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Magnesium in PDB 5bsm: Crystal Structure of 4-Coumarate:Coa Ligase Complexed with Magnesium and Adenosine Triphosphate

Enzymatic activity of Crystal Structure of 4-Coumarate:Coa Ligase Complexed with Magnesium and Adenosine Triphosphate

All present enzymatic activity of Crystal Structure of 4-Coumarate:Coa Ligase Complexed with Magnesium and Adenosine Triphosphate:
6.2.1.12;

Protein crystallography data

The structure of Crystal Structure of 4-Coumarate:Coa Ligase Complexed with Magnesium and Adenosine Triphosphate, PDB code: 5bsm was solved by Z.Li, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.357, 96.311, 122.573, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 4-Coumarate:Coa Ligase Complexed with Magnesium and Adenosine Triphosphate (pdb code 5bsm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of 4-Coumarate:Coa Ligase Complexed with Magnesium and Adenosine Triphosphate, PDB code: 5bsm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5bsm

Go back to Magnesium Binding Sites List in 5bsm
Magnesium binding site 1 out of 2 in the Crystal Structure of 4-Coumarate:Coa Ligase Complexed with Magnesium and Adenosine Triphosphate


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 4-Coumarate:Coa Ligase Complexed with Magnesium and Adenosine Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:22.8
occ:1.00
O A:HOH770 2.0 26.3 1.0
O2G A:ATP600 2.0 19.3 1.0
O2B A:ATP600 2.1 20.1 1.0
O A:HOH728 2.1 16.3 1.0
O A:HOH817 2.2 21.8 1.0
O A:HOH864 2.4 23.7 1.0
PB A:ATP600 3.2 18.9 1.0
PG A:ATP600 3.2 20.4 1.0
O3A A:ATP600 3.5 20.6 1.0
O3B A:ATP600 3.6 20.8 1.0
O3G A:ATP600 3.8 20.0 1.0
NH2 A:ARG435 4.1 20.2 1.0
NZ A:LYS197 4.2 32.2 1.0
O1A A:ATP600 4.3 20.1 1.0
OE1 A:GLU337 4.4 22.1 1.0
OE2 A:GLU337 4.4 21.5 1.0
O3' A:ATP600 4.4 19.0 1.0
PA A:ATP600 4.4 21.4 1.0
O1G A:ATP600 4.5 20.5 1.0
CE A:MET335 4.5 21.2 1.0
O A:HOH712 4.5 21.5 1.0
O5' A:ATP600 4.6 21.2 1.0
O1B A:ATP600 4.6 20.5 1.0
C5' A:ATP600 4.7 20.4 1.0
C4' A:ATP600 4.7 21.0 1.0
CB A:SER189 4.7 20.8 1.0
CD A:GLU337 4.8 21.7 1.0
CE A:LYS197 4.8 30.3 1.0
CG A:MET335 5.0 20.3 1.0

Magnesium binding site 2 out of 2 in 5bsm

Go back to Magnesium Binding Sites List in 5bsm
Magnesium binding site 2 out of 2 in the Crystal Structure of 4-Coumarate:Coa Ligase Complexed with Magnesium and Adenosine Triphosphate


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 4-Coumarate:Coa Ligase Complexed with Magnesium and Adenosine Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:29.5
occ:1.00
O2G B:ATP600 2.0 28.7 1.0
O B:HOH815 2.1 20.3 1.0
O B:HOH719 2.1 31.3 1.0
O B:HOH726 2.1 25.1 1.0
O2B B:ATP600 2.2 29.2 1.0
O B:HOH736 2.3 25.8 1.0
PG B:ATP600 3.2 30.2 1.0
PB B:ATP600 3.5 25.9 1.0
O1G B:ATP600 3.6 32.0 1.0
O3B B:ATP600 3.8 27.0 1.0
O3A B:ATP600 4.0 28.1 1.0
NH2 B:ARG435 4.0 22.0 1.0
O3G B:ATP600 4.5 31.6 1.0
NZ B:LYS197 4.5 46.6 1.0
OE2 B:GLU337 4.5 26.2 1.0
CE B:MET335 4.6 23.4 1.0
OE1 B:GLU337 4.6 23.2 1.0
O3' B:ATP600 4.6 19.5 1.0
O2A B:ATP600 4.8 22.9 1.0
O1B B:ATP600 4.8 29.3 1.0
C5' B:ATP600 4.8 23.8 1.0
PA B:ATP600 4.9 25.3 1.0
O5' B:ATP600 4.9 25.0 1.0
CB B:SER189 4.9 28.3 1.0
C4' B:ATP600 4.9 23.0 1.0
CG B:MET335 5.0 22.2 1.0
CD B:GLU337 5.0 23.4 1.0

Reference:

Z.Li, S.K.Nair. Structural Basis For Specificity and Flexibility in A Plant 4-Coumarate:Coa Ligase. Structure V. 23 2032 2015.
ISSN: ISSN 0969-2126
PubMed: 26412334
DOI: 10.1016/J.STR.2015.08.012
Page generated: Sun Sep 29 01:17:39 2024

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