Atomistry » Magnesium » PDB 3wqc-3x1d » 3wql
Atomistry »
  Magnesium »
    PDB 3wqc-3x1d »
      3wql »

Magnesium in PDB 3wql: Crystal Structure of RV3378C with MG2+ and Ppi

Enzymatic activity of Crystal Structure of RV3378C with MG2+ and Ppi

All present enzymatic activity of Crystal Structure of RV3378C with MG2+ and Ppi:
3.1.7.8; 3.1.7.9;

Protein crystallography data

The structure of Crystal Structure of RV3378C with MG2+ and Ppi, PDB code: 3wql was solved by H.C.Chan, X.Feng, T.P.Ko, C.H.Huang, Y.Hu, Y.Zheng, S.Bogue, C.Nakano, T.Hoshino, L.Zhang, P.Lv, W.Liu, D.C.Crick, P.H.Liang, A.H.Wang, E.Oldfield, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 208.420, 56.525, 114.435, 90.00, 90.28, 90.00
R / Rfree (%) 19.8 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of RV3378C with MG2+ and Ppi (pdb code 3wql). 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 RV3378C with MG2+ and Ppi, PDB code: 3wql:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3wql

Go back to Magnesium Binding Sites List in 3wql
Magnesium binding site 1 out of 8 in the Crystal Structure of RV3378C with MG2+ and Ppi


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 RV3378C with MG2+ and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:32.3
occ:1.00
 O A:HOH546 2.7 9.2 1.0
O A:HOH425 2.8 16.2 1.0
OD2 A:ASP34 3.0 25.6 1.0
N A:PHE207 3.3 12.4 1.0
CG A:PRO32 3.4 14.1 1.0
CA A:GLY206 3.5 13.1 1.0
CB A:ASP34 3.6 21.1 1.0
C A:GLY206 3.7 13.8 1.0
CG A:ASP34 3.8 23.0 1.0
CE1 A:PHE213 3.9 12.5 1.0
CB A:PHE207 3.9 15.1 1.0
CZ A:PHE213 4.0 12.4 1.0
CA A:PHE207 4.2 15.2 1.0
O A:PRO32 4.3 13.2 1.0
O A:ILE205 4.4 9.4 1.0
CB A:PRO32 4.4 15.0 1.0
MG A:MG302 4.4 24.1 1.0
CZ A:PHE204 4.5 8.5 1.0
CD A:PRO32 4.5 14.4 1.0
CE1 A:PHE204 4.5 8.6 1.0
O A:PHE207 4.6 16.6 1.0
O A:GLY206 4.6 11.5 1.0
N A:GLY206 4.7 12.1 1.0
C A:PHE207 4.9 14.9 1.0
CA A:ASP34 4.9 20.1 1.0
OD1 A:ASP34 5.0 22.1 1.0
C A:ILE205 5.0 10.0 1.0

Magnesium binding site 2 out of 8 in 3wql

Go back to Magnesium Binding Sites List in 3wql
Magnesium binding site 2 out of 8 in the Crystal Structure of RV3378C with MG2+ and Ppi


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 RV3378C with MG2+ and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:24.1
occ:1.00
 O A:ARG209 2.2 9.3 1.0
O A:HOH546 2.4 9.2 1.0
O A:PHE207 2.5 16.6 1.0
OG A:SER211 2.9 19.8 1.0
C A:ARG209 3.4 12.2 1.0
C A:PHE207 3.7 14.9 1.0
N A:SER211 3.8 10.7 1.0
CB A:SER211 3.9 13.7 1.0
O A:SER211 4.0 11.1 1.0
N A:ARG209 4.0 13.1 1.0
N A:PHE207 4.1 12.4 1.0
CA A:ARG209 4.2 13.9 1.0
C A:GLY208 4.2 14.1 1.0
O A:HOH479 4.3 28.1 1.0
CA A:SER211 4.3 11.8 1.0
C A:PHE210 4.4 10.4 1.0
N A:PHE210 4.4 13.3 1.0
MG A:MG301 4.4 32.3 1.0
CA A:PHE207 4.5 15.2 1.0
CB A:ARG209 4.5 15.8 1.0
C A:SER211 4.5 12.1 1.0
O A:GLY208 4.6 14.2 1.0
CA A:PHE210 4.6 11.1 1.0
OD2 A:ASP34 4.6 25.6 1.0
N A:GLY208 4.7 15.0 1.0
CA A:GLY208 4.8 12.4 1.0

Magnesium binding site 3 out of 8 in 3wql

Go back to Magnesium Binding Sites List in 3wql
Magnesium binding site 3 out of 8 in the Crystal Structure of RV3378C with MG2+ and Ppi


