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Magnesium in PDB 1kj8: Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar

Protein crystallography data

The structure of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar, PDB code: 1kj8 was solved by J.B.Thoden, S.M.Firestine, S.J.Benkovic, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.100, 179.300, 75.800, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1kj8:

The structure of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar (pdb code 1kj8). 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 Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar, PDB code: 1kj8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1kj8

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Magnesium binding site 1 out of 4 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar


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 Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg393

b:16.8
occ:1.00
O3G A:ATP1 2.0 17.1 1.0
O A:HOH410 2.0 14.7 1.0
O2B A:ATP1 2.0 14.2 1.0
O A:HOH533 2.2 21.7 1.0
OE2 A:GLU279 2.3 14.0 1.0
OE1 A:GLU279 2.3 14.2 1.0
CD A:GLU279 2.6 17.4 1.0
PG A:ATP1 3.2 19.3 1.0
PB A:ATP1 3.3 16.4 1.0
O3B A:ATP1 3.5 16.1 1.0
O2G A:ATP1 3.7 15.0 1.0
MG A:MG394 3.8 12.9 1.0
O A:HOH527 4.0 20.5 1.0
O A:HOH508 4.0 25.3 1.0
NH1 A:ARG114 4.0 13.7 1.0
CG A:GLU279 4.1 12.4 1.0
O2A A:ATP1 4.1 19.8 1.0
O A:SER159 4.2 25.3 1.0
O3A A:ATP1 4.2 21.1 1.0
OE2 A:GLU84 4.3 19.8 1.0
O1B A:ATP1 4.3 14.8 1.0
OE1 A:GLU84 4.3 25.6 1.0
O A:HOH461 4.4 16.0 1.0
NH2 A:ARG114 4.4 17.7 1.0
O1G A:ATP1 4.5 18.3 1.0
PA A:ATP1 4.6 16.4 1.0
CZ A:ARG114 4.6 13.9 1.0
O1A A:ATP1 4.7 18.6 1.0
CB A:SER160 4.7 39.8 1.0
CA A:SER160 4.7 20.4 1.0
CD A:GLU84 4.8 43.4 1.0
OE1 A:GLU267 4.8 20.5 1.0
CB A:GLU279 4.9 10.7 1.0

Magnesium binding site 2 out of 4 in 1kj8

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Magnesium binding site 2 out of 4 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar


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 Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg394

b:12.9
occ:1.00
O2A A:ATP1 2.0 19.8 1.0
OE1 A:GLU279 2.0 14.2 1.0
OE1 A:GLU267 2.1 20.5 1.0
O2G A:ATP1 2.1 15.0 1.0
O A:HOH404 2.2 12.6 1.0
OE2 A:GLU267 2.2 18.6 1.0
CD A:GLU267 2.5 17.8 1.0
CD A:GLU279 3.1 17.4 1.0
PG A:ATP1 3.2 19.3 1.0
PA A:ATP1 3.4 16.4 1.0
O3B A:ATP1 3.5 16.1 1.0
CG A:GLU279 3.7 12.4 1.0
MG A:MG393 3.8 16.8 1.0
O3G A:ATP1 3.8 17.1 1.0
CG A:GLU267 4.0 14.9 1.0
O3A A:ATP1 4.0 21.1 1.0
O A:HOH402 4.0 8.4 1.0
O2B A:ATP1 4.0 14.2 1.0
O A:HOH455 4.1 19.3 1.0
PB A:ATP1 4.1 16.4 1.0
OE2 A:GLU279 4.2 14.0 1.0
O A:HOH423 4.2 13.6 1.0
O1A A:ATP1 4.3 18.6 1.0
O5' A:ATP1 4.4 14.7 1.0
O3' A:ATP1 4.5 14.7 1.0
O1G A:ATP1 4.5 18.3 1.0
C5' A:ATP1 4.5 15.4 1.0
NE2 A:HIS285 4.6 13.7 1.0
O A:HOH508 4.6 25.3 1.0
O A:HOH533 4.7 21.7 1.0
CB A:GLU267 4.8 14.0 1.0

