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Magnesium in PDB 6c07: Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum

Enzymatic activity of Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum

All present enzymatic activity of Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum:
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum, PDB code: 6c07 was solved by J.F.Ohren, R.E.Viola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.85
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.390, 62.060, 191.583, 90.00, 90.65, 90.00
R / Rfree (%) 15.7 / 20.4

Other elements in 6c07:

The structure of Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum (pdb code 6c07). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum, PDB code: 6c07:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6c07

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Magnesium binding site 1 out of 7 in the Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum


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 S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:22.6
occ:1.00
 O A:HOH692 2.0 20.4 1.0
O B:HOH643 2.1 24.2 1.0
O A:ALA267 2.1 20.3 1.0
O A:HOH682 2.1 21.0 1.0
O A:HOH786 2.2 26.0 1.0
OD1 A:ASP266 2.2 24.0 1.0
CG A:ASP266 3.1 28.9 1.0
C A:ALA267 3.3 16.0 1.0
OD2 A:ASP266 3.5 25.4 1.0
HA2 A:GLY268 3.7 18.7 1.0
N A:ALA267 3.9 17.2 1.0
H A:ALA267 3.9 20.6 1.0
OE2 B:GLU62 3.9 27.3 1.0
HB3 A:ALA267 4.0 23.9 1.0
O A:HOH644 4.0 29.9 1.0
O A:HOH616 4.0 33.2 1.0
OD1 A:ASP36 4.1 20.5 1.0
CA A:ALA267 4.1 17.9 1.0
C A:ASP266 4.2 18.4 1.0
OD2 A:ASP36 4.2 23.1 1.0
HB2 A:PRO35 4.2 20.6 1.0
O B:HOH685 4.3 25.4 1.0
N A:GLY268 4.3 18.7 1.0
CB A:ASP266 4.4 24.8 1.0
CA A:GLY268 4.5 15.6 1.0
CG A:ASP36 4.5 22.0 1.0
HD12 A:LEU269 4.5 30.4 1.0
HA A:ASP266 4.5 26.3 1.0
CB A:ALA267 4.5 19.9 1.0
O A:ASP266 4.6 18.9 1.0
O A:HOH914 4.6 40.1 1.0
O A:HOH830 4.6 46.2 1.0
CA A:ASP266 4.7 21.9 1.0
HG3 B:GLU62 4.7 24.9 1.0
HE1 A:HIS34 4.7 29.7 1.0
HB3 A:ASP266 4.9 29.8 1.0
CD B:GLU62 5.0 29.1 1.0
HB1 A:ALA267 5.0 23.9 1.0
HB2 A:ASP266 5.0 29.8 1.0
HA A:ALA267 5.0 21.6 1.0

Magnesium binding site 2 out of 7 in 6c07

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Magnesium binding site 2 out of 7 in the Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum


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 S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:47.9
occ:0.96
 O A:HOH773 2.0 45.0 1.0
O A:HOH822 2.0 36.9 1.0
O A:HOH729 2.1 45.2 1.0
O B:HOH679 2.1 41.2 1.0
OD2 A:ASP139 2.4 37.2 1.0
O A:HOH632 2.4 36.6 1.0
CG A:ASP139 3.4 35.0 1.0
HE21 B:GLN191 3.6 49.0 1.0
OD1 A:ASP139 3.8 34.6 1.0
O A:HOH606 3.8 56.2 1.0
OD1 A:ASP299 4.0 47.1 1.0
OE1 B:GLU28 4.1 45.7 1.0
NE2 B:GLN191 4.2 40.8 1.0
HE22 B:GLN191 4.2 49.0 1.0
OD2 A:ASP299 4.2 59.1 1.0
HA2 A:GLY141 4.5 31.3 1.0
CG A:ASP299 4.5 45.3 1.0
CB A:ASP139 4.7 33.2 1.0
CD B:GLU28 4.8 39.9 1.0
HB2 A:ASP139 4.8 39.9 1.0
OE2 B:GLU28 4.8 42.7 1.0
HB3 A:ASP139 4.9 39.9 1.0
O A:HOH728 5.0 38.1 1.0

Magnesium binding site 3 out of 7 in 6c07

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Magnesium binding site 3 out of 7 in the Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum


