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

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

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

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase, PDB code: 4xgv 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) 31.51 / 1.88
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.197, 70.645, 85.961, 75.70, 72.45, 69.28
R / Rfree (%) 16.3 / 20.1

Other elements in 4xgv:

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

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Escherichia Coli Flavin Trafficking Protein, An Fmn Transferase (pdb code 4xgv). 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, PDB code: 4xgv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4xgv

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:20.8
occ:1.00
 O A:ASP280 2.3 18.6 1.0
O A:HOH721 2.3 26.7 1.0
OD1 A:ASP280 2.3 17.2 1.0
O A:THR166 2.4 20.6 1.0
OG1 A:THR284 2.4 18.8 1.0
OD1 A:ASP283 2.5 23.7 1.0
O A:HOH698 2.5 33.2 1.0
CG A:ASP280 3.3 17.1 1.0
HB A:THR166 3.3 27.6 1.0
C A:ASP280 3.3 17.9 1.0
HA A:ASP280 3.3 18.7 1.0
H A:THR284 3.5 25.7 1.0
CG A:ASP283 3.5 21.3 1.0
C A:THR166 3.5 22.5 1.0
CB A:THR284 3.6 22.0 1.0
HB A:THR284 3.6 26.4 1.0
HB2 A:SER236 3.7 33.1 1.0
CA A:ASP280 3.7 15.6 1.0
OD2 A:ASP283 3.8 18.4 1.0
HA A:THR166 3.8 26.3 1.0
N A:THR284 4.0 21.4 1.0
CA A:THR166 4.1 21.9 1.0
CB A:ASP280 4.1 17.3 1.0
CB A:THR166 4.1 23.0 1.0
OD2 A:ASP280 4.1 16.0 1.0
O A:HOH616 4.1 32.3 1.0
O A:HOH759 4.2 27.7 1.0
HA A:VAL167 4.3 19.7 1.0
CA A:THR284 4.3 20.2 1.0
HB3 A:ASP280 4.4 20.8 1.0
HG A:SER234 4.5 21.4 1.0
N A:ALA281 4.5 16.7 1.0
HA A:THR284 4.5 24.3 1.0
HA A:ALA281 4.6 16.9 1.0
CB A:SER236 4.6 27.6 1.0
N A:VAL167 4.7 18.2 1.0
O A:HOH646 4.7 14.6 1.0
HG21 A:THR284 4.7 32.4 1.0
OG A:SER234 4.7 17.9 1.0
O A:HOH639 4.7 25.7 1.0
CG2 A:THR284 4.7 27.0 1.0
HG12 A:VAL167 4.8 18.8 1.0
H A:ASP283 4.8 18.4 1.0
HB2 A:ASP280 4.9 20.8 1.0
HG A:SER236 4.9 38.7 1.0
HG22 A:THR166 4.9 34.9 1.0
CB A:ASP283 4.9 18.7 1.0
OG1 A:THR166 4.9 23.6 1.0
HG13 A:VAL167 4.9 18.8 1.0
OG A:SER236 5.0 32.2 1.0
C A:ASP283 5.0 20.2 1.0
CA A:ALA281 5.0 14.1 1.0
CA A:VAL167 5.0 16.4 1.0

Calcium binding site 2 out of 4 in 4xgv

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:22.5
occ:1.00
 O B:ASP280 2.3 19.4 1.0
OD1 B:ASP280 2.4 19.8 1.0
OG1 B:THR284 2.4 20.4 1.0
O B:HOH759 2.4 25.4 1.0
OD1 B:ASP283 2.4 24.6 1.0
O B:HOH712 2.5 28.1 1.0
O B:THR166 2.5 22.4 1.0
CG B:ASP280 3.3 22.4 1.0
C B:ASP280 3.3 18.9 1.0
HA B:ASP280 3.4 23.4 1.0
H B:THR284 3.4 23.3 1.0
HB B:THR166 3.5 29.8 1.0
CG B:ASP283 3.5 22.3 1.0
CB B:THR284 3.6 20.4 1.0
C B:THR166 3.6 21.3 1.0
HB B:THR284 3.7 24.5 1.0
CA B:ASP280 3.7 19.5 1.0
OD2 B:ASP283 3.8 25.3 1.0
N B:THR284 3.9 19.4 1.0
HA B:THR166 4.0 26.2 1.0
CB B:ASP280 4.0 20.4 1.0
OD2 B:ASP280 4.1 19.2 1.0
CA B:THR166 4.2 21.8 1.0
CA B:THR284 4.3 19.6 1.0
CB B:THR166 4.3 24.8 1.0
HA B:VAL167 4.3 20.2 1.0
HB2 B:SER236 4.3 31.9 1.0
HA B:THR284 4.4 23.5 1.0
O B:HOH692 4.4 26.2 1.0
HB3 B:ASP280 4.4 24.5 1.0
O B:HOH773 4.4 22.6 1.0
N B:ALA281 4.5 15.9 1.0
HA B:ALA281 4.5 20.4 1.0
HG B:SER234 4.6 35.0 1.0
O B:HOH707 4.6 36.4 1.0
O B:HOH635 4.7 16.7 1.0
HG12 B:VAL167 4.7 24.0 1.0
O B:HOH772 4.7 44.4 1.0
OG B:SER234 4.8 29.2 1.0
N B:VAL167 4.8 16.3 1.0
CG2 B:THR284 4.8 24.1 1.0
HG21 B:THR284 4.8 28.9 1.0
HB2 B:ASP280 4.8 24.5 1.0
C B:ASP283 4.9 19.8 1.0
H B:ASP283 4.9 21.6 1.0
CB B:ASP283 4.9 18.6 1.0
CA B:ALA281 5.0 17.0 1.0
HG23 B:THR284 5.0 28.9 1.0

