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Magnesium in PDB 6qla: Crystal Structure of the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library

Enzymatic activity of Crystal Structure of the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library

All present enzymatic activity of Crystal Structure of the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library:
3.1.1.3;

Protein crystallography data

The structure of Crystal Structure of the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library, PDB code: 6qla was solved by K.M.Boyko, D.Garsia, A.Y.Nikolaeva, D.A.Korzhenevskiy, M.V.Kryukova, L.E.Petrovskaya, K.A.Novototskaya-Vlasova, E.M.Rivkina, D.A.Dolgikh, M.P.Kirpichnikov, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.46 / 1.43
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.140, 92.180, 74.460, 90.00, 106.41, 90.00
R / Rfree (%) 15.6 / 18.4

Other elements in 6qla:

The structure of Crystal Structure of the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library (pdb code 6qla). 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 the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library, PDB code: 6qla:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6qla

Go back to Magnesium Binding Sites List in 6qla
Magnesium binding site 1 out of 3 in the Crystal Structure of the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library


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 the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:27.7
occ:0.80
 O A:HOH532 2.0 22.4 0.5
O B:HOH613 2.1 23.5 1.0
O B:HOH743 2.1 32.1 1.0
O A:HOH529 2.1 24.4 1.0
O A:HOH705 2.1 26.1 0.5
OE1 A:GLU293 3.5 20.6 1.0
NH1 A:ARG327 3.9 15.6 1.0
O A:HOH734 4.0 35.4 1.0
O A:HOH669 4.1 16.1 0.5
O B:HOH565 4.1 20.1 1.0
CD A:GLU293 4.1 21.3 1.0
NH2 A:ARG327 4.2 15.9 1.0
OE2 A:GLU293 4.4 29.8 1.0
O B:SER292 4.5 11.1 1.0
CZ A:ARG327 4.6 14.9 1.0
OD1 B:ASP291 4.6 15.4 1.0
N B:SER292 4.8 9.6 1.0
CA B:ASP291 4.8 11.5 1.0
O B:HOH727 4.8 26.3 1.0
O B:VAL290 5.0 13.0 1.0

Magnesium binding site 2 out of 3 in 6qla

Go back to Magnesium Binding Sites List in 6qla
Magnesium binding site 2 out of 3 in the Crystal Structure of the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library


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 the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:24.0
occ:0.80
 O B:HOH580 2.0 16.9 0.5
O A:HOH558 2.1 23.8 1.0
O B:HOH531 2.1 21.6 1.0
OE1 B:GLU293 3.4 24.4 1.0
O B:HOH634 3.9 18.8 0.5
O A:HOH718 4.0 44.5 1.0
NH1 B:ARG327 4.0 17.7 1.0
CD B:GLU293 4.1 21.2 1.0
O A:HOH517 4.1 18.4 1.0
NH2 B:ARG327 4.2 18.3 1.0
OE2 B:GLU293 4.4 27.9 1.0
O A:SER292 4.5 11.2 1.0
CZ B:ARG327 4.6 17.2 1.0
OD1 A:ASP291 4.6 14.9 1.0
O B:HOH727 4.7 26.3 1.0
N A:SER292 4.8 10.3 1.0
CA A:ASP291 4.8 11.4 1.0
CG B:GLU293 5.0 13.9 1.0

Magnesium binding site 3 out of 3 in 6qla

Go back to Magnesium Binding Sites List in 6qla
Magnesium binding site 3 out of 3 in the Crystal Structure of the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library


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 the PMGL2 Esterase (Point Mutant 1) From Permafrost Metagenomic Library within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:40.3
occ:1.00
 O B:HOH664 2.1 37.8 1.0
O B:HOH689 2.1 46.4 1.0
O B:HOH539 2.1 37.3 1.0
ND2 B:ASN79 2.1 22.9 1.0
O B:HOH547 2.8 36.8 1.0
CG B:ASN79 3.3 21.4 1.0
OE2 B:GLU161 3.5 45.0 1.0
OD1 B:ASN79 3.6 22.4 1.0
O B:HOH668 4.2 31.6 1.0
O B:HOH685 4.2 40.0 1.0
CB B:ASN79 4.5 18.6 1.0
CD B:GLU161 4.7 38.4 1.0
CA B:ASN79 4.8 17.1 1.0

Reference:

K.M.Boyko, M.V.Kryukova, A.Y.Nikolaeva, D.A.Korzhenevskiy, L.E.Petrovskaya, K.A.Novototskaya-Vlasova, E.M.Rivkina, D.A.Dolgikh, M.P.Kirpichnikov, V.O.Popov. Crystal Structure of the PMGL2 Esterase with Gcsag Motif Around the Catalytic Serine To Be Published.
Page generated: Tue Oct 1 15:31:31 2024

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