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Magnesium in PDB 7lo2: S-Adenosylmethionine Synthetase Cocrystallized with Ctp

Enzymatic activity of S-Adenosylmethionine Synthetase Cocrystallized with Ctp

All present enzymatic activity of S-Adenosylmethionine Synthetase Cocrystallized with Ctp:
2.5.1.6;

Protein crystallography data

The structure of S-Adenosylmethionine Synthetase Cocrystallized with Ctp, PDB code: 7lo2 was solved by L.L.Tan, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.22 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.139, 118.32, 144.456, 90, 90, 90
R / Rfree (%) 16.6 / 19.5

Other elements in 7lo2:

The structure of S-Adenosylmethionine Synthetase Cocrystallized with Ctp also contains other interesting chemical elements:

Potassium (K) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S-Adenosylmethionine Synthetase Cocrystallized with Ctp (pdb code 7lo2). 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 Cocrystallized with Ctp, PDB code: 7lo2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7lo2

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Magnesium binding site 1 out of 8 in the S-Adenosylmethionine Synthetase Cocrystallized with Ctp


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 Cocrystallized with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:39.9
occ:1.00
 O3 A:PO4404 2.0 35.0 0.9
O A:HOH505 2.1 41.4 1.0
O3 A:POP405 2.1 49.1 0.8
OD2 A:ASP16 2.2 30.2 1.0
O A:HOH532 2.2 35.6 1.0
O A:HOH531 2.2 40.5 1.0
CG A:ASP16 3.1 30.6 1.0
P A:PO4404 3.2 45.1 0.9
OD1 A:ASP16 3.4 28.7 1.0
O1 A:PO4404 3.4 50.7 0.9
P1 A:POP405 3.4 74.2 0.8
NZ A:LYS245 3.6 35.7 1.0
O1 A:POP405 3.8 62.9 0.8
O2 A:PO4404 4.2 53.5 0.9
O A:POP405 4.2 63.6 0.8
NH2 A:ARG244 4.2 33.5 1.0
O4 A:PO4404 4.2 37.5 0.9
K B:K404 4.3 79.9 1.0
O A:HOH516 4.3 50.4 1.0
CE1 A:HIS14 4.4 34.3 1.0
O2 A:POP405 4.4 65.0 0.8
CB A:ASP16 4.4 26.8 1.0
O A:CYS239 4.4 38.0 0.5
O A:CYS239 4.5 37.8 0.5
CB A:ARG244 4.6 27.3 1.0
OE2 B:GLU42 4.6 52.1 1.0
CZ A:ARG244 4.7 33.3 1.0
NE A:ARG244 4.8 28.9 1.0
CE A:LYS245 4.8 34.0 1.0
O A:ARG244 4.9 31.6 1.0

Magnesium binding site 2 out of 8 in 7lo2

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Magnesium binding site 2 out of 8 in the S-Adenosylmethionine Synthetase Cocrystallized with Ctp


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 Cocrystallized with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:56.2
occ:1.00
 O A:HOH640 2.8 33.8 1.0
O2 A:PO4404 3.0 53.5 0.9
O A:ARG244 3.0 31.6 1.0
O5 A:POP405 3.0 66.6 0.8
O A:HOH513 3.3 41.0 1.0
NZ A:LYS245 3.4 35.7 1.0
N B:GLY260 3.5 39.5 1.0
O A:HOH503 3.5 50.7 1.0
CD A:LYS245 4.0 32.3 1.0
CE A:LYS245 4.0 34.0 1.0
C A:ARG244 4.0 30.6 1.0
CA A:LYS245 4.0 28.2 1.0
O A:HOH652 4.1 36.0 1.0
CA B:GLY260 4.1 40.0 1.0
C B:GLY259 4.1 43.6 1.0
P A:PO4404 4.2 45.1 0.9
CA B:GLY259 4.2 44.7 1.0
O B:HOH574 4.3 40.6 1.0
O3 A:PO4404 4.4 35.0 0.9
P2 A:POP405 4.4 83.5 0.8
N A:LYS245 4.5 27.9 1.0
O4 A:PO4404 4.5 37.5 0.9
O A:HOH654 4.6 52.2 1.0
CG A:LYS245 4.7 26.2 1.0
C A:LYS245 4.8 29.8 1.0
O6 A:POP405 4.8 58.0 0.8
CB A:LYS245 4.9 25.7 1.0
CG1 A:VAL248 4.9 35.3 1.0

