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Strontium in PDB 6eel: Crystal Structure of Myoferlin C2A with Divalent Cation

Protein crystallography data

The structure of Crystal Structure of Myoferlin C2A with Divalent Cation, PDB code: 6eel was solved by R.B.Sutton, F.M.Harsini, A.M.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.34 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.350, 83.110, 94.280, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.2

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of Myoferlin C2A with Divalent Cation (pdb code 6eel). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 6 binding sites of Strontium where determined in the Crystal Structure of Myoferlin C2A with Divalent Cation, PDB code: 6eel:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6;

Strontium binding site 1 out of 6 in 6eel

Go back to Strontium Binding Sites List in 6eel
Strontium binding site 1 out of 6 in the Crystal Structure of Myoferlin C2A with Divalent Cation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of Myoferlin C2A with Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr201

b:31.3
occ:1.00
 O A:HOH337 2.4 36.4 1.0
O A:PHE79 2.5 31.7 1.0
OD2 A:ASP28 2.6 25.7 1.0
OD1 A:ASP78 2.6 19.7 1.0
O A:HOH392 2.7 30.9 1.0
CG A:ASP78 3.5 24.8 1.0
C A:PHE79 3.7 31.6 1.0
CG A:ASP28 3.7 21.0 1.0
OD2 A:ASP78 3.9 28.1 1.0
SR A:SR202 4.1 27.2 1.0
CB A:ASP28 4.2 18.4 1.0
OE2 A:GLU80 4.4 53.2 1.0
N A:PHE79 4.4 26.7 1.0
C A:ASP78 4.4 19.8 1.0
N A:ASP28 4.5 18.3 1.0
N A:GLU80 4.5 35.3 1.0
CD A:GLU80 4.5 50.1 1.0
O A:ASP78 4.5 20.4 1.0
O A:LYS26 4.6 23.3 1.0
CA A:GLU80 4.6 40.7 1.0
CA A:PHE79 4.6 28.7 1.0
OD1 A:ASP28 4.7 20.2 1.0
CB A:ASP78 4.7 20.4 1.0
O A:HOH346 4.7 31.5 1.0
CG A:GLU80 4.8 44.9 1.0
CA A:PRO27 4.9 21.6 1.0
OE1 A:GLU80 5.0 52.6 1.0
CA A:ASP28 5.0 17.4 1.0

Strontium binding site 2 out of 6 in 6eel

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Strontium binding site 2 out of 6 in the Crystal Structure of Myoferlin C2A with Divalent Cation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of Myoferlin C2A with Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr202

b:27.2
occ:1.00
 OD1 A:ASN47 2.3 25.6 1.0
OD2 A:ASP28 2.5 25.7 1.0
O A:LYS26 2.6 23.3 1.0
OD1 A:ASP28 2.7 20.2 1.0
CG A:ASP28 2.9 21.0 1.0
CG A:ASN47 3.4 27.3 1.0
C A:LYS26 3.8 24.8 1.0
ND2 A:ASN47 4.0 33.9 1.0
SR A:SR201 4.1 31.3 1.0
N A:LYS26 4.4 27.1 1.0
CB A:ASP28 4.4 18.4 1.0
N A:ASN47 4.6 20.1 1.0
CB A:ASN47 4.6 26.1 1.0
C A:PRO27 4.6 19.9 1.0
CA A:LYS26 4.6 26.3 1.0
O A:HOH346 4.6 31.5 1.0
CA A:ASN47 4.7 23.4 1.0
N A:ASP28 4.8 18.3 1.0
O A:PRO27 4.8 22.6 1.0
N A:PRO27 4.8 22.3 1.0
CA A:PRO27 4.8 21.6 1.0

Strontium binding site 3 out of 6 in 6eel

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Strontium binding site 3 out of 6 in the Crystal Structure of Myoferlin C2A with Divalent Cation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structure of Myoferlin C2A with Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr201

b:30.1
occ:1.00
 O B:HOH361 2.4 35.1 1.0
OD2 B:ASP28 2.5 26.8 1.0
O B:PHE79 2.5 35.5 1.0
O B:HOH401 2.5 34.2 1.0
OD1 B:ASP78 2.6 21.1 1.0
O B:HOH340 2.7 36.2 1.0
O B:HOH405 2.7 33.4 1.0
CG B:ASP78 3.5 24.3 1.0
C B:PHE79 3.6 33.9 1.0
CG B:ASP28 3.7 26.5 1.0
OD2 B:ASP78 3.9 23.4 1.0
CB B:ASP28 4.2 24.4 1.0
SR B:SR202 4.2 33.3 1.0
N B:PHE79 4.4 29.2 1.0
C B:ASP78 4.4 22.5 1.0
O B:HOH416 4.5 28.7 1.0
O B:ASP78 4.5 23.1 1.0
N B:ASP28 4.5 23.9 1.0
N B:GLU80 4.5 36.4 1.0
CA B:PHE79 4.6 31.1 1.0
CB B:ASP78 4.6 22.8 1.0
CA B:GLU80 4.7 43.1 1.0
O B:LYS26 4.7 33.1 1.0
OD1 B:ASP28 4.7 25.6 1.0
CD B:GLU80 4.8 58.5 1.0
O B:HOH442 4.8 42.6 1.0
OE1 B:GLU80 4.8 63.9 1.0
CA B:PRO27 4.9 26.2 1.0

