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Magnesium in PDB 1xbt: Crystal Structure of Human Thymidine Kinase 1

Enzymatic activity of Crystal Structure of Human Thymidine Kinase 1

All present enzymatic activity of Crystal Structure of Human Thymidine Kinase 1:
2.7.1.21;

Protein crystallography data

The structure of Crystal Structure of Human Thymidine Kinase 1, PDB code: 1xbt was solved by M.Welin, U.Kosinska, N.E.Mikkelsen, C.Carnrot, C.Zhu, L.Wang, S.Eriksson, B.Munch-Petersen, H.Eklund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.07 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.672, 123.177, 116.000, 90.00, 130.20, 90.00
R / Rfree (%) 20.1 / 23.2

Other elements in 1xbt:

The structure of Crystal Structure of Human Thymidine Kinase 1 also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Thymidine Kinase 1 (pdb code 1xbt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Human Thymidine Kinase 1, PDB code: 1xbt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1xbt

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Magnesium binding site 1 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


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 Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1194

b:36.0
occ:1.00
 O1A A:TTP1195 2.0 37.6 1.0
O1B A:TTP1195 2.4 39.0 1.0
O1G A:TTP1195 3.0 30.1 1.0
OG A:SER33 3.2 28.6 1.0
PA A:TTP1195 3.3 38.0 1.0
O A:HOH1218 3.3 42.3 1.0
PB A:TTP1195 3.5 39.3 1.0
NH2 A:ARG60 3.6 53.0 1.0
O3A A:TTP1195 3.7 38.5 1.0
OE2 A:GLU98 3.9 41.0 1.0
O3B A:TTP1195 3.9 37.6 1.0
PG A:TTP1195 4.0 31.7 1.0
O5' A:TTP1195 4.0 37.2 1.0
CB A:SER33 4.2 25.5 1.0
OD2 A:ASP97 4.4 38.3 1.0
O2A A:TTP1195 4.6 36.8 1.0
CD A:GLU98 4.6 38.3 1.0
OD1 A:ASP97 4.7 37.5 1.0
CZ A:ARG60 4.7 53.2 1.0
O2G A:TTP1195 4.7 33.9 1.0
CG A:GLU98 4.7 34.5 1.0
O A:HOH1214 4.8 38.2 1.0
O2B A:TTP1195 4.9 40.0 1.0
CG A:ASP97 5.0 34.8 1.0

Magnesium binding site 2 out of 8 in 1xbt

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Magnesium binding site 2 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


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 Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2194

b:41.6
occ:1.00
 O1A B:TTP2195 2.1 35.9 1.0
O1B B:TTP2195 2.6 40.9 1.0
OG B:SER33 2.7 28.5 1.0
O1G B:TTP2195 2.8 34.3 1.0
O3B B:TTP2195 2.8 39.8 1.0
PB B:TTP2195 3.2 39.6 1.0
PA B:TTP2195 3.3 36.3 1.0
PG B:TTP2195 3.5 35.2 1.0
O3A B:TTP2195 3.5 38.3 1.0
CB B:SER33 4.0 25.2 1.0
OE2 B:GLU98 4.1 40.6 1.0
O B:HOH2216 4.1 30.9 1.0
NH2 B:ARG60 4.1 57.7 1.0
O2G B:TTP2195 4.2 37.4 1.0
O2A B:TTP2195 4.3 37.1 1.0
OD2 B:ASP97 4.3 37.8 1.0
OD1 B:ASP97 4.3 36.1 1.0
O5' B:TTP2195 4.5 35.8 1.0
O3G B:TTP2195 4.6 35.1 1.0
O2B B:TTP2195 4.6 38.7 1.0
O B:HOH2226 4.7 27.8 1.0
CG B:GLU98 4.8 34.5 1.0
CG B:ASP97 4.8 34.0 1.0
N B:SER33 4.9 24.5 1.0
CD B:GLU98 4.9 38.5 1.0

Magnesium binding site 3 out of 8 in 1xbt

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Magnesium binding site 3 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


