Atomistry » Magnesium » PDB 5h2f-5hi8 » 5h5k
Atomistry »
  Magnesium »
    PDB 5h2f-5hi8 »
      5h5k »

Magnesium in PDB 5h5k: Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5

Enzymatic activity of Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5

All present enzymatic activity of Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5:
2.7.4.9;

Protein crystallography data

The structure of Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 5h5k was solved by A.Biswas, J.Jeyakanthan, K.Sekar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.840, 51.863, 53.595, 92.00, 92.30, 112.22
R / Rfree (%) 19.4 / 25.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 (pdb code 5h5k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 5h5k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5h5k

Go back to Magnesium Binding Sites List in 5h5k
Magnesium binding site 1 out of 2 in the Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:48.9
occ:1.00
O1G A:ATP202 2.1 58.5 1.0
OG1 A:THR14 2.1 38.5 1.0
O A:HOH314 2.2 40.5 1.0
O1B A:ATP202 2.5 42.3 1.0
O A:HOH308 2.6 40.7 1.0
CB A:THR14 3.2 37.4 1.0
O1A A:ATP202 3.3 57.1 1.0
PG A:ATP202 3.4 66.0 1.0
O1P A:C5P206 3.5 81.3 1.0
PB A:ATP202 3.7 39.3 1.0
O3B A:ATP202 3.7 49.7 1.0
CG2 A:THR14 4.0 38.1 1.0
P A:C5P206 4.1 76.4 1.0
O2P A:C5P206 4.1 73.2 1.0
O2G A:ATP202 4.1 54.0 1.0
OD2 A:ASP89 4.2 46.5 1.0
O3P A:C5P206 4.4 82.5 1.0
CA A:THR14 4.4 35.7 1.0
O A:HOH301 4.5 53.2 1.0
PA A:ATP202 4.5 52.6 1.0
N A:THR14 4.5 35.5 1.0
O A:HOH335 4.5 38.6 1.0
O3G A:ATP202 4.5 66.1 1.0
O3A A:ATP202 4.6 46.8 1.0
OD1 A:ASP89 4.7 46.9 1.0
CG A:ASP89 4.9 41.2 1.0
O2B A:ATP202 4.9 41.8 1.0

Magnesium binding site 2 out of 2 in 5h5k

Go back to Magnesium Binding Sites List in 5h5k
Magnesium binding site 2 out of 2 in the Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Atp and Cmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:56.5
occ:1.00
O1G B:ATP202 2.1 80.7 1.0
OG1 B:THR14 2.1 47.0 1.0
O1B B:ATP202 2.4 53.0 1.0
O1P B:C5P203 2.8 62.7 1.0
PG B:ATP202 3.3 86.8 1.0
CB B:THR14 3.4 42.8 1.0
O2G B:ATP202 3.7 59.0 1.0
PB B:ATP202 3.7 50.6 1.0
O2P B:C5P203 3.7 63.5 1.0
O3B B:ATP202 3.8 62.5 1.0
P B:C5P203 3.8 64.3 1.0
OD2 B:ASP89 3.9 41.9 1.0
CG2 B:THR14 4.2 40.6 1.0
O1A B:ATP202 4.2 58.9 1.0
N B:THR14 4.4 37.0 1.0
CA B:THR14 4.4 42.1 1.0
OD1 B:ASP89 4.5 42.5 1.0
O3G B:ATP202 4.6 76.5 1.0
CG B:ASP89 4.7 39.5 1.0
O3A B:ATP202 4.7 56.9 1.0
O2B B:ATP202 4.8 42.2 1.0
PA B:ATP202 4.9 61.6 1.0
O3P B:C5P203 4.9 73.6 1.0
O5' B:C5P203 4.9 68.5 1.0

Reference:

A.Biswas, A.Shukla, S.K.Chaudhary, R.Santhosh, J.Jeyakanthan, K.Sekar. Structural Studies of A Hyperthermophilic Thymidylate Kinase Enzyme Reveal Conformational Substates Along the Reaction Coordinate Febs J. V. 284 2527 2017.
ISSN: ISSN 1742-4658
PubMed: 28627020
DOI: 10.1111/FEBS.14140
Page generated: Sun Sep 29 15:40:53 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy