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Calcium in PDB 5olw: 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation

Enzymatic activity of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation

All present enzymatic activity of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation:
5.4.2.6;

Protein crystallography data

The structure of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation, PDB code: 5olw was solved by M.W.Bowler, J.Von Velsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 2.28
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 61.005, 73.971, 120.440, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 26.2

Other elements in 5olw:

The structure of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation (pdb code 5olw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation, PDB code: 5olw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5olw

Go back to Calcium Binding Sites List in 5olw
Calcium binding site 1 out of 5 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:34.1
occ:1.00
 OD1 A:ASN127 2.2 36.7 1.0
OE2 B:GLU124 2.2 37.7 1.0
OE2 A:GLU124 2.2 48.9 1.0
O B:GLU124 2.3 37.2 1.0
OD1 B:ASN127 2.4 30.0 1.0
O A:GLU124 2.4 38.2 1.0
CD A:GLU124 3.2 54.2 1.0
CD B:GLU124 3.3 37.9 1.0
C A:GLU124 3.4 30.4 1.0
CG A:ASN127 3.4 37.1 1.0
C B:GLU124 3.4 37.2 1.0
CG B:ASN127 3.6 39.3 1.0
CG B:GLU124 3.9 38.1 1.0
CG A:GLU124 3.9 26.2 1.0
OE1 A:GLU124 4.1 50.9 1.0
N A:ASN127 4.2 33.4 1.0
ND2 A:ASN127 4.2 26.5 1.0
N B:ASN127 4.2 33.9 1.0
N A:ARG125 4.2 36.6 1.0
CA A:ASN127 4.2 32.9 1.0
OE1 B:GLU124 4.3 33.6 1.0
CA A:ARG125 4.3 29.9 1.0
CA A:GLU124 4.3 35.1 1.0
N B:ARG125 4.3 40.5 1.0
CA B:ASN127 4.3 29.9 1.0
CA B:GLU124 4.3 29.2 1.0
CA B:ARG125 4.3 39.0 1.0
O A:HOH453 4.3 32.3 1.0
C A:ARG125 4.3 29.0 1.0
C B:ARG125 4.4 34.9 1.0
O B:ARG125 4.4 35.8 1.0
CB A:ASN127 4.4 31.4 1.0
O B:HOH456 4.4 37.4 1.0
O A:ARG125 4.5 32.5 1.0
ND2 B:ASN127 4.5 30.2 1.0
CB B:ASN127 4.6 32.2 1.0
CB A:GLU124 4.7 26.1 1.0
CB B:GLU124 4.7 28.4 1.0
N A:MET126 5.0 36.0 1.0

Calcium binding site 2 out of 5 in 5olw

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Calcium binding site 2 out of 5 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:36.4
occ:1.00
 OD2 A:ASP8 2.1 39.1 1.0
O A:HOH465 2.2 37.5 1.0
O A:HOH436 2.3 31.8 1.0
OD1 A:ASP170 2.3 37.9 1.0
O A:ASP10 2.5 29.7 1.0
OE1 A:GLU169 2.8 38.1 1.0
OG A:SER171 3.0 50.4 1.0
CG A:ASP8 3.4 39.7 1.0
CG A:ASP170 3.4 32.5 1.0
CD A:GLU169 3.7 42.0 1.0
C A:ASP10 3.7 32.6 1.0
OE2 A:GLU169 3.8 46.3 1.0
OD2 A:ASP170 3.8 31.7 1.0
O A:HOH407 4.0 34.8 1.0
OD1 A:ASP8 4.2 39.9 1.0
CB A:SER171 4.2 39.4 1.0
CB A:ASP8 4.3 26.2 1.0
N A:ASP170 4.3 28.8 1.0
N A:SER171 4.4 30.2 1.0
CA A:ASP10 4.5 34.1 1.0
CB A:ASP10 4.5 24.0 1.0
CB A:ASP170 4.6 31.8 1.0
N A:GLY11 4.6 35.3 1.0
OD2 A:ASP10 4.7 48.8 1.0
O A:HOH404 4.7 31.3 1.0
CA A:GLY11 4.7 28.6 1.0
N A:ASP10 4.7 31.6 1.0
C A:ASP170 4.8 37.1 1.0
CA A:ASP170 4.8 32.5 1.0
CA A:SER171 4.9 34.7 1.0