Magnesium binding site 3 out of 8 in 7lo2

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Magnesium binding site 3 out of 8 in the S-Adenosylmethionine Synthetase Cocrystallized with Ctp


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 Cocrystallized with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:33.8
occ:1.00
 O3 B:PO4402 2.0 31.2 0.9
O B:HOH573 2.1 34.1 1.0
O A:HOH572 2.1 32.5 1.0
O2 B:POP405 2.1 30.7 1.0
O6 B:POP405 2.1 34.2 1.0
OD2 A:ASP271 2.2 30.5 1.0
P1 B:POP405 3.2 31.4 1.0
CG A:ASP271 3.2 34.4 1.0
P B:PO4402 3.3 33.3 0.9
P2 B:POP405 3.3 36.4 1.0
O B:POP405 3.3 35.9 1.0
OD1 A:ASP271 3.6 32.7 1.0
O2 B:PO4402 3.7 29.9 0.9
O B:HOH551 3.8 34.2 1.0
O B:HOH547 3.9 31.3 1.0
O4 B:PO4402 3.9 27.3 0.9
O1 B:POP405 3.9 31.4 1.0
O A:HOH534 4.0 31.1 1.0
NZ A:LYS265 4.1 28.5 1.0
O B:HOH561 4.1 40.3 1.0
O4 B:POP405 4.1 30.9 1.0
O3 B:POP405 4.4 32.2 1.0
O5 B:POP405 4.4 35.9 1.0
NZ B:LYS245 4.4 29.9 1.0
OD2 A:ASP118 4.4 35.7 1.0
O B:HOH604 4.5 39.0 1.0
O1 B:PO4402 4.5 31.3 0.9
CB A:ASP271 4.5 26.6 1.0
CA A:GLY260 4.6 29.8 1.0
MG B:MG401 4.7 27.8 1.0
O A:HOH629 4.7 27.4 1.0
O A:HOH554 4.8 46.4 1.0
NZ B:LYS165 4.8 28.6 1.0

Magnesium binding site 4 out of 8 in 7lo2

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Magnesium binding site 4 out of 8 in the S-Adenosylmethionine Synthetase Cocrystallized with Ctp


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 Cocrystallized with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:27.8
occ:1.00
 O4 B:PO4402 2.0 27.3 0.9
O4 B:POP405 2.0 30.9 1.0
O1 B:POP405 2.0 31.4 1.0
OD2 B:ASP16 2.1 28.1 1.0
O B:HOH518 2.1 30.7 1.0
O B:HOH557 2.2 29.1 1.0
CG B:ASP16 3.1 28.2 1.0
P2 B:POP405 3.2 36.4 1.0
P1 B:POP405 3.3 31.4 1.0
OD1 B:ASP16 3.3 28.6 1.0
P B:PO4402 3.4 33.3 0.9
O B:POP405 3.5 35.9 1.0
NZ B:LYS245 3.6 29.9 1.0
O6 B:POP405 3.8 34.2 1.0
K B:K403 3.9 70.4 1.0
O3 B:PO4402 4.0 31.2 0.9
O B:HOH512 4.0 43.1 1.0
O2 B:POP405 4.1 30.7 1.0
O2 B:PO4402 4.1 29.9 0.9
CE1 B:HIS14 4.1 31.6 1.0
NH2 B:ARG244 4.2 31.6 1.0
O B:CYS239 4.4 36.0 0.5
O3 B:POP405 4.4 32.2 1.0
CB B:ASP16 4.4 23.9 1.0
O B:CYS239 4.4 35.8 0.5
O1 B:PO4402 4.4 31.3 0.9
O5 B:POP405 4.5 35.9 1.0
CE B:LYS245 4.6 28.6 1.0
MG A:MG403 4.7 33.8 1.0
NE2 B:HIS14 4.7 27.7 1.0
CZ B:ARG244 4.8 28.7 1.0
NE B:ARG244 4.8 31.2 1.0
CB B:ARG244 4.8 28.4 1.0

