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Magnesium in PDB 8yh1: Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor.

Enzymatic activity of Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor.

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor.:
2.7.4.22;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor., PDB code: 8yh1 was solved by K.Fukui, A.Nishiwaki, N.Nakagawa, S.Kuramitsu, R.Masui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.32 / 2.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 150.217, 232.197, 284.841, 90, 90, 90
R / Rfree (%) 18.8 / 21

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor. (pdb code 8yh1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor., PDB code: 8yh1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8yh1

Go back to Magnesium Binding Sites List in 8yh1
Magnesium binding site 1 out of 6 in the Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor.


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 Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:70.3
occ:1.00
 O2B A:ADP301 2.5 63.6 1.0
O A:HOH407 2.9 52.3 1.0
O2A A:ADP301 3.0 84.5 1.0
O2B A:UDP302 3.2 83.7 1.0
O3B A:UDP302 3.4 47.0 1.0
OG A:SER136 3.4 47.7 1.0
NZ A:LYS9 3.4 33.9 1.0
O1A A:UDP302 3.6 57.1 1.0
PB A:ADP301 3.7 63.3 1.0
NZ A:LYS157 3.7 34.0 1.0
PB A:UDP302 3.7 84.7 1.0
OD1 A:ASP138 3.8 38.9 1.0
O1B A:ADP301 3.8 57.1 1.0
OD2 A:ASP138 3.9 28.6 1.0
CG A:ASP138 4.1 39.1 1.0
PA A:UDP302 4.1 41.2 1.0
O3A A:UDP302 4.1 49.7 1.0
PA A:ADP301 4.3 63.0 1.0
O2A A:UDP302 4.3 46.3 1.0
O3A A:ADP301 4.5 58.1 1.0
OG1 A:THR137 4.5 41.6 1.0
CE A:LYS9 4.6 25.1 1.0
CB A:SER136 4.6 46.9 1.0
O5' A:ADP301 4.8 78.6 1.0
O3B A:ADP301 4.9 63.8 1.0
CE A:LYS157 4.9 26.1 1.0

Magnesium binding site 2 out of 6 in 8yh1

Go back to Magnesium Binding Sites List in 8yh1
Magnesium binding site 2 out of 6 in the Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor.


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 Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg308

b:79.9
occ:1.00
 O1B C:ADP301 2.3 74.5 1.0
O1A C:ADP301 2.4 89.8 1.0
O2B C:UDP302 2.7 81.9 0.8
PA C:ADP301 3.0 111.0 1.0
O2A C:ADP301 3.2 98.7 1.0
O3A C:ADP301 3.5 69.5 1.0
PB C:ADP301 3.5 104.3 1.0
OG C:SER11 3.6 40.1 1.0
PB C:UDP302 3.7 85.5 0.8
O1B C:UDP302 3.9 35.5 0.8
CG C:GLU13 4.1 48.6 1.0
NH2 C:ARG55 4.2 77.6 1.0
O C:HOH440 4.3 56.2 1.0
O3B C:UDP302 4.3 48.7 0.8
O2B C:ADP301 4.4 88.3 1.0
O5' C:ADP301 4.5 113.4 1.0
CB C:SER11 4.6 36.0 1.0
O3B C:ADP301 4.6 77.5 1.0
CB C:ASN158 4.8 55.8 1.0
ND2 C:ASN158 4.9 50.4 1.0

Magnesium binding site 3 out of 6 in 8yh1

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Magnesium binding site 3 out of 6 in the Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor.


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 Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg306

b:54.5
occ:1.00
 O1B E:ADP301 2.0 64.7 1.0
O1P E:U5P302 2.3 43.7 1.0
OG E:SER11 3.2 43.1 1.0
N E:GLY12 3.3 46.8 1.0
PB E:ADP301 3.5 66.0 1.0
CA E:SER11 3.5 55.4 1.0
CB E:SER11 3.7 45.2 1.0
P E:U5P302 3.7 52.5 1.0
N E:GLY51 3.7 56.3 1.0
C E:SER11 3.9 45.8 1.0
N E:ALA50 3.9 55.1 1.0
CA E:GLY49 4.0 38.2 1.0
O2B E:ADP301 4.2 45.8 1.0
NZ E:LYS9 4.2 43.8 1.0
O E:HOH402 4.2 47.8 1.0
CA E:GLY51 4.3 51.6 1.0
O3B E:ADP301 4.3 44.1 1.0
O2P E:U5P302 4.3 68.9 1.0
C E:GLY49 4.3 46.8 1.0
CA E:GLY12 4.3 37.2 1.0
O3A E:ADP301 4.3 58.7 1.0
O E:HOH430 4.5 54.9 1.0
O5' E:U5P302 4.6 54.8 1.0
O3P E:U5P302 4.6 41.6 1.0
C E:ALA50 4.7 45.9 1.0
N E:GLU13 4.7 43.6 1.0
N E:SER11 4.7 43.5 1.0
N E:GLY49 4.8 47.6 1.0
O E:LEU10 4.8 42.5 1.0
OG1 E:THR137 4.8 46.0 1.0
CA E:ALA50 4.9 48.5 1.0
O2A E:ADP301 4.9 68.1 1.0

Magnesium binding site 4 out of 6 in 8yh1

Go back to Magnesium Binding Sites List in 8yh1
Magnesium binding site 4 out of 6 in the Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor.


