Magnesium in PDB 7r3b: S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam

Enzymatic activity of S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam

All present enzymatic activity of S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam:
2.5.1.6;

Protein crystallography data

The structure of S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam, PDB code: 7r3b was solved by A.Shahar, D.Kleiner, S.Bershtein, R.Zarivach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.41 / 2.82
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.426, 110.927, 112.661, 93.82, 104.03, 99.59
R / Rfree (%) 15.6 / 27.5

Other elements in 7r3b:

The structure of S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam also contains other interesting chemical elements:

Potassium (K) 5 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam (pdb code 7r3b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam, PDB code: 7r3b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 7r3b

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Magnesium binding site 1 out of 16 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


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 From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:98.0
occ:1.00
 K A:K506 2.9 110.2 1.0
OE2 B:GLU44 3.1 84.5 1.0
O A:ALA251 3.3 70.0 1.0
O1B A:PPK502 3.4 111.3 1.0
OD1 A:ASP250 3.4 85.1 1.0
O2B A:PPK502 3.5 159.2 1.0
N A:ALA251 3.8 73.7 1.0
CB A:ALA251 3.9 61.1 1.0
CG A:ASP250 4.0 82.9 1.0
PB A:PPK502 4.0 150.9 1.0
C A:ALA251 4.0 66.3 1.0
CA A:ALA251 4.1 63.6 1.0
CD B:GLU44 4.2 71.5 1.0
OD2 A:ASP250 4.2 97.2 1.0
CG B:GLU44 4.6 72.2 1.0
OE1 B:GLU57 4.7 136.5 1.0
C A:ASP250 4.9 79.2 1.0
CB A:ASP250 5.0 73.4 1.0

Magnesium binding site 2 out of 16 in 7r3b

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Magnesium binding site 2 out of 16 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


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 From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:83.0
occ:1.00
 O3G A:PPK502 2.7 139.0 1.0
OE2 A:GLU10 3.0 90.3 1.0
O4A A:PPK502 3.1 126.6 1.0
NZ A:LYS257 3.6 65.2 1.0
CD A:GLU10 3.7 93.8 1.0
OE1 A:GLU10 3.9 102.9 1.0
N B:GLY272 3.9 69.8 1.0
PG A:PPK502 4.0 142.2 1.0
C B:GLY271 4.0 75.2 1.0
O B:GLY271 4.0 87.4 1.0
OD2 B:ASP283 4.0 96.6 1.0
CA B:GLY272 4.2 68.0 1.0
O2G A:PPK502 4.4 97.3 1.0
PA A:PPK502 4.6 138.8 1.0
N3B A:PPK502 4.6 149.2 1.0
O B:GLY270 4.7 75.1 1.0
CG B:ASP283 4.9 96.0 1.0
CA B:GLY271 4.9 76.0 1.0
OD1 B:ASP283 4.9 112.7 1.0
CG A:GLU10 5.0 84.6 1.0
CE A:LYS257 5.0 63.1 1.0

Magnesium binding site 3 out of 16 in 7r3b

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Magnesium binding site 3 out of 16 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


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 From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:98.2
occ:1.00
 OD2 A:ASP129 3.4 138.2 1.0
OD2 A:ASP283 3.4 106.2 1.0
OE1 B:GLU10 3.5 96.2 1.0
O3G B:PPK501 3.7 126.9 1.0
OE2 B:GLU10 3.7 111.5 1.0
OD1 A:ASP129 3.7 136.6 1.0
OD1 A:ASP283 3.8 120.4 1.0
CG A:ASP129 3.9 135.3 1.0
CD B:GLU10 3.9 91.2 1.0
CG A:ASP283 4.1 89.6 1.0
O4A B:PPK501 4.7 119.2 1.0
NZ B:LYS176 4.8 92.8 1.0
N A:GLY272 4.9 88.3 1.0

Magnesium binding site 4 out of 16 in 7r3b

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Magnesium binding site 4 out of 16 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


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 From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:70.7
occ:1.00
 O2B B:PPK501 1.9 106.2 1.0
PB B:PPK501 2.8 140.3 1.0
OD1 B:ASP18 3.0 54.6 1.0
OE2 A:GLU44 3.1 72.1 1.0
OD2 B:ASP18 3.2 59.2 1.0
N3B B:PPK501 3.2 149.6 1.0
O1B B:PPK501 3.4 126.4 1.0
CG B:ASP18 3.5 52.1 1.0
O B:ALA251 3.5 65.1 1.0
CD1 B:LEU253 3.7 69.2 1.0
NH1 B:ARG256 4.0 105.1 1.0
C B:ALA251 4.1 61.2 1.0
CZ B:ARG256 4.2 97.6 1.0
CD A:GLU44 4.2 69.4 1.0
O3A B:PPK501 4.2 152.8 1.0
CA B:GLY252 4.2 56.0 1.0
NH2 B:ARG256 4.3 113.1 1.0
N B:LEU253 4.4 61.9 1.0
N B:GLY252 4.5 56.5 1.0
CB B:ARG256 4.6 64.8 1.0
C B:GLY252 4.7 63.8 1.0
NE B:ARG256 4.7 82.7 1.0
CG B:ARG256 4.8 61.1 1.0
PG B:PPK501 4.8 147.6 1.0
CG A:GLU44 4.9 61.0 1.0
CB B:ASP18 5.0 50.6 1.0