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 Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3194

b:44.8
occ:1.00
 O1A C:TTP3195 2.1 36.3 1.0
O1G C:TTP3195 2.4 37.8 1.0
OG C:SER33 2.6 28.9 1.0
O1B C:TTP3195 2.7 42.7 1.0
O3B C:TTP3195 2.8 42.6 1.0
O C:HOH3215 2.9 42.8 1.0
PB C:TTP3195 3.3 42.7 1.0
PG C:TTP3195 3.3 37.6 1.0
PA C:TTP3195 3.3 38.3 1.0
O3A C:TTP3195 3.6 41.1 1.0
CB C:SER33 3.7 25.6 1.0
OD2 C:ASP97 4.2 37.9 1.0
OD1 C:ASP97 4.2 35.9 1.0
NH2 C:ARG60 4.2 55.0 1.0
O2G C:TTP3195 4.3 40.5 1.0
O3G C:TTP3195 4.3 39.4 1.0
O2A C:TTP3195 4.3 38.2 1.0
O5' C:TTP3195 4.4 39.4 1.0
N C:SER33 4.4 24.7 1.0
OE2 C:GLU98 4.5 40.9 1.0
CA C:SER33 4.6 25.5 1.0
CG C:ASP97 4.7 34.1 1.0
CG C:GLU98 4.7 35.3 1.0
O C:HOH3207 4.7 36.0 1.0
O2B C:TTP3195 4.7 42.3 1.0
O C:HOH3200 4.8 32.2 1.0
CD C:GLU98 4.9 38.6 1.0

Magnesium binding site 4 out of 8 in 1xbt

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Magnesium binding site 4 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


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 Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4194

b:35.1
occ:1.00
 O D:HOH4229 2.0 32.6 1.0
O1G D:TTP4195 2.1 29.9 1.0
O1A D:TTP4195 2.2 27.1 1.0
OG D:SER33 2.2 27.4 1.0
O1B D:TTP4195 2.4 32.1 1.0
PG D:TTP4195 3.3 28.2 1.0
CB D:SER33 3.4 25.1 1.0
PB D:TTP4195 3.4 30.7 1.0
O3B D:TTP4195 3.5 31.1 1.0
PA D:TTP4195 3.5 28.0 1.0
O3A D:TTP4195 3.9 29.5 1.0
OD1 D:ASP97 4.1 35.5 1.0
O D:HOH4206 4.2 28.3 1.0
N D:SER33 4.2 24.6 1.0
O D:HOH4212 4.2 41.3 1.0
O2G D:TTP4195 4.3 30.5 1.0
O3G D:TTP4195 4.3 28.9 1.0
CA D:SER33 4.4 25.4 1.0
OD2 D:ASP97 4.4 38.0 1.0
O2A D:TTP4195 4.5 25.5 1.0
O5' D:TTP4195 4.6 27.3 1.0
OE2 D:GLU98 4.6 39.5 1.0
NH2 D:ARG60 4.6 40.8 1.0
CG D:ASP97 4.8 34.2 1.0
O2B D:TTP4195 4.8 33.0 1.0

Magnesium binding site 5 out of 8 in 1xbt

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Magnesium binding site 5 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


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 Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg5194

b:41.1
occ:1.00
 O1A E:TTP5195 2.1 38.9 1.0
OG E:SER33 2.3 28.6 1.0
O1G E:TTP5195 2.5 39.6 1.0
O1B E:TTP5195 3.0 44.7 1.0
O3B E:TTP5195 3.3 43.1 1.0
CB E:SER33 3.4 25.6 1.0
PG E:TTP5195 3.5 39.3 1.0
PA E:TTP5195 3.5 38.0 1.0
O E:HOH5219 3.6 36.0 1.0
PB E:TTP5195 3.7 43.4 1.0
OD1 E:ASP97 3.7 35.9 1.0
OD2 E:ASP97 3.8 36.7 1.0
O3A E:TTP5195 4.0 40.8 1.0
CG E:ASP97 4.2 33.4 1.0
N E:SER33 4.3 24.6 1.0
OE2 E:GLU98 4.4 41.1 1.0
CA E:SER33 4.4 25.5 1.0
O2G E:TTP5195 4.4 41.4 1.0
O2A E:TTP5195 4.5 37.8 1.0
CG E:GLU98 4.5 35.3 1.0
O5' E:TTP5195 4.6 37.8 1.0
O3G E:TTP5195 4.6 41.7 1.0
NH2 E:ARG60 4.6 54.4 1.0
CD E:GLU98 4.8 39.0 1.0
O E:HOH5215 4.8 42.8 1.0

Magnesium binding site 6 out of 8 in 1xbt

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Magnesium binding site 6 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


