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Calcium in PDB 1sl6: Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.

Protein crystallography data

The structure of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X., PDB code: 1sl6 was solved by Y.Guo, H.Feinberg, E.Conroy, D.A.Mitchell, R.Alvarez, O.Blixt, M.E.Taylor, W.I.Weis, K.Drickamer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.96 / 2.25
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 153.750, 153.750, 128.702, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 25.6

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. (pdb code 1sl6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 24 binding sites of Calcium where determined in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X., PDB code: 1sl6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 24 in 1sl6

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Calcium binding site 1 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


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 Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:49.0
occ:1.00
OD1 A:ASP367 2.2 49.1 1.0
OE2 A:GLU336 2.2 55.6 1.0
OD1 A:ASN362 2.4 58.0 1.0
O A:GLU366 2.4 49.4 1.0
O A:HOH400 2.4 40.8 1.0
OD2 A:ASP332 2.5 50.7 1.0
OE1 A:GLU336 2.6 56.5 1.0
OD1 A:ASP332 2.7 53.0 1.0
CD A:GLU336 2.7 57.6 1.0
CG A:ASP332 2.9 52.5 1.0
CG A:ASN362 3.2 56.1 1.0
C A:GLU366 3.3 49.4 1.0
CG A:ASP367 3.4 50.3 1.0
CA A:ASP367 3.7 46.7 1.0
N A:ASP367 3.9 47.5 1.0
CA A:CA3 3.9 56.9 1.0
CB A:ASP367 4.0 47.4 1.0
CB A:ASN362 4.0 54.9 1.0
ND2 A:ASN362 4.0 54.7 1.0
N A:GLU366 4.2 53.3 1.0
CG A:GLU336 4.2 56.3 1.0
OD2 A:ASP367 4.4 51.8 1.0
CA A:GLU366 4.4 50.5 1.0
CB A:ASP332 4.4 51.8 1.0
CZ2 A:TRP339 4.5 48.7 1.0
OD1 A:ASN365 4.6 55.9 1.0
CA A:ASN362 4.6 56.0 1.0
O A:ASP332 4.7 52.4 1.0
OD2 A:ASP378 4.7 45.2 1.0
N A:GLY337 4.8 59.7 1.0
CA A:GLU336 4.9 61.0 1.0
CH2 A:TRP339 4.9 47.2 1.0
O A:HOH401 5.0 60.2 1.0
C A:ASN365 5.0 55.0 1.0
CB A:GLU336 5.0 59.3 1.0
C A:ASP367 5.0 46.0 1.0

Calcium binding site 2 out of 24 in 1sl6

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Calcium binding site 2 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


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 Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:48.4
occ:1.00
OD1 A:ASP378 2.3 44.5 1.0
O4 A:FUC13 2.4 60.6 1.0
OE1 A:GLU366 2.5 55.2 1.0
O3 A:FUC13 2.5 65.7 1.0
O A:ASP378 2.5 45.2 1.0
OD1 A:ASN377 2.5 41.6 1.0
OD1 A:ASN361 2.6 48.3 1.0
OE1 A:GLU359 2.9 50.3 1.0
C4 A:FUC13 3.2 66.9 1.0
CG A:ASP378 3.3 44.5 1.0
C3 A:FUC13 3.3 67.6 1.0
CD A:GLU366 3.3 53.2 1.0
CG A:ASN361 3.5 50.3 1.0
CG A:ASN377 3.6 45.4 1.0
OE2 A:GLU366 3.6 52.9 1.0
C A:ASP378 3.6 45.1 1.0
CD A:GLU359 3.6 50.0 1.0
ND2 A:ASN361 3.8 50.9 1.0
N A:ASP378 3.8 42.0 1.0
OE2 A:GLU359 3.9 49.4 1.0
OD2 A:ASP378 3.9 45.2 1.0
C2 A:FUC13 4.0 71.4 1.0
ND2 A:ASN377 4.0 45.8 1.0
CA A:ASP378 4.2 44.3 1.0
CB A:ASP378 4.3 41.9 1.0
N A:ASN361 4.3 52.4 1.0
N A:ASN362 4.6 53.6 1.0
CG A:GLU366 4.6 51.0 1.0
C5 A:FUC13 4.6 68.7 1.0
CB A:ASN361 4.7 49.1 1.0
N A:SER363 4.7 58.9 1.0
N A:ASN379 4.8 45.8 1.0
O2 A:FUC13 4.8 72.0 1.0
C A:ASN377 4.8 42.7 1.0
CB A:GLU366 4.8 50.3 1.0
CG A:GLU359 4.8 46.7 1.0
CB A:SER363 4.9 60.8 1.0
CB A:ASN377 4.9 43.4 1.0
CA A:ASN361 4.9 51.9 1.0