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 S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:30.6
occ:0.84
 O B:HOH795 2.1 45.4 1.0
O B:HOH811 2.3 49.5 1.0
O B:HOH766 2.3 35.1 1.0
O B:GLY182 2.4 31.3 1.0
O B:HOH647 2.5 30.7 1.0
O B:HOH694 2.5 39.6 1.0
C B:GLY182 3.6 31.7 1.0
HA B:TRP183 3.8 28.9 1.0
HZ3 B:LYS102 4.0 33.8 1.0
O B:HOH823 4.1 47.9 1.0
O B:LEU184 4.1 18.5 1.0
OD2 B:ASP218 4.3 30.3 1.0
HA2 B:GLY182 4.4 46.6 1.0
O B:HOH656 4.4 30.7 1.0
N B:TRP183 4.4 28.2 1.0
O B:HOH757 4.4 55.2 1.0
CA B:TRP183 4.4 24.0 1.0
HZ2 B:LYS102 4.5 33.8 1.0
O B:HOH758 4.5 31.6 1.0
CA B:GLY182 4.5 38.8 1.0
NZ B:LYS102 4.7 28.2 1.0
HA3 B:GLY182 4.7 46.6 1.0
OD1 B:ASP218 4.7 30.8 1.0
C B:TRP183 4.7 21.2 1.0
HE2 B:LYS102 4.8 38.0 1.0
O B:HOH673 4.9 34.1 1.0
CG B:ASP218 4.9 25.8 1.0

Magnesium binding site 4 out of 7 in 6c07

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Magnesium binding site 4 out of 7 in the Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:27.7
occ:0.73
 O A:HOH698 1.9 33.6 1.0
O B:HOH671 2.0 25.9 1.0
OD1 B:ASP266 2.1 39.2 1.0
O B:ALA267 2.1 22.1 1.0
O B:HOH763 2.2 33.5 1.0
O B:HOH705 2.3 32.4 1.0
C B:ALA267 3.2 20.8 1.0
CG B:ASP266 3.3 37.8 1.0
HB3 B:ALA267 3.7 31.6 1.0
HA2 B:GLY268 3.7 19.4 1.0
O B:HOH626 3.8 49.7 1.0
HB3 B:ASP266 3.8 33.3 1.0
N B:ALA267 3.8 24.2 1.0
H B:ALA267 3.8 29.1 1.0
CA B:ALA267 3.9 21.0 1.0
OE2 A:GLU62 4.0 35.0 1.0
CB B:ASP266 4.1 27.8 1.0
OD2 B:ASP266 4.2 44.7 1.0
N B:GLY268 4.2 16.3 1.0
C B:ASP266 4.2 22.0 1.0
OD1 B:ASP36 4.3 19.7 1.0
O A:HOH717 4.3 25.7 1.0
CB B:ALA267 4.3 26.4 1.0
HD12 B:LEU269 4.3 36.2 1.0
CA B:GLY268 4.5 16.2 1.0
OD2 B:ASP36 4.5 20.2 1.0
HG2 B:PRO35 4.5 32.5 1.0
O B:HOH877 4.5 35.8 1.0
HG3 A:GLU62 4.6 25.8 1.0
O B:HOH634 4.6 33.0 1.0
HB1 B:ALA267 4.7 31.6 1.0
CG B:ASP36 4.7 20.3 1.0
CA B:ASP266 4.7 25.2 1.0
O B:ASP266 4.8 19.8 1.0
HA B:ALA267 4.9 25.2 1.0
HB2 B:ASP266 4.9 33.3 1.0
HD13 B:LEU269 4.9 36.2 1.0
HD11 B:LEU269 4.9 36.2 1.0
CD1 B:LEU269 4.9 30.1 1.0
HA B:ASP266 5.0 30.2 1.0
CD A:GLU62 5.0 30.0 1.0
O A:HOH613 5.0 37.1 1.0

Magnesium binding site 5 out of 7 in 6c07

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Magnesium binding site 5 out of 7 in the Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:37.3
occ:0.89
 O C:HOH609 1.9 27.9 1.0
O C:ALA267 2.0 21.5 1.0
O D:HOH642 2.2 31.8 1.0
O C:HOH653 2.3 26.4 1.0
OD1 C:ASP266 2.4 39.1 1.0
O C:HOH845 2.4 35.8 1.0
OD2 C:ASP266 2.8 45.3 1.0
CG C:ASP266 2.8 33.4 1.0
C C:ALA267 3.2 24.4 1.0
HA2 C:GLY268 3.7 24.7 1.0
N C:ALA267 3.7 23.2 1.0
H C:ALA267 3.8 27.9 1.0
O C:HOH623 3.8 41.5 1.0
HB3 C:ALA267 3.8 26.4 1.0
CA C:ALA267 4.0 22.9 1.0
OE2 D:GLU62 4.0 34.0 1.0
OD1 C:ASP36 4.1 20.4 1.0
C C:ASP266 4.1 25.2 1.0
CB C:ASP266 4.2 27.8 1.0
N C:GLY268 4.2 20.9 1.0
OD2 C:ASP36 4.2 22.7 1.0
HB2 C:PRO35 4.3 27.1 1.0
CB C:ALA267 4.4 21.9 1.0
CA C:GLY268 4.4 20.6 1.0
CG C:ASP36 4.5 20.1 1.0
O D:HOH634 4.5 30.7 1.0
HD12 C:LEU269 4.6 31.5 1.0
O C:ASP266 4.6 22.9 1.0
CA C:ASP266 4.6 23.7 1.0
HA C:ASP266 4.6 28.5 1.0
HE1 C:HIS34 4.6 31.1 1.0
HB3 C:ASP266 4.6 33.3 1.0
HG3 D:GLU62 4.7 29.4 1.0
CL C:CL502 4.8 47.9 1.0
HB2 C:ASP266 4.8 33.3 1.0
O C:HOH824 4.8 45.6 1.0
HA C:ALA267 4.8 27.6 1.0
O D:HOH812 4.8 46.7 1.0
HB1 C:ALA267 4.9 26.4 1.0
HG2 C:PRO35 4.9 35.2 1.0