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 Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg6194

b:48.6
occ:1.00
 O1A F:TTP6195 2.1 35.5 1.0
O1G F:TTP6195 2.2 37.0 1.0
OG F:SER33 2.6 28.6 1.0
O1B F:TTP6195 2.7 37.3 1.0
O F:HOH6219 3.1 39.5 1.0
CB F:SER33 3.4 25.4 1.0
PG F:TTP6195 3.5 35.1 1.0
PA F:TTP6195 3.5 35.2 1.0
O3B F:TTP6195 3.6 39.0 1.0
PB F:TTP6195 3.6 36.8 1.0
OD2 F:ASP97 3.9 38.1 1.0
OD1 F:ASP97 4.0 35.6 1.0
O3A F:TTP6195 4.0 37.8 1.0
NH2 F:ARG60 4.3 53.3 1.0
N F:SER33 4.4 24.7 1.0
O F:HOH6220 4.4 41.0 1.0
O5' F:TTP6195 4.4 36.4 1.0
O2G F:TTP6195 4.4 38.2 1.0
CG F:ASP97 4.4 34.2 1.0
CA F:SER33 4.5 25.4 1.0
O3G F:TTP6195 4.5 37.0 1.0
OE2 F:GLU98 4.5 39.0 1.0
O2A F:TTP6195 4.6 34.3 1.0
CG F:GLU98 4.8 34.8 1.0

Magnesium binding site 7 out of 8 in 1xbt

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Magnesium binding site 7 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg7194

b:34.9
occ:1.00
 O1A G:TTP7195 2.0 28.2 1.0
O1G G:TTP7195 2.0 29.4 1.0
O G:HOH7228 2.1 32.4 1.0
OG G:SER33 2.2 27.3 1.0
O1B G:TTP7195 2.3 31.4 1.0
PB G:TTP7195 3.4 30.2 1.0
PA G:TTP7195 3.4 28.6 1.0
PG G:TTP7195 3.4 28.9 1.0
CB G:SER33 3.5 25.1 1.0
O3B G:TTP7195 3.7 31.0 1.0
O3A G:TTP7195 3.8 29.0 1.0
OD2 G:ASP97 4.0 37.9 1.0
OD1 G:ASP97 4.3 35.6 1.0
O5' G:TTP7195 4.3 28.8 1.0
O2G G:TTP7195 4.3 29.7 1.0
N G:SER33 4.4 24.5 1.0
OE2 G:GLU98 4.4 38.7 1.0
O3G G:TTP7195 4.4 29.7 1.0
NH2 G:ARG60 4.5 37.5 1.0
O G:HOH7202 4.5 26.3 1.0
CA G:SER33 4.5 25.4 1.0
O2A G:TTP7195 4.5 26.8 1.0
CB G:SER63 4.6 53.7 1.0
CG G:ASP97 4.6 33.7 1.0
O2B G:TTP7195 4.8 32.1 1.0
CG G:GLU98 4.9 34.6 1.0

Magnesium binding site 8 out of 8 in 1xbt

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Magnesium binding site 8 out of 8 in the Crystal Structure of Human Thymidine Kinase 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Human Thymidine Kinase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg8194

b:36.7
occ:1.00
 O1G H:TTP8195 2.1 31.1 1.0
O1B H:TTP8195 2.3 30.0 1.0
O1A H:TTP8195 2.3 28.7 1.0
O H:HOH8217 2.4 31.8 1.0
OG H:SER33 2.5 26.6 1.0
PB H:TTP8195 3.3 27.2 1.0
PG H:TTP8195 3.3 30.4 1.0
CB H:SER33 3.3 25.4 1.0
O3B H:TTP8195 3.4 31.1 1.0
PA H:TTP8195 3.6 29.1 1.0
O3A H:TTP8195 3.9 28.9 1.0
O2G H:TTP8195 4.1 31.8 1.0
O H:HOH8205 4.2 32.4 1.0
OD2 H:ASP97 4.3 37.0 1.0
OD1 H:ASP97 4.3 35.8 1.0
N H:SER33 4.3 24.6 1.0
CA H:SER33 4.4 25.4 1.0
NH2 H:ARG60 4.5 39.6 1.0
O3G H:TTP8195 4.5 31.9 1.0
O5' H:TTP8195 4.7 27.0 1.0
O2B H:TTP8195 4.7 29.9 1.0
O2A H:TTP8195 4.7 27.7 1.0
OE2 H:GLU98 4.7 40.2 1.0
CG H:ASP97 4.8 33.5 1.0

Reference:

M.Welin, U.Kosinska, N.E.Mikkelsen, C.Carnrot, C.Zhu, L.Wang, S.Eriksson, B.Munch-Petersen, H.Eklund. Structures of Thymidine Kinase 1 of Human and Mycoplasmic Origin Proc.Natl.Acad.Sci.Usa V. 101 17970 2004.
ISSN: ISSN 0027-8424
PubMed: 15611477
DOI: 10.1073/PNAS.0406332102
Page generated: Tue Aug 13 17:29:24 2024

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