Magnesium binding site 5 out of 8 in 7lo2

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Magnesium binding site 5 out of 8 in the S-Adenosylmethionine Synthetase Cocrystallized with Ctp


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 Cocrystallized with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:43.1
occ:1.00
 O3 C:POP405 1.9 43.5 0.6
OD2 C:ASP16 1.9 32.2 1.0
O6 C:POP405 2.0 33.9 0.6
O4 D:PO4403 2.1 43.7 1.0
O C:HOH524 2.2 37.7 1.0
O C:HOH518 2.3 32.9 1.0
CG C:ASP16 2.8 35.3 1.0
P1 C:POP405 3.1 66.6 0.6
OD1 C:ASP16 3.1 30.8 1.0
P2 C:POP405 3.2 58.7 0.6
O C:POP405 3.4 61.4 0.6
P D:PO4403 3.5 51.5 1.0
NZ C:LYS245 3.5 39.3 1.0
O1 D:PO4403 3.7 56.5 1.0
O5 C:POP405 3.8 47.3 0.6
O2 C:POP405 3.8 57.2 0.6
CE1 C:HIS14 4.2 37.4 1.0
O1 C:POP405 4.2 64.7 0.6
CB C:ASP16 4.2 30.4 1.0
O C:HOH560 4.4 57.9 1.0
O C:CYS239 4.4 43.0 0.6
O3 D:PO4403 4.4 57.7 1.0
O4 C:POP405 4.4 57.0 0.6
O C:CYS239 4.4 41.9 0.4
NH2 C:ARG244 4.4 34.5 1.0
O2 D:PO4403 4.4 41.0 1.0
CB C:ARG244 4.5 28.1 1.0
K C:K404 4.6 81.2 1.0
OE2 D:GLU42 4.8 45.9 1.0
CE C:LYS245 4.8 31.1 1.0
CZ C:ARG244 4.8 37.7 1.0
NE C:ARG244 4.8 32.1 1.0
NE2 C:HIS14 4.9 35.2 1.0
O C:ARG244 4.9 29.5 1.0
MG C:MG402 4.9 55.9 1.0

Magnesium binding site 6 out of 8 in 7lo2

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Magnesium binding site 6 out of 8 in the S-Adenosylmethionine Synthetase Cocrystallized with Ctp


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 Cocrystallized with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:55.9
occ:1.00
 O5 C:POP405 1.8 47.3 0.6
O3 D:PO4403 1.8 57.7 1.0
O C:HOH503 2.9 122.6 1.0
P D:PO4403 3.0 51.5 1.0
O1 D:PO4403 3.2 56.5 1.0
P2 C:POP405 3.3 58.7 0.6
O C:HOH655 3.5 61.6 1.0
NZ C:LYS245 3.5 39.3 1.0
O4 D:PO4403 3.6 43.7 1.0
OD2 D:ASP271 3.6 48.9 1.0
O C:POP405 4.0 61.4 0.6
O6 C:POP405 4.1 33.9 0.6
O4 C:POP405 4.1 57.0 0.6
O2 D:PO4403 4.2 41.0 1.0
CE C:LYS245 4.2 31.1 1.0
OE2 C:GLU8 4.4 59.9 0.5
CA D:GLY260 4.5 40.4 1.0
CG D:ASP271 4.7 53.0 1.0
N D:GLY260 4.7 38.4 1.0
OE1 C:GLU8 4.7 55.1 0.5
MG C:MG401 4.9 43.1 1.0

Magnesium binding site 7 out of 8 in 7lo2

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Magnesium binding site 7 out of 8 in the S-Adenosylmethionine Synthetase Cocrystallized with Ctp