Magnesium binding site 6 out of 7 in 6c07

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Magnesium binding site 6 out of 7 in the Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg504

b:44.2
occ:0.88
 O C:HOH747 1.9 40.4 1.0
O C:HOH642 2.0 42.8 1.0
O D:HOH638 2.0 49.0 1.0
O C:HOH832 2.2 43.3 1.0
OD2 C:ASP139 2.3 33.9 1.0
O C:HOH703 2.3 44.9 1.0
CG C:ASP139 3.3 40.2 1.0
HE22 D:GLN191 3.5 41.2 1.0
OD1 C:ASP139 3.7 36.3 1.0
OD2 C:ASP299 3.9 57.2 1.0
NE2 D:GLN191 4.1 34.3 1.0
HE21 D:GLN191 4.1 41.2 1.0
OD1 C:ASP299 4.1 46.9 1.0
OE1 D:GLU28 4.2 39.5 1.0
O C:HOH784 4.3 43.9 1.0
CG C:ASP299 4.4 41.1 1.0
O D:HOH793 4.5 53.9 1.0
CB C:ASP139 4.6 30.2 1.0
HA2 C:GLY141 4.7 40.5 1.0
HB3 C:ASP139 4.7 36.2 1.0
HB2 C:ASP139 4.7 36.2 1.0
CD D:GLU28 4.8 42.2 1.0
OE2 D:GLU28 4.8 40.7 1.0

Magnesium binding site 7 out of 7 in 6c07

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Magnesium binding site 7 out of 7 in the Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of S-Adenosylmethionine Synthetase (Metk/Mat) From Cryptosporidium Parvum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:24.8
occ:0.61
 O D:HOH653 2.0 37.9 1.0
OD2 D:ASP36 2.0 24.6 1.0
O D:HOH803 2.1 33.0 1.0
O D:HOH639 2.1 33.0 1.0
O D:HOH686 2.3 33.5 1.0
O D:HOH615 2.3 28.6 1.0
HZ3 D:LYS273 3.0 55.8 1.0
CG D:ASP36 3.0 25.0 1.0
HZ2 D:LYS273 3.0 55.8 1.0
OD1 D:ASP36 3.3 18.5 1.0
HE1 D:HIS34 3.4 31.9 1.0
NZ D:LYS273 3.4 46.5 1.0
HZ1 D:LYS273 3.8 55.8 1.0
HB3 D:ARG272 3.8 27.0 1.0
O D:HOH793 4.2 53.9 1.0
O C:HOH812 4.2 17.4 1.0
CE1 D:HIS34 4.3 26.6 1.0
HH21 D:ARG272 4.3 29.5 1.0
CB D:ASP36 4.3 24.8 1.0
HB2 D:ASP36 4.4 29.8 1.0
HB2 D:ARG272 4.4 27.0 1.0
OD2 D:ASP266 4.5 54.7 1.0
O D:ARG272 4.5 24.0 1.0
CB D:ARG272 4.6 22.5 1.0
HE2 D:LYS273 4.6 41.3 1.0
O D:HOH758 4.6 47.0 1.0
CE D:LYS273 4.6 34.4 1.0
O D:ALA267 4.7 23.8 1.0
NH2 D:ARG272 4.7 24.6 1.0
HB3 D:ASP36 4.7 29.8 1.0
HE2 D:HIS34 4.8 25.7 1.0
HE D:ARG272 4.8 27.5 1.0
HG2 D:LYS273 4.9 23.5 1.0
HA2 D:GLY268 4.9 21.2 1.0
NE2 D:HIS34 4.9 21.4 1.0
HH22 D:ARG272 5.0 29.5 1.0

Reference:

J.Ohren, G.G.Parungao, R.E.Viola. Structure of A Critical Metabolic Enzyme: S-Adenosylmethionine Synthetase From Cryptosporidium Parvum. Acta Crystallogr F Struct V. 75 290 2019BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30950830
DOI: 10.1107/S2053230X19002772
Page generated: Mon Sep 30 20:05:19 2024

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