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 RV3378C with MG2+ and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:25.5
occ:1.00
 O B:HOH465 2.8 12.9 1.0
OD2 B:ASP34 2.9 19.3 1.0
O B:HOH413 2.9 10.9 1.0
N B:PHE207 3.3 11.9 1.0
CB B:ASP34 3.5 16.6 1.0
CG B:PRO32 3.6 13.1 1.0
CG B:ASP34 3.6 19.0 1.0
CA B:GLY206 3.6 8.3 1.0
C B:GLY206 3.7 10.8 1.0
CZ B:PHE213 3.8 9.9 1.0
CE1 B:PHE213 3.8 9.3 1.0
CB B:PHE207 3.8 11.6 1.0
CA B:PHE207 4.1 13.1 1.0
MG B:MG302 4.3 26.5 1.0
O B:PRO32 4.3 15.8 1.0
CB B:PRO32 4.4 12.1 1.0
O B:PHE207 4.5 14.6 1.0
CE1 B:PHE204 4.7 9.9 1.0
O B:ILE205 4.7 10.6 1.0
O B:GLY206 4.7 9.3 1.0
CZ B:PHE204 4.7 7.7 1.0
CD B:PRO32 4.8 11.6 1.0
C B:PHE207 4.8 12.3 1.0
OD1 B:ASP34 4.8 23.4 1.0
N B:GLY206 4.9 10.2 1.0
CA B:ASP34 4.9 14.4 1.0

Magnesium binding site 4 out of 8 in 3wql

Go back to Magnesium Binding Sites List in 3wql
Magnesium binding site 4 out of 8 in the Crystal Structure of RV3378C with MG2+ and Ppi


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 RV3378C with MG2+ and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:26.5
occ:1.00
 O B:PHE207 2.3 14.6 1.0
O B:ARG209 2.3 14.2 1.0
O B:HOH465 2.6 12.9 1.0
O B:HOH427 2.8 49.5 1.0
C B:ARG209 3.5 12.4 1.0
C B:PHE207 3.5 12.3 1.0
OG B:SER211 3.5 21.1 1.0
N B:ARG209 3.8 10.2 1.0
CA B:ARG209 4.0 13.4 1.0
N B:PHE207 4.1 11.9 1.0
C B:GLY208 4.1 12.1 1.0
O B:SER211 4.1 7.8 1.0
N B:SER211 4.2 10.2 1.0
MG B:MG301 4.3 25.5 1.0
CB B:ARG209 4.3 12.1 1.0
CA B:PHE207 4.3 13.1 1.0
N B:GLY208 4.5 14.1 1.0
OD2 B:ASP34 4.5 19.3 1.0
CB B:SER211 4.5 13.0 1.0
O B:GLY208 4.5 11.2 1.0
N B:PHE210 4.6 9.5 1.0
CA B:GLY208 4.6 12.7 1.0
CA B:SER211 4.8 10.5 1.0
C B:PHE210 4.8 10.8 1.0
C B:SER211 4.8 8.1 1.0
CA B:PHE210 4.8 10.0 1.0
CB B:PHE207 4.8 11.6 1.0
O A:HOH632 5.0 54.0 1.0

Magnesium binding site 5 out of 8 in 3wql

Go back to Magnesium Binding Sites List in 3wql
Magnesium binding site 5 out of 8 in the Crystal Structure of RV3378C with MG2+ and Ppi


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 RV3378C with MG2+ and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:26.0
occ:1.00
 O C:HOH504 2.7 14.1 1.0
O C:HOH433 2.8 16.3 1.0
OD2 C:ASP34 3.1 32.5 1.0
N C:PHE207 3.3 16.0 1.0
CG C:PRO32 3.5 12.3 1.0
CB C:ASP34 3.6 23.8 1.0
CA C:GLY206 3.6 13.1 1.0
C C:GLY206 3.7 13.8 1.0
CG C:ASP34 3.7 26.9 1.0
CZ C:PHE213 3.8 14.0 1.0
CE1 C:PHE213 3.8 14.3 1.0
CB C:PHE207 3.9 16.2 1.0
O C:HOH505 4.0 45.7 1.0
CA C:PHE207 4.2 16.4 1.0
O C:PRO32 4.3 16.2 1.0
MG C:MG302 4.4 22.9 1.0
O C:PHE207 4.4 18.0 1.0
CB C:PRO32 4.5 14.1 1.0
O C:ILE205 4.5 11.8 1.0
CZ C:PHE204 4.6 9.1 1.0
CE1 C:PHE204 4.6 15.5 1.0
CD C:PRO32 4.6 13.0 1.0
O C:GLY206 4.7 13.2 1.0
C C:PHE207 4.8 17.3 1.0
N C:GLY206 4.9 12.3 1.0
CA C:ASP34 4.9 20.0 1.0
OD1 C:ASP34 5.0 29.3 1.0

Magnesium binding site 6 out of 8 in 3wql

Go back to Magnesium Binding Sites List in 3wql
Magnesium binding site 6 out of 8 in the Crystal Structure of RV3378C with MG2+ and Ppi