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 Cocrystallized with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:33.3
occ:0.84
 O3 D:PO4404 2.0 33.2 0.8
O6 D:POP405 2.0 34.5 0.9
O C:HOH585 2.1 36.0 1.0
O2 D:POP405 2.2 36.5 0.9
O C:HOH600 2.2 36.2 1.0
OD2 C:ASP271 2.3 31.1 1.0
P2 D:POP405 3.1 31.3 0.9
O D:POP405 3.2 34.5 0.9
P1 D:POP405 3.3 34.8 0.9
P D:PO4404 3.3 36.1 0.8
CG C:ASP271 3.3 32.6 1.0
OD1 C:ASP271 3.6 34.3 1.0
O4 D:PO4404 3.8 31.1 0.8
O4 D:POP405 3.8 30.1 0.9
O1 D:PO4404 3.8 26.9 0.8
O D:HOH535 3.9 39.5 1.0
O D:HOH536 4.0 41.7 1.0
O D:HOH520 4.0 28.7 1.0
NZ C:LYS265 4.0 26.9 1.0
O1 D:POP405 4.1 29.6 0.9
O D:HOH611 4.2 38.5 1.0
O C:HOH539 4.3 33.4 1.0
O5 D:POP405 4.3 33.1 0.9
OD2 C:ASP118 4.4 38.4 1.0
NZ D:LYS245 4.4 25.6 1.0
O3 D:POP405 4.4 37.0 0.9
O2 D:PO4404 4.5 36.6 0.8
CA C:GLY260 4.6 25.4 1.0
CB C:ASP271 4.6 28.9 1.0
MG D:MG402 4.7 31.7 1.0
O C:HOH615 4.9 26.2 1.0
O C:HOH582 4.9 46.7 1.0
NZ D:LYS165 4.9 26.9 1.0

Magnesium binding site 8 out of 8 in 7lo2

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Magnesium binding site 8 out of 8 in the S-Adenosylmethionine Synthetase Cocrystallized with Ctp


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 Cocrystallized with Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:31.7
occ:1.00
 O1 D:PO4404 2.0 26.9 0.8
OD2 D:ASP16 2.1 31.2 1.0
O4 D:POP405 2.1 30.1 0.9
O D:HOH517 2.1 30.8 1.0
O1 D:POP405 2.1 29.6 0.9
O D:HOH578 2.2 29.7 1.0
CG D:ASP16 3.0 28.2 1.0
P1 D:POP405 3.3 34.8 0.9
P2 D:POP405 3.3 31.3 0.9
OD1 D:ASP16 3.4 27.6 1.0
P D:PO4404 3.4 36.1 0.8
O D:POP405 3.5 34.5 0.9
NZ D:LYS245 3.5 25.6 1.0
O C:HOH508 3.8 45.2 1.0
O2 D:POP405 3.9 36.5 0.9
O3 D:PO4404 4.0 33.2 0.8
O6 D:POP405 4.1 34.5 0.9
O4 D:PO4404 4.2 31.1 0.8
CE1 D:HIS14 4.2 29.3 1.0
NH2 D:ARG244 4.3 32.0 1.0
O D:HOH501 4.3 44.2 1.0
CB D:ASP16 4.4 25.4 1.0
O2 D:PO4404 4.4 36.6 0.8
O D:CYS239 4.4 33.5 0.3
O5 D:POP405 4.4 33.1 0.9
O D:CYS239 4.4 33.0 0.7
O3 D:POP405 4.5 37.0 0.9
CE D:LYS245 4.6 26.5 1.0
MG C:MG403 4.7 33.3 0.8
CB D:ARG244 4.7 28.0 1.0
NE D:ARG244 4.8 31.9 1.0
CZ D:ARG244 4.8 29.1 1.0
NE2 D:HIS14 4.9 31.9 1.0
O D:ARG244 5.0 27.1 1.0
OE2 C:GLU42 5.0 45.2 1.0

Reference:

P.Laurino, C.J.Jackson. S-Adenosylmethionine Synthetase To Be Published.
Page generated: Wed Oct 2 23:29:58 2024

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