Calcium binding site 3 out of 24 in 1sl6

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Calcium binding site 3 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


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 Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:56.9
occ:1.00
OE1 A:GLU336 2.2 56.5 1.0
OD1 A:ASN365 2.4 55.9 1.0
O A:HOH401 2.4 60.2 1.0
OD2 A:ASP367 2.5 51.8 1.0
O A:HOH402 2.5 54.6 1.0
OD1 A:ASP367 2.6 49.1 1.0
CG A:ASP367 2.8 50.3 1.0
CG A:ASN365 3.4 55.9 1.0
CD A:GLU336 3.4 57.6 1.0
ND2 A:ASN365 3.8 53.7 1.0
CA A:CA1 3.9 49.0 1.0
CB A:GLU336 4.2 59.3 1.0
CG A:GLU336 4.2 56.3 1.0
CB A:ASP367 4.3 47.4 1.0
OE2 A:GLU336 4.3 55.6 1.0
OD1 A:ASN362 4.4 58.0 1.0
O A:ASP332 4.5 52.4 1.0
CA A:GLU336 4.6 61.0 1.0
CB A:ASN365 4.7 54.8 1.0
OD1 A:ASP332 4.9 53.0 1.0
ND2 A:ASN362 4.9 54.7 1.0
OD2 A:ASP332 4.9 50.7 1.0

Calcium binding site 4 out of 24 in 1sl6

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Calcium binding site 4 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


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 Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:62.3
occ:1.00
OD2 A:ASP256 2.5 62.7 1.0
O E:HOH422 2.6 52.7 1.0
OE1 A:GLU253 2.7 79.2 1.0
CG A:ASP256 3.5 63.1 1.0
CD A:GLU253 3.5 78.7 1.0
OE2 A:GLU253 3.6 79.5 1.0
CB A:ASP256 3.8 60.6 1.0
OG E:SER350 4.1 46.2 1.0
OG E:SER348 4.3 51.5 1.0
OD1 A:ASP256 4.6 64.3 1.0
CB E:SER348 4.7 47.5 1.0
CG A:GLU253 4.9 77.6 1.0
CB E:SER350 5.0 40.8 1.0
CA A:GLU253 5.0 76.0 1.0

Calcium binding site 5 out of 24 in 1sl6

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Calcium binding site 5 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


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 Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:40.1
occ:1.00
OD1 B:ASP367 2.2 46.6 1.0
O B:HOH400 2.3 39.6 1.0
OD2 B:ASP332 2.4 40.2 1.0
OD1 B:ASN362 2.5 45.3 1.0
O B:GLU366 2.5 43.6 1.0
OD1 B:ASP332 2.5 39.9 1.0
OE1 B:GLU336 2.6 49.1 1.0
OE2 B:GLU336 2.6 50.1 1.0
CG B:ASP332 2.8 41.0 1.0
CD B:GLU336 2.9 49.4 1.0
CG B:ASN362 3.2 47.9 1.0
C B:GLU366 3.3 44.3 1.0
CG B:ASP367 3.4 47.7 1.0
CA B:ASP367 3.7 43.9 1.0
N B:ASP367 3.8 43.2 1.0
CA B:CA3 3.9 46.6 1.0
CB B:ASN362 3.9 47.6 1.0
CB B:ASP367 4.0 45.0 1.0
N B:GLU366 4.1 47.8 1.0
ND2 B:ASN362 4.1 46.4 1.0
O B:HOH424 4.2 51.7 1.0
CB B:ASP332 4.3 40.1 1.0
CA B:GLU366 4.3 46.2 1.0
CG B:GLU336 4.4 48.6 1.0
OD2 B:ASP367 4.4 48.9 1.0
CZ2 B:TRP339 4.5 43.1 1.0
CA B:ASN362 4.5 49.9 1.0
O B:ASP332 4.5 43.0 1.0
O B:HOH401 4.7 37.2 1.0
OD2 B:ASP378 4.7 42.8 1.0
OD1 B:ASN365 4.7 48.1 1.0
CH2 B:TRP339 4.9 40.7 1.0
N B:GLY337 4.9 49.0 1.0
C B:ASP367 4.9 43.0 1.0
C B:ASN365 4.9 49.9 1.0

Calcium binding site 6 out of 24 in 1sl6

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Calcium binding site 6 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


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 Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:44.1
occ:1.00
OD1 B:ASP378 2.2 42.4 1.0
OD1 B:ASN377 2.4 40.1 1.0
O3 B:FUC13 2.4 47.3 0.5
O B:ASP378 2.4 39.1 1.0
O4 B:FUC13 2.5 48.0 0.5
OD1 B:ASN361 2.5 46.9 1.0
OE1 B:GLU366 2.5 51.7 1.0
OE1 B:GLU359 2.5 47.5 1.0
C4 B:FUC13 3.2 50.7 0.5
C3 B:FUC13 3.2 51.0 0.5
CG B:ASP378 3.3 41.5 1.0
CD B:GLU359 3.3 50.4 1.0
CG B:ASN361 3.3 49.2 1.0
CG B:ASN377 3.4 40.0 1.0
C B:ASP378 3.5 41.6 1.0
OE2 B:GLU359 3.6 50.3 1.0
CD B:GLU366 3.6 50.2 1.0
N B:ASP378 3.7 41.3 1.0
ND2 B:ASN361 3.7 48.8 1.0
ND2 B:ASN377 3.8 41.6 1.0
C2 B:FUC13 3.8 55.2 0.5
OD2 B:ASP378 3.9 42.8 1.0
CA B:ASP378 4.0 41.5 1.0
OE2 B:GLU366 4.1 49.0 1.0
CB B:ASP378 4.2 41.5 1.0
N B:ASN361 4.3 48.6 1.0
O2 B:FUC13 4.5 56.4 0.5
CG B:GLU359 4.6 48.5 1.0
C B:ASN377 4.6 40.7 1.0
CB B:ASN361 4.6 49.0 1.0
C5 B:FUC13 4.7 52.1 0.5
CB B:ASN377 4.7 39.4 1.0
N B:ASN379 4.7 42.5 1.0
N B:ASN362 4.7 49.0 1.0
CG B:GLU366 4.8 45.9 1.0
CA B:ASN361 4.9 49.4 1.0
CA B:ASN377 4.9 40.7 1.0
CB B:GLU366 4.9 47.3 1.0
N B:SER363 5.0 54.1 1.0

Calcium binding site 7 out of 24 in 1sl6

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Calcium binding site 7 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


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 Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:46.6
occ:1.00
OD1 B:ASN365 2.2 48.1 1.0
O B:HOH402 2.3 44.2 1.0
OE1 B:GLU336 2.4 49.1 1.0
O B:HOH401 2.4 37.2 1.0
OD1 B:ASP367 2.5 46.6 1.0
OD2 B:ASP367 2.6 48.9 1.0
CG B:ASP367 2.9 47.7 1.0
CG B:ASN365 3.3 46.0 1.0
CD B:GLU336 3.6 49.4 1.0
ND2 B:ASN365 3.8 46.5 1.0
CA B:CA1 3.9 40.1 1.0
OD1 B:ASN362 4.2 45.3 1.0
CB B:GLU336 4.2 48.5 1.0
CG B:GLU336 4.3 48.6 1.0
CB B:ASP367 4.3 45.0 1.0
O B:ASP332 4.5 43.0 1.0
OE2 B:GLU336 4.5 50.1 1.0
CB B:ASN365 4.6 47.9 1.0
OD1 B:ASP332 4.6 39.9 1.0
ND2 B:ASN362 4.7 46.4 1.0
CA B:GLU336 4.8 49.1 1.0
CA B:ASN365 4.8 50.9 1.0
CG B:ASN362 4.8 47.9 1.0
OD2 B:ASP332 5.0 40.2 1.0

