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Magnesium in PDB 2j4l: Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution

Enzymatic activity of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution:
2.7.4.22;

Protein crystallography data

The structure of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution, PDB code: 2j4l was solved by K.S.Jensen, E.Johansson, K.F.Jensen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.63 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.750, 79.030, 223.470, 90.00, 96.56, 90.00
R / Rfree (%) 24.6 / 27.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution (pdb code 2j4l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution, PDB code: 2j4l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 2j4l

Go back to Magnesium Binding Sites List in 2j4l
Magnesium binding site 1 out of 7 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom 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 Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1228

b:55.1
occ:1.00
 O3A B:UTP1227 2.7 95.4 1.0
O1A B:UTP1227 2.9 87.6 1.0
PA B:UTP1227 3.3 84.4 1.0
O5' B:UTP1227 3.5 80.1 1.0
O3B B:UTP1227 3.6 0.9 1.0
PB B:UTP1227 3.6 0.4 1.0
O1B B:UTP1227 3.9 0.8 1.0
O3' B:UTP1227 4.1 69.5 1.0
C3' B:UTP1227 4.2 68.8 1.0
CB B:SER118 4.4 52.1 1.0
C5' B:UTP1227 4.5 72.2 1.0
O2A B:UTP1227 4.7 88.5 1.0
O3G B:UTP1227 4.8 0.9 1.0
C4' B:UTP1227 4.9 69.8 1.0
PG B:UTP1227 4.9 0.3 1.0
O2B B:UTP1227 4.9 0.1 1.0

Magnesium binding site 2 out of 7 in 2j4l

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Magnesium binding site 2 out of 7 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom 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 Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1228

b:66.3
occ:1.00
 O3B C:UTP1227 2.6 95.8 1.0
NH2 C:ARG48 2.7 77.1 1.0
O1A C:UTP1227 3.1 74.1 1.0
O3A C:UTP1227 3.2 81.0 1.0
O1G C:UTP1227 3.2 0.1 1.0
PB C:UTP1227 3.4 88.6 1.0
PG C:UTP1227 3.5 0.3 1.0
PA C:UTP1227 3.6 71.9 1.0
O1B C:UTP1227 3.7 89.7 1.0
O5' C:UTP1227 3.8 68.2 1.0
CZ C:ARG48 4.0 77.8 1.0
O3G C:UTP1227 4.2 0.1 1.0
O C:GLY179 4.2 94.6 1.0
N C:TYR181 4.3 94.6 1.0
O C:TYR181 4.6 92.9 1.0
O2B C:UTP1227 4.7 89.2 1.0
CB C:TYR181 4.7 93.7 1.0
O2G C:UTP1227 4.7 0.0 1.0
NH1 C:ARG48 4.8 76.3 1.0
C5' C:UTP1227 4.8 61.1 1.0
NE C:ARG48 4.9 77.1 1.0
CA C:TYR181 4.9 93.5 1.0

Magnesium binding site 3 out of 7 in 2j4l

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Magnesium binding site 3 out of 7 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1228

b:56.5
occ:1.00
 O3A D:UTP1227 2.6 95.4 1.0
O1B D:UTP1227 2.6 0.4 1.0
PB D:UTP1227 3.0 0.6 1.0
PA D:UTP1227 3.7 84.6 1.0
O3B D:UTP1227 3.7 0.3 1.0
O1A D:UTP1227 3.7 87.2 1.0
O3' D:UTP1227 3.8 73.4 1.0
C3' D:UTP1227 4.0 68.9 1.0
O5' D:UTP1227 4.2 80.6 1.0
O2B D:UTP1227 4.3 0.4 1.0
CB D:SER118 4.3 56.4 1.0
C5' D:UTP1227 4.8 73.2 1.0
C4' D:UTP1227 4.9 69.6 1.0
O2A D:UTP1227 5.0 84.5 1.0

Magnesium binding site 4 out of 7 in 2j4l

Go back to Magnesium Binding Sites List in 2j4l
Magnesium binding site 4 out of 7 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1228

