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Magnesium in PDB 2shk: The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp

Enzymatic activity of The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp

All present enzymatic activity of The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp:
2.7.1.71;

Protein crystallography data

The structure of The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp, PDB code: 2shk was solved by T.Krell, J.R.Coggins, A.J.Lapthorn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.500, 108.500, 92.800, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 26.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp (pdb code 2shk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp, PDB code: 2shk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2shk

Go back to Magnesium Binding Sites List in 2shk
Magnesium binding site 1 out of 4 in the The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:38.9
occ:1.00
 O A:HOH904 2.3 20.5 1.0
O A:ALA147 2.3 33.0 1.0
O A:GLN144 2.3 36.7 1.0
O A:HOH946 2.4 49.8 1.0
C A:ALA147 3.3 34.0 1.0
C A:GLN144 3.5 39.0 1.0
O A:HOH959 4.0 48.2 1.0
CA A:ALA147 4.1 33.7 1.0
N A:ALA147 4.1 34.3 1.0
NH1 A:ARG92 4.2 36.6 1.0
CB A:ALA147 4.2 34.5 1.0
O A:ASP145 4.3 35.0 1.0
C A:ASP145 4.4 37.4 1.0
N A:HIS148 4.4 32.5 1.0
CA A:GLN144 4.4 39.0 1.0
N A:ASP145 4.5 36.8 1.0
CA A:ASP145 4.6 39.8 1.0
CA A:HIS148 4.8 31.6 1.0
C A:VAL146 4.8 35.1 1.0
OE1 A:GLN144 4.9 42.1 1.0
N A:VAL146 5.0 35.0 1.0

Magnesium binding site 2 out of 4 in 2shk

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Magnesium binding site 2 out of 4 in the The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:38.9
occ:1.00
 O A:ARG92 2.4 33.7 1.0
O A:GLY95 2.5 34.6 1.0
O A:ALA93 2.6 44.9 1.0
C A:GLY95 3.4 34.8 1.0
C A:ALA93 3.5 43.0 1.0
C A:ARG92 3.5 35.5 1.0
N A:GLY95 3.6 36.6 1.0
CA A:GLY95 3.8 36.0 1.0
C A:HIS94 4.0 37.7 1.0
CA A:ALA93 4.1 41.2 1.0
N A:ALA93 4.3 37.1 1.0
N A:HIS94 4.4 42.6 1.0
O A:HIS94 4.5 34.6 1.0
N A:THR96 4.5 33.3 1.0
O A:MET91 4.6 37.4 1.0
CA A:ARG92 4.6 36.6 1.0
CE1 A:HIS148 4.6 37.7 1.0
CA A:HIS94 4.6 39.8 1.0
OG1 A:THR96 5.0 26.5 1.0

Magnesium binding site 3 out of 4 in 2shk

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Magnesium binding site 3 out of 4 in the The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:34.5
occ:1.00
 O B:HOH967 2.2 42.9 1.0
O B:ALA147 2.4 30.1 1.0
O B:GLN144 2.4 36.1 1.0
O B:HOH924 2.5 32.3 1.0
C B:ALA147 3.5 31.3 1.0
C B:GLN144 3.6 35.4 1.0
O B:HOH959 3.8 46.7 1.0
CA B:ALA147 4.2 31.4 1.0
CB B:ALA147 4.3 31.0 1.0
N B:ALA147 4.3 29.6 1.0
CA B:GLN144 4.4 35.3 1.0
NH1 B:ARG92 4.5 31.0 1.0
O B:ASP145 4.5 29.0 1.0
C B:ASP145 4.5 31.1 1.0
N B:HIS148 4.6 30.4 1.0
OE1 B:GLN144 4.6 41.0 1.0
N B:ASP145 4.6 34.5 1.0
CA B:ASP145 4.7 33.6 1.0
CA B:HIS148 4.8 30.4 1.0
CB B:GLN144 4.9 34.7 1.0
O B:HIS148 5.0 30.0 1.0

Magnesium binding site 4 out of 4 in 2shk

Go back to Magnesium Binding Sites List in 2shk
Magnesium binding site 4 out of 4 in the The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Three-Dimensional Structure of Shikimate Kinase From Erwinia Chrysanthemi Complexed with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg904

b:73.5
occ:1.00
 O2B B:ADP905 2.4 0.9 1.0
OG1 B:THR16 2.6 48.9 1.0
O B:HOH958 2.9 67.0 1.0
OD2 B:ASP32 3.2 55.2 1.0
PB B:ADP905 3.8 0.3 1.0
O3B B:ADP905 3.9 0.7 1.0
CB B:THR16 3.9 49.0 1.0
O1A B:ADP905 3.9 0.3 1.0
CG B:ASP32 4.3 53.5 1.0
N B:THR16 4.3 47.9 1.0
O B:HOH911 4.3 34.9 1.0
OD2 B:ASP34 4.6 58.3 1.0
OD1 B:ASP32 4.6 55.6 1.0
O3A B:ADP905 4.7 0.3 1.0
CA B:THR16 4.7 49.9 1.0
CB B:LYS15 4.8 47.1 1.0
O1B B:ADP905 4.8 0.0 1.0
PA B:ADP905 4.9 0.2 1.0
CG2 B:THR16 4.9 49.1 1.0
O B:THR77 5.0 42.0 1.0

Reference:

T.Krell, J.E.Coyle, M.J.Horsburgh, J.R.Coggins, A.J.Lapthorn. Crystallization and Preliminary X-Ray Crystallographic Analysis of Shikimate Kinase From Erwinia Chrysanthemi. Acta Crystallogr.,Sect.D V. 53 612 1997.
ISSN: ISSN 0907-4449
PubMed: 15299895
DOI: 10.1107/S0907444997004319
Page generated: Wed Aug 14 03:24:39 2024

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