Calcium binding site 3 out of 5 in 5olw

Go back to Calcium Binding Sites List in 5olw
Calcium binding site 3 out of 5 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:64.5
occ:1.00
 O A:HOH457 2.7 29.0 1.0
O A:PRO89 2.7 33.9 1.0
O A:HOH514 2.8 30.5 1.0
O A:HOH518 3.1 39.8 1.0
CG2 A:VAL92 3.4 26.4 1.0
C A:PRO89 3.5 33.1 1.0
CB A:VAL92 3.5 27.0 1.0
CB A:PRO89 3.7 32.6 1.0
CD2 A:LEU97 3.8 25.6 1.0
CA A:PRO89 3.8 27.0 1.0
O A:HOH448 3.9 38.9 1.0
CG1 A:VAL92 4.3 27.4 1.0
CB A:LEU97 4.5 21.2 1.0
O A:HOH522 4.5 51.5 1.0
N A:ALA90 4.6 29.9 1.0
CG A:LEU97 4.6 35.0 1.0
O A:MET126 4.7 33.2 1.0
CA A:VAL92 4.7 26.5 1.0
N A:VAL92 4.8 37.8 1.0
CA A:ALA90 5.0 36.6 1.0
CD1 A:LEU97 5.0 35.6 1.0

Calcium binding site 4 out of 5 in 5olw

Go back to Calcium Binding Sites List in 5olw
Calcium binding site 4 out of 5 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:94.8
occ:1.00
 O A:HOH503 2.4 64.9 1.0
O A:HOH447 2.6 30.3 1.0
O A:HOH516 2.6 59.5 1.0
O A:HOH510 2.8 61.4 1.0
O A:HOH417 2.9 47.0 1.0
O A:HOH523 3.3 56.9 1.0
O A:HOH520 4.1 40.7 1.0
O A:HOH521 4.2 49.8 1.0
O A:HOH495 4.4 40.6 1.0
O A:HOH469 4.4 44.0 1.0
O A:HOH429 4.4 25.7 1.0
OH A:TYR93 4.5 25.9 1.0
O A:HOH428 4.6 37.0 1.0
OD2 A:ASP170 4.9 31.7 1.0

Calcium binding site 5 out of 5 in 5olw

Go back to Calcium Binding Sites List in 5olw
Calcium binding site 5 out of 5 in the 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 5-Fluorotryptophan Labeled Beta-Phosphoglucomutase in An Open Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:51.2
occ:1.00
 OD2 B:ASP8 2.2 60.2 1.0
OD1 B:ASP170 2.3 48.0 1.0
O B:HOH405 2.3 41.4 1.0
O B:HOH415 2.4 41.1 1.0
O B:ASP10 2.6 44.3 1.0
OE1 B:GLU169 3.0 46.6 1.0
OG B:SER171 3.2 54.6 1.0
CG B:ASP8 3.4 48.6 1.0
CG B:ASP170 3.4 40.5 1.0
C B:ASP10 3.7 43.6 1.0
OD2 B:ASP170 3.9 39.8 1.0
CD B:GLU169 4.0 45.9 1.0
OD1 B:ASP8 4.1 51.0 1.0
OE2 B:GLU169 4.2 47.6 1.0
CB B:SER171 4.3 50.6 1.0
OD2 B:ASP10 4.4 68.9 1.0
CB B:ASP10 4.4 41.2 1.0
CB B:ASP8 4.4 33.6 1.0
N B:ASP170 4.5 38.6 1.0
N B:SER171 4.5 43.7 1.0
CA B:ASP10 4.5 39.4 1.0
CB B:ASP170 4.7 31.0 1.0
N B:ASP10 4.7 38.8 1.0
N B:GLY11 4.7 33.1 1.0
CG B:ASP10 4.8 51.8 1.0
CA B:GLY11 4.9 32.7 1.0
C B:ASP170 4.9 38.4 1.0
CA B:ASP170 4.9 37.5 1.0

Reference:

A.Ampaw, M.Carroll, J.Von Velsen, D.Bhattasali, A.Cohen, M.W.Bowler, D.L.Jakeman. Observing Enzyme Ternary Transition State Analogue Complexes BY19F uc(Nmr) Spectroscopy. Chem Sci V. 8 8427 2017.
ISSN: ISSN 2041-6520
PubMed: 29619190
DOI: 10.1039/C7SC04204C
Page generated: Mon Jul 15 09:51:07 2024

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