Magnesium in PDB 6ltw: Crystal Structure of Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis

Enzymatic activity of Crystal Structure of Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis

All present enzymatic activity of Crystal Structure of Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis:
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis, PDB code: 6ltw was solved by R.K.Singh, F.Michailidou, A.Rentmeister, D.Kuemmel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.08 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.877, 100.360, 66.842, 90.00, 95.86, 90.00
R / Rfree (%) 15.6 / 19.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis (pdb code 6ltw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis, PDB code: 6ltw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6ltw

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Magnesium binding site 1 out of 4 in the Crystal Structure of Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis


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 Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:20.1
occ:1.00
 O4 A:PO4504 1.9 21.4 1.0
O3 A:PO4503 1.9 24.8 1.0
O A:HOH730 2.1 25.1 1.0
O A:HOH651 2.1 21.6 1.0
OD2 A:ASP36 2.1 16.2 1.0
O A:HOH669 2.2 22.2 1.0
CG A:ASP36 3.0 18.4 1.0
P A:PO4503 3.3 25.6 1.0
P A:PO4504 3.3 23.9 1.0
OD1 A:ASP36 3.4 19.5 1.0
O1 A:PO4503 3.5 36.7 1.0
O3 A:PO4504 3.6 27.9 1.0
NZ A:LYS273 3.6 19.6 1.0
O2 A:PO4503 4.0 30.2 1.0
OD2 A:ASP266 4.1 30.8 1.0
CE1 A:HIS34 4.1 21.1 1.0
O B:HOH633 4.1 35.0 1.0
NH2 A:ARG272 4.1 21.6 1.0
O1 A:PO4504 4.3 23.8 1.0
O2 A:PO4504 4.3 24.3 1.0
O A:ALA267 4.3 24.1 1.0
O4 A:PO4503 4.4 29.4 1.0
CB A:ASP36 4.4 18.5 1.0
CB A:ARG272 4.6 17.1 1.0
NE2 A:HIS34 4.7 20.1 1.0
CZ A:ARG272 4.8 20.6 1.0
CE A:LYS273 4.8 17.7 1.0
NE A:ARG272 4.8 20.9 1.0
CG A:ASP266 4.9 30.2 1.0
OE2 B:GLU62 4.9 29.6 1.0

Magnesium binding site 2 out of 4 in 6ltw

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Magnesium binding site 2 out of 4 in the Crystal Structure of Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis


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 Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:40.0
occ:1.00
 O A:HOH603 2.2 39.0 1.0
O2 B:PO4503 2.4 21.9 1.0
O2 B:PO4504 2.4 26.6 1.0
O B:HOH623 2.6 32.4 1.0
O B:HOH624 3.1 23.8 1.0
O4 B:PO4504 3.1 37.2 1.0
OD2 A:ASP299 3.3 19.1 1.0
P B:PO4503 3.4 22.6 1.0
O3 B:PO4503 3.4 24.8 1.0
P B:PO4504 3.4 25.1 1.0
OD1 A:ASP299 3.8 23.5 1.0
CG A:ASP299 3.9 22.4 1.0
NZ B:LYS273 4.0 18.5 1.0
O B:HOH751 4.1 22.8 1.0
O1 B:PO4503 4.1 18.8 1.0
O A:HOH698 4.3 27.8 1.0
O3 B:PO4504 4.4 23.3 1.0
CA A:GLY288 4.5 18.3 1.0
O4 B:PO4503 4.5 25.9 1.0
OE2 B:GLU28 4.6 20.9 1.0
O1 B:PO4504 4.6 28.6 1.0
NZ B:LYS189 4.6 23.7 1.0
CE B:LYS273 4.7 17.9 1.0
O A:HOH720 4.8 19.9 1.0
OD2 A:ASP139 4.8 29.8 1.0
N A:GLY288 4.9 17.1 1.0

Magnesium binding site 3 out of 4 in 6ltw

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Magnesium binding site 3 out of 4 in the Crystal Structure of Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis


