Magnesium in PDB 6ojr: Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda

Enzymatic activity of Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda

All present enzymatic activity of Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda:
1.13.11.43;

Protein crystallography data

The structure of Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda, PDB code: 6ojr was solved by E.Kuatsjah, M.M.Verstraete, M.J.Kobylarz, A.K.N.Liu, M.E.P.Murphy, L.D.Eltis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.27 / 2.30
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.364, 181.364, 94.983, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda (pdb code 6ojr). 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 Sphingomonas Paucimobilis TMY1009 Apo-Lsda, PDB code: 6ojr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6ojr

Go back to Magnesium Binding Sites List in 6ojr
Magnesium binding site 1 out of 3 in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda


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 Sphingomonas Paucimobilis TMY1009 Apo-Lsda within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:43.6
occ:1.00
OD2 A:ASP372 2.3 44.4 1.0
OG1 A:THR390 2.7 30.7 1.0
HE3 A:LYS375 2.8 53.7 1.0
HH22 A:ARG347 2.8 53.4 1.0
HB2 A:TRP405 2.9 35.8 1.0
HB2 A:ASP372 3.0 54.0 1.0
HB3 A:ASP372 3.1 54.0 1.0
CG A:ASP372 3.1 49.0 1.0
HG21 A:THR390 3.2 39.5 1.0
CB A:ASP372 3.3 45.0 1.0
HG1 A:THR390 3.3 36.8 1.0
HG3 A:LYS375 3.3 57.6 1.0
HE2 A:LYS375 3.4 53.7 1.0
NH2 A:ARG347 3.5 44.5 1.0
CE A:LYS375 3.5 44.7 1.0
HH21 A:ARG347 3.5 53.4 1.0
HG23 A:THR390 3.6 39.5 1.0
CG2 A:THR390 3.7 32.9 1.0
CB A:THR390 3.8 33.6 1.0
CB A:TRP405 3.8 29.9 1.0
HG2 A:LYS375 3.8 57.6 1.0
HD1 A:TRP405 3.9 41.4 1.0
CG A:LYS375 3.9 48.0 1.0
HA A:TRP405 4.1 38.3 1.0
CG A:TRP405 4.2 35.3 1.0
CD1 A:TRP405 4.2 34.5 1.0
HB A:THR390 4.2 40.3 1.0
CD A:LYS375 4.3 42.9 1.0
OD1 A:ASP372 4.3 49.4 1.0
HG A:SER403 4.4 39.9 1.0
CA A:TRP405 4.5 31.9 1.0
HB3 A:TRP405 4.5 35.8 1.0
HZ1 A:LYS375 4.5 74.5 1.0
HG22 A:THR390 4.6 39.5 1.0
NZ A:LYS375 4.6 62.1 1.0
HH12 A:ARG347 4.7 50.1 1.0
CZ A:ARG347 4.7 43.9 1.0
HD2 A:LYS375 4.7 51.5 1.0
OD1 A:ASN389 4.7 31.8 1.0
CA A:ASP372 4.8 45.4 1.0
N A:TRP405 4.8 31.2 1.0
HA A:THR390 4.9 39.4 1.0
OG A:SER403 4.9 33.2 1.0
CA A:THR390 5.0 32.8 1.0
HZ2 A:LYS375 5.0 74.5 1.0

Magnesium binding site 2 out of 3 in 6ojr

Go back to Magnesium Binding Sites List in 6ojr
Magnesium binding site 2 out of 3 in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda


