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Magnesium in PDB 6ltv: Crystal Structure of I122A/I330A Variant of S-Adenosylmethionine Synthetase From Cryptosporidium Hominis in Complex with Onb-Sam (2- Nitro Benzyme S-Adenosyl-Methionine)

Enzymatic activity of Crystal Structure of I122A/I330A Variant of S-Adenosylmethionine Synthetase From Cryptosporidium Hominis in Complex with Onb-Sam (2- Nitro Benzyme S-Adenosyl-Methionine)

All present enzymatic activity of Crystal Structure of I122A/I330A Variant of S-Adenosylmethionine Synthetase From Cryptosporidium Hominis in Complex with Onb-Sam (2- Nitro Benzyme S-Adenosyl-Methionine):
2.5.1.6;

Protein crystallography data

The structure of Crystal Structure of I122A/I330A Variant of S-Adenosylmethionine Synthetase From Cryptosporidium Hominis in Complex with Onb-Sam (2- Nitro Benzyme S-Adenosyl-Methionine), PDB code: 6ltv 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) 48.28 / 1.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.169, 100.167, 66.945, 90.00, 95.99, 90.00
R / Rfree (%) 16.2 / 19.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of I122A/I330A Variant of S-Adenosylmethionine Synthetase From Cryptosporidium Hominis in Complex with Onb-Sam (2- Nitro Benzyme S-Adenosyl-Methionine) (pdb code 6ltv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of I122A/I330A Variant of S-Adenosylmethionine Synthetase From Cryptosporidium Hominis in Complex with Onb-Sam (2- Nitro Benzyme S-Adenosyl-Methionine), PDB code: 6ltv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ltv

Go back to Magnesium Binding Sites List in 6ltv
Magnesium binding site 1 out of 2 in the Crystal Structure of I122A/I330A Variant of S-Adenosylmethionine Synthetase From Cryptosporidium Hominis in Complex with Onb-Sam (2- Nitro Benzyme S-Adenosyl-Methionine)


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 I122A/I330A Variant of S-Adenosylmethionine Synthetase From Cryptosporidium Hominis in Complex with Onb-Sam (2- Nitro Benzyme S-Adenosyl-Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:16.3
occ:1.00
 O2G A:3PO501 1.9 16.3 1.0
O5' A:3PO501 2.0 17.8 1.0
O A:HOH645 2.1 19.3 1.0
OD2 A:ASP36 2.1 16.4 1.0
O2B A:3PO501 2.1 18.9 1.0
O A:HOH635 2.2 19.2 1.0
CG A:ASP36 3.1 16.3 1.0
PB A:3PO501 3.1 19.4 1.0
PA A:3PO501 3.2 19.6 1.0
PG A:3PO501 3.3 19.0 1.0
OD1 A:ASP36 3.3 16.9 1.0
O3A A:3PO501 3.4 18.3 1.0
O3B A:3PO501 3.5 18.6 1.0
NZ A:LYS273 3.7 18.1 1.0
O A:HOH731 3.8 22.9 1.0
CE1 A:HIS34 4.1 16.1 1.0
O1A A:3PO501 4.1 15.9 1.0
O3G A:3PO501 4.1 17.4 1.0
OD2 A:ASP266 4.2 23.6 1.0
O1G A:3PO501 4.3 17.5 1.0
O2A A:3PO501 4.3 17.9 1.0
NH2 A:ARG272 4.3 18.1 1.0
CB A:ASP36 4.4 15.7 1.0
O A:ALA267 4.4 20.1 1.0
O1B A:3PO501 4.5 19.4 1.0
CE A:LYS273 4.7 17.0 1.0
NE2 A:HIS34 4.7 15.9 1.0
CB A:ARG272 4.8 16.4 1.0
CZ A:ARG272 4.9 18.3 1.0

Magnesium binding site 2 out of 2 in 6ltv

Go back to Magnesium Binding Sites List in 6ltv
Magnesium binding site 2 out of 2 in the Crystal Structure of I122A/I330A Variant of S-Adenosylmethionine Synthetase From Cryptosporidium Hominis in Complex with Onb-Sam (2- Nitro Benzyme S-Adenosyl-Methionine)


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 I122A/I330A Variant of S-Adenosylmethionine Synthetase From Cryptosporidium Hominis in Complex with Onb-Sam (2- Nitro Benzyme S-Adenosyl-Methionine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:17.3
occ:1.00
 O1A B:3PO501 1.9 15.9 1.0
O B:HOH660 2.0 17.6 1.0
O3G B:3PO501 2.0 17.7 1.0
O1B B:3PO501 2.1 19.5 1.0
OD2 B:ASP36 2.1 17.3 1.0
O B:HOH627 2.2 18.1 1.0
CG B:ASP36 3.0 17.3 1.0
PB B:3PO501 3.1 19.8 1.0
PG B:3PO501 3.2 19.4 1.0
PA B:3PO501 3.2 18.7 1.0
OD1 B:ASP36 3.3 17.1 1.0
O3B B:3PO501 3.5 20.9 1.0
O3A B:3PO501 3.5 19.1 1.0
NZ B:LYS273 3.7 17.7 1.0
O A:HOH725 3.9 22.6 1.0
O2G B:3PO501 4.1 16.4 1.0
CE1 B:HIS34 4.1 15.9 1.0
O5' B:3PO501 4.2 16.2 1.0
OD2 B:ASP266 4.2 23.6 1.0
NH2 B:ARG272 4.3 18.0 1.0
O B:ALA267 4.3 20.6 1.0
O1G B:3PO501 4.4 18.4 1.0
O2A B:3PO501 4.4 19.4 1.0
CB B:ASP36 4.4 16.9 1.0
O2B B:3PO501 4.5 18.0 1.0
CE B:LYS273 4.7 17.1 1.0
NE2 B:HIS34 4.8 15.9 1.0
CB B:ARG272 4.8 17.0 1.0
CZ B:ARG272 4.9 17.9 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: Tue Oct 1 10:36:41 2024

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