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Magnesium in PDB 3etj: Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi

Enzymatic activity of Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi

All present enzymatic activity of Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi:
4.1.1.21;

Protein crystallography data

The structure of Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi, PDB code: 3etj was solved by H.M.Holden, J.B.Thoden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.800, 70.500, 88.700, 90.00, 124.30, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3etj:

The structure of Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi (pdb code 3etj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi, PDB code: 3etj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3etj

Go back to Magnesium Binding Sites List in 3etj
Magnesium binding site 1 out of 4 in the Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:15.6
occ:1.00
O A:HOH694 2.0 33.1 1.0
OE2 A:GLU226 2.1 33.6 1.0
O2 A:PI403 2.1 22.0 1.0
O2A A:ADP400 2.2 17.2 1.0
OE1 A:GLU238 2.3 20.2 1.0
O2B A:ADP400 2.3 26.8 1.0
CD A:GLU226 3.1 25.1 1.0
CD A:GLU238 3.3 26.3 1.0
P A:PI403 3.3 25.4 1.0
PB A:ADP400 3.4 21.2 1.0
OE1 A:GLU226 3.4 27.3 1.0
PA A:ADP400 3.5 19.5 1.0
O4 A:PI403 3.7 27.7 1.0
O3A A:ADP400 3.7 25.1 1.0
O1B A:ADP400 3.7 15.2 1.0
O A:HOH471 3.8 39.3 1.0
O1 A:PI403 3.8 19.5 1.0
MG A:MG402 3.8 18.1 1.0
O A:HOH463 3.8 20.0 1.0
CG A:GLU238 3.9 20.4 1.0
OE2 A:GLU238 4.2 18.2 1.0
C5' A:ADP400 4.2 21.4 1.0
O5' A:ADP400 4.3 18.1 1.0
ND2 A:ASN237 4.3 22.1 1.0
NE2 A:HIS244 4.4 14.6 1.0
CG A:GLU226 4.5 13.3 1.0
O A:HOH625 4.5 22.3 1.0
O3 A:PI403 4.5 27.4 1.0
O A:HOH605 4.6 29.1 1.0
O3' A:ADP400 4.6 16.9 1.0
O1A A:ADP400 4.6 31.7 1.0
O3B A:ADP400 4.8 23.9 1.0
O A:HOH635 4.8 17.9 1.0
NE2 A:HIS184 4.9 18.7 1.0
CB A:GLU226 5.0 14.3 1.0

Magnesium binding site 2 out of 4 in 3etj

Go back to Magnesium Binding Sites List in 3etj
Magnesium binding site 2 out of 4 in the Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:18.1
occ:1.00
O1B A:ADP400 1.9 15.2 1.0
O A:HOH635 2.0 17.9 1.0
O A:HOH695 2.0 19.9 1.0
O1 A:PI403 2.0 19.5 1.0
OE1 A:GLU238 2.3 20.2 1.0
OE2 A:GLU238 2.4 18.2 1.0
CD A:GLU238 2.6 26.3 1.0
PB A:ADP400 3.2 21.2 1.0
P A:PI403 3.3 25.4 1.0
O2B A:ADP400 3.5 26.8 1.0
O2 A:PI403 3.6 22.0 1.0
O A:HOH471 3.8 39.3 1.0
MG A:MG401 3.8 15.6 1.0
O4 A:PI403 3.9 27.7 1.0
O A:HOH554 4.0 27.9 1.0
NH2 A:ARG80 4.1 23.2 1.0
O3A A:ADP400 4.1 25.1 1.0
OE1 A:GLU51 4.1 31.6 1.0
O A:GLY125 4.1 28.5 1.0
CG A:GLU238 4.1 20.4 1.0
O3B A:ADP400 4.2 23.9 1.0
CA A:TYR126 4.3 35.6 1.0
OE2 A:GLU51 4.3 32.4 1.0
NH2 A:ARG242 4.5 19.2 1.0
O3 A:PI403 4.5 27.4 1.0
O2A A:ADP400 4.6 17.2 1.0
CD A:GLU51 4.6 44.7 1.0
CB A:TYR126 4.7 79.2 1.0
NH1 A:ARG80 4.7 22.8 1.0
CZ A:ARG80 4.8 26.6 1.0
OE2 A:GLU226 4.8 33.6 1.0
PA A:ADP400 4.8 19.5 1.0
O A:LEU239 4.9 17.4 1.0
C A:GLY125 4.9 99.9 1.0
CB A:GLU238 5.0 23.8 1.0
N A:TYR126 5.0 27.9 1.0

