Atomistry » Magnesium » PDB 4s1l-4tny » 4s35
Atomistry »
  Magnesium »
    PDB 4s1l-4tny »
      4s35 »

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

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