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Calcium in PDB 6u2m: Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635

Protein crystallography data

The structure of Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635, PDB code: 6u2m was solved by C.Deo, E.R.Schreiter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 122.58 / 2.00
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.560, 60.662, 122.600, 90.00, 91.02, 90.00
R / Rfree (%) 18.6 / 22.6

Other elements in 6u2m:

The structure of Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635 also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Silicon (Si) 2 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635 (pdb code 6u2m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635, PDB code: 6u2m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6u2m

Go back to Calcium Binding Sites List in 6u2m
Calcium binding site 1 out of 8 in the Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635


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 A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:59.8
occ:1.00
O A:HOH784 2.4 45.0 1.0
O A:THR404 2.5 32.0 1.0
OD1 A:ASN402 2.5 42.1 1.0
OD1 A:ASP398 2.6 33.7 1.0
OE1 A:GLU409 2.7 41.4 1.0
OE2 A:GLU409 2.7 45.2 1.0
OD1 A:ASP400 2.9 56.0 1.0
CD A:GLU409 3.1 41.4 1.0
CG A:ASP398 3.3 34.8 1.0
CG A:ASN402 3.5 44.4 1.0
C A:THR404 3.6 36.6 1.0
CG A:ASP400 3.6 56.6 1.0
ND2 A:ASN402 3.9 42.0 1.0
OD2 A:ASP400 3.9 75.6 1.0
OD2 A:ASP398 3.9 34.7 1.0
CB A:ASP398 4.0 34.4 1.0
CA A:ASP398 4.1 34.2 1.0
N A:THR404 4.2 40.8 1.0
OG1 A:THR404 4.3 42.4 1.0
N A:ASP400 4.3 41.4 1.0
CA A:ILE405 4.4 32.0 1.0
N A:ILE405 4.4 32.0 1.0
N A:ALA399 4.4 33.6 1.0
CA A:THR404 4.5 39.5 1.0
N A:ASN402 4.6 40.4 1.0
CG A:GLU409 4.6 39.2 1.0
N A:GLY403 4.6 40.0 1.0
N A:ASP406 4.6 36.9 1.0
C A:ASP398 4.7 34.1 1.0
CB A:ASN402 4.7 43.3 1.0
N A:GLY401 4.7 37.6 1.0
CB A:ASP400 4.8 47.9 1.0
C A:ILE405 4.9 34.3 1.0
CA A:ASP400 5.0 43.3 1.0

Calcium binding site 2 out of 8 in 6u2m

Go back to Calcium Binding Sites List in 6u2m
Calcium binding site 2 out of 8 in the Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635


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 A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:45.5
occ:1.00
O A:TYR441 2.2 39.6 1.0
OD1 A:ASP437 2.2 53.4 1.0
OD1 A:ASP435 2.4 41.5 1.0
O A:HOH802 2.4 45.6 1.0
OD1 A:ASN439 2.4 44.0 1.0
OE2 A:GLU446 2.5 44.9 1.0
OE1 A:GLU446 2.6 41.4 1.0
CD A:GLU446 2.9 42.8 1.0
CG A:ASP437 3.3 53.1 1.0
CG A:ASN439 3.4 47.4 1.0
C A:TYR441 3.4 40.8 1.0
CG A:ASP435 3.5 44.6 1.0
OD2 A:ASP437 3.9 61.1 1.0
N A:TYR441 4.0 39.5 1.0
ND2 A:ASN439 4.0 42.4 1.0
N A:ASN439 4.1 42.2 1.0
CA A:ASP435 4.2 43.0 1.0
N A:ASP437 4.2 50.5 1.0
CA A:TYR441 4.2 41.4 1.0
CB A:ASP435 4.3 40.7 1.0
C A:ASP435 4.3 43.4 1.0
CB A:ASN439 4.3 45.5 1.0
OD2 A:ASP435 4.4 40.6 1.0
CG A:GLU446 4.4 45.9 1.0
N A:GLY438 4.4 45.7 1.0
N A:LYS436 4.5 44.9 1.0
N A:ILE442 4.5 41.0 1.0
CB A:ASP437 4.5 49.4 1.0
CB A:TYR441 4.5 43.8 1.0
CA A:ASN439 4.6 44.1 1.0
CA A:ILE442 4.7 40.5 1.0
CA A:ASP437 4.7 51.0 1.0
N A:GLY440 4.7 42.0 1.0
N A:SER443 4.8 41.8 1.0
C A:ASP437 4.9 50.3 1.0
C A:ASN439 4.9 45.9 1.0
O A:HOH780 4.9 60.9 1.0
O A:ASP435 4.9 42.3 1.0