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 Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:18.2
occ:1.00
 O1 B:PO4503 1.8 18.8 1.0
O B:HOH682 1.9 21.6 1.0
O3 B:PO4504 2.0 23.3 1.0
OD2 B:ASP36 2.1 18.8 1.0
O B:HOH695 2.1 20.8 1.0
O B:HOH759 2.1 25.5 1.0
CG B:ASP36 3.1 19.5 1.0
P B:PO4503 3.3 22.6 1.0
P B:PO4504 3.3 25.1 1.0
OD1 B:ASP36 3.4 19.6 1.0
O4 B:PO4504 3.6 37.2 1.0
NZ B:LYS273 3.6 18.5 1.0
O3 B:PO4503 3.7 24.8 1.0
O A:HOH622 4.0 34.7 1.0
O2 B:PO4504 4.0 26.6 1.0
NH2 B:ARG272 4.1 21.7 1.0
CE1 B:HIS34 4.2 19.1 1.0
OD2 B:ASP266 4.2 32.4 1.0
O4 B:PO4503 4.3 25.9 1.0
O2 B:PO4503 4.3 21.9 1.0
O B:ALA267 4.3 23.9 1.0
O1 B:PO4504 4.4 28.6 1.0
CB B:ASP36 4.4 18.9 1.0
CB B:ARG272 4.6 18.0 1.0
NE2 B:HIS34 4.7 20.4 1.0
CZ B:ARG272 4.7 20.3 1.0
NE B:ARG272 4.8 20.9 1.0
CE B:LYS273 4.8 17.9 1.0
OE2 A:GLU62 4.9 29.6 1.0
CG B:ASP266 4.9 30.9 1.0

Magnesium binding site 4 out of 4 in 6ltw

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Magnesium binding site 4 out of 4 in the Crystal Structure of Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis


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 Apo Form of I122A/I330A Variant of S- Adenosylmethionine Synthetase From Cryptosporidium Hominis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:47.4
occ:1.00
 O2 A:PO4504 2.4 24.3 1.0
O A:HOH625 2.5 28.1 1.0
O2 A:PO4503 2.5 30.2 1.0
O B:HOH767 2.9 35.7 1.0
O A:HOH645 3.0 23.8 1.0
OD2 B:ASP299 3.3 19.8 1.0
O1 A:PO4503 3.3 36.7 1.0
P A:PO4504 3.4 23.9 1.0
O3 A:PO4504 3.5 27.9 1.0
P A:PO4503 3.5 25.6 1.0
OD1 B:ASP299 3.7 24.4 1.0
CG B:ASP299 3.8 22.3 1.0
O4 A:PO4504 4.1 21.4 1.0
O A:HOH792 4.1 24.1 1.0
NZ A:LYS273 4.1 19.6 1.0
O B:HOH679 4.3 29.3 1.0
OE2 A:GLU28 4.5 19.1 1.0
NZ A:LYS189 4.5 22.0 1.0
CA B:GLY288 4.5 19.1 1.0
O3 A:PO4503 4.5 24.8 1.0
O1 A:PO4504 4.6 23.8 1.0
O4 A:PO4503 4.6 29.4 1.0
O B:HOH717 4.6 18.8 1.0
CE A:LYS273 4.7 17.7 1.0
OD2 B:ASP139 4.9 31.1 1.0
O B:GLN140 4.9 23.4 1.0
N B:GLY288 5.0 16.6 1.0

Reference:

F.Michailidou, N.Klocker, N.Cornelissen, R.K.Singh, A.Peters, A.Ovcharenko, D.Kummel, A.Rentmeister. Engineered Sam Synthetases For Enzymatic Generation of Adomet Analogs with Photocaging Groups and Reversible Dna Modification in Cascade Reactions. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 33017502
DOI: 10.1002/ANIE.202012623
Page generated: Mon Jan 25 08:58:05 2021

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