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 RV3378C with MG2+ and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:22.9
occ:1.00
 O C:ARG209 2.2 9.9 1.0
O C:PHE207 2.4 18.0 1.0
O C:HOH504 2.5 14.1 1.0
OG C:SER211 2.8 17.5 1.0
C C:ARG209 3.4 13.5 1.0
O C:HOH505 3.5 45.7 1.0
C C:PHE207 3.6 17.3 1.0
N C:ARG209 3.9 14.3 1.0
N C:SER211 3.9 12.5 1.0
CB C:SER211 4.0 14.2 1.0
CA C:ARG209 4.1 15.6 1.0
C C:GLY208 4.1 16.7 1.0
O C:SER211 4.1 12.7 1.0
N C:PHE207 4.2 16.0 1.0
CB C:ARG209 4.4 14.9 1.0
O C:HOH432 4.4 31.5 1.0
CA C:SER211 4.4 12.0 1.0
O C:GLY208 4.4 15.4 1.0
N C:PHE210 4.4 12.4 1.0
MG C:MG301 4.4 26.0 1.0
C C:PHE210 4.5 13.2 1.0
CA C:PHE207 4.5 16.4 1.0
N C:GLY208 4.6 16.5 1.0
CA C:GLY208 4.6 16.4 1.0
C C:SER211 4.6 12.5 1.0
CA C:PHE210 4.6 12.9 1.0

Magnesium binding site 7 out of 8 in 3wql

Go back to Magnesium Binding Sites List in 3wql
Magnesium binding site 7 out of 8 in the Crystal Structure of RV3378C with MG2+ and Ppi


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 RV3378C with MG2+ and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:34.5
occ:1.00
 O D:HOH485 2.7 10.4 1.0
O D:HOH483 2.8 15.2 1.0
N D:PHE207 3.1 14.1 1.0
OD2 D:ASP34 3.2 22.4 1.0
CA D:GLY206 3.3 10.9 1.0
C D:GLY206 3.5 12.4 1.0
CG D:PRO32 3.7 9.7 1.0
CB D:ASP34 3.8 17.9 1.0
CE1 D:PHE213 3.8 10.4 1.0
CZ D:PHE213 3.8 11.0 1.0
CB D:PHE207 3.9 14.6 1.0
CG D:ASP34 4.0 20.8 1.0
CA D:PHE207 4.1 14.8 1.0
MG D:MG302 4.3 29.3 1.0
O D:ILE205 4.4 9.7 1.0
O D:PHE207 4.4 16.2 1.0
CE1 D:PHE204 4.5 13.0 1.0
CZ D:PHE204 4.5 13.2 1.0
O D:PRO32 4.5 16.0 1.0
N D:GLY206 4.6 11.8 1.0
O D:GLY206 4.6 12.1 1.0
CB D:PRO32 4.6 12.3 1.0
CD D:PRO32 4.7 10.0 1.0
O D:HOH608 4.8 35.9 1.0
C D:PHE207 4.8 14.8 1.0
O D:SER211 4.9 4.8 1.0
C D:ILE205 4.9 12.1 1.0

Magnesium binding site 8 out of 8 in 3wql

Go back to Magnesium Binding Sites List in 3wql
Magnesium binding site 8 out of 8 in the Crystal Structure of RV3378C with MG2+ and Ppi


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 RV3378C with MG2+ and Ppi within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:29.3
occ:1.00
 O D:ARG209 2.3 13.9 1.0
O D:HOH485 2.4 10.4 1.0
O D:PHE207 2.4 16.2 1.0
O D:HOH666 2.6 50.2 1.0
OG D:SER211 2.8 15.7 1.0
C D:ARG209 3.5 13.1 1.0
O D:HOH608 3.6 35.9 1.0
C D:PHE207 3.6 14.8 1.0
N D:ARG209 4.0 10.4 1.0
N D:SER211 4.0 7.7 1.0
O D:SER211 4.0 4.8 1.0
CB D:SER211 4.1 10.8 1.0
O D:HOH528 4.1 41.7 1.0
CA D:ARG209 4.1 13.5 1.0
N D:PHE207 4.1 14.1 1.0
C D:GLY208 4.2 14.1 1.0
MG D:MG301 4.3 34.5 1.0
CB D:ARG209 4.4 13.8 1.0
CA D:PHE207 4.4 14.8 1.0
CA D:SER211 4.5 8.2 1.0
O D:HOH609 4.5 40.0 1.0
N D:PHE210 4.5 10.8 1.0
C D:PHE210 4.6 9.3 1.0
O D:GLY208 4.6 13.5 1.0
C D:SER211 4.6 7.4 1.0
N D:GLY208 4.6 15.2 1.0
OD2 D:ASP34 4.7 22.4 1.0
CA D:PHE210 4.7 8.7 1.0
CA D:GLY208 4.7 12.7 1.0

Reference:

H.C.Chan, X.Feng, T.P.Ko, C.H.Huang, Y.Hu, Y.Zheng, S.Bogue, C.Nakano, T.Hoshino, L.Zhang, P.Lv, W.Liu, D.C.Crick, P.H.Liang, A.H.Wang, E.Oldfield, R.T.Guo. Structure and Inhibition of Tuberculosinol Synthase and Decaprenyl Diphosphate Synthase From Mycobacterium Tuberculosis. J.Am.Chem.Soc. V. 136 2892 2014.
ISSN: ISSN 0002-7863
PubMed: 24475925
DOI: 10.1021/JA413127V
Page generated: Mon Dec 14 09:01:35 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