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Magnesium in PDB 7c1z: Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana

Protein crystallography data

The structure of Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana, PDB code: 7c1z was solved by S.H.Kim, S.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.72 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.613, 47.917, 91.928, 90.00, 108.95, 90.00
R / Rfree (%) 18.6 / 23.7

Other elements in 7c1z:

The structure of Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana (pdb code 7c1z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana, PDB code: 7c1z:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7c1z

Go back to Magnesium Binding Sites List in 7c1z
Magnesium binding site 1 out of 4 in the Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:59.6
occ:1.00
O A:HOH535 2.5 47.9 1.0
O1B A:ATP404 2.7 54.5 1.0
O A:HOH510 2.7 40.8 1.0
O A:SER181 2.8 30.6 1.0
OG1 A:THR237 2.9 38.3 1.0
CG2 A:THR237 3.4 28.5 1.0
MG A:MG403 3.5 53.4 1.0
CB A:THR237 3.7 33.3 1.0
O A:HOH517 3.8 45.9 1.0
C A:SER181 4.0 27.4 1.0
N A:ASN183 4.0 34.4 1.0
PB A:ATP404 4.0 52.4 1.0
C A:PRO182 4.1 30.4 1.0
CA A:GLY310 4.3 31.0 1.0
OE1 A:GLU160 4.3 37.0 1.0
O3A A:ATP404 4.4 55.9 1.0
O A:PRO182 4.4 25.2 1.0
CA A:PRO182 4.6 26.5 1.0
OE2 A:GLU160 4.6 41.3 1.0
OE1 A:GLU186 4.6 34.9 1.0
CA A:ASN183 4.7 33.5 1.0
O2B A:ATP404 4.7 52.0 1.0
N A:PRO182 4.7 29.5 1.0
CB A:SER181 4.8 27.5 1.0
O1A A:ATP404 4.8 37.7 1.0
CB A:ASN183 4.8 28.6 1.0
CD A:GLU160 4.9 40.6 1.0
C A:GLY310 4.9 33.6 1.0
O2G A:ATP404 4.9 80.7 1.0
O A:GLY310 4.9 38.8 1.0
CA A:THR237 5.0 29.5 1.0

Magnesium binding site 2 out of 4 in 7c1z

Go back to Magnesium Binding Sites List in 7c1z
Magnesium binding site 2 out of 4 in the Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:53.4
occ:1.00
O A:HOH517 2.2 45.9 1.0
O1B A:ATP404 2.3 54.5 1.0
O A:HOH549 2.3 47.7 1.0
O A:HOH510 2.8 40.8 1.0
O A:HOH501 2.8 51.5 1.0
O2G A:ATP404 3.2 80.7 1.0
PB A:ATP404 3.4 52.4 1.0
MG A:MG402 3.5 59.6 1.0
O3B A:ATP404 3.5 0.7 1.0
OE2 A:GLU160 3.7 41.3 1.0
PG A:ATP404 3.9 78.9 1.0
OD2 A:ASP311 4.2 45.7 1.0
O1G A:ATP404 4.2 74.9 1.0
O A:HOH535 4.4 47.9 1.0
CD A:GLU160 4.4 40.6 1.0
CA A:GLY310 4.5 31.0 1.0
O2B A:ATP404 4.5 52.0 1.0
O3A A:ATP404 4.5 55.9 1.0
OE1 A:GLU160 4.6 37.0 1.0
OE2 A:GLU186 4.7 42.4 1.0
OE1 A:GLU186 4.8 34.9 1.0
O A:VAL162 4.9 30.9 1.0
C A:GLY310 4.9 33.6 1.0

Magnesium binding site 3 out of 4 in 7c1z

Go back to Magnesium Binding Sites List in 7c1z
Magnesium binding site 3 out of 4 in the Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:45.0
occ:1.00
O B:HOH526 2.5 44.5 1.0
O B:SER181 2.6 29.8 1.0
O B:HOH536 2.6 37.9 1.0
OG1 B:THR237 3.0 38.9 1.0
O1B B:ATP404 3.0 84.8 1.0
N B:ASN183 3.5 40.2 1.0
CG2 B:THR237 3.6 30.7 1.0
MG B:MG403 3.6 64.2 1.0
C B:PRO182 3.6 28.6 1.0
OE2 B:GLU160 3.7 35.5 1.0
C B:SER181 3.7 31.9 1.0
CB B:THR237 3.9 35.2 1.0
OE1 B:GLU186 4.0 37.3 1.0
O B:HOH517 4.0 53.6 1.0
CA B:PRO182 4.1 32.7 1.0
O B:PRO182 4.1 29.4 1.0
PB B:ATP404 4.2 84.4 1.0
CA B:ASN183 4.3 39.2 1.0
N B:PRO182 4.4 29.9 1.0
O3A B:ATP404 4.4 87.7 1.0
CB B:ASN183 4.5 33.5 1.0
CB B:SER181 4.6 27.9 1.0
CD B:GLU160 4.7 35.6 1.0
CA B:GLY310 4.7 32.3 1.0
OG B:SER181 4.8 28.5 1.0
O2B B:ATP404 4.8 93.2 1.0
CA B:SER181 4.8 28.1 1.0
OE1 B:GLU160 4.9 39.6 1.0
O1A B:ATP404 5.0 73.7 1.0

Magnesium binding site 4 out of 4 in 7c1z

Go back to Magnesium Binding Sites List in 7c1z
Magnesium binding site 4 out of 4 in the Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:64.2
occ:1.00
O B:HOH533 2.0 50.1 1.0
O1B B:ATP404 2.2 84.8 1.0
O B:HOH543 2.4 52.3 1.0
O1G B:ATP404 2.4 93.4 1.0
O B:HOH526 2.6 44.5 1.0
O B:HOH517 2.7 53.6 1.0
PB B:ATP404 3.5 84.4 1.0
MG B:MG402 3.6 45.0 1.0
PG B:ATP404 3.7 90.4 1.0
O3B B:ATP404 3.8 0.9 1.0
OE2 B:GLU186 4.0 45.6 1.0
OE1 B:GLU160 4.0 39.6 1.0
O B:VAL162 4.2 39.2 1.0
OE1 B:GLU186 4.2 37.3 1.0
O2G B:ATP404 4.4 88.8 1.0
CD B:GLU186 4.5 37.3 1.0
O2B B:ATP404 4.5 93.2 1.0
OE2 B:GLU160 4.5 35.5 1.0
O3A B:ATP404 4.6 87.7 1.0
OD2 B:ASP311 4.6 47.5 1.0
CD B:GLU160 4.6 35.6 1.0
CA B:GLY310 4.7 32.3 1.0
ND2 B:ASN183 4.7 30.3 1.0
C B:VAL162 4.8 36.7 1.0
O B:HOH536 4.8 37.9 1.0
O3G B:ATP404 4.8 95.4 1.0
CA B:VAL162 4.9 29.8 1.0

Reference:

S.H.Kim, S.Rhee. Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana To Be Published.
Page generated: Tue Dec 15 03:31:14 2020

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