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Magnesium in PDB 1nlk: Crystal Structure of Myxococcus Xanthus Nucleoside Diphosphate Kinase and Its Interaction with A Nucleotide Substrate at 2.0 Angstroms Resolution

Enzymatic activity of Crystal Structure of Myxococcus Xanthus Nucleoside Diphosphate Kinase and Its Interaction with A Nucleotide Substrate at 2.0 Angstroms Resolution

All present enzymatic activity of Crystal Structure of Myxococcus Xanthus Nucleoside Diphosphate Kinase and Its Interaction with A Nucleotide Substrate at 2.0 Angstroms Resolution:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Myxococcus Xanthus Nucleoside Diphosphate Kinase and Its Interaction with A Nucleotide Substrate at 2.0 Angstroms Resolution, PDB code: 1nlk was solved by R.L.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 63.500, 63.500, 159.500, 90.00, 90.00, 90.00
R / Rfree (%) 23 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Myxococcus Xanthus Nucleoside Diphosphate Kinase and Its Interaction with A Nucleotide Substrate at 2.0 Angstroms Resolution (pdb code 1nlk). 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 Myxococcus Xanthus Nucleoside Diphosphate Kinase and Its Interaction with A Nucleotide Substrate at 2.0 Angstroms Resolution, PDB code: 1nlk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1nlk

Go back to Magnesium Binding Sites List in 1nlk
Magnesium binding site 1 out of 2 in the Crystal Structure of Myxococcus Xanthus Nucleoside Diphosphate Kinase and Its Interaction with A Nucleotide Substrate at 2.0 Angstroms Resolution


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 Myxococcus Xanthus Nucleoside Diphosphate Kinase and Its Interaction with A Nucleotide Substrate at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg146

b:20.0
occ:1.00
 O2A R:ADP1 2.7 32.5 0.2
O1A R:ADP1 3.4 29.2 0.5
CE1 R:HIS54 3.7 44.1 1.0
O2A R:ADP1 3.7 27.0 0.5
PA R:ADP1 3.7 33.1 0.2
O3A R:ADP1 3.8 33.7 0.2
OD2 R:ASP120 3.8 34.8 1.0
NE2 R:HIS54 4.0 45.5 1.0
PA R:ADP1 4.1 25.4 0.5
O1A R:ADP1 4.5 38.5 0.2
CG R:ASP120 4.8 31.6 1.0
ND1 R:HIS54 4.9 43.2 1.0
O5' R:ADP1 4.9 33.3 0.2

Magnesium binding site 2 out of 2 in 1nlk

Go back to Magnesium Binding Sites List in 1nlk
Magnesium binding site 2 out of 2 in the Crystal Structure of Myxococcus Xanthus Nucleoside Diphosphate Kinase and Its Interaction with A Nucleotide Substrate at 2.0 Angstroms Resolution


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 Myxococcus Xanthus Nucleoside Diphosphate Kinase and Its Interaction with A Nucleotide Substrate at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg146

b:20.0
occ:1.00
 O1A L:ADP1 2.5 34.4 0.5
O3B L:ADP1 2.8 37.5 0.5
O3A L:ADP1 2.9 32.9 0.5
O3A L:ADP1 3.0 36.6 0.5
PA L:ADP1 3.2 34.6 0.5
PA L:ADP1 3.2 34.1 0.5
O1A L:ADP1 3.3 35.5 0.5
PB L:ADP1 3.4 41.5 0.5
OD2 L:ASP120 3.5 43.2 1.0
O2A L:ADP1 3.5 32.2 0.5
CB L:ASP120 3.5 29.6 1.0
O2B L:ADP1 3.6 36.3 0.5
O5' L:ADP1 3.9 29.2 0.5
CG L:ASP120 4.0 38.9 1.0
O3B L:ADP1 4.1 41.0 0.5
PB L:ADP1 4.1 39.9 0.5
O L:GLY118 4.2 11.4 1.0
CA L:ASP120 4.5 22.0 1.0
O2A L:ADP1 4.5 32.1 0.5
N L:ASP120 4.7 15.6 1.0
O1B L:ADP1 4.7 34.3 0.5
O5' L:ADP1 4.8 29.4 0.5
O1B L:ADP1 4.8 34.3 0.5

Reference:

R.L.Williams, D.A.Oren, J.Munoz-Dorado, S.Inouye, M.Inouye, E.Arnold. Crystal Structure of Myxococcus Xanthus Nucleoside Diphosphate Kinase and Its Interaction with A Nucleotide Substrate at 2.0 A Resolution. J.Mol.Biol. V. 234 1230 1993.
ISSN: ISSN 0022-2836
PubMed: 8263923
DOI: 10.1006/JMBI.1993.1673
Page generated: Sun Aug 10 01:47:00 2025

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