Atomistry » Magnesium » PDB 5z79-5zki » 5z7w
Atomistry »
  Magnesium »
    PDB 5z79-5zki »
      5z7w »

Magnesium in PDB 5z7w: Crystal Structure of Striga Hermonthica HTL1 (SHHTL1)

Protein crystallography data

The structure of Crystal Structure of Striga Hermonthica HTL1 (SHHTL1), PDB code: 5z7w was solved by Y.Xu, T.Miyakawa, A.Nakamura, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.95 / 1.66
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.170, 138.770, 49.410, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.9

Other elements in 5z7w:

The structure of Crystal Structure of Striga Hermonthica HTL1 (SHHTL1) also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Striga Hermonthica HTL1 (SHHTL1) (pdb code 5z7w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Striga Hermonthica HTL1 (SHHTL1), PDB code: 5z7w:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5z7w

Go back to Magnesium Binding Sites List in 5z7w
Magnesium binding site 1 out of 3 in the Crystal Structure of Striga Hermonthica HTL1 (SHHTL1)


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 Striga Hermonthica HTL1 (SHHTL1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:31.9
occ:0.47
OD2 A:ASP129 2.0 35.1 1.0
O A:HOH611 2.1 47.9 1.0
CG A:ASP129 3.2 34.1 1.0
CB A:ASP129 3.8 28.4 1.0
O A:HOH425 4.2 29.1 1.0
OD1 A:ASP129 4.2 37.8 1.0
O A:HOH696 4.7 36.2 1.0

Magnesium binding site 2 out of 3 in 5z7w

Go back to Magnesium Binding Sites List in 5z7w
Magnesium binding site 2 out of 3 in the Crystal Structure of Striga Hermonthica HTL1 (SHHTL1)


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 Striga Hermonthica HTL1 (SHHTL1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:21.5
occ:1.00
OG A:SER95 2.8 22.6 1.0
O3 A:GOL304 3.1 52.7 1.0
O1 A:GOL304 3.1 48.1 1.0
N A:PHE26 3.1 17.6 1.0
N A:VAL96 3.2 15.7 1.0
CB A:PHE26 3.2 19.6 1.0
CB A:SER95 3.3 22.3 1.0
CB A:VAL96 3.4 14.9 1.0
CG1 A:VAL96 3.5 15.5 1.0
CD1 A:ILE193 3.7 17.5 1.0
CA A:PHE26 3.8 17.2 1.0
O A:HOH414 3.8 22.6 1.0
CA A:VAL96 3.9 15.6 1.0
C1 A:GOL304 4.0 47.0 1.0
C A:GLY25 4.1 18.4 1.0
C A:SER95 4.1 16.2 1.0
CA A:GLY25 4.2 17.1 1.0
C3 A:GOL304 4.3 50.5 1.0
CA A:SER95 4.3 16.4 1.0
C2 A:GOL304 4.5 46.9 1.0
CG A:PHE26 4.5 20.4 1.0
CG2 A:ILE193 4.6 18.6 1.0
NE2 A:HIS246 4.7 17.1 1.0
CG2 A:VAL96 4.7 17.2 1.0
O A:PHE26 4.8 17.6 1.0
C A:PHE26 4.8 16.4 1.0
O A:HOH440 4.8 19.9 1.0
CG1 A:ILE193 4.9 15.5 1.0

Magnesium binding site 3 out of 3 in 5z7w

Go back to Magnesium Binding Sites List in 5z7w
Magnesium binding site 3 out of 3 in the Crystal Structure of Striga Hermonthica HTL1 (SHHTL1)


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 Striga Hermonthica HTL1 (SHHTL1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:18.5
occ:1.00
OG B:SER95 2.9 19.7 1.0
N B:PHE26 3.2 17.0 1.0
N B:VAL96 3.2 16.8 1.0
O1 B:GOL304 3.2 42.8 1.0
CB B:SER95 3.3 15.1 1.0
CB B:PHE26 3.3 17.0 1.0
CB B:VAL96 3.4 15.6 1.0
CG1 B:VAL96 3.5 16.3 1.0
C1 B:GOL304 3.7 43.1 1.0
CA B:PHE26 3.8 17.3 1.0
CD1 B:ILE193 3.9 19.0 1.0
CA B:VAL96 3.9 16.0 1.0
O2 B:GOL304 3.9 41.9 1.0
O B:HOH521 4.0 29.1 1.0
C B:SER95 4.2 16.4 1.0
C B:GLY25 4.2 18.1 1.0
CA B:GLY25 4.2 16.2 1.0
CG2 B:ILE193 4.3 20.7 1.0
CA B:SER95 4.3 14.6 1.0
C2 B:GOL304 4.4 42.4 1.0
CG B:PHE26 4.6 19.0 1.0
NE2 B:HIS246 4.8 16.9 1.0
CG2 B:VAL96 4.8 15.9 1.0
O B:HOH466 4.8 19.9 1.0
CG1 B:ILE193 4.9 19.4 1.0
OH B:TYR124 4.9 19.4 1.0
C B:PHE26 4.9 15.9 1.0
O B:PHE26 4.9 16.5 1.0

Reference:

Y.Xu, T.Miyakawa, S.Nosaki, A.Nakamura, Y.Lyu, H.Nakamura, U.Ohto, H.Ishida, T.Shimizu, T.Asami, M.Tanokura. Structural Analysis of Htl and D14 Proteins Reveals the Basis For Ligand Selectivity in Striga. Nat Commun V. 9 3947 2018.
ISSN: ESSN 2041-1723
PubMed: 30258184
DOI: 10.1038/S41467-018-06452-2
Page generated: Mon Sep 30 11:45:51 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy