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Magnesium in PDB 2jat: Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound

Enzymatic activity of Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound

All present enzymatic activity of Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound:
2.7.1.113;

Protein crystallography data

The structure of Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound, PDB code: 2jat was solved by M.Welin, L.Wang, S.Eriksson, H.Eklund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.60
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 83.931, 83.931, 53.310, 90.00, 90.00, 120.00
R / Rfree (%) 22.2 / 26.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound (pdb code 2jat). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound, PDB code: 2jat:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2jat

Go back to Magnesium Binding Sites List in 2jat
Magnesium binding site 1 out of 2 in the Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1203

b:65.1
occ:1.00
O1P A:DCM1205 2.0 50.0 1.0
O2 A:POP1204 2.2 58.0 1.0
OG A:SER14 3.3 36.7 1.0
P A:DCM1205 3.4 51.9 1.0
OD2 A:ASP77 3.5 35.9 1.0
O2P A:DCM1205 3.5 51.5 1.0
P1 A:POP1204 3.5 56.2 1.0
O3 A:POP1204 3.8 57.5 1.0
CB A:SER14 3.9 34.4 1.0
OD1 A:ASP77 4.1 36.5 1.0
O A:POP1204 4.2 58.6 1.0
CG A:ASP77 4.2 36.2 1.0
N A:SER14 4.2 33.9 1.0
O3P A:DCM1205 4.2 50.3 1.0
CE A:LYS13 4.4 32.5 1.0
O5' A:DCM1205 4.5 52.8 1.0
O4 A:POP1204 4.5 58.9 1.0
CA A:SER14 4.6 34.5 1.0
O1 A:POP1204 4.6 57.1 1.0
CB A:LYS13 4.8 34.4 1.0
C5' A:DCM1205 5.0 53.0 1.0

Magnesium binding site 2 out of 2 in 2jat

Go back to Magnesium Binding Sites List in 2jat
Magnesium binding site 2 out of 2 in the Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Deoxyadenosine Kinase From M.Mycoides with Products Dcmp and A Flexible Dcdp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1202

b:69.0
occ:1.00
O1P B:DCM1204 2.0 49.8 1.0
O5 B:POP1203 2.2 60.5 1.0
OG B:SER14 3.3 36.7 1.0
P2 B:POP1203 3.4 58.8 1.0
P B:DCM1204 3.5 51.8 1.0
OD2 B:ASP77 3.6 35.8 1.0
O4 B:POP1203 3.6 59.9 1.0
O2P B:DCM1204 3.7 52.2 1.0
CB B:SER14 3.9 34.4 1.0
O B:POP1203 3.9 60.7 1.0
OD1 B:ASP77 4.2 36.4 1.0
O3P B:DCM1204 4.2 49.6 1.0
N B:SER14 4.2 33.9 1.0
CG B:ASP77 4.3 36.2 1.0
O1 B:POP1203 4.4 61.1 1.0
CE B:LYS13 4.4 32.6 1.0
O5' B:DCM1204 4.6 52.9 1.0
CA B:SER14 4.6 34.5 1.0
O6 B:POP1203 4.6 59.9 1.0
CB B:LYS13 4.8 34.5 1.0
P1 B:POP1203 4.9 62.1 1.0

Reference:

M.Welin, L.Wang, S.Eriksson, H.Eklund. Structure-Function Analysis of A Bacterial Deoxyadenosine Kinase Reveals the Basis For Substrate Specificity. J.Mol.Biol. V. 366 1615 2007.
ISSN: ISSN 0022-2836
PubMed: 17229440
DOI: 10.1016/J.JMB.2006.12.010
Page generated: Wed Aug 14 00:41:57 2024

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