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 Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg306

b:53.2
occ:1.00
 O1B G:ADP301 2.4 60.2 1.0
O2P G:U5P302 2.6 57.1 1.0
PB G:ADP301 3.5 89.5 1.0
O2B G:ADP301 3.5 95.4 1.0
P G:U5P302 3.6 58.9 1.0
NZ G:LYS9 3.7 39.8 1.0
O3P G:U5P302 3.8 60.7 1.0
OG G:SER11 3.8 45.2 1.0
CA G:GLY49 3.9 29.9 1.0
N G:GLY12 3.9 44.3 1.0
CA G:SER11 4.0 46.9 1.0
N G:ALA50 4.1 33.0 1.0
O1A G:ADP301 4.1 69.1 1.0
N G:GLY51 4.2 52.5 1.0
O1P G:U5P302 4.2 65.4 1.0
CB G:SER11 4.2 42.4 1.0
OG1 G:THR137 4.3 41.3 1.0
O2A G:ADP301 4.3 104.1 1.0
C G:GLY49 4.4 36.8 1.0
PA G:ADP301 4.4 78.8 1.0
O3A G:ADP301 4.5 71.5 1.0
C G:SER11 4.5 45.2 1.0
O3B G:ADP301 4.6 69.8 1.0
CE G:LYS9 4.7 38.9 1.0
CA G:GLY51 4.7 56.2 1.0
N G:GLY49 4.8 42.2 1.0
O G:LEU10 4.9 39.6 1.0
O5' G:U5P302 5.0 60.8 1.0
CA G:GLY12 5.0 53.8 1.0

Magnesium binding site 5 out of 6 in 8yh1

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Magnesium binding site 5 out of 6 in the Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor.


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 Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg303

b:69.9
occ:1.00
 O1B H:ADP301 2.1 84.6 1.0
O2P H:U5P302 2.3 65.6 1.0
OG H:SER11 3.1 51.1 1.0
N H:GLY12 3.1 44.0 1.0
CA H:SER11 3.4 57.0 1.0
PB H:ADP301 3.6 105.4 1.0
CB H:SER11 3.7 54.5 1.0
P H:U5P302 3.7 52.4 1.0
C H:SER11 3.8 47.8 1.0
CA H:GLY49 3.8 32.5 1.0
N H:GLY51 3.9 48.9 1.0
N H:ALA50 3.9 49.6 1.0
CA H:GLY12 4.2 63.2 1.0
NZ H:LYS9 4.2 47.0 1.0
C H:GLY49 4.2 44.8 1.0
O2A H:ADP301 4.3 99.5 1.0
O3P H:U5P302 4.3 57.9 1.0
O H:HOH406 4.4 61.5 1.0
O2B H:ADP301 4.4 89.0 1.0
O3B H:ADP301 4.4 68.9 1.0
CA H:GLY51 4.4 59.1 1.0
O3A H:ADP301 4.5 57.5 1.0
O5' H:U5P302 4.6 72.8 1.0
O1P H:U5P302 4.6 50.2 1.0
N H:GLY49 4.6 43.6 1.0
N H:SER11 4.7 49.2 1.0
O H:LEU10 4.7 49.3 1.0
N H:GLU13 4.7 46.4 1.0
OG1 H:THR137 4.8 47.4 1.0
C H:ALA50 4.9 44.8 1.0
PA H:ADP301 4.9 93.1 1.0
O H:SER11 5.0 50.7 1.0
CA H:ALA50 5.0 39.6 1.0

Magnesium binding site 6 out of 6 in 8yh1

Go back to Magnesium Binding Sites List in 8yh1
Magnesium binding site 6 out of 6 in the Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor.


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 Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg303

b:82.5
occ:1.00
 O2B I:UDP301 3.5 90.6 0.8
OG I:SER11 3.7 71.5 1.0
CB I:SER11 4.0 71.7 1.0
CB I:ASN158 4.0 87.7 1.0
NZ I:LYS9 4.2 61.4 1.0
PB I:UDP301 4.3 77.6 0.8
O3B I:UDP301 4.4 73.2 0.8
N I:ASN158 4.5 98.5 1.0
O1B I:UDP301 4.8 73.7 0.8
CA I:ASN158 4.9 91.9 1.0

Reference:

K.Fukui, A.Nishiwaki, N.Nakagawa, S.Kuramitsu, R.Masui. The Crystal Structure of Thermus Thermophilus Ump Kinase Complexed with A Phosphoryl Group Acceptor and Donor. To Be Published.
Page generated: Fri Aug 15 21:27:21 2025

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