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Magnesium in PDB 3fkb: Structure of Ndpk H122G and Tenofovir-Diphosphate

Enzymatic activity of Structure of Ndpk H122G and Tenofovir-Diphosphate

All present enzymatic activity of Structure of Ndpk H122G and Tenofovir-Diphosphate:
2.7.4.6;

Protein crystallography data

The structure of Structure of Ndpk H122G and Tenofovir-Diphosphate, PDB code: 3fkb was solved by S.Morera, Y.X.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.420, 104.570, 69.210, 90.00, 117.96, 90.00
R / Rfree (%) 18.1 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Ndpk H122G and Tenofovir-Diphosphate (pdb code 3fkb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Ndpk H122G and Tenofovir-Diphosphate, PDB code: 3fkb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3fkb

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Magnesium binding site 1 out of 6 in the Structure of Ndpk H122G and Tenofovir-Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Ndpk H122G and Tenofovir-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg156

b:12.1
occ:1.00
 O2B A:TNM160 2.1 16.9 1.0
O A:HOH1016 2.1 10.7 1.0
O A:HOH1019 2.1 9.4 1.0
O1A A:TNM160 2.1 19.0 1.0
O A:HOH1335 2.1 8.4 1.0
O A:HOH1020 2.1 12.3 1.0
PB A:TNM160 3.2 16.9 1.0
PA A:TNM160 3.3 16.9 1.0
O1B A:TNM160 3.5 17.3 1.0
O3A A:TNM160 3.7 17.3 1.0
C9' A:TNM160 3.8 18.8 1.0
O A:HOH1626 4.1 15.0 1.0
O A:HOH1017 4.2 18.7 1.0
O A:HOH1513 4.2 15.4 1.0
NH2 A:ARG92 4.2 9.3 1.0
O A:HOH1018 4.2 13.7 1.0
O A:HOH1066 4.2 14.7 1.0
O A:GLY123 4.4 7.2 1.0
O A:HOH1550 4.4 12.3 1.0
O3B A:TNM160 4.5 18.8 1.0
O A:HOH1858 4.5 8.6 1.0
O A:HOH1625 4.6 16.0 1.0
O2A A:TNM160 4.6 20.4 1.0
CE1 A:TYR56 4.6 11.6 1.0
O A:HOH1023 5.0 31.1 1.0

Magnesium binding site 2 out of 6 in 3fkb

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Magnesium binding site 2 out of 6 in the Structure of Ndpk H122G and Tenofovir-Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Ndpk H122G and Tenofovir-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg156

b:15.8
occ:1.00
 O1A B:TNM160 2.0 19.1 1.0
O2B B:TNM160 2.0 22.5 1.0
O B:HOH2040 2.0 18.6 1.0
O B:HOH1554 2.0 18.9 1.0
O B:HOH1814 2.1 18.9 1.0
O B:HOH1597 2.1 19.1 1.0
PB B:TNM160 3.2 18.6 1.0
PA B:TNM160 3.2 21.7 1.0
O1B B:TNM160 3.6 20.9 1.0
O3A B:TNM160 3.7 21.7 1.0
C9' B:TNM160 3.8 23.4 1.0
O B:HOH2258 4.0 28.9 1.0
O B:HOH1010 4.1 19.4 1.0
O B:HOH1173 4.1 26.2 1.0
O B:HOH1008 4.1 21.6 1.0
NH2 B:ARG92 4.2 10.8 1.0
O B:HOH1842 4.2 29.9 1.0
O B:HOH1009 4.3 19.4 1.0
O B:GLY123 4.4 8.8 1.0
O3B B:TNM160 4.5 21.2 1.0
O2A B:TNM160 4.5 24.3 1.0
O B:HOH1455 4.7 12.6 1.0
CE1 B:TYR56 4.7 17.1 1.0
O B:HOH1815 4.9 23.8 1.0

Magnesium binding site 3 out of 6 in 3fkb

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Magnesium binding site 3 out of 6 in the Structure of Ndpk H122G and Tenofovir-Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Ndpk H122G and Tenofovir-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg156

b:20.8
occ:1.00
 O1A C:TNM160 2.0 30.3 1.0
O C:HOH1850 2.0 17.6 1.0
O C:HOH1849 2.1 14.0 1.0
O C:HOH1851 2.1 16.7 1.0
O2B C:TNM160 2.1 22.8 1.0
O C:HOH1014 2.2 20.1 1.0
PB C:TNM160 3.2 24.3 1.0
PA C:TNM160 3.3 28.8 1.0
O1B C:TNM160 3.5 23.3 1.0
O3A C:TNM160 3.7 26.7 1.0
C9' C:TNM160 3.9 31.1 1.0
O C:HOH1848 4.0 26.1 1.0
O C:HOH2043 4.1 24.2 1.0
O C:HOH1852 4.1 23.6 1.0
O C:HOH1853 4.2 19.0 1.0
O C:HOH1854 4.3 22.2 1.0
NH1 C:ARG92 4.3 17.5 1.0
O C:GLY123 4.3 12.2 1.0
O C:HOH1771 4.4 17.2 1.0
O C:HOH1772 4.5 14.8 1.0
O2A C:TNM160 4.5 30.9 1.0
O3B C:TNM160 4.5 23.4 1.0
CE1 C:TYR56 4.7 19.3 1.0

