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Calcium in PDB 4xgw: Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant

Enzymatic activity of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant

All present enzymatic activity of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant:
2.7.1.180;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant, PDB code: 4xgw was solved by D.R.Tomchick, C.A.Brautigam, R.K.Deka, M.V.Norgard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.92 / 1.75
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.216, 70.650, 86.276, 75.72, 71.91, 69.72
R / Rfree (%) 17.2 / 19.9

Other elements in 4xgw:

The structure of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant (pdb code 4xgw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant, PDB code: 4xgw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4xgw

Go back to Calcium Binding Sites List in 4xgw
Calcium binding site 1 out of 4 in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant


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 Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:24.9
occ:1.00
 O A:ASP280 2.3 19.0 1.0
OD1 A:ASP280 2.4 17.6 1.0
O A:THR166 2.4 20.4 1.0
OG1 A:THR284 2.4 20.9 1.0
OD1 A:ASP283 2.4 25.5 1.0
O A:HOH743 2.4 24.3 1.0
C A:ASP280 3.3 16.9 1.0
CG A:ASP280 3.3 18.5 1.0
HB A:THR166 3.4 24.1 1.0
H A:THR284 3.4 21.9 1.0
HA A:ASP280 3.4 18.9 1.0
CG A:ASP283 3.4 24.3 1.0
C A:THR166 3.5 19.8 1.0
CB A:THR284 3.6 21.3 1.0
HB A:THR284 3.6 25.6 1.0
HA A:THR166 3.7 23.3 1.0
OD2 A:ASP283 3.7 24.2 1.0
CA A:ASP280 3.7 15.8 1.0
HB2 A:SER236 3.9 32.3 1.0
N A:THR284 3.9 18.2 1.0
CA A:THR166 4.0 19.4 1.0
CB A:ASP280 4.0 17.9 1.0
OD2 A:ASP280 4.1 16.5 1.0
CB A:THR166 4.1 20.1 1.0
HG A:SER236 4.2 43.7 1.0
O A:HOH602 4.2 39.5 1.0
CA A:THR284 4.3 19.0 1.0
HA A:VAL167 4.3 21.6 1.0
HA A:ALA281 4.3 21.8 1.0
N A:ALA281 4.4 18.2 1.0
HB3 A:ASP280 4.4 21.4 1.0
HA A:THR284 4.4 22.8 1.0
OG A:SER236 4.6 36.4 1.0
N A:VAL167 4.6 17.0 1.0
O A:HOH611 4.6 19.6 1.0
CB A:SER236 4.7 26.9 1.0
H A:ASP283 4.7 21.3 1.0
HG A:SER234 4.7 22.5 1.0
HG12 A:VAL167 4.7 26.8 1.0
HG21 A:THR284 4.7 27.3 1.0
CG2 A:THR284 4.7 22.7 1.0
CA A:ALA281 4.8 18.2 1.0
HG22 A:THR166 4.8 29.0 1.0
CB A:ASP283 4.8 19.6 1.0
C A:ASP283 4.8 20.6 1.0
HB2 A:ASP280 4.9 21.4 1.0
HG13 A:VAL167 4.9 26.8 1.0
OG A:SER234 4.9 18.8 1.0
CA A:VAL167 4.9 18.0 1.0

Calcium binding site 2 out of 4 in 4xgw

Go back to Calcium Binding Sites List in 4xgw
Calcium binding site 2 out of 4 in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant


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 Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:27.9
occ:1.00
 O B:ASP280 2.3 18.9 1.0
OD1 B:ASP280 2.3 19.0 1.0
OG1 B:THR284 2.4 22.3 1.0
O B:THR166 2.4 22.0 1.0
OD1 B:ASP283 2.5 32.4 1.0
O B:HOH669 2.7 40.3 1.0
CG B:ASP280 3.2 19.6 1.0
C B:ASP280 3.3 19.7 1.0
HA B:ASP280 3.4 24.2 1.0
H B:THR284 3.4 23.1 1.0
CG B:ASP283 3.5 27.5 1.0
HB B:THR166 3.5 32.1 1.0
CB B:THR284 3.6 22.8 1.0
C B:THR166 3.6 20.5 1.0
HB B:THR284 3.7 27.3 1.0
CA B:ASP280 3.7 20.1 1.0
OD2 B:ASP283 3.7 31.8 1.0
HA B:THR166 3.9 26.0 1.0
N B:THR284 3.9 19.2 1.0
CB B:ASP280 4.0 16.9 1.0
OD2 B:ASP280 4.1 21.6 1.0
CA B:THR166 4.2 21.6 1.0
CA B:THR284 4.2 21.0 1.0
HA B:VAL167 4.3 22.4 1.0
CB B:THR166 4.3 26.8 1.0
HB3 B:ASP280 4.3 20.3 1.0
O B:HOH668 4.3 30.7 1.0
HA B:ALA281 4.4 23.7 1.0
HA B:THR284 4.4 25.2 1.0
N B:ALA281 4.4 19.1 1.0
O B:HOH702 4.6 41.6 1.0
O B:HOH619 4.6 21.0 1.0
HG12 B:VAL167 4.6 28.7 1.0
HB2 B:SER236 4.6 53.3 1.0
HG B:SER234 4.7 35.5 1.0
N B:VAL167 4.7 17.9 1.0
CG2 B:THR284 4.7 23.7 1.0
HG21 B:THR284 4.7 28.4 1.0
OG B:SER234 4.8 29.6 1.0
HB2 B:ASP280 4.8 20.3 1.0
CA B:ALA281 4.8 19.8 1.0
H B:ASP283 4.9 21.9 1.0
C B:ASP283 4.9 21.6 1.0
CB B:ASP283 4.9 22.3 1.0
HG13 B:VAL167 4.9 28.7 1.0
HG23 B:THR284 4.9 28.4 1.0
CA B:VAL167 5.0 18.7 1.0

Calcium binding site 3 out of 4 in 4xgw

Go back to Calcium Binding Sites List in 4xgw
Calcium binding site 3 out of 4 in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:26.3
occ:1.00
 O C:ASP280 2.3 19.3 1.0
OD1 C:ASP280 2.3 19.9 1.0
OG1 C:THR284 2.4 23.5 1.0
O C:THR166 2.4 20.7 1.0
O C:HOH730 2.5 23.1 1.0
OD1 C:ASP283 2.5 34.6 1.0
O C:HOH683 2.9 30.1 1.0
CG C:ASP280 3.2 19.5 1.0
C C:ASP280 3.3 21.9 1.0
HA C:ASP280 3.4 23.8 1.0
HB C:THR166 3.5 29.6 1.0
H C:THR284 3.5 22.6 1.0
CG C:ASP283 3.5 27.7 1.0
C C:THR166 3.5 20.4 1.0
CB C:THR284 3.6 23.3 1.0
HB C:THR284 3.7 27.9 1.0
CA C:ASP280 3.7 19.8 1.0
OD2 C:ASP283 3.8 25.4 1.0
HA C:THR166 3.8 24.8 1.0
CB C:ASP280 4.0 17.9 1.0
N C:THR284 4.0 18.9 1.0
OD2 C:ASP280 4.0 19.1 1.0
CA C:THR166 4.1 20.6 1.0
CB C:THR166 4.2 24.6 1.0
CA C:THR284 4.3 19.9 1.0
HA C:VAL167 4.3 22.0 1.0
O C:HOH689 4.3 30.8 1.0
HB3 C:ASP280 4.3 21.5 1.0
HA C:THR284 4.4 23.9 1.0
HA C:ALA281 4.4 24.9 1.0
N C:ALA281 4.4 21.4 1.0
HB2 C:SER236 4.5 31.5 1.0
O C:HOH611 4.6 23.5 1.0
HG C:SER234 4.6 33.2 1.0
N C:VAL167 4.7 18.1 1.0
O C:HOH663 4.7 35.1 1.0
HG21 C:THR284 4.7 34.3 1.0
CG2 C:THR284 4.7 28.6 1.0
HB2 C:ASP280 4.8 21.5 1.0
HG12 C:VAL167 4.8 27.8 1.0
OG C:SER234 4.8 27.7 1.0
H C:ASP283 4.9 24.0 1.0
CA C:ALA281 4.9 20.8 1.0
C C:ASP283 4.9 21.6 1.0
HG22 C:THR166 4.9 34.7 1.0
CB C:ASP283 4.9 22.9 1.0
CA C:VAL167 5.0 18.4 1.0
HG23 C:THR284 5.0 34.3 1.0