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 Sphingomonas Paucimobilis TMY1009 Apo-Lsda within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:36.6
occ:1.00
H A:ILE354 2.3 30.2 1.0
OE2 A:GLU356 2.4 45.4 1.0
HD2 A:ARG353 2.5 31.8 1.0
O A:HOH750 2.6 34.0 1.0
HA A:ARG353 2.7 30.2 1.0
HH11 A:ARG353 2.7 39.3 1.0
HG12 A:ILE354 2.8 36.1 1.0
N A:ILE354 3.1 25.2 1.0
CD A:ARG353 3.4 26.5 1.0
HB3 A:ARG353 3.4 29.7 1.0
CD A:GLU356 3.4 46.3 1.0
CA A:ARG353 3.4 25.1 1.0
HG13 A:ILE354 3.5 36.1 1.0
HD3 A:ARG353 3.5 31.8 1.0
NH1 A:ARG353 3.5 32.8 1.0
O A:HOH870 3.6 38.2 1.0
CG1 A:ILE354 3.6 30.1 1.0
HG3 A:GLU356 3.6 52.7 1.0
C A:ARG353 3.7 28.9 1.0
O A:HOH741 3.7 29.7 1.0
O A:ILE354 3.8 29.7 1.0
CB A:ARG353 3.8 24.8 1.0
HH12 A:ARG353 4.0 39.3 1.0
CA A:ILE354 4.1 31.4 1.0
CG A:GLU356 4.1 43.9 1.0
O A:HOH858 4.2 38.6 1.0
CG A:ARG353 4.2 27.0 1.0
HG23 A:ILE354 4.3 34.6 1.0
C A:ILE354 4.3 30.9 1.0
NE A:ARG353 4.3 39.6 1.0
OE1 A:GLU356 4.3 61.6 1.0
CB A:ILE354 4.4 30.2 1.0
CZ A:ARG353 4.4 30.6 1.0
O A:PRO352 4.5 30.9 1.0
HD11 A:ILE354 4.6 38.6 1.0
N A:ARG353 4.6 27.4 1.0
HG2 A:GLU356 4.7 52.7 1.0
CD1 A:ILE354 4.7 32.2 1.0
O A:HOH846 4.7 44.0 1.0
HB2 A:ARG353 4.7 29.7 1.0
HG2 A:ARG353 4.8 32.4 1.0
O A:MET284 4.8 25.4 1.0
CG2 A:ILE354 4.9 28.8 1.0
HA A:ILE354 4.9 37.7 1.0
HG3 A:ARG353 4.9 32.4 1.0
O A:ARG353 4.9 24.0 1.0

Magnesium binding site 3 out of 3 in 6ojr

Go back to Magnesium Binding Sites List in 6ojr
Magnesium binding site 3 out of 3 in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda


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 Sphingomonas Paucimobilis TMY1009 Apo-Lsda within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:46.0
occ:1.00
HE22 A:GLN469 1.6 44.9 1.0
NE2 A:GLN469 2.4 37.5 1.0
HE21 A:GLN469 2.7 44.9 1.0
O A:ILE412 2.8 27.1 1.0
HG1 A:THR388 2.9 46.9 1.0
HB1 A:ALA411 3.0 41.0 1.0
OG1 A:THR388 3.1 39.1 1.0
O A:HOH735 3.2 45.0 1.0
HG2 A:GLN413 3.3 36.6 1.0
CD A:GLN469 3.5 37.7 1.0
C A:ILE412 3.5 27.9 1.0
HB3 A:ALA411 3.5 41.0 1.0
H A:ILE412 3.5 34.4 1.0
HA A:GLN413 3.6 35.8 1.0
CB A:ALA411 3.7 34.1 1.0
O A:HOH616 3.7 33.9 1.0
OE1 A:GLN469 3.8 40.2 1.0
N A:ILE412 3.8 28.7 1.0
CG A:GLN413 4.1 30.5 1.0
N A:GLN413 4.1 25.1 1.0
HG3 A:GLN413 4.1 36.6 1.0
H A:THR388 4.2 42.2 1.0
CA A:GLN413 4.3 29.8 1.0
CA A:ILE412 4.3 29.2 1.0
HB2 A:ALA411 4.3 41.0 1.0
C A:ALA411 4.4 28.4 1.0
O A:THR388 4.4 35.1 1.0
CB A:THR388 4.5 35.7 1.0
CA A:ALA411 4.7 31.9 1.0
HA A:ILE412 4.8 35.0 1.0
H A:GLN413 4.8 30.1 1.0
HD13 A:LEU369 4.8 31.2 1.0
CG A:GLN469 4.8 39.2 1.0
HB2 A:GLN469 4.8 35.1 1.0
CB A:GLN413 4.8 27.9 1.0
OD2 A:ASP436 4.9 27.7 1.0
HG2 A:GLN469 4.9 47.0 1.0
HB A:THR388 5.0 42.8 1.0
N A:THR388 5.0 35.1 1.0
HE1 A:HIS438 5.0 56.4 1.0
HA A:GLN469 5.0 33.1 1.0

Reference:

E.Kuatsjah, M.M.Verstraete, M.J.Kobylarz, A.K.N.Liu, M.E.P.Murphy, L.D.Eltis. Identification of Functionally Important Residues and Structural Features in A Bacterial Lignostilbene Dioxygenase. J.Biol.Chem. V. 294 12911 2019.
ISSN: ESSN 1083-351X
PubMed: 31292192
DOI: 10.1074/JBC.RA119.009428
Page generated: Mon Dec 14 23:43:34 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