Magnesium in PDB 6qbd: Crystal Structure of Nlppya P41A, D44N, N48E Mutant

Protein crystallography data

The structure of Crystal Structure of Nlppya P41A, D44N, N48E Mutant, PDB code: 6qbd was solved by T.Lenarcic, M.Podobnik, G.Anderluh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.28 / 1.95
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.391, 87.391, 115.967, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nlppya P41A, D44N, N48E Mutant (pdb code 6qbd). 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 Nlppya P41A, D44N, N48E Mutant, PDB code: 6qbd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6qbd

Go back to Magnesium Binding Sites List in 6qbd
Magnesium binding site 1 out of 3 in the Crystal Structure of Nlppya P41A, D44N, N48E Mutant


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 Nlppya P41A, D44N, N48E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:26.4
occ:1.00
O A:HOH401 2.1 24.4 1.0
O A:HOH496 2.1 24.5 1.0
O A:HOH459 2.2 19.8 1.0
OD1 A:ASP104 2.2 20.9 1.0
O A:HOH545 2.2 25.5 1.0
OE2 A:GLU106 2.3 27.4 0.9
CG A:ASP104 3.2 17.8 1.0
CD A:GLU106 3.4 28.0 0.9
OD2 A:ASP104 3.7 15.6 1.0
OD2 A:ASP93 4.1 23.6 1.0
O A:TRP105 4.2 17.6 1.0
O A:HOH442 4.2 22.0 1.0
CG A:GLU106 4.2 16.6 1.0
O A:HOH495 4.2 16.0 1.0
OE1 A:GLU106 4.3 26.1 0.9
O A:HIS159 4.3 22.0 1.0
CB A:ASP104 4.5 12.8 1.0
N A:TRP105 4.6 12.8 1.0
NE2 A:HIS101 4.6 29.5 0.9
CE1 A:HIS101 4.6 24.6 0.9
CA A:ASP104 4.7 13.8 1.0
C A:TRP105 4.9 16.4 1.0

Magnesium binding site 2 out of 3 in 6qbd

Go back to Magnesium Binding Sites List in 6qbd
Magnesium binding site 2 out of 3 in the Crystal Structure of Nlppya P41A, D44N, N48E Mutant


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 Nlppya P41A, D44N, N48E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:14.3
occ:1.00
O A:HOH520 3.2 20.8 1.0
N A:ALA115 3.3 15.0 1.0
CB A:ASN114 3.6 17.7 1.0
CB A:ALA115 3.8 14.0 1.0
CA A:ASN114 4.1 17.3 1.0
CA A:ALA115 4.1 17.8 1.0
C A:ASN114 4.2 14.7 1.0
CD1 A:TYR82 4.5 13.3 1.0
CG A:ASN114 4.6 23.6 1.0
OD1 A:ASN114 4.8 22.8 1.0
N A:ALA116 4.8 15.8 1.0
CB A:TYR82 4.9 16.7 1.0
C A:ALA115 5.0 21.9 1.0

Magnesium binding site 3 out of 3 in 6qbd

Go back to Magnesium Binding Sites List in 6qbd
Magnesium binding site 3 out of 3 in the Crystal Structure of Nlppya P41A, D44N, N48E Mutant


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 Nlppya P41A, D44N, N48E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:32.2
occ:1.00
O B:HOH505 2.1 22.6 1.0
OD1 B:ASP104 2.1 22.3 1.0
O B:HOH424 2.2 21.1 1.0
O B:HOH402 2.3 27.6 1.0
O B:HOH565 2.4 33.5 1.0
OE2 B:GLU106 2.5 32.6 0.9
CG B:ASP104 3.2 19.1 1.0
CD B:GLU106 3.6 29.3 0.9
OD2 B:ASP104 3.7 16.2 1.0
OD2 B:ASP93 3.8 24.9 1.0
O B:HOH483 4.0 16.4 1.0
O B:HOH446 4.0 29.1 1.0
O B:TRP105 4.1 17.1 1.0
CG B:GLU106 4.3 22.4 1.0
O B:HOH511 4.4 33.3 1.0
O B:HIS159 4.4 25.1 1.0
CB B:ASP104 4.4 13.9 1.0
OE1 B:GLU106 4.4 30.0 0.9
CE1 B:HIS101 4.5 20.9 0.9
N B:TRP105 4.5 12.9 1.0
NE2 B:HIS101 4.5 27.9 0.9
CA B:ASP104 4.6 13.9 1.0
CG B:ASP93 4.9 23.7 1.0
C B:TRP105 4.9 14.9 1.0

Reference:

T.Lenarcic, K.Pirc, V.Hodnik, I.Albert, J.Borisek, A.Magistrato, T.Nurnberger, M.Podobnik, G.Anderluh. Molecular Basis For Functional Diversity Among Microbial NEP1-Like Proteins. Plos Pathog. V. 15 07951 2019.
ISSN: ESSN 1553-7374
PubMed: 31479498
DOI: 10.1371/JOURNAL.PPAT.1007951
Page generated: Mon Dec 14 23:51:57 2020

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