Atomistry » Magnesium » PDB 3fcw-3fpk » 3fkb
Atomistry »
  Magnesium »
    PDB 3fcw-3fpk »
      3fkb »

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

Go back to Magnesium Binding Sites List in 3fkb
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

Go back to Magnesium Binding Sites List in 3fkb
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

Go back to Magnesium Binding Sites List in 3fkb
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

Go back to Magnesium Binding Sites List in 3fkb
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

Go back to Magnesium Binding Sites List in 3fkb
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

Go back to Magnesium Binding Sites List in 3fkb
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: Mon Dec 14 08:08:47 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy