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Magnesium in PDB 6ude: Crystal Structure of Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol

Enzymatic activity of Crystal Structure of Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol

All present enzymatic activity of Crystal Structure of Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol:
2.7.1.30;

Protein crystallography data

The structure of Crystal Structure of Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol, PDB code: 6ude was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.73 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.730, 185.930, 103.460, 90.00, 105.78, 90.00
R / Rfree (%) 16.5 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol (pdb code 6ude). 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 Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol, PDB code: 6ude:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6ude

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Magnesium binding site 1 out of 4 in the Crystal Structure of Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol


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 Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:53.1
occ:1.00
 O1B A:ADP600 1.9 55.3 1.0
N A:THR15 2.8 21.5 1.0
OG1 A:THR15 2.8 39.7 1.0
O A:HOH769 2.9 41.8 1.0
N A:SER16 3.0 23.8 1.0
PB A:ADP600 3.3 44.1 1.0
N A:THR14 3.4 23.0 1.0
CA A:THR15 3.5 26.7 1.0
NH2 A:ARG18 3.6 35.6 1.0
C A:GLY13 3.6 26.3 1.0
C A:THR15 3.6 23.4 1.0
OG1 A:THR267 3.6 25.0 1.0
CA A:GLY13 3.7 22.5 1.0
CB A:THR15 3.7 35.7 1.0
O A:SER16 3.7 27.0 1.0
C A:THR14 3.8 25.6 1.0
OG A:SER16 3.9 38.4 1.0
O2B A:ADP600 3.9 49.3 1.0
CA A:SER16 4.1 26.6 1.0
O3B A:ADP600 4.1 43.7 1.0
CA A:THR14 4.1 27.3 1.0
O A:GLY13 4.3 23.5 1.0
C A:SER16 4.4 25.7 1.0
CB A:SER16 4.4 32.4 1.0
CG2 A:THR15 4.4 35.7 1.0
O A:HOH737 4.4 31.4 1.0
O3A A:ADP600 4.4 37.9 1.0
CZ A:ARG18 4.6 47.9 1.0
O1A A:ADP600 4.6 27.9 1.0
CB A:THR14 4.6 25.1 1.0
N A:GLY13 4.6 26.7 1.0
O A:THR15 4.8 28.1 1.0
O A:THR14 5.0 26.9 1.0

Magnesium binding site 2 out of 4 in 6ude

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Magnesium binding site 2 out of 4 in the Crystal Structure of Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol


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 Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:53.5
occ:1.00
 O2B B:ADP600 1.9 57.7 1.0
N B:THR15 2.5 31.0 1.0
N B:SER16 2.9 30.4 1.0
CB B:THR15 3.0 31.3 1.0
CA B:THR15 3.0 35.1 1.0
O B:HOH759 3.1 34.3 1.0
N B:THR14 3.2 30.8 1.0
PB B:ADP600 3.3 54.2 1.0
C B:GLY13 3.4 31.7 1.0
C B:THR15 3.4 33.4 1.0
NH2 B:ARG18 3.5 59.6 1.0
CA B:GLY13 3.5 31.3 1.0
O B:SER16 3.6 31.1 1.0
OG1 B:THR267 3.6 29.2 1.0
C B:THR14 3.6 32.2 1.0
OG1 B:THR15 3.7 41.3 1.0
O1B B:ADP600 3.7 49.9 1.0
CA B:THR14 3.9 29.6 1.0
CA B:SER16 4.0 31.0 1.0
OG B:SER16 4.1 53.7 1.0
O B:GLY13 4.1 29.9 1.0
O3B B:ADP600 4.1 55.9 1.0
CG2 B:THR15 4.1 43.9 1.0
C B:SER16 4.2 24.8 1.0
O B:HOH708 4.3 33.4 1.0
CZ B:ARG18 4.4 61.0 1.0
O3A B:ADP600 4.4 52.7 1.0
CB B:THR14 4.5 30.3 1.0
N B:GLY13 4.6 31.7 1.0
CB B:SER16 4.6 42.8 1.0
O2A B:ADP600 4.6 34.7 1.0
O B:THR15 4.6 30.5 1.0
O B:THR14 4.7 31.0 1.0
CB B:THR267 5.0 22.5 1.0