Calcium binding site 3 out of 8 in 6u2m

Go back to Calcium Binding Sites List in 6u2m
Calcium binding site 3 out of 8 in the Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635


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 A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:60.2
occ:1.00
O A:HOH788 2.1 66.5 1.0
OD1 A:ASP471 2.2 53.5 1.0
OE1 A:GLU482 2.4 58.6 1.0
OD1 A:ASP473 2.4 69.2 1.0
O A:GLN477 2.5 50.4 1.0
OD1 A:ASP475 2.5 61.7 1.0
OE2 A:GLU482 2.6 51.0 1.0
CD A:GLU482 2.8 54.5 1.0
CG A:ASP471 3.3 57.2 1.0
CG A:ASP473 3.3 74.5 1.0
CG A:ASP475 3.4 63.0 1.0
C A:GLN477 3.5 52.2 1.0
OD2 A:ASP473 3.6 78.3 1.0
OD2 A:ASP475 3.8 64.0 1.0
CA A:ASP471 4.0 58.0 1.0
OD2 A:ASP471 4.1 60.3 1.0
CB A:ASP471 4.1 56.5 1.0
N A:ASP475 4.2 66.0 1.0
N A:ASP473 4.3 67.8 1.0
N A:GLN477 4.3 50.4 1.0
N A:VAL478 4.4 47.8 1.0
CA A:VAL478 4.4 46.9 1.0
CG A:GLU482 4.4 52.4 1.0
C A:ASP471 4.4 60.3 1.0
CA A:GLN477 4.4 53.9 1.0
N A:ASN479 4.5 47.0 1.0
CB A:ASP475 4.5 62.3 1.0
N A:ILE472 4.6 64.7 1.0
CB A:ASP473 4.6 71.8 1.0
N A:GLY474 4.6 65.0 1.0
CA A:ASP475 4.7 61.7 1.0
CA A:ASP473 4.8 69.5 1.0
CB A:GLN477 4.8 61.0 1.0
CG A:ASN479 4.9 52.9 1.0
C A:ASP473 5.0 70.9 1.0
C A:VAL478 5.0 45.9 1.0
ND2 A:ASN479 5.0 52.3 1.0
O A:ASP471 5.0 59.2 1.0

Calcium binding site 4 out of 8 in 6u2m

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Calcium binding site 4 out of 8 in the Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635


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 A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca605

b:49.3
occ:1.00
O A:HOH766 2.2 58.0 1.0
OD1 A:ASP362 2.3 41.4 1.0
OD1 A:ASP366 2.3 54.7 1.0
OE1 A:GLU373 2.4 49.9 1.0
O A:THR368 2.4 54.3 1.0
OD1 A:ASP364 2.4 55.6 1.0
OE2 A:GLU373 2.5 55.4 1.0
CD A:GLU373 2.8 50.8 1.0
CG A:ASP366 3.3 59.5 1.0
CG A:ASP364 3.4 54.2 1.0
CG A:ASP362 3.5 44.3 1.0
C A:THR368 3.6 47.7 1.0
OD2 A:ASP364 3.7 56.3 1.0
OD2 A:ASP366 3.9 66.2 1.0
CA A:ASP362 4.0 42.2 1.0
N A:ASP366 4.1 52.7 1.0
CB A:ASP362 4.2 41.8 1.0
N A:THR368 4.2 43.9 1.0
CB A:ASP366 4.3 56.6 1.0
C A:ASP362 4.3 46.4 1.0
CG A:GLU373 4.4 48.2 1.0
OD2 A:ASP362 4.4 44.8 1.0
N A:ILE369 4.4 42.5 1.0
CA A:THR368 4.5 50.1 1.0
CA A:ILE369 4.5 40.3 1.0
OG1 A:THR368 4.6 62.3 1.0
N A:ASP364 4.6 45.6 1.0
CA A:ASP366 4.6 52.3 1.0
N A:LYS363 4.6 49.0 1.0
CB A:ASP364 4.7 48.7 1.0
O A:HOH726 4.7 49.3 1.0
N A:GLY365 4.8 50.1 1.0
O A:ASP362 4.8 44.0 1.0
N A:GLY367 4.8 47.0 1.0
C A:ASP366 4.9 51.4 1.0
N A:THR370 5.0 40.5 1.0
CA A:ASP364 5.0 48.4 1.0

