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Magnesium in PDB 1mj5: Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution

Enzymatic activity of Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution

All present enzymatic activity of Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution:
3.8.1.5;

Protein crystallography data

The structure of Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution, PDB code: 1mj5 was solved by A.J.Oakley, J.Damborsky, M.C.Wilce, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.76 / 0.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.390, 68.380, 80.720, 90.00, 90.00, 90.00
R / Rfree (%) 11.2 / 14.1

Other elements in 1mj5:

The structure of Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution (pdb code 1mj5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution, PDB code: 1mj5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1mj5

Go back to Magnesium Binding Sites List in 1mj5
Magnesium binding site 1 out of 3 in the Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2001

b:6.0
occ:1.00
 O A:HOH3013 2.0 7.5 1.0
O A:HOH3032 2.1 7.0 1.0
O A:HOH3461 4.1 23.0 0.5
OE1 A:GLU161 4.2 14.3 1.0
OE2 A:GLU161 4.2 11.7 1.0
CD A:GLU161 4.7 8.9 1.0

Magnesium binding site 2 out of 3 in 1mj5

Go back to Magnesium Binding Sites List in 1mj5
Magnesium binding site 2 out of 3 in the Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:8.4
occ:1.00
 O A:HOH3039 2.1 10.1 1.0
O A:HOH3143 2.1 8.5 1.0
O A:HOH3114 2.1 8.6 1.0
HE A:ARG20 3.3 7.2 0.3
HG3 A:ARG20 3.6 2.8 0.3
HB2 A:ARG20 3.9 11.4 0.7
NE A:ARG20 4.1 6.0 0.3
OD2 A:ASP70 4.1 6.0 1.0
HH22 A:ARG20 4.1 10.4 0.3
O A:HOH3027 4.2 6.9 1.0
HD3 A:ARG20 4.2 14.2 0.7
O A:HOH3015 4.2 6.6 1.0
OE1 A:GLU15 4.2 14.1 1.0
OE2 A:GLU15 4.3 10.6 1.0
O A:HOH3479 4.3 26.7 0.5
H A:ARG20 4.3 6.1 0.7
O A:GLY18 4.4 6.2 1.0
CG A:ARG20 4.4 2.4 0.3
HG2 A:ARG20 4.5 2.8 0.3
HA A:ARG19 4.7 6.1 1.0
CD A:GLU15 4.7 9.3 1.0
NH2 A:ARG20 4.8 8.6 0.3
H A:ARG20 4.8 6.3 0.3
CD A:ARG20 4.8 3.0 0.3
CZ A:ARG20 4.8 7.6 0.3
CB A:ARG20 4.9 9.5 0.7
N A:ARG20 4.9 5.0 0.7

Magnesium binding site 3 out of 3 in 1mj5

Go back to Magnesium Binding Sites List in 1mj5
Magnesium binding site 3 out of 3 in the Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Linb (Haloalkane Dehalogenase) From Sphingomonas Paucimobilis UT26 at Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2003

b:9.7
occ:1.00
 O A:HOH3083 2.0 11.4 1.0
O A:HOH3219 4.1 20.7 1.0
OE1 A:GLU10 4.1 25.8 0.6
OE2 A:GLU10 4.2 21.2 0.6
OE2 A:GLU10 4.6 30.9 0.4
CD A:GLU10 4.6 16.6 0.6
OE1 A:GLU10 4.7 31.9 0.4

Reference:

A.J.Oakley, M.Klvana, M.Otyepka, Y.Nagata, M.C.Wilce, J.Damborsky. Crystal Structure of Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis UT26 at 0.95 A Resolution: Dynamics of Catalytic Residues. Biochemistry V. 43 870 2004.
ISSN: ISSN 0006-2960
PubMed: 14744129
DOI: 10.1021/BI034748G
Page generated: Sun Aug 10 01:05:38 2025

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