Magnesium binding site 5 out of 16 in 7r3b

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Magnesium binding site 5 out of 16 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


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 From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:86.0
occ:1.00
 O1B C:ANP501 2.3 152.4 1.0
OE2 D:GLU44 2.9 122.3 1.0
PB C:ANP501 2.9 146.7 1.0
O2B C:ANP501 3.2 136.2 1.0
OD2 C:ASP18 3.4 58.0 1.0
N3B C:ANP501 3.5 164.8 1.0
O C:ALA251 3.5 75.9 1.0
K C:K504 3.6 121.2 1.0
OD1 C:ASP18 3.6 73.4 1.0
CG C:ASP18 3.9 60.7 1.0
CD D:GLU44 4.0 91.0 1.0
C C:ALA251 4.2 74.5 1.0
NH1 C:ARG256 4.3 71.3 1.0
CD1 C:LEU253 4.3 65.1 1.0
CZ C:ARG256 4.4 69.5 1.0
NH2 C:ARG256 4.4 77.0 1.0
O3A C:ANP501 4.4 152.2 1.0
CA C:GLY252 4.7 61.0 1.0
CG D:GLU44 4.7 87.7 1.0
OD1 C:ASP250 4.7 110.8 1.0
N C:GLY252 4.8 65.2 1.0
OE1 D:GLU44 4.8 85.8 1.0
PG C:ANP501 4.9 150.8 1.0
CB C:ALA251 5.0 73.8 1.0
NE C:ARG256 5.0 66.4 1.0
O3G C:ANP501 5.0 89.8 1.0

Magnesium binding site 6 out of 16 in 7r3b

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Magnesium binding site 6 out of 16 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


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 From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:82.3
occ:1.00
 O1A D:ANP501 3.0 111.0 1.0
OD2 C:ASP129 3.3 89.2 1.0
OD1 C:ASP129 3.3 92.0 1.0
CG C:ASP129 3.4 92.0 1.0
OD2 C:ASP283 3.6 126.2 1.0
OE1 D:GLU10 3.7 93.6 1.0
O3G D:ANP501 3.8 139.2 1.0
NZ D:LYS176 4.1 84.0 1.0
OD1 C:ASP283 4.2 116.5 1.0
OE2 D:GLU10 4.3 87.2 1.0
CG C:ASP283 4.3 90.1 1.0
PA D:ANP501 4.3 110.0 1.0
CD D:GLU10 4.4 79.6 1.0
CB C:ASP129 4.6 98.8 1.0
O2A D:ANP501 4.8 93.5 1.0
CE D:LYS176 5.0 69.2 1.0

Magnesium binding site 7 out of 16 in 7r3b

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Magnesium binding site 7 out of 16 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


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 From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:95.3
occ:1.00
 O2G C:ANP501 2.5 152.3 1.0
OD2 D:ASP283 2.6 101.4 1.0
O1G C:ANP501 3.2 120.2 1.0
PG C:ANP501 3.5 150.8 1.0
CG D:ASP283 3.5 103.3 1.0
O1A C:ANP501 3.6 123.3 1.0
OD1 D:ASP283 3.7 116.4 1.0
OD2 D:ASP129 3.8 102.1 1.0
O3G C:ANP501 4.1 89.8 1.0
CG D:ASP129 4.2 111.7 1.0
OD1 D:ASP129 4.3 120.4 1.0
CA D:GLY272 4.3 80.3 1.0
OE1 C:GLU10 4.5 111.4 1.0
OE2 C:GLU10 4.5 97.6 1.0
N D:GLY272 4.5 81.1 1.0
PA C:ANP501 4.8 128.1 1.0
CD C:GLU10 4.9 101.9 1.0
NZ D:LYS277 4.9 92.7 1.0
CB D:ASP283 4.9 86.1 1.0
N3B C:ANP501 4.9 164.8 1.0

Magnesium binding site 8 out of 16 in 7r3b

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Magnesium binding site 8 out of 16 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