Calcium binding site 4 out of 4 in 4xgw

Go back to Calcium Binding Sites List in 4xgw
Calcium binding site 4 out of 4 in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, E169K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:21.6
occ:1.00
 O D:ASP280 2.2 18.1 1.0
OD1 D:ASP280 2.3 17.7 1.0
O D:HOH759 2.4 23.3 1.0
O D:THR166 2.4 19.7 1.0
OG1 D:THR284 2.4 22.9 1.0
OD1 D:ASP283 2.4 26.0 1.0
C D:ASP280 3.3 16.1 1.0
CG D:ASP280 3.3 17.6 1.0
HB D:THR166 3.3 21.1 1.0
CG D:ASP283 3.4 24.5 1.0
H D:THR284 3.4 20.7 1.0
O D:HOH712 3.4 42.6 1.0
HA D:ASP280 3.4 19.7 1.0
C D:THR166 3.5 18.6 1.0
CB D:THR284 3.5 22.3 1.0
HB D:THR284 3.5 26.8 1.0
OD2 D:ASP283 3.7 22.0 1.0
HB2 D:SER236 3.7 28.4 1.0
HA D:THR166 3.7 20.3 1.0
CA D:ASP280 3.8 16.4 1.0
N D:THR284 3.9 17.3 1.0
CA D:THR166 4.0 16.9 1.0
CB D:ASP280 4.1 16.6 1.0
CB D:THR166 4.1 17.6 1.0
OD2 D:ASP280 4.1 18.2 1.0
CA D:THR284 4.2 19.1 1.0
O D:HOH603 4.3 31.6 1.0
HA D:VAL167 4.3 16.4 1.0
HA D:ALA281 4.3 19.6 1.0
N D:ALA281 4.4 16.2 1.0
HB3 D:ASP280 4.4 20.0 1.0
HA D:THR284 4.4 22.9 1.0
HG D:SER236 4.5 39.8 1.0
CB D:SER236 4.6 23.7 1.0
N D:VAL167 4.6 13.5 1.0
HG D:SER234 4.7 20.9 1.0
H D:ASP283 4.7 16.9 1.0
HG21 D:THR284 4.7 28.0 1.0
CG2 D:THR284 4.7 23.4 1.0
HG22 D:THR166 4.7 26.9 1.0
HG12 D:VAL167 4.8 20.0 1.0
CA D:ALA281 4.8 16.3 1.0
CB D:ASP283 4.8 18.8 1.0
OG D:SER236 4.8 33.1 1.0
C D:ASP283 4.8 16.6 1.0
O D:HOH614 4.8 18.9 1.0
HG13 D:VAL167 4.8 20.0 1.0
HB2 D:ASP280 4.9 20.0 1.0
OG D:SER234 4.9 17.4 1.0
HB3 D:SER236 5.0 28.4 1.0
CA D:VAL167 5.0 13.7 1.0
O D:ALA281 5.0 15.5 1.0
CG2 D:THR166 5.0 22.4 1.0

Reference:

R.K.Deka, C.A.Brautigam, W.Z.Liu, D.R.Tomchick, M.V.Norgard. Molecular Insights Into the Enzymatic Diversity of Flavin-Trafficking Protein (Ftp; Formerly Apbe) in Flavoprotein Biogenesis in the Bacterial Periplasm. Microbiologyopen V. 5 21 2016.
ISSN: ESSN 2045-8827
PubMed: 26626129
DOI: 10.1002/MBO3.306
Page generated: Sun Jul 14 14:34:22 2024

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