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Magnesium in PDB 5h56: Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5

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

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

Protein crystallography data

The structure of Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 5h56 was solved by A.Biswas, J.Jeyakanthan, K.Sekar, S.Kuramitsu, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.482, 62.414, 76.144, 90.00, 91.02, 90.00
R / Rfree (%) 15.6 / 18.5

Other elements in 5h56:

The structure of Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 (pdb code 5h56). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 5h56:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5h56

Go back to Magnesium Binding Sites List in 5h56
Magnesium binding site 1 out of 6 in the Adp and Dtdp 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 Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:5.2
occ:1.00
 O2B A:ADP201 2.1 7.9 1.0
O1B A:TYD202 2.1 11.6 0.7
O A:HOH339 2.1 8.8 1.0
O A:HOH313 2.1 9.9 1.0
OG1 A:THR14 2.1 7.8 1.0
O A:HOH319 2.2 8.6 1.0
CB A:THR14 3.2 7.7 1.0
PB A:ADP201 3.3 8.1 1.0
PB A:TYD202 3.4 14.7 0.7
O3B A:ADP201 3.5 8.2 1.0
O3B A:TYD202 3.8 14.0 0.7
O A:HOH425 4.0 36.4 1.0
O1A A:TYD202 4.0 11.2 1.0
O A:HOH362 4.0 12.5 1.0
N A:THR14 4.0 7.6 1.0
O2A A:ADP201 4.0 8.0 1.0
OD2 A:ASP89 4.1 9.6 1.0
NH1 A:ARG145 4.2 14.8 0.7
CG2 A:THR14 4.2 7.8 1.0
CA A:THR14 4.2 7.5 1.0
O2A A:TYD202 4.3 12.1 1.0
O3A A:ADP201 4.3 8.4 1.0
OD1 A:ASP89 4.3 9.6 1.0
O3A A:TYD202 4.4 12.7 1.0
O1B A:ADP201 4.4 8.0 1.0
PA A:TYD202 4.4 11.7 1.0
O2B A:TYD202 4.6 14.3 0.7
PA A:ADP201 4.6 8.1 1.0
CG A:ASP89 4.7 8.8 1.0
O A:HOH448 4.7 26.9 1.0
NZ A:LYS13 4.8 7.4 1.0

Magnesium binding site 2 out of 6 in 5h56

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Magnesium binding site 2 out of 6 in the Adp and Dtdp 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 Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:13.9
occ:1.00
 O A:HOH369 2.1 28.0 1.0
O A:LYS103 2.3 12.8 1.0
O A:HOH414 2.3 32.3 1.0
O A:HOH432 2.4 31.3 1.0
OE2 A:GLU57 2.4 18.8 1.0
OE1 A:GLU57 2.6 19.4 1.0
CD A:GLU57 2.9 18.8 1.0
C A:LYS103 3.5 11.5 1.0
CA A:LYS103 4.3 11.7 0.5
CA A:LYS103 4.3 11.3 0.5
O A:HOH438 4.3 34.7 1.0
CG A:GLU57 4.4 17.3 1.0
N A:GLY104 4.4 11.1 1.0
CB A:LYS103 4.5 12.4 0.5
CB A:LYS103 4.5 11.6 0.5
CA A:GLY104 4.5 11.4 1.0
C A:GLY104 4.8 11.2 1.0
O A:HOH333 4.8 19.1 1.0

Magnesium binding site 3 out of 6 in 5h56

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Magnesium binding site 3 out of 6 in the Adp and Dtdp 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 3 of Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:13.0
occ:1.00
 O A:HOH389 2.8 28.9 1.0
O A:HOH381 2.9 31.4 1.0
OD1 A:ASN114 3.2 10.4 1.0
CB A:ASN114 3.6 9.1 1.0
CG A:ASN114 3.9 9.2 1.0
CD1 A:ILE96 3.9 8.0 1.0
CG2 A:VAL92 4.0 9.4 1.0
CG A:LYS111 4.0 13.8 1.0
CB A:VAL92 4.1 9.0 1.0
CA A:LYS111 4.3 10.9 1.0
CB A:LYS111 4.3 12.2 1.0
O A:LYS111 4.6 10.2 1.0
OE1 A:GLU166 4.7 26.6 1.0
O A:HOH462 4.7 26.6 1.0
CG1 A:VAL92 4.7 9.4 1.0
CG1 A:ILE96 4.8 7.8 1.0
CD A:LYS111 4.9 16.0 1.0
C A:LYS111 4.9 10.5 1.0