Strontium binding site 4 out of 6 in 6eel

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Strontium binding site 4 out of 6 in the Crystal Structure of Myoferlin C2A with Divalent Cation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Crystal Structure of Myoferlin C2A with Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr202

b:33.3
occ:1.00
 OD1 B:ASN47 2.2 29.9 1.0
O B:LYS26 2.4 33.1 1.0
OD2 B:ASP28 2.6 26.8 1.0
O B:HOH399 2.6 25.8 1.0
OD1 B:ASP28 2.6 25.6 1.0
O B:HOH405 2.7 33.4 1.0
CG B:ASP28 3.0 26.5 1.0
CG B:ASN47 3.4 34.3 1.0
C B:LYS26 3.6 33.9 1.0
ND2 B:ASN47 4.0 42.9 1.0
SR B:SR201 4.2 30.1 1.0
N B:LYS26 4.3 36.5 1.0
O B:HOH416 4.3 28.7 1.0
O B:HOH361 4.4 35.1 1.0
CB B:ASP28 4.4 24.4 1.0
CA B:LYS26 4.5 37.1 1.0
CB B:ASN47 4.5 35.2 1.0
N B:ASN47 4.5 31.5 1.0
C B:PRO27 4.5 25.3 1.0
CA B:ASN47 4.6 32.2 1.0
N B:PRO27 4.6 32.4 1.0
O B:PRO27 4.7 24.2 1.0
CA B:PRO27 4.7 26.2 1.0
N B:ASP28 4.7 23.9 1.0
CB B:LYS26 4.9 41.1 1.0

Strontium binding site 5 out of 6 in 6eel

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Strontium binding site 5 out of 6 in the Crystal Structure of Myoferlin C2A with Divalent Cation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Crystal Structure of Myoferlin C2A with Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr201

b:27.6
occ:1.00
 O C:HOH388 2.2 37.9 1.0
OD2 C:ASP28 2.4 23.9 1.0
O C:HOH343 2.5 32.0 1.0
OD1 C:ASP78 2.6 19.0 1.0
O C:PHE79 2.6 43.6 1.0
OE2 C:GLU80 2.7 52.3 1.0
O C:HOH386 2.9 42.1 1.0
CG C:ASP78 3.5 21.1 1.0
CG C:ASP28 3.6 23.2 1.0
C C:PHE79 3.8 42.6 1.0
CD C:GLU80 3.8 56.2 1.0
OD2 C:ASP78 3.8 23.0 1.0
CB C:ASP28 4.1 21.6 1.0
OE1 C:GLU80 4.2 58.1 1.0
SR C:SR202 4.3 30.1 1.0
N C:ASP28 4.4 19.8 1.0
N C:PHE79 4.5 39.0 1.0
C C:ASP78 4.5 17.4 1.0
O C:ASP78 4.6 19.5 1.0
N C:GLU80 4.6 44.5 1.0
OD1 C:ASP28 4.6 25.1 1.0
O C:LYS26 4.6 28.4 1.0
CA C:PHE79 4.7 40.0 1.0
CB C:ASP78 4.7 20.5 1.0
CA C:GLU80 4.7 48.5 1.0
CA C:PRO27 4.8 24.0 1.0
CA C:ASP28 4.9 19.7 1.0
O C:HOH313 5.0 31.8 1.0
CG C:GLU80 5.0 52.4 1.0
O C:HOH394 5.0 35.0 1.0

Strontium binding site 6 out of 6 in 6eel

Go back to Strontium Binding Sites List in 6eel
Strontium binding site 6 out of 6 in the Crystal Structure of Myoferlin C2A with Divalent Cation


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Crystal Structure of Myoferlin C2A with Divalent Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr202

b:30.1
occ:1.00
 OD1 C:ASN47 2.2 30.2 1.0
O C:HOH386 2.3 42.1 1.0
O C:HOH394 2.4 35.0 1.0
O C:LYS26 2.6 28.4 1.0
O C:HOH382 2.6 32.2 1.0
OD1 C:ASP28 2.6 25.1 1.0
OD2 C:ASP28 2.7 23.9 1.0
CG C:ASP28 3.0 23.2 1.0
CG C:ASN47 3.3 28.4 1.0
C C:LYS26 3.8 30.0 1.0
ND2 C:ASN47 3.9 30.6 1.0
SR C:SR201 4.3 27.6 1.0
N C:LYS26 4.3 38.0 1.0
O C:HOH343 4.4 32.0 1.0
CB C:ASN47 4.5 29.4 1.0
N C:ASN47 4.5 24.4 1.0
CB C:ASP28 4.5 21.6 1.0
O C:HOH325 4.5 41.5 1.0
CA C:LYS26 4.6 34.9 1.0
CA C:ASN47 4.6 25.7 1.0
C C:PRO27 4.7 21.4 1.0
O C:PRO27 4.8 21.4 1.0
N C:PRO27 4.8 26.9 1.0
O C:HOH313 4.9 31.8 1.0
N C:ASP28 4.9 19.8 1.0
CA C:PRO27 4.9 24.0 1.0
CB C:LYS26 5.0 36.4 1.0
O C:HOH388 5.0 37.9 1.0

Reference:

F.M.Harsini, A.A.Bui, A.M.Rice, S.Chebrolu, K.L.Fuson, A.Turtoi, M.Bradberry, E.R.Chapman, R.B.Sutton. Structural Basis For the Distinct Membrane Binding Activity of the Homologous C2A Domains of Myoferlin and Dysferlin. J.Mol.Biol. V. 431 2112 2019.
ISSN: ESSN 1089-8638
PubMed: 31004665
DOI: 10.1016/J.JMB.2019.04.006
Page generated: Fri Oct 11 06:39:02 2024

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