Magnesium binding site 3 out of 4 in 6ude

Go back to Magnesium Binding Sites List in 6ude
Magnesium binding site 3 out of 4 in the Crystal Structure of Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol


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 Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:54.0
occ:1.00
 O3B C:ADP600 2.6 52.3 1.0
O C:HOH762 2.7 39.4 1.0
N C:THR15 2.9 23.2 1.0
N C:SER16 3.0 24.1 1.0
NH2 C:ARG18 3.1 49.2 1.0
CB C:THR15 3.3 36.3 1.0
CA C:THR15 3.4 35.8 1.0
N C:THR14 3.4 29.1 1.0
O C:SER16 3.5 32.8 1.0
CA C:GLY13 3.5 25.0 1.0
PB C:ADP600 3.5 45.9 1.0
C C:GLY13 3.6 24.3 1.0
C C:THR15 3.6 28.7 1.0
OG C:SER16 3.7 45.4 1.0
O3A C:ADP600 3.7 43.1 1.0
O1B C:ADP600 3.8 41.8 1.0
OG1 C:THR15 3.8 46.1 1.0
OG1 C:THR267 3.9 23.7 1.0
CZ C:ARG18 4.0 53.0 1.0
CA C:SER16 4.0 26.1 1.0
C C:THR14 4.0 26.0 1.0
C C:SER16 4.2 28.1 1.0
CA C:THR14 4.3 24.2 1.0
CB C:SER16 4.3 35.5 1.0
O C:GLY13 4.3 25.9 1.0
O C:HOH725 4.3 29.6 1.0
O1A C:ADP600 4.4 31.7 1.0
N C:GLY13 4.5 32.9 1.0
CG2 C:THR15 4.5 34.4 1.0
NE C:ARG18 4.6 58.2 1.0
NH1 C:ARG18 4.6 45.4 1.0
PA C:ADP600 4.8 36.7 1.0
O C:THR15 4.8 26.1 1.0
CB C:THR14 4.9 18.9 1.0
O2B C:ADP600 4.9 56.8 1.0

Magnesium binding site 4 out of 4 in 6ude

Go back to Magnesium Binding Sites List in 6ude
Magnesium binding site 4 out of 4 in the Crystal Structure of Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol


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 Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:61.8
occ:1.00
 O D:HOH770 2.8 40.2 1.0
O3B D:ADP600 2.9 51.0 1.0
N D:THR15 2.9 24.7 1.0
CB D:THR15 3.0 28.0 1.0
N D:SER16 3.1 27.7 1.0
CA D:THR15 3.3 25.2 1.0
N D:THR14 3.5 25.7 1.0
OG1 D:THR15 3.5 45.0 1.0
O3A D:ADP600 3.5 50.0 1.0
PB D:ADP600 3.5 52.0 1.0
OG1 D:THR267 3.6 26.3 1.0
NH1 D:ARG18 3.6 57.5 1.0
C D:THR15 3.6 33.8 1.0
CA D:GLY13 3.7 26.0 1.0
C D:GLY13 3.7 26.6 1.0
O1B D:ADP600 3.8 51.1 1.0
O D:SER16 3.8 26.4 1.0
OG D:SER16 3.9 35.5 1.0
C D:THR14 4.0 25.8 1.0
CG2 D:THR15 4.2 32.7 1.0
CA D:SER16 4.2 27.1 1.0
CA D:THR14 4.3 24.0 1.0
CZ D:ARG18 4.3 59.8 1.0
O D:HOH721 4.4 33.7 1.0
C D:SER16 4.4 28.3 1.0
O2A D:ADP600 4.5 34.9 1.0
O D:GLY13 4.5 25.4 1.0
CB D:SER16 4.5 33.4 1.0
PA D:ADP600 4.7 35.3 1.0
N D:GLY13 4.7 27.9 1.0
C5' D:ADP600 4.8 31.2 1.0
NH2 D:ARG18 4.8 60.8 1.0
CB D:THR14 4.8 29.0 1.0
O D:THR15 4.8 30.6 1.0
NE D:ARG18 4.9 61.8 1.0
CB D:THR267 4.9 21.6 1.0

Reference:

J.N.Phan, J.Abendroth, D.M.Dranow, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Glycerol Kinase From Elizabethkingia Anophelis NUHP1 in Complex with Adp and Glycerol To Be Published.
Page generated: Tue Oct 1 20:58:40 2024

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