Calcium binding site 3 out of 4 in 4xgv

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:26.1
occ:1.00
 OD1 C:ASP280 2.3 20.9 1.0
O C:ASP280 2.4 22.1 1.0
OG1 C:THR284 2.4 18.5 1.0
O C:HOH748 2.4 24.6 1.0
O C:THR166 2.5 26.6 1.0
OD1 C:ASP283 2.5 35.3 1.0
O C:HOH703 2.6 32.4 1.0
CG C:ASP280 3.2 20.9 1.0
C C:ASP280 3.3 21.5 1.0
HA C:ASP280 3.3 21.6 1.0
HB C:THR166 3.4 29.5 1.0
H C:THR284 3.5 20.3 1.0
CG C:ASP283 3.5 24.5 1.0
C C:THR166 3.6 24.5 1.0
CB C:THR284 3.7 19.6 1.0
CA C:ASP280 3.7 18.0 1.0
HB C:THR284 3.8 23.6 1.0
OD2 C:ASP283 3.8 23.2 1.0
HA C:THR166 3.9 28.5 1.0
CB C:ASP280 4.0 16.7 1.0
N C:THR284 4.0 16.9 1.0
OD2 C:ASP280 4.0 17.6 1.0
CA C:THR166 4.2 23.7 1.0
CB C:THR166 4.2 24.6 1.0
HA C:VAL167 4.3 19.5 1.0
HB3 C:ASP280 4.3 20.1 1.0
CA C:THR284 4.3 19.6 1.0
O C:HOH763 4.4 27.2 1.0
HB2 C:SER236 4.4 28.8 1.0
O C:HOH730 4.4 34.3 1.0
HA C:THR284 4.4 23.5 1.0
N C:ALA281 4.5 19.5 1.0
HA C:ALA281 4.5 22.5 1.0
HG C:SER234 4.5 27.1 1.0
O C:HOH663 4.6 26.6 1.0
O C:HOH620 4.6 21.8 1.0
N C:VAL167 4.7 17.9 1.0
OG C:SER234 4.8 22.6 1.0
HG12 C:VAL167 4.8 24.8 1.0
HB2 C:ASP280 4.8 20.1 1.0
CG2 C:THR284 4.8 25.2 1.0
HG21 C:THR284 4.8 30.2 1.0
C C:ASP283 4.9 18.2 1.0
H C:ASP283 4.9 21.3 1.0
CB C:ASP283 4.9 22.4 1.0
CA C:ALA281 4.9 18.8 1.0
HG13 C:VAL167 5.0 24.8 1.0

Calcium binding site 4 out of 4 in 4xgv

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:20.5
occ:1.00
 O D:ASP280 2.3 19.4 1.0
OD1 D:ASP280 2.3 16.5 1.0
O D:HOH760 2.4 23.4 1.0
O D:THR166 2.4 16.1 1.0
OD1 D:ASP283 2.4 20.5 1.0
OG1 D:THR284 2.5 19.3 1.0
O D:HOH724 2.5 35.9 1.0
CG D:ASP280 3.2 16.3 1.0
C D:ASP280 3.3 18.4 1.0
HA D:ASP280 3.3 16.7 1.0
HB D:THR166 3.4 16.9 1.0
CG D:ASP283 3.4 22.9 1.0
H D:THR284 3.5 21.3 1.0
C D:THR166 3.5 17.1 1.0
CB D:THR284 3.7 21.2 1.0
HB2 D:SER236 3.7 33.2 1.0
HB D:THR284 3.7 25.5 1.0
CA D:ASP280 3.7 13.9 1.0
OD2 D:ASP283 3.7 23.2 1.0
HA D:THR166 3.8 22.1 1.0
N D:THR284 4.0 17.7 1.0
CB D:ASP280 4.0 15.7 1.0
OD2 D:ASP280 4.1 13.6 1.0
CA D:THR166 4.1 18.4 1.0
O D:HOH613 4.1 30.3 1.0
CB D:THR166 4.2 14.1 1.0
HA D:VAL167 4.3 12.9 1.0
CA D:THR284 4.3 18.5 1.0
O D:HOH781 4.4 33.3 1.0
HB3 D:ASP280 4.4 18.8 1.0
HG D:SER234 4.4 22.4 1.0
HA D:ALA281 4.5 19.9 1.0
N D:ALA281 4.5 18.7 1.0
O D:HOH665 4.5 29.0 1.0
HA D:THR284 4.5 22.2 1.0
HG D:SER236 4.5 38.0 1.0
CB D:SER236 4.6 27.7 1.0
O D:HOH780 4.7 29.6 1.0
OG D:SER234 4.7 18.7 1.0
N D:VAL167 4.7 11.9 1.0
O D:HOH620 4.7 12.2 1.0
H D:ASP283 4.7 17.1 1.0
HG21 D:THR284 4.8 28.8 1.0
CG2 D:THR284 4.8 24.0 1.0
HG12 D:VAL167 4.8 23.2 1.0
HB2 D:ASP280 4.8 18.8 1.0
OG D:SER236 4.8 31.7 1.0
CB D:ASP283 4.8 17.4 1.0
C D:ASP283 4.9 15.7 1.0
HG22 D:THR166 4.9 19.8 1.0
CA D:ALA281 4.9 16.6 1.0
HG13 D:VAL167 5.0 23.2 1.0
CA D:VAL167 5.0 10.8 1.0
HB3 D:SER236 5.0 33.2 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: Sat Dec 12 05:12:06 2020

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