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 From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:80.1
occ:1.00
 O2B D:ANP501 2.9 144.5 1.0
OE2 C:GLU44 3.1 91.6 1.0
OD1 D:ASP18 3.1 60.5 1.0
K D:K504 3.2 92.6 1.0
OD2 D:ASP18 3.3 66.3 1.0
N3B D:ANP501 3.5 154.7 1.0
CD1 D:LEU253 3.5 72.0 1.0
CZ D:ARG256 3.6 68.3 1.0
CG D:ASP18 3.6 60.3 1.0
PB D:ANP501 3.7 156.4 1.0
NH1 D:ARG256 3.7 79.2 1.0
NH2 D:ARG256 3.8 69.2 1.0
NE D:ARG256 4.1 65.5 1.0
CD C:GLU44 4.1 77.1 1.0
O D:ALA251 4.1 74.4 1.0
CB D:ARG256 4.2 57.7 1.0
O1B D:ANP501 4.3 185.4 1.0
CG D:ARG256 4.4 58.6 1.0
PG D:ANP501 4.4 145.6 1.0
O1G D:ANP501 4.5 113.9 1.0
O2G D:ANP501 4.5 116.8 1.0
N D:LEU253 4.6 64.2 1.0
CA D:GLY252 4.6 57.8 1.0
C D:ALA251 4.6 63.8 1.0
CD D:ARG256 4.7 60.4 1.0
OE1 C:GLU44 4.8 60.9 1.0
CG C:GLU44 4.8 78.5 1.0
CG D:LEU253 4.9 70.8 1.0
N D:GLY252 4.9 58.7 1.0
C D:GLY252 4.9 64.0 1.0

Magnesium binding site 9 out of 16 in 7r3b

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Magnesium binding site 9 out of 16 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:84.5
occ:1.00
 O2B E:ANP501 1.8 126.3 1.0
O1B E:ANP501 2.4 103.1 1.0
PB E:ANP501 2.4 145.9 1.0
O E:ALA251 2.7 68.3 1.0
OD1 E:ASP250 3.3 72.5 1.0
OE2 F:GLU44 3.4 77.9 1.0
N3B E:ANP501 3.6 161.8 1.0
C E:ALA251 3.6 58.8 1.0
O3A E:ANP501 3.7 147.6 1.0
N E:ALA251 4.1 49.7 1.0
CG E:ASP250 4.1 78.1 1.0
CB E:ALA251 4.1 50.7 1.0
CA E:ALA251 4.2 51.7 1.0
OD2 E:ASP18 4.2 66.1 1.0
N E:GLY252 4.6 57.8 1.0
CD F:GLU44 4.6 78.8 1.0
OD2 E:ASP250 4.6 102.0 1.0
OD1 E:ASP18 4.7 76.5 1.0
CG E:ASP18 4.8 61.7 1.0
CA E:GLY252 4.9 54.2 1.0

Magnesium binding site 10 out of 16 in 7r3b

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Magnesium binding site 10 out of 16 in the S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of S-Adenosylmethionine Synthetase From Lactobacillus Plantarum Complexed with Amppnp, Methionine and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:91.7
occ:1.00
 O3G E:ANP501 2.8 155.3 1.0
O1G E:ANP501 3.3 150.3 1.0
OD2 F:ASP283 3.5 105.4 1.0
OD2 F:ASP129 3.5 98.2 1.0
OD1 F:ASP129 3.5 96.0 1.0
PG E:ANP501 3.7 155.8 1.0
CG F:ASP129 3.7 101.9 1.0
OE1 E:GLU10 3.8 103.2 1.0
O2A E:ANP501 3.8 121.9 1.0
NZ E:LYS176 3.9 111.6 1.0
OE2 E:GLU10 4.1 100.1 1.0
OD1 F:ASP283 4.1 118.7 1.0
CG F:ASP283 4.2 100.9 1.0
CD E:GLU10 4.3 90.3 1.0
O1A E:ANP501 4.4 105.2 1.0
O2G E:ANP501 4.4 114.1 1.0
PA E:ANP501 4.6 131.7 1.0
CE E:LYS176 4.8 98.8 1.0
CB F:ASP129 4.9 122.5 1.0
NZ E:LYS257 4.9 60.3 1.0

Reference:

D.Kleiner, Z.Shapiro Tuchman, F.Shmulevich, A.Shahar, R.Zarivach, M.Kosloff, S.Bershtein. Evolution of Homo-Oligomerization of Methionine S-Adenosyltransferases Is Replete with Structure-Function Constrains. Protein Sci. V. 31 E4352 2022.
ISSN: ESSN 1469-896X
PubMed: 35762725
DOI: 10.1002/PRO.4352
Page generated: Thu Apr 6 21:05:40 2023

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