Magnesium binding site 3 out of 4 in 1kj8

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Magnesium binding site 3 out of 4 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar


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 Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg393

b:51.5
occ:1.00
O3G B:ATP397 2.0 91.6 1.0
O B:HOH684 2.6 40.0 1.0
OE2 B:GLU279 2.7 32.9 1.0
OE1 B:GLU279 2.9 31.5 1.0
O2B B:ATP397 3.0 54.6 1.0
CD B:GLU279 3.1 35.6 1.0
PG B:ATP397 3.4 95.9 1.0
NH2 B:ARG114 3.8 0.0 1.0
PB B:ATP397 3.9 62.0 1.0
O B:HOH740 3.9 42.8 1.0
O3B B:ATP397 4.0 97.2 1.0
O B:HOH556 4.0 41.8 1.0
O2G B:ATP397 4.0 77.5 1.0
OE1 B:GLU84 4.1 62.9 1.0
O3A B:ATP397 4.1 39.5 1.0
O B:SER159 4.2 0.0 1.0
O B:HOH482 4.4 35.5 1.0
MG B:MG394 4.5 39.7 1.0
O1G B:ATP397 4.6 92.8 1.0
CG B:GLU279 4.6 31.7 1.0
CZ B:ARG114 4.6 93.2 1.0
O B:HOH708 4.7 51.2 1.0
CA B:SER160 4.9 95.0 1.0
CD B:GLU84 4.9 88.2 1.0
NE B:ARG114 5.0 38.5 1.0

Magnesium binding site 4 out of 4 in 1kj8

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Magnesium binding site 4 out of 4 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar


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 Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg394

b:39.7
occ:1.00
O2G B:ATP397 2.2 77.5 1.0
O2A B:ATP397 2.2 61.7 1.0
O B:HOH605 2.2 37.2 1.0
OE2 B:GLU267 2.3 46.0 1.0
OE1 B:GLU279 2.3 31.5 1.0
O3B B:ATP397 2.8 97.2 1.0
OE1 B:GLU267 2.8 64.8 1.0
CD B:GLU267 2.9 95.5 1.0
PG B:ATP397 3.0 95.9 1.0
CD B:GLU279 3.3 35.6 1.0
PA B:ATP397 3.3 46.1 1.0
O3A B:ATP397 3.5 39.5 1.0
PB B:ATP397 3.7 62.0 1.0
O3G B:ATP397 3.8 91.6 1.0
CG B:GLU279 4.0 31.7 1.0
C5' B:ATP397 4.1 42.3 1.0
O B:HOH489 4.2 25.2 1.0
O1G B:ATP397 4.2 92.8 1.0
O3' B:ATP397 4.3 30.9 1.0
O5' B:ATP397 4.3 68.6 1.0
OE2 B:GLU279 4.3 32.9 1.0
CG B:GLU267 4.4 21.2 1.0
O B:HOH677 4.4 42.1 1.0
O1A B:ATP397 4.4 37.2 1.0
O B:HOH740 4.4 42.8 1.0
MG B:MG393 4.5 51.5 1.0
O2B B:ATP397 4.6 54.6 1.0
C3' B:ATP397 4.7 31.6 1.0
O1B B:ATP397 4.9 0.0 1.0
C4' B:ATP397 5.0 43.8 1.0

Reference:

J.B.Thoden, S.M.Firestine, S.J.Benkovic, H.M.Holden. Purt-Encoded Glycinamide Ribonucleotide Transformylase. Accommodation of Adenosine Nucleotide Analogs Within the Active Site. J.Biol.Chem. V. 277 23898 2002.
ISSN: ISSN 0021-9258
PubMed: 11953435
DOI: 10.1074/JBC.M202251200
Page generated: Mon Dec 14 06:20:29 2020

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