Calcium binding site 5 out of 8 in 6u2m

Go back to Calcium Binding Sites List in 6u2m
Calcium binding site 5 out of 8 in the Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca602

b:51.8
occ:1.00
O C:HOH741 2.1 55.4 1.0
OD1 C:ASP362 2.3 43.5 1.0
O C:THR368 2.3 54.1 1.0
OD1 C:ASP366 2.3 57.5 1.0
OE1 C:GLU373 2.4 48.9 1.0
OE2 C:GLU373 2.6 52.3 1.0
OD1 C:ASP364 2.6 56.8 1.0
CD C:GLU373 2.9 52.0 1.0
CG C:ASP366 3.3 60.5 1.0
CG C:ASP364 3.4 59.8 1.0
CG C:ASP362 3.5 42.9 1.0
C C:THR368 3.5 48.3 1.0
OD2 C:ASP364 3.6 67.4 1.0
OD2 C:ASP366 3.8 66.0 1.0
CA C:ASP362 4.0 43.1 1.0
CB C:ASP362 4.2 43.2 1.0
N C:ASP366 4.2 49.5 1.0
N C:THR368 4.2 45.5 1.0
C C:ASP362 4.3 49.9 1.0
OG1 C:THR368 4.3 63.5 1.0
OD2 C:ASP362 4.3 42.9 1.0
CG C:GLU373 4.4 49.2 1.0
CA C:THR368 4.4 48.6 1.0
N C:ILE369 4.4 44.0 1.0
CB C:ASP366 4.4 57.6 1.0
N C:LYS363 4.5 54.1 1.0
N C:ASP364 4.6 53.5 1.0
CA C:ILE369 4.6 41.2 1.0
CA C:ASP366 4.7 52.0 1.0
N C:GLY365 4.8 49.2 1.0
CB C:ASP364 4.8 51.5 1.0
O C:ASP362 4.8 46.4 1.0
N C:GLY367 4.9 48.7 1.0
C C:ASP366 5.0 51.0 1.0

Calcium binding site 6 out of 8 in 6u2m

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Calcium binding site 6 out of 8 in the Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:59.3
occ:1.00
O C:HOH752 2.4 45.5 1.0
OD1 C:ASN402 2.5 41.8 1.0
O C:THR404 2.5 31.8 1.0
OD1 C:ASP398 2.5 37.7 1.0
OE1 C:GLU409 2.6 40.5 1.0
OE2 C:GLU409 2.7 44.1 1.0
OD1 C:ASP400 3.0 59.5 1.0
CD C:GLU409 3.1 43.1 1.0
CG C:ASP398 3.2 39.6 1.0
CG C:ASN402 3.4 47.2 1.0
C C:THR404 3.5 37.4 1.0
ND2 C:ASN402 3.7 42.6 1.0
CG C:ASP400 3.9 57.6 1.0
OD2 C:ASP398 3.9 36.3 1.0
CB C:ASP398 3.9 37.4 1.0
CA C:ASP398 4.1 37.6 1.0
N C:THR404 4.1 38.1 1.0
OD2 C:ASP400 4.2 70.4 1.0
N C:ASP400 4.3 40.6 1.0
CA C:ILE405 4.4 37.0 1.0
N C:ALA399 4.4 34.5 1.0
OG1 C:THR404 4.4 41.0 1.0
N C:ILE405 4.4 35.6 1.0
CA C:THR404 4.4 38.4 1.0
N C:ASN402 4.6 42.4 1.0
CG C:GLU409 4.6 41.7 1.0
C C:ASP398 4.7 36.8 1.0
CB C:ASN402 4.7 44.4 1.0
N C:GLY403 4.7 41.7 1.0
N C:ASP406 4.7 38.4 1.0
N C:GLY401 4.8 38.4 1.0
OD2 C:ASP406 4.9 63.1 1.0
C C:ILE405 4.9 36.3 1.0
CB C:ASP400 5.0 50.8 1.0
CA C:ASN402 5.0 43.2 1.0