b:73.6
occ:1.00
 O3B E:UTP1227 2.9 91.4 1.0
O1A E:UTP1227 3.0 72.2 1.0
O3A E:UTP1227 3.1 79.2 1.0
CG E:TYR181 3.1 0.1 1.0
CD1 E:TYR181 3.1 0.4 1.0
CD2 E:TYR181 3.5 0.5 1.0
PA E:UTP1227 3.5 70.3 1.0
CE1 E:TYR181 3.5 0.0 1.0
O1G E:UTP1227 3.5 97.5 1.0
CA E:TYR181 3.5 0.7 1.0
O5' E:UTP1227 3.6 68.1 1.0
CB E:TYR181 3.6 0.5 1.0
PB E:UTP1227 3.7 84.7 1.0
CE2 E:TYR181 3.8 0.2 1.0
CZ E:TYR181 3.8 1.0 1.0
PG E:UTP1227 3.9 99.0 1.0
O E:GLY179 4.0 90.8 1.0
O E:THR180 4.2 96.8 1.0
N E:TYR181 4.3 99.6 1.0
CB E:SER118 4.4 42.9 1.0
O1B E:UTP1227 4.5 84.8 1.0
C E:THR180 4.6 97.4 1.0
C E:TYR181 4.6 98.7 1.0
C5' E:UTP1227 4.6 65.0 1.0
OH E:TYR181 4.7 0.6 1.0
O3G E:UTP1227 4.8 98.4 1.0
N E:GLU182 4.8 95.9 1.0
O2B E:UTP1227 4.8 85.5 1.0
O2A E:UTP1227 4.9 70.7 1.0
O2G E:UTP1227 5.0 97.0 1.0

Magnesium binding site 5 out of 7 in 2j4l

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Magnesium binding site 5 out of 7 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1228

b:79.0
occ:1.00
 O3A I:UTP1227 3.3 0.2 1.0
O1A I:UTP1227 3.3 97.1 1.0
O5' I:UTP1227 3.5 90.9 1.0
PA I:UTP1227 3.6 96.2 1.0
O3B I:UTP1227 4.0 0.5 1.0
C3' I:UTP1227 4.1 76.3 1.0
O3' I:UTP1227 4.1 78.2 1.0
PB I:UTP1227 4.2 1.0 1.0
C5' I:UTP1227 4.4 81.3 1.0
O1B I:UTP1227 4.4 0.0 1.0
C4' I:UTP1227 4.8 78.0 1.0
CB I:SER118 4.9 72.5 1.0

Magnesium binding site 6 out of 7 in 2j4l

Go back to Magnesium Binding Sites List in 2j4l
Magnesium binding site 6 out of 7 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg1228

b:64.3
occ:1.00
 O3A J:UTP1227 2.5 93.9 1.0
O2B J:UTP1227 2.8 0.3 1.0
PB J:UTP1227 2.9 0.8 1.0
C5' J:UTP1227 3.2 76.6 1.0
O1B J:UTP1227 3.3 99.9 1.0
O5' J:UTP1227 3.5 81.4 1.0
C3' J:UTP1227 3.6 72.7 1.0
PA J:UTP1227 3.8 83.5 1.0
C4' J:UTP1227 4.0 74.1 1.0
O3' J:UTP1227 4.2 72.2 1.0
O3B J:UTP1227 4.4 0.7 1.0
CB J:SER118 4.4 61.8 1.0
O2A J:UTP1227 4.6 85.3 1.0
O1A J:UTP1227 4.7 85.1 1.0
C2' J:UTP1227 4.8 71.9 1.0

Magnesium binding site 7 out of 7 in 2j4l

Go back to Magnesium Binding Sites List in 2j4l
Magnesium binding site 7 out of 7 in the Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Uridylate Kinase From Sulfolobus Solfataricus in Complex with Utp to 2.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1228

b:55.0
occ:1.00
 O5' L:UTP1227 3.0 80.3 1.0
O1A L:UTP1227 3.1 84.8 1.0
PA L:UTP1227 3.4 82.4 1.0
O3A L:UTP1227 3.4 92.5 1.0
O3B L:UTP1227 3.4 0.9 1.0
O2G L:UTP1227 4.0 0.1 1.0
C5' L:UTP1227 4.0 78.0 1.0
C3' L:UTP1227 4.1 75.1 1.0
PB L:UTP1227 4.2 99.8 1.0
O3' L:UTP1227 4.4 78.1 1.0
PG L:UTP1227 4.5 0.0 1.0
CB L:SER118 4.6 56.9 1.0
C4' L:UTP1227 4.6 77.0 1.0
O2A L:UTP1227 4.9 84.9 1.0
O1B L:UTP1227 4.9 99.2 1.0

Reference:

K.S.Jensen, E.Johansson, K.F.Jensen. Structural and Enzymatic Investigation of the Sulfolobus Solfataricus Uridylate Kinase Shows Competitive Utp Inhibition and the Lack of Gtp Stimulation Biochemistry V. 46 2745 2007.
ISSN: ISSN 0006-2960
PubMed: 17297917
DOI: 10.1021/BI0618159
Page generated: Wed Aug 14 00:24:42 2024

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