Atomistry » Magnesium » PDB 4z40-4zgn » 4zd6
Atomistry »
  Magnesium »
    PDB 4z40-4zgn »
      4zd6 »

Magnesium in PDB 4zd6: Halohydrin Hydrogen-Halide-Lyase, Hheb

Protein crystallography data

The structure of Halohydrin Hydrogen-Halide-Lyase, Hheb, PDB code: 4zd6 was solved by F.Watanabe, F.Yu, A.Ohtaki, Y.Yamanaka, K.Noguchi, M.Yohda, M.Odaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.31 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 121.484, 216.380, 104.517, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.7

Other elements in 4zd6:

The structure of Halohydrin Hydrogen-Halide-Lyase, Hheb also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Halohydrin Hydrogen-Halide-Lyase, Hheb (pdb code 4zd6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Halohydrin Hydrogen-Halide-Lyase, Hheb, PDB code: 4zd6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4zd6

Go back to Magnesium Binding Sites List in 4zd6
Magnesium binding site 1 out of 3 in the Halohydrin Hydrogen-Halide-Lyase, Hheb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Halohydrin Hydrogen-Halide-Lyase, Hheb within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:19.3
occ:1.00
O B:HOH498 2.2 36.2 1.0
OE2 B:GLU107 4.1 35.4 1.0
OE1 B:GLU107 4.4 32.6 1.0
CD B:GLU107 4.7 31.3 1.0

Magnesium binding site 2 out of 3 in 4zd6

Go back to Magnesium Binding Sites List in 4zd6
Magnesium binding site 2 out of 3 in the Halohydrin Hydrogen-Halide-Lyase, Hheb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Halohydrin Hydrogen-Halide-Lyase, Hheb within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:19.0
occ:1.00
O A:HOH434 2.0 24.5 1.0
O E:HOH427 2.0 19.1 1.0
O A:HOH554 2.1 27.3 1.0
O E:HOH519 2.1 24.5 1.0
O E:HOH607 2.2 25.9 1.0
O E:HOH489 2.3 25.4 1.0
O B:HOH417 4.0 26.9 1.0
OE1 E:GLU81 4.1 18.6 1.0
O E:HOH539 4.1 18.4 1.0
O B:HOH569 4.1 22.6 1.0
O E:HOH613 4.2 22.1 1.0
O F:HOH548 4.4 37.3 1.0
OE2 E:GLU81 4.4 20.3 1.0
OD2 A:ASP212 4.5 18.2 1.0
OD2 E:ASP79 4.6 20.5 1.0
O F:HOH537 4.6 18.3 1.0
CB E:ASP79 4.6 15.5 1.0
CD E:GLU81 4.7 17.8 1.0
CB A:ASP209 4.8 15.4 1.0
OD2 A:ASP209 4.9 24.5 1.0
NH2 B:ARG197 4.9 16.9 1.0
CG A:ASP209 5.0 20.6 1.0

Magnesium binding site 3 out of 3 in 4zd6

Go back to Magnesium Binding Sites List in 4zd6
Magnesium binding site 3 out of 3 in the Halohydrin Hydrogen-Halide-Lyase, Hheb


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Halohydrin Hydrogen-Halide-Lyase, Hheb within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg304

b:13.4
occ:0.65
O E:HOH543 2.2 20.1 1.0
O E:ARG54 2.3 16.0 1.0
O E:HOH452 2.4 20.9 1.0
O E:HOH476 2.5 20.7 0.5
C E:ARG54 3.4 16.5 1.0
CA E:ARG54 4.1 15.4 1.0
O E:HOH450 4.3 23.4 1.0
C E:ALA55 4.4 17.7 1.0
N E:ALA55 4.5 14.5 1.0
O E:ALA55 4.5 19.9 1.0
N E:GLY56 4.5 17.2 1.0
CG E:ARG54 4.6 23.0 1.0
CA E:ALA55 4.7 16.1 1.0
O E:GLU53 4.7 19.1 1.0
O E:HOH466 4.9 28.2 1.0
O E:HOH575 4.9 18.0 1.0
CB E:ARG54 5.0 18.4 1.0
CA E:GLY56 5.0 19.9 1.0

Reference:

F.Watanabe, F.Yu, A.Ohtaki, Y.Yamanaka, K.Noguchi, M.Yohda, M.Odaka. Crystal Structures of Halohydrin Hydrogen-Halide-Lyases From Corynebacterium Sp. N-1074 Proteins V. 83 2230 2015.
ISSN: ESSN 1097-0134
PubMed: 26422370
DOI: 10.1002/PROT.24938
Page generated: Mon Dec 14 19:56:49 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy