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Calcium in PDB 4gi8: Crystal Structure of the Mutb F164L Mutant From Crystals Soaked with the Substrate Sucrose

Enzymatic activity of Crystal Structure of the Mutb F164L Mutant From Crystals Soaked with the Substrate Sucrose

All present enzymatic activity of Crystal Structure of the Mutb F164L Mutant From Crystals Soaked with the Substrate Sucrose:
5.4.11.99;

Protein crystallography data

The structure of Crystal Structure of the Mutb F164L Mutant From Crystals Soaked with the Substrate Sucrose, PDB code: 4gi8 was solved by A.Lipski, R.Haser, N.Aghajari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.92 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.140, 86.110, 118.100, 90.00, 97.89, 90.00
R / Rfree (%) 15.7 / 19.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Mutb F164L Mutant From Crystals Soaked with the Substrate Sucrose (pdb code 4gi8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Mutb F164L Mutant From Crystals Soaked with the Substrate Sucrose, PDB code: 4gi8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4gi8

Go back to Calcium Binding Sites List in 4gi8
Calcium binding site 1 out of 2 in the Crystal Structure of the Mutb F164L Mutant From Crystals Soaked with the Substrate Sucrose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Mutb F164L Mutant From Crystals Soaked with the Substrate Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:13.5
occ:1.00
O A:HOH4185 2.3 27.3 1.0
OD1 A:ASP22 2.3 16.4 1.0
OD2 A:ASP30 2.4 15.1 1.0
O A:ILE28 2.4 13.2 1.0
OD1 A:ASN24 2.4 19.2 1.0
OD1 A:ASP26 2.5 18.6 1.0
O A:HOH4477 2.6 39.4 1.0
CG A:ASP26 3.3 19.3 1.0
CG A:ASP22 3.3 15.8 1.0
CG A:ASP30 3.4 14.2 1.0
CG A:ASN24 3.5 20.3 1.0
OD2 A:ASP26 3.5 21.2 1.0
C A:ILE28 3.6 13.6 1.0
CB A:ASP30 3.9 13.1 1.0
OD2 A:ASP22 4.1 16.6 1.0
ND2 A:ASN24 4.2 20.5 1.0
N A:ASN24 4.2 18.2 1.0
N A:THR23 4.2 17.4 1.0
CB A:ASP22 4.2 14.7 1.0
CA A:ASP22 4.2 14.7 1.0
N A:ILE28 4.3 14.1 1.0
CA A:ILE28 4.3 14.3 1.0
C A:GLY29 4.4 11.6 1.0
O A:GLU75 4.4 15.5 1.0
O A:GLY29 4.5 11.5 1.0
OD1 A:ASP30 4.5 14.7 1.0
CB A:ASN24 4.5 19.0 1.0
CB A:ASP26 4.6 18.3 1.0
N A:GLY29 4.6 11.9 1.0
CB A:ILE28 4.6 14.2 1.0
N A:ASP26 4.6 17.7 1.0
N A:ASP30 4.6 11.7 1.0
CA A:GLY29 4.7 11.1 1.0
C A:ASP22 4.7 16.1 1.0
CA A:ASN24 4.7 18.9 1.0
CA A:ASP30 4.9 12.2 1.0
CA A:ASP26 5.0 16.8 1.0
C A:ASN24 5.0 18.0 1.0

Calcium binding site 2 out of 2 in 4gi8

Go back to Calcium Binding Sites List in 4gi8
Calcium binding site 2 out of 2 in the Crystal Structure of the Mutb F164L Mutant From Crystals Soaked with the Substrate Sucrose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Mutb F164L Mutant From Crystals Soaked with the Substrate Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:14.9
occ:1.00
OD1 B:ASP22 2.3 15.8 1.0
O B:HOH876 2.3 21.7 1.0
O B:ILE28 2.4 14.0 1.0
OD2 B:ASP30 2.4 15.0 1.0
OD1 B:ASN24 2.4 17.9 1.0
OD1 B:ASP26 2.4 19.1 1.0
O B:HOH910 2.4 26.2 1.0
CG B:ASP26 3.2 21.2 1.0
CG B:ASP22 3.3 15.1 1.0
CG B:ASN24 3.4 19.9 1.0
OD2 B:ASP26 3.5 22.4 1.0
CG B:ASP30 3.5 14.2 1.0
C B:ILE28 3.6 13.4 1.0
CB B:ASP30 3.9 13.4 1.0
OD2 B:ASP22 4.1 15.9 1.0
ND2 B:ASN24 4.1 20.5 1.0
CB B:ASP22 4.2 14.9 1.0
N B:ASN24 4.2 18.8 1.0
N B:THR23 4.2 16.1 1.0
N B:ILE28 4.2 14.3 1.0
CA B:ASP22 4.3 14.4 1.0
CA B:ILE28 4.3 14.1 1.0
C B:GLY29 4.4 11.7 1.0
O B:GLU75 4.4 17.3 1.0
O B:GLY29 4.4 12.1 1.0
CB B:ASP26 4.5 20.4 1.0
N B:GLY29 4.6 12.7 1.0
N B:ASP26 4.6 20.0 1.0
OD1 B:ASP30 4.6 14.4 1.0
CB B:ASN24 4.6 18.7 1.0
CB B:ILE28 4.6 15.0 1.0
N B:ASP30 4.7 12.1 1.0
CA B:GLY29 4.7 11.6 1.0
C B:ASP22 4.8 15.7 1.0
CA B:ASN24 4.8 18.7 1.0
CA B:ASP30 4.9 13.3 1.0
CA B:ASP26 4.9 18.6 1.0

Reference:

A.Lipski, H.Watzlawick, S.Ravaud, X.Robert, M.Rhimi, R.Haser, R.Mattes, N.Aghajari. Mutations Inducing An Active-Site Aperture in Rhizobium Sp. Sucrose Isomerase Confer Hydrolytic Activity Acta Crystallogr.,Sect.D V. 69 298 2013.
ISSN: ISSN 0907-4449
PubMed: 23385465
DOI: 10.1107/S0907444912045532
Page generated: Sat Dec 12 04:48:08 2020

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