Calcium binding site 7 out of 8 in 6u2m

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Calcium binding site 7 out of 8 in the Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca604

b:50.6
occ:1.00
O C:TYR441 2.2 46.6 1.0
OD1 C:ASP437 2.4 54.4 1.0
OD1 C:ASP435 2.4 42.0 1.0
O C:HOH783 2.5 53.2 1.0
OE1 C:GLU446 2.5 45.0 1.0
OD1 C:ASN439 2.5 42.2 1.0
OE2 C:GLU446 2.6 47.0 1.0
CD C:GLU446 2.8 46.5 1.0
CG C:ASN439 3.4 45.1 1.0
CG C:ASP437 3.4 55.8 1.0
C C:TYR441 3.4 44.5 1.0
CG C:ASP435 3.6 42.0 1.0
OD2 C:ASP437 4.1 62.7 1.0
ND2 C:ASN439 4.1 42.1 1.0
N C:ASN439 4.1 43.2 1.0
N C:TYR441 4.1 41.6 1.0
CA C:ASP435 4.2 41.6 1.0
N C:ASP437 4.2 50.9 1.0
CA C:TYR441 4.3 44.3 1.0
CG C:GLU446 4.3 47.9 1.0
CB C:ASN439 4.4 45.4 1.0
C C:ASP435 4.4 43.2 1.0
CB C:ASP435 4.4 41.9 1.0
OD2 C:ASP435 4.4 42.0 1.0
N C:ILE442 4.4 48.6 1.0
CB C:ASP437 4.5 51.8 1.0
CB C:TYR441 4.5 47.6 1.0
CA C:ILE442 4.5 45.4 1.0
N C:LYS436 4.5 46.6 1.0
N C:GLY438 4.6 47.0 1.0
CA C:ASN439 4.6 45.9 1.0
N C:SER443 4.7 47.5 1.0
CA C:ASP437 4.7 52.5 1.0
N C:GLY440 4.8 43.8 1.0
C C:ASN439 4.9 43.2 1.0
C C:ASP437 4.9 51.0 1.0
O C:ASP435 5.0 44.9 1.0

Calcium binding site 8 out of 8 in 6u2m

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Calcium binding site 8 out of 8 in the Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2, Bound to JF635 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca605

b:55.6
occ:1.00
OD1 C:ASP475 2.3 59.0 1.0
OD1 C:ASP471 2.3 52.8 1.0
OD1 C:ASP473 2.3 73.9 1.0
O C:HOH769 2.4 51.0 1.0
OE1 C:GLU482 2.4 62.1 1.0
O C:GLN477 2.5 52.0 1.0
OE2 C:GLU482 2.6 56.1 1.0
CD C:GLU482 2.9 55.2 1.0
CG C:ASP475 3.2 64.3 1.0
CG C:ASP473 3.3 76.4 1.0
CG C:ASP471 3.4 56.2 1.0
C C:GLN477 3.6 53.3 1.0
OD2 C:ASP473 3.7 81.5 1.0
OD2 C:ASP475 3.7 68.8 1.0
N C:ASP475 4.1 67.6 1.0
N C:GLN477 4.1 54.5 1.0
CA C:ASP471 4.2 58.5 1.0
OD2 C:ASP471 4.2 56.4 1.0
CB C:ASP471 4.3 57.0 1.0
CB C:ASP475 4.3 66.2 1.0
CG C:GLU482 4.4 53.6 1.0
N C:ASP473 4.4 70.9 1.0
CA C:VAL478 4.4 51.3 1.0
CA C:GLN477 4.4 55.2 1.0
N C:ASN479 4.4 51.8 1.0
N C:VAL478 4.4 53.5 1.0
C C:ASP471 4.5 59.6 1.0
N C:GLY474 4.5 65.8 1.0
CB C:ASP473 4.6 72.0 1.0
CA C:ASP475 4.7 66.8 1.0
CB C:GLN477 4.8 59.9 1.0
CA C:ASP473 4.8 74.1 1.0
N C:ILE472 4.8 62.0 1.0
ND2 C:ASN479 4.8 55.8 1.0
N C:GLY476 4.9 60.7 1.0
C C:ASP473 4.9 72.1 1.0
C C:VAL478 4.9 51.5 1.0
O C:ASP471 4.9 60.0 1.0
C C:ASP475 4.9 64.2 1.0
CG C:ASN479 5.0 55.8 1.0

Reference:

C.Deo, L.D.Lavis, E.R.Schreiter. Crystal Structure of A Halotag-Based Calcium Indicator, Halocamp V2 To Be Published.
Page generated: Sat Dec 12 07:46:39 2020

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