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Magnesium in PDB 2jas: Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp

Enzymatic activity of Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp

All present enzymatic activity of Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp:
2.7.1.113;

Protein crystallography data

The structure of Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp, PDB code: 2jas 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) 47.00 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 190.845, 100.850, 109.486, 90.00, 124.58, 90.00
R / Rfree (%) 23.3 / 27.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp (pdb code 2jas). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp, PDB code: 2jas:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2jas

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Magnesium binding site 1 out of 6 in the Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp


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 Bound Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1202

b:44.6
occ:1.00
 O2A A:DTP1201 2.0 44.4 1.0
O2G A:DTP1201 2.1 34.3 1.0
O1B A:DTP1201 2.2 37.8 1.0
PB A:DTP1201 3.4 40.0 1.0
PG A:DTP1201 3.4 38.3 1.0
PA A:DTP1201 3.4 42.9 1.0
O3B A:DTP1201 3.8 39.2 1.0
O3A A:DTP1201 3.8 41.2 1.0
O1G A:DTP1201 4.1 38.2 1.0
OE2 A:GLU150 4.1 39.8 1.0
CG1 A:VAL9 4.2 34.5 1.0
O5' A:DTP1201 4.2 44.8 1.0
OE1 A:GLU150 4.4 40.5 1.0
N A:GLY10 4.4 34.9 1.0
CA A:GLY146 4.5 44.4 1.0
O1A A:DTP1201 4.5 42.7 1.0
O3G A:DTP1201 4.6 37.5 1.0
CD A:GLU150 4.7 40.0 1.0
O2B A:DTP1201 4.7 38.5 1.0
CA A:GLY10 4.9 35.0 1.0
OG A:SER14 5.0 36.4 1.0

Magnesium binding site 2 out of 6 in 2jas

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Magnesium binding site 2 out of 6 in the Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp


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 Bound Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1201

b:47.5
occ:1.00
 O1B B:DTP1202 2.1 33.5 1.0
O2A B:DTP1202 2.1 37.1 1.0
O2G B:DTP1202 2.2 36.0 1.0
PB B:DTP1202 3.3 35.7 1.0
PA B:DTP1202 3.4 37.4 1.0
PG B:DTP1202 3.5 38.8 1.0
OE2 B:GLU150 3.5 39.5 1.0
O3A B:DTP1202 3.8 36.5 1.0
O3B B:DTP1202 3.8 38.3 1.0
OE1 B:GLU150 4.0 40.0 1.0
CG1 B:VAL9 4.0 34.9 1.0
O1G B:DTP1202 4.2 39.5 1.0
CD B:GLU150 4.2 39.9 1.0
O5' B:DTP1202 4.2 37.6 1.0
N B:GLY10 4.3 35.0 1.0
O1A B:DTP1202 4.6 39.2 1.0
CA B:GLY146 4.6 43.8 1.0
O2B B:DTP1202 4.6 36.4 1.0
O3G B:DTP1202 4.7 38.6 1.0
C3' B:DTP1202 4.9 36.4 1.0
CA B:VAL9 4.9 34.9 1.0
O3' B:DTP1202 5.0 34.7 1.0
CB B:VAL9 5.0 34.8 1.0
C4' B:DTP1202 5.0 35.9 1.0

Magnesium binding site 3 out of 6 in 2jas

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Magnesium binding site 3 out of 6 in the Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1201

b:46.4
occ:1.00
 O1B C:DTP1202 2.1 26.2 1.0
O2A C:DTP1202 2.3 29.4 1.0
O2G C:DTP1202 2.4 30.4 1.0
PB C:DTP1202 3.5 29.3 1.0
PG C:DTP1202 3.6 32.8 1.0
PA C:DTP1202 3.6 29.1 1.0
OE2 C:GLU150 3.8 39.7 1.0
OE1 C:GLU150 4.0 40.9 1.0
O3B C:DTP1202 4.0 31.3 1.0
O3A C:DTP1202 4.0 29.5 1.0
N C:GLY10 4.1 35.5 1.0
O1G C:DTP1202 4.1 33.1 1.0
CG1 C:VAL9 4.2 35.0 1.0
CA C:GLY146 4.3 39.0 1.0
CD C:GLU150 4.3 40.1 1.0
O1A C:DTP1202 4.5 29.8 1.0
CA C:GLY10 4.6 35.2 1.0
C5' C:DTP1202 4.7 27.5 1.0
O5' C:DTP1202 4.7 28.1 1.0
O2B C:DTP1202 4.7 28.3 1.0
O3G C:DTP1202 4.9 32.1 1.0
C C:VAL9 5.0 35.6 1.0