Magnesium binding site 3 out of 4 in 3etj

Go back to Magnesium Binding Sites List in 3etj
Magnesium binding site 3 out of 4 in the Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:17.8
occ:1.00
OE2 B:GLU226 2.0 23.8 1.0
O B:HOH659 2.1 27.6 1.0
O2A B:ADP400 2.1 21.7 1.0
OE2 B:GLU238 2.1 17.6 1.0
O2B B:ADP400 2.3 29.1 1.0
O2 B:PI403 2.3 38.0 1.0
CD B:GLU226 3.1 23.9 1.0
CD B:GLU238 3.2 19.5 1.0
PA B:ADP400 3.4 24.9 1.0
PB B:ADP400 3.4 30.7 1.0
OE1 B:GLU226 3.4 35.4 1.0
P B:PI403 3.5 99.9 1.0
O4 B:PI403 3.7 32.5 1.0
O B:HOH530 3.7 38.4 1.0
O3A B:ADP400 3.7 25.5 1.0
MG B:MG402 3.7 25.6 1.0
O1 B:PI403 3.8 28.6 1.0
CG B:GLU238 3.8 18.9 1.0
O1B B:ADP400 3.9 27.0 1.0
OE1 B:GLU238 4.2 20.8 1.0
ND2 B:ASN237 4.3 19.1 1.0
O B:HOH665 4.4 32.6 1.0
C5' B:ADP400 4.4 17.5 1.0
O5' B:ADP400 4.4 18.0 1.0
CG B:GLU226 4.4 17.8 1.0
O3' B:ADP400 4.4 21.1 1.0
O1A B:ADP400 4.5 24.5 1.0
NE2 B:HIS244 4.6 20.8 1.0
O3 B:PI403 4.7 35.1 1.0
O3B B:ADP400 4.7 47.4 1.0
NE2 B:HIS184 4.9 22.6 1.0
O B:HOH660 4.9 23.5 1.0
CB B:GLU226 5.0 17.3 1.0

Magnesium binding site 4 out of 4 in 3etj

Go back to Magnesium Binding Sites List in 3etj
Magnesium binding site 4 out of 4 in the Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure E. Coli Purk in Complex with Mg, Adp, and Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:25.6
occ:1.00
O B:HOH661 1.9 24.8 1.0
O1B B:ADP400 1.9 27.0 1.0
O1 B:PI403 2.1 28.6 1.0
O B:HOH660 2.2 23.5 1.0
OE2 B:GLU238 2.3 17.6 1.0
OE1 B:GLU238 2.4 20.8 1.0
CD B:GLU238 2.7 19.5 1.0
PB B:ADP400 3.1 30.7 1.0
P B:PI403 3.3 99.9 1.0
O2B B:ADP400 3.3 29.1 1.0
O2 B:PI403 3.4 38.0 1.0
MG B:MG401 3.7 17.8 1.0
O4 B:PI403 3.8 32.5 1.0
O3A B:ADP400 4.2 25.5 1.0
CG B:GLU238 4.2 18.9 1.0
O3B B:ADP400 4.3 47.4 1.0
O B:HOH482 4.3 30.6 1.0
NH2 B:ARG80 4.3 27.6 1.0
O3 B:PI403 4.4 35.1 1.0
O2A B:ADP400 4.5 21.7 1.0
OE2 B:GLU51 4.5 26.1 1.0
OE1 B:GLU51 4.7 37.0 1.0
NH2 B:ARG242 4.7 18.7 1.0
OE2 B:GLU226 4.7 23.8 1.0
NH1 B:ARG80 4.8 26.8 1.0
PA B:ADP400 4.9 24.9 1.0
O B:LEU239 5.0 17.8 1.0
CZ B:ARG80 5.0 31.6 1.0

Reference:

J.B.Thoden, H.M.Holden, S.M.Firestine. Structural Analysis of the Active Site Geometry of N(5)-Carboxyaminoimidazole Ribonucleotide Synthetase From Escherichia Coli. Biochemistry V. 47 13346 2008.
ISSN: ISSN 0006-2960
PubMed: 19053251
DOI: 10.1021/BI801734Z
Page generated: Mon Dec 14 08:07:04 2020

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