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Magnesium in PDB 3wxl: Crystal Structure of Trypanosoma Brucei Gambiense Glycerol Kinase Complex with Adp, MG2+, and Glycerol

Enzymatic activity of Crystal Structure of Trypanosoma Brucei Gambiense Glycerol Kinase Complex with Adp, MG2+, and Glycerol

All present enzymatic activity of Crystal Structure of Trypanosoma Brucei Gambiense Glycerol Kinase Complex with Adp, MG2+, and Glycerol:
2.7.1.30;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Brucei Gambiense Glycerol Kinase Complex with Adp, MG2+, and Glycerol, PDB code: 3wxl was solved by E.O.Balogun, D.K.Inaoka, T.Shiba, Y.Kido, C.Tsuge, T.Nara, T.Aoki, T.Honma, A.Tanaka, M.Inoue, S.Matsuoka, P.A.M.Michels, K.Kita, S.Harada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.115, 153.840, 120.098, 90.00, 89.95, 90.00
R / Rfree (%) 21.2 / 25.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trypanosoma Brucei Gambiense Glycerol Kinase Complex with Adp, MG2+, and Glycerol (pdb code 3wxl). 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 Trypanosoma Brucei Gambiense Glycerol Kinase Complex with Adp, MG2+, and Glycerol, PDB code: 3wxl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3wxl

Go back to Magnesium Binding Sites List in 3wxl
Magnesium binding site 1 out of 2 in the Crystal Structure of Trypanosoma Brucei Gambiense Glycerol Kinase Complex with Adp, MG2+, 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 Trypanosoma Brucei Gambiense Glycerol Kinase Complex with Adp, MG2+, and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:32.6
occ:1.00
O B:HOH876 2.0 32.8 1.0
O2B B:ADP603 2.0 30.3 1.0
O B:HOH884 2.1 33.0 1.0
O2B B:ADP602 2.1 41.1 1.0
PB B:ADP603 3.3 30.9 1.0
PB B:ADP602 3.3 41.2 1.0
O1B B:ADP603 3.6 30.9 1.0
O3B B:ADP602 3.6 41.4 1.0
NH1 B:ARG22 3.7 25.9 1.0
O1A B:ADP603 4.0 30.9 1.0
O B:HOH984 4.0 33.2 1.0
O1A B:ADP602 4.0 42.0 1.0
O3A B:ADP603 4.3 30.6 1.0
N7 B:ADP603 4.3 29.8 1.0
O1B B:ADP602 4.3 41.2 1.0
NH2 B:ARG24 4.4 28.6 1.0
O3B B:ADP603 4.4 30.2 1.0
O3A B:ADP602 4.4 41.6 1.0
C8 B:ADP603 4.6 29.9 1.0
PA B:ADP602 4.6 42.0 1.0
PA B:ADP603 4.8 30.7 1.0
CZ B:ARG22 4.8 25.5 1.0
O2A B:ADP602 4.9 42.2 1.0

Magnesium binding site 2 out of 2 in 3wxl

Go back to Magnesium Binding Sites List in 3wxl
Magnesium binding site 2 out of 2 in the Crystal Structure of Trypanosoma Brucei Gambiense Glycerol Kinase Complex with Adp, MG2+, 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 Trypanosoma Brucei Gambiense Glycerol Kinase Complex with Adp, MG2+, and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:37.9
occ:1.00
O2B D:ADP603 2.0 35.3 1.0
O D:HOH865 2.1 40.9 1.0
O2B D:ADP602 2.1 39.5 1.0
O D:HOH728 2.1 31.5 1.0
O D:HOH820 2.3 46.6 1.0
O D:HOH745 2.3 27.5 1.0
PB D:ADP603 3.3 36.0 1.0
PB D:ADP602 3.5 40.1 1.0
O1B D:ADP603 3.7 35.9 1.0
O D:HOH902 3.8 61.6 1.0
NH2 D:ARG22 3.9 31.4 1.0
O1B D:ADP602 3.9 40.3 1.0
NH1 D:ARG24 4.0 30.2 1.0
O2A D:ADP603 4.1 37.2 1.0
O3A D:ADP603 4.1 36.2 1.0
N7 D:ADP602 4.2 33.7 1.0
O1A D:ADP603 4.3 36.2 1.0
O2A D:ADP602 4.3 38.8 1.0
PA D:ADP603 4.3 36.4 1.0
O3A D:ADP602 4.4 39.3 1.0
O3B D:ADP603 4.4 35.5 1.0
O3B D:ADP602 4.5 39.9 1.0
O D:HOH936 4.6 43.3 1.0
O D:HOH793 4.7 46.1 1.0
C8 D:ADP602 4.8 33.7 1.0
O D:HOH934 4.8 40.4 1.0

Reference:

E.O.Balogun, D.K.Inaoka, T.Shiba, Y.Kido, C.Tsuge, T.Nara, T.Aoki, T.Honma, A.Tanaka, M.Inoue, S.Matsuoka, P.A.Michels, K.Kita, S.Harada. Molecular Basis For the Reverse Reaction of African Human Trypanosomes Glycerol Kinase. Mol.Microbiol. V. 94 1315 2014.
ISSN: ISSN 0950-382X
PubMed: 25315291
DOI: 10.1111/MMI.12831
Page generated: Mon Dec 14 09:02:01 2020

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