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Magnesium in PDB 1ndc: X-Ray Structure of Nucleoside Diphosphate Kinase Complexed with Dtdp and MG2+ at 2 A Resolution

Enzymatic activity of X-Ray Structure of Nucleoside Diphosphate Kinase Complexed with Dtdp and MG2+ at 2 A Resolution

All present enzymatic activity of X-Ray Structure of Nucleoside Diphosphate Kinase Complexed with Dtdp and MG2+ at 2 A Resolution:
2.7.4.6;

Protein crystallography data

The structure of X-Ray Structure of Nucleoside Diphosphate Kinase Complexed with Dtdp and MG2+ at 2 A Resolution, PDB code: 1ndc was solved by J.Cherfils, S.Morera, J.Janin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.00 / 2.00
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 79.800, 79.800, 160.600, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Nucleoside Diphosphate Kinase Complexed with Dtdp and MG2+ at 2 A Resolution (pdb code 1ndc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the X-Ray Structure of Nucleoside Diphosphate Kinase Complexed with Dtdp and MG2+ at 2 A Resolution, PDB code: 1ndc:

Magnesium binding site 1 out of 1 in 1ndc

Go back to Magnesium Binding Sites List in 1ndc
Magnesium binding site 1 out of 1 in the X-Ray Structure of Nucleoside Diphosphate Kinase Complexed with Dtdp and MG2+ at 2 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Nucleoside Diphosphate Kinase Complexed with Dtdp and MG2+ at 2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg161

b:8.0
occ:1.00
 O A:HOH204 1.9 8.8 1.0
O A:HOH243 2.0 7.3 1.0
O A:HOH224 2.0 9.0 1.0
O A:HOH264 2.1 9.0 1.0
O1A A:TYD160 2.1 8.1 1.0
O2B A:TYD160 2.1 7.3 1.0
PA A:TYD160 3.4 7.1 1.0
PB A:TYD160 3.4 6.8 1.0
O3A A:TYD160 3.7 8.8 1.0
OD2 A:ASP125 3.9 18.4 1.0
O A:HOH235 4.2 15.5 1.0
NH1 A:ARG92 4.2 8.8 1.0
O A:HOH249 4.3 18.0 1.0
O1B A:TYD160 4.3 7.4 1.0
OE2 A:GLU58 4.4 14.3 1.0
O A:HOH218 4.4 8.3 1.0
O2A A:TYD160 4.4 9.7 1.0
CG A:ASP125 4.4 10.3 1.0
O A:HOH225 4.4 22.9 1.0
O3B A:TYD160 4.4 9.3 1.0
CB A:ASP125 4.4 8.9 1.0
O A:HOH246 4.4 9.4 1.0
O5' A:TYD160 4.5 4.4 1.0
C5' A:TYD160 4.5 6.2 1.0
NE2 A:HIS59 4.6 5.1 1.0
O A:GLY123 4.7 5.1 1.0
CE1 A:HIS122 4.9 2.0 1.0
CZ A:ARG92 5.0 10.5 1.0

Reference:

J.Cherfils, S.Morera, I.Lascu, M.Veron, J.Janin. X-Ray Structure of Nucleoside Diphosphate Kinase Complexed with Thymidine Diphosphate and MG2+ at 2-A Resolution. Biochemistry V. 33 9062 1994.
ISSN: ISSN 0006-2960
PubMed: 8049207
DOI: 10.1021/BI00197A006
Page generated: Mon Dec 14 06:31:56 2020

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