Magnesium binding site 4 out of 6 in 5h56

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Magnesium binding site 4 out of 6 in the Adp and Dtdp 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 4 of Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:7.3
occ:1.00
 O1B B:TYD202 2.1 11.3 0.7
O1B B:ADP201 2.1 7.8 1.0
O B:HOH377 2.1 10.5 1.0
O B:HOH332 2.1 10.9 1.0
O B:HOH337 2.1 8.3 1.0
OG1 B:THR14 2.2 8.0 1.0
CB B:THR14 3.3 7.6 1.0
PB B:ADP201 3.3 8.6 1.0
PB B:TYD202 3.4 13.9 0.7
O2B B:ADP201 3.5 8.8 1.0
O2B B:TYD202 3.8 12.1 0.7
O2A B:TYD202 3.9 12.4 1.0
O B:HOH358 4.0 14.7 1.0
N B:THR14 4.1 7.3 1.0
O1A B:ADP201 4.1 9.7 1.0
OD2 B:ASP89 4.1 9.4 1.0
CG2 B:THR14 4.2 8.0 1.0
CA B:THR14 4.2 7.5 1.0
NH1 B:ARG145 4.3 32.5 1.0
O1A B:TYD202 4.3 13.2 1.0
O3A B:TYD202 4.3 12.6 1.0
OD1 B:ASP89 4.3 9.3 1.0
PA B:TYD202 4.3 12.5 1.0
O3B B:ADP201 4.4 8.1 1.0
O3A B:ADP201 4.4 9.1 1.0
O3B B:TYD202 4.5 14.2 0.7
CG B:ASP89 4.7 8.9 1.0
PA B:ADP201 4.7 9.3 1.0
NZ B:LYS13 4.8 7.6 1.0
CB B:LYS13 5.0 7.6 1.0

Magnesium binding site 5 out of 6 in 5h56

Go back to Magnesium Binding Sites List in 5h56
Magnesium binding site 5 out of 6 in the Adp and Dtdp 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 5 of Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:16.5
occ:1.00
 O B:LYS103 2.3 12.4 1.0
O B:HOH322 2.3 33.1 1.0
O B:HOH403 2.3 27.6 1.0
OE1 B:GLU57 2.5 20.8 1.0
OE2 B:GLU57 2.5 20.8 1.0
CD B:GLU57 2.8 19.0 1.0
C B:LYS103 3.5 12.7 1.0
CA B:LYS103 4.2 13.1 1.0
CG B:GLU57 4.3 17.1 1.0
O B:HOH428 4.4 35.4 1.0
CB B:LYS103 4.4 14.9 1.0
N B:GLY104 4.5 12.0 1.0
CA B:GLY104 4.7 12.6 1.0
C B:GLY104 5.0 12.7 1.0

Magnesium binding site 6 out of 6 in 5h56

Go back to Magnesium Binding Sites List in 5h56
Magnesium binding site 6 out of 6 in the Adp and Dtdp 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 6 of Adp and Dtdp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:13.5
occ:1.00
 O B:HOH378 2.8 32.0 1.0
O B:HOH340 3.0 29.7 1.0
OD1 B:ASN114 3.2 11.1 1.0
CB B:ASN114 3.6 9.8 1.0
CD1 B:ILE96 3.8 8.8 1.0
CG B:ASN114 3.8 9.9 1.0
CG2 B:VAL92 4.0 11.1 1.0
CG B:LYS111 4.0 14.3 1.0
CB B:VAL92 4.1 10.6 1.0
CA B:LYS111 4.3 12.0 1.0
CB B:LYS111 4.3 13.2 1.0
O B:LYS111 4.5 10.8 1.0
OE1 B:GLU166 4.8 25.7 1.0
CG1 B:VAL92 4.8 11.4 1.0
CG1 B:ILE96 4.8 8.7 1.0
O B:HOH440 4.9 31.1 1.0
C B:LYS111 4.9 11.7 1.0
CD B:LYS111 5.0 15.8 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: Mon Dec 14 20:26:01 2020

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