Magnesium binding site 4 out of 6 in 2jas

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Magnesium binding site 4 out of 6 in the Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1202

b:67.2
occ:1.00
 O2G D:DTP1201 2.1 41.4 1.0
O2A D:DTP1201 2.2 46.1 1.0
O1B D:DTP1201 2.3 46.7 1.0
PG D:DTP1201 3.5 43.6 1.0
PB D:DTP1201 3.5 46.1 1.0
PA D:DTP1201 3.5 46.8 1.0
O3B D:DTP1201 3.9 45.4 1.0
OE2 D:GLU150 4.0 39.9 1.0
O3A D:DTP1201 4.0 46.2 1.0
O5' D:DTP1201 4.1 47.7 1.0
N D:GLY10 4.1 35.1 1.0
CG1 D:VAL9 4.1 35.2 1.0
O1G D:DTP1201 4.2 44.0 1.0
CA D:GLY146 4.4 43.5 1.0
OE1 D:GLU150 4.5 40.1 1.0
O3G D:DTP1201 4.6 44.3 1.0
CD D:GLU150 4.7 39.8 1.0
CA D:GLY10 4.7 35.2 1.0
O1A D:DTP1201 4.8 47.4 1.0
O2B D:DTP1201 4.9 45.2 1.0

Magnesium binding site 5 out of 6 in 2jas

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Magnesium binding site 5 out of 6 in the Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1202

b:60.1
occ:1.00
 O1B E:DTP1201 2.2 43.6 1.0
O2G E:DTP1201 2.2 45.6 1.0
O2A E:DTP1201 2.3 48.4 1.0
PB E:DTP1201 3.5 46.8 1.0
PG E:DTP1201 3.6 46.1 1.0
PA E:DTP1201 3.7 48.4 1.0
OE2 E:GLU150 3.8 40.5 1.0
O3B E:DTP1201 3.9 46.6 1.0
O3A E:DTP1201 4.0 47.4 1.0
CG1 E:VAL9 4.2 34.5 1.0
O1G E:DTP1201 4.2 46.5 1.0
CA E:GLY146 4.3 44.6 1.0
C5' E:DTP1201 4.3 43.9 1.0
OE1 E:GLU150 4.4 41.2 1.0
CD E:GLU150 4.5 41.0 1.0
O5' E:DTP1201 4.5 47.0 1.0
N E:GLY10 4.7 35.5 1.0
O3G E:DTP1201 4.7 45.0 1.0
O2B E:DTP1201 4.8 44.9 1.0
O1A E:DTP1201 4.8 48.9 1.0
N E:ARG147 4.9 44.6 1.0

Magnesium binding site 6 out of 6 in 2jas

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Magnesium binding site 6 out of 6 in the Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Deoxyadenosine Kinase From M.Mycoides with Bound Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1202

b:46.9
occ:1.00
 O1B F:DTP1201 2.1 43.2 1.0
O2A F:DTP1201 2.2 46.5 1.0
O2G F:DTP1201 2.2 42.4 1.0
PB F:DTP1201 3.3 45.5 1.0
PA F:DTP1201 3.4 45.5 1.0
PG F:DTP1201 3.4 44.9 1.0
O3B F:DTP1201 3.7 45.8 1.0
O3A F:DTP1201 3.7 45.0 1.0
OE2 F:GLU150 3.8 40.2 1.0
O5' F:DTP1201 4.1 46.1 1.0
O1G F:DTP1201 4.1 45.8 1.0
CG1 F:VAL9 4.2 35.0 1.0
N F:GLY10 4.3 35.4 1.0
OE1 F:GLU150 4.3 39.9 1.0
CA F:GLY146 4.4 42.2 1.0
CD F:GLU150 4.5 40.2 1.0
O3G F:DTP1201 4.6 44.5 1.0
O2B F:DTP1201 4.7 44.4 1.0
O1A F:DTP1201 4.7 47.4 1.0
CA F:GLY10 4.8 35.4 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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