60.9 1.0
P1 R:POP401 3.3 56.3 1.0
NZ R:LYS245 3.3 62.2 1.0
OD1 R:ASP16 3.3 54.6 1.0
O R:POP401 3.6 61.7 1.0
O4 R:POP401 4.0 68.0 1.0
OD2 R:ASP238 4.1 78.5 1.0
NH2 R:ARG244 4.1 62.5 1.0
O1 R:POP401 4.1 65.7 1.0
CE1 R:HIS14 4.2 58.3 1.0
O2 R:POP401 4.3 56.9 1.0
CB R:ASP16 4.3 62.3 1.0
MG B:MG404 4.4 81.9 1.0
O5 R:POP401 4.4 60.8 1.0
O R:CYS239 4.5 49.6 0.5
CB R:ARG244 4.5 56.0 1.0
CE R:LYS245 4.5 62.4 1.0
O R:CYS239 4.5 50.1 0.5
O R:ARG244 4.5 60.6 1.0
CZ R:ARG244 4.6 59.7 1.0
NE R:ARG244 4.6 58.5 1.0
NE2 R:HIS14 4.7 61.0 1.0
CG R:ASP238 5.0 79.7 1.0

Reference:

C.J.Jackson, P.L.Laurino. Protein and Substrate Flexibility Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferase To Be Published.
Page generated: Fri Sep 24 15:24:54 2021

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