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Magnesium in PDB 4s35: Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5

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

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

Protein crystallography data

The structure of Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 4s35 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 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.479, 62.615, 73.577, 90.00, 97.97, 90.00
R / Rfree (%) 14.6 / 17.4

Other elements in 4s35:

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

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5 (pdb code 4s35). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase (AQ_969) From Aquifex Aeolicus VF5, PDB code: 4s35:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4s35

Go back to Magnesium Binding Sites List in 4s35
Magnesium binding site 1 out of 4 in the Amppcp and Tmp 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 Amppcp and Tmp 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:8.6
occ:1.00
 O2G A:ACP201 2.0 9.8 1.0
O A:HOH301 2.1 10.1 1.0
O A:HOH302 2.1 9.8 1.0
OG1 A:THR14 2.1 7.8 1.0
O1B A:ACP201 2.1 7.5 1.0
O A:HOH303 2.1 11.2 1.0
CB A:THR14 3.2 8.0 1.0
PG A:ACP201 3.2 11.6 1.0
PB A:ACP201 3.3 8.5 1.0
C3B A:ACP201 3.5 9.6 1.0
O3G A:ACP201 3.9 10.8 1.0
O2P A:TMP202 3.9 7.7 0.5
O A:HOH407 4.0 35.4 1.0
N A:THR14 4.0 7.6 1.0
OD2 A:ASP89 4.1 10.7 1.0
O1A A:ACP201 4.1 10.4 1.0
CG2 A:THR14 4.1 9.2 1.0
CA A:THR14 4.2 7.4 1.0
O1P A:TMP202 4.2 9.1 0.5
OD1 A:ASP89 4.2 9.8 1.0
O2P A:TMP202 4.3 17.6 0.5
O3A A:ACP201 4.3 9.2 1.0
O A:HOH455 4.4 29.9 1.0
O2B A:ACP201 4.4 8.7 1.0
O A:HOH389 4.5 21.1 1.0
O1G A:ACP201 4.5 13.0 1.0
CG A:ASP89 4.5 9.7 1.0
P A:TMP202 4.6 11.4 0.5
O A:HOH408 4.6 38.4 1.0
O A:HOH457 4.6 30.4 1.0
PA A:ACP201 4.7 9.2 1.0
CB A:LYS13 5.0 9.2 1.0
CE A:LYS13 5.0 9.1 1.0

Magnesium binding site 2 out of 4 in 4s35

Go back to Magnesium Binding Sites List in 4s35
Magnesium binding site 2 out of 4 in the Amppcp and Tmp 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 Amppcp and Tmp 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:22.5
occ:1.00
 O A:ASP83 2.9 13.5 1.0
N A:PHE30 3.0 7.2 1.0
O A:PHE30 3.5 9.3 1.0
CA A:TYR29 3.5 7.6 1.0
CD1 A:TYR29 3.6 7.5 1.0
C A:TYR29 3.7 7.8 1.0
CB A:TYR29 3.8 7.6 1.0
CA A:PHE30 3.9 7.9 1.0
CB A:PHE30 4.1 9.4 1.0
C A:ASP83 4.1 14.2 1.0
C A:PHE30 4.2 8.9 1.0
CG A:TYR29 4.2 7.2 1.0
CG2 A:VAL85 4.5 9.3 1.0
N A:VAL85 4.5 8.7 1.0
CA A:LYS84 4.6 13.2 1.0
CG A:PHE30 4.6 9.1 1.0
CE1 A:TYR29 4.7 7.7 1.0
N A:LYS84 4.8 12.0 1.0
O A:GLY28 4.8 8.8 1.0
CB A:ASP83 4.9 15.4 1.0
N A:TYR29 4.9 8.2 1.0
C A:LYS84 4.9 11.0 1.0
O A:TYR29 4.9 8.1 1.0

Magnesium binding site 3 out of 4 in 4s35

Go back to Magnesium Binding Sites List in 4s35
Magnesium binding site 3 out of 4 in the Amppcp and Tmp 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 Amppcp and Tmp 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:10.4
occ:1.00
 O B:HOH303 2.0 12.4 1.0
O1G B:ACP201 2.1 10.9 1.0
O B:HOH301 2.1 9.9 1.0
O B:HOH302 2.1 12.2 1.0
OG1 B:THR14 2.1 11.6 1.0
O1B B:ACP201 2.1 12.7 1.0
PG B:ACP201 3.2 12.9 1.0
CB B:THR14 3.2 12.3 1.0
PB B:ACP201 3.3 11.3 1.0
C3B B:ACP201 3.6 12.3 1.0
O3P B:TMP202 4.0 15.1 1.0
O B:HOH360 4.0 29.0 1.0
O B:HOH357 4.0 25.6 1.0
O2G B:ACP201 4.0 12.7 1.0
N B:THR14 4.1 11.2 1.0
OD2 B:ASP89 4.1 12.6 1.0
O2A B:ACP201 4.1 13.5 1.0
CA B:THR14 4.2 10.9 1.0
CG2 B:THR14 4.2 13.2 1.0
O2P B:TMP202 4.2 15.7 1.0
O B:HOH368 4.2 28.2 1.0
OD1 B:ASP89 4.2 12.0 1.0
O2B B:ACP201 4.4 9.7 1.0
O3A B:ACP201 4.4 12.3 1.0
O3G B:ACP201 4.5 15.3 1.0
O B:HOH323 4.6 30.2 1.0
P B:TMP202 4.6 17.3 1.0
CG B:ASP89 4.6 11.4 1.0
PA B:ACP201 4.6 12.2 1.0
O B:HOH358 4.7 26.0 1.0
O B:HOH315 4.8 23.9 1.0
CE B:LYS13 5.0 12.4 1.0

Magnesium binding site 4 out of 4 in 4s35

Go back to Magnesium Binding Sites List in 4s35
Magnesium binding site 4 out of 4 in the Amppcp and Tmp 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 Amppcp and Tmp 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:24.5
occ:1.00
 OE1 B:GLU153 2.5 33.2 1.0
NH1 B:ARG156 3.1 19.9 1.0
N B:VAL133 3.2 12.1 1.0
CD B:GLU153 3.2 27.1 1.0
OE2 B:GLU153 3.2 35.4 1.0
O B:HOH395 3.4 26.3 1.0
CG2 B:VAL133 3.5 13.8 1.0
CD B:ARG156 3.6 16.7 1.0
O B:HOH394 3.6 28.7 1.0
CB B:VAL133 3.7 12.9 1.0
CA B:PRO132 3.8 14.4 1.0
C B:PRO132 4.0 12.3 1.0
CA B:VAL133 4.0 11.9 1.0
CZ B:ARG156 4.1 21.3 1.0
CB B:PRO132 4.3 17.2 1.0
NE B:ARG156 4.3 16.6 1.0
CG B:GLU153 4.6 21.0 1.0
CG B:ARG156 4.9 14.7 1.0
O B:ILE131 4.9 14.6 1.0
N B:ASP134 5.0 13.8 1.0

Reference:

A.Biswas, J.Jeyakanthan, K.Sekar. Structural Studies of A Hyperthermophilic Thymidylate Kinase Enzyme Reveal Conformational Sub-States Along the Reaction Coordinate Febs J. 2017.
ISSN: ISSN 1742-464X
Page generated: Tue Aug 20 03:45:09 2024

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