Magnesium in PDB 6h98: Native Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola.

Protein crystallography data

The structure of Native Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola., PDB code: 6h98 was solved by F.Leisinger, R.Burn, M.Meury, P.Lukat, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.51 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 129.380, 43.222, 89.069, 90.00, 108.50, 90.00
R / Rfree (%) 16.5 / 20.4

Other elements in 6h98:

The structure of Native Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Native Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola. (pdb code 6h98). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Native Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola., PDB code: 6h98:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6h98

Go back to Magnesium Binding Sites List in 6h98
Magnesium binding site 1 out of 3 in the Native Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Native Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:30.9
occ:1.00
O A:HOH935 2.1 31.1 1.0
O A:HOH733 2.9 12.4 1.0
OH A:TYR355 3.4 34.6 1.0
CE2 A:TYR188 3.7 9.9 1.0
CA A:GLY256 3.8 12.2 1.0
CD2 A:TYR188 3.8 10.8 1.0
CE1 A:TYR375 3.8 21.7 1.0
CE1 A:TYR355 4.1 21.6 1.0
CZ A:TYR355 4.1 21.0 1.0
N A:GLY256 4.2 9.9 1.0
CZ A:TYR188 4.5 14.0 1.0
OH A:TYR375 4.6 26.5 1.0
CD1 A:TYR375 4.6 19.3 1.0
CG A:TYR188 4.6 10.5 1.0
CZ A:TYR375 4.7 20.1 1.0
CZ2 A:TRP416 4.8 11.2 1.0
C A:GLY256 4.8 11.2 1.0
O A:HOH769 4.8 26.3 1.0
O A:HOH748 4.9 17.2 1.0
CH2 A:TRP416 4.9 13.5 1.0
O A:HOH801 4.9 14.1 1.0
CE2 A:TRP416 4.9 11.8 1.0
CH2 A:TRP216 5.0 19.5 1.0

Magnesium binding site 2 out of 3 in 6h98

Go back to Magnesium Binding Sites List in 6h98
Magnesium binding site 2 out of 3 in the Native Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Native Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:11.8
occ:1.00
O A:TRP216 2.2 10.1 1.0
O A:ASP437 2.3 9.9 1.0
O A:THR414 2.3 12.9 1.0
OD1 A:ASN217 2.3 12.6 1.0
O A:HOH773 2.5 10.8 1.0
OD1 A:ASP437 2.7 12.1 1.0
C A:ASP437 3.1 11.7 1.0
C A:TRP216 3.1 11.2 1.0
C A:THR414 3.3 13.3 1.0
CG A:ASN217 3.5 13.8 1.0
CG A:ASP437 3.5 10.0 1.0
CA A:ASN217 3.5 10.9 1.0
N A:ASN217 3.6 8.2 1.0
NH2 A:ARG266 3.7 11.4 1.0
CA A:THR414 3.8 11.3 1.0
N A:GLY438 3.9 11.3 1.0
CA A:GLY438 3.9 9.7 1.0
CA A:ASP437 3.9 8.7 1.0
CB A:ASN217 4.1 13.2 1.0
CB A:ASP437 4.2 7.5 1.0
CB A:THR414 4.2 13.2 1.0
C A:GLY438 4.2 13.1 1.0
O A:HOH695 4.2 16.5 1.0
O A:GLY438 4.2 11.0 1.0
OD2 A:ASP437 4.3 11.5 1.0
CA A:TRP216 4.3 10.8 1.0
CB A:TRP216 4.3 12.3 1.0
N A:GLY415 4.4 10.9 1.0
O A:THR215 4.5 9.6 1.0
ND2 A:ASN217 4.6 19.9 1.0
CZ A:ARG266 4.6 10.9 1.0
CA A:GLY415 4.7 12.0 1.0
NH1 A:ARG266 4.7 11.7 1.0
C A:ASN217 4.8 9.7 1.0
O A:HOH761 4.9 10.3 1.0

Magnesium binding site 3 out of 3 in 6h98

Go back to Magnesium Binding Sites List in 6h98
Magnesium binding site 3 out of 3 in the Native Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Native Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:37.4
occ:1.00
O A:HOH651 2.2 32.8 1.0
O A:HOH609 2.3 28.5 1.0
O A:HOH995 2.4 44.3 1.0
OE2 A:GLU125 4.3 36.8 1.0
OE1 A:GLU125 4.4 44.1 1.0
CD A:GLU125 4.8 43.9 1.0

Reference:

F.Leisinger, R.Burn, M.Meury, P.Lukat, F.P.Seebeck. Structural and Mechanistic Basis For Anaerobic Ergothioneine Biosynthesis. J.Am.Chem.Soc. V. 141 6906 2019.
ISSN: ESSN 1520-5126
PubMed: 30943021
DOI: 10.1021/JACS.8B12596
Page generated: Mon Dec 14 22:48:37 2020

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