Magnesium binding site 4 out of 6 in 3fkb

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Magnesium binding site 4 out of 6 in the Structure of Ndpk H122G and Tenofovir-Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Ndpk H122G and Tenofovir-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg156

b:27.3
occ:1.00
 O1A D:TNV160 2.0 26.0 1.0
O D:HOH1001 2.0 29.6 1.0
O3G D:TNV160 2.1 26.2 1.0
O2B D:TNV160 2.1 26.3 1.0
O D:HOH1831 2.2 20.8 1.0
O D:HOH1834 2.2 26.6 1.0
PG D:TNV160 3.2 28.6 1.0
PA D:TNV160 3.2 25.3 1.0
PB D:TNV160 3.3 25.9 1.0
O1G D:TNV160 3.5 26.9 1.0
O3B D:TNV160 3.6 28.6 1.0
O3A D:TNV160 3.7 25.2 1.0
OE2 D:GLU58 3.7 21.6 1.0
C9' D:TNV160 3.8 26.4 1.0
NH1 D:ARG92 4.0 13.2 1.0
O D:HOH1531 4.1 15.9 1.0
O D:HOH1805 4.2 16.4 1.0
NE2 D:HIS59 4.2 14.3 1.0
O D:HOH1004 4.3 21.6 1.0
O D:GLY123 4.4 10.3 1.0
O2A D:TNV160 4.5 26.6 1.0
O2G D:TNV160 4.5 27.8 1.0
O1B D:TNV160 4.6 24.6 1.0
CD D:GLU58 4.6 19.8 1.0

Magnesium binding site 5 out of 6 in 3fkb

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Magnesium binding site 5 out of 6 in the Structure of Ndpk H122G and Tenofovir-Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Ndpk H122G and Tenofovir-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg156

b:11.7
occ:1.00
 O2B E:TNM160 2.0 13.8 1.0
O E:HOH1029 2.0 12.1 1.0
O E:HOH1026 2.1 11.5 1.0
O1A E:TNM160 2.1 11.6 1.0
O E:HOH1024 2.1 10.3 1.0
O E:HOH1025 2.2 11.3 1.0
PB E:TNM160 3.1 13.1 1.0
PA E:TNM160 3.3 13.1 1.0
O1B E:TNM160 3.5 12.8 1.0
O3A E:TNM160 3.6 12.7 1.0
C9' E:TNM160 3.9 11.9 1.0
O E:HOH1864 4.1 11.6 1.0
NH2 E:ARG92 4.1 9.2 1.0
O E:HOH1033 4.1 16.2 1.0
O E:HOH1547 4.2 11.0 1.0
O E:HOH1028 4.2 13.9 1.0
O E:HOH1491 4.3 13.5 1.0
O E:HOH1030 4.3 12.8 1.0
O E:GLY123 4.4 10.1 1.0
O3B E:TNM160 4.4 13.8 1.0
O E:HOH1545 4.6 12.7 1.0
O2A E:TNM160 4.6 13.9 1.0
O E:HOH1408 4.7 9.8 1.0
CE1 E:TYR56 4.7 10.8 1.0

Magnesium binding site 6 out of 6 in 3fkb

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Magnesium binding site 6 out of 6 in the Structure of Ndpk H122G and Tenofovir-Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Ndpk H122G and Tenofovir-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg156

b:12.0
occ:1.00
 O2B F:TNM160 2.0 15.8 1.0
O F:HOH1045 2.0 13.4 1.0
O F:HOH1046 2.1 13.1 1.0
O F:HOH1044 2.1 15.7 1.0
O1A F:TNM160 2.1 16.9 1.0
O F:HOH1043 2.1 11.5 1.0
PB F:TNM160 3.2 16.0 1.0
PA F:TNM160 3.3 16.7 1.0
O1B F:TNM160 3.5 15.7 1.0
O3A F:TNM160 3.7 15.9 1.0
C9' F:TNM160 3.9 17.6 1.0
NH1 F:ARG92 4.1 11.5 1.0
O F:HOH1051 4.1 22.2 1.0
O F:HOH1049 4.1 14.3 1.0
O F:HOH1869 4.2 19.0 1.0
O F:HOH1047 4.2 13.4 1.0
O F:HOH1039 4.2 14.2 1.0
O F:HOH1037 4.3 14.1 1.0
O F:GLY123 4.3 8.6 1.0
O F:HOH1040 4.5 11.9 1.0
O3B F:TNM160 4.5 16.3 1.0
O2A F:TNM160 4.6 19.3 1.0
O F:HOH1048 4.6 10.1 1.0
CE1 F:TYR56 4.7 10.8 1.0

Reference:

K.Koch, Y.X.Chen, J.Y.Feng, K.Borroto-Esoda, D.Deville-Bonne, S.Gallois-Montbrun, J.Janin, S.Morera. Nucleoside Diphosphate Kinase and the Activation of Antiviral Phosphonate Analogs of Nucleotides: Binding Mode and Phosphorylation of Tenofovir Derivatives Nucleosides Nucleotides V. 28 776 2009NUCLEIC Acids.
ISSN: ISSN 1525-7770
PubMed: 20183617
DOI: 10.1080/15257770903155899
Page generated: Wed Aug 14 13:49:08 2024

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