Calcium binding site 8 out of 24 in 1sl6

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Calcium binding site 8 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


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 Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4

b:76.8
occ:1.00
OE1 B:GLU253 2.2 83.1 1.0
O F:HOH424 2.3 66.6 1.0
OD2 B:ASP256 2.7 72.9 1.0
CD B:GLU253 3.0 83.2 1.0
OE2 B:GLU253 3.1 83.6 1.0
CG B:ASP256 3.5 71.5 1.0
CB B:ASP256 3.8 69.2 1.0
OG F:SER350 3.9 48.4 1.0
OG F:SER348 4.3 48.7 1.0
CG B:GLU253 4.5 81.7 1.0
OD1 B:ASP256 4.5 75.0 1.0
CB F:SER348 4.6 42.7 1.0
CA B:GLU253 4.9 80.8 1.0
CB F:SER350 4.9 45.2 1.0
O F:HOH440 4.9 49.1 1.0

Calcium binding site 9 out of 24 in 1sl6

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Calcium binding site 9 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:46.9
occ:1.00
OD2 C:ASP332 2.4 43.4 1.0
O C:HOH17 2.4 39.7 1.0
O C:GLU366 2.4 41.9 1.0
OD1 C:ASN362 2.4 54.0 1.0
OD1 C:ASP367 2.5 42.1 1.0
OE2 C:GLU336 2.6 51.8 1.0
OE1 C:GLU336 2.6 49.8 1.0
OD1 C:ASP332 2.7 48.2 1.0
CG C:ASP332 2.9 45.1 1.0
CD C:GLU336 2.9 52.4 1.0
CG C:ASN362 3.3 54.2 1.0
C C:GLU366 3.3 42.0 1.0
CG C:ASP367 3.5 44.5 1.0
CA C:ASP367 3.7 42.7 1.0
CA C:CA3 3.8 41.9 1.0
N C:ASP367 3.9 40.5 1.0
CB C:ASN362 3.9 52.4 1.0
CB C:ASP367 4.1 43.3 1.0
N C:GLU366 4.2 44.3 1.0
ND2 C:ASN362 4.3 53.9 1.0
CZ2 C:TRP339 4.3 39.7 1.0
CB C:ASP332 4.4 44.3 1.0
CA C:GLU366 4.4 42.8 1.0
CG C:GLU336 4.4 51.8 1.0
OD1 C:ASN365 4.5 43.2 1.0
CA C:ASN362 4.5 52.1 1.0
OD2 C:ASP367 4.5 47.0 1.0
OD2 C:ASP378 4.6 42.3 1.0
O C:ASP332 4.7 45.4 1.0
CH2 C:TRP339 4.8 41.8 1.0
O C:HOH18 4.9 39.5 1.0
C C:ASP367 4.9 43.8 1.0
N C:GLY337 5.0 52.6 1.0
CA C:GLU336 5.0 53.0 1.0

Calcium binding site 10 out of 24 in 1sl6

Go back to Calcium Binding Sites List in 1sl6
Calcium binding site 10 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2

b:47.3
occ:1.00
OD1 C:ASP378 2.1 41.9 1.0
OE1 C:GLU359 2.4 58.9 1.0
O4 C:FUC13 2.4 77.1 1.0
OD1 C:ASN377 2.4 40.6 1.0
O C:ASP378 2.5 42.2 1.0
O3 C:FUC13 2.5 76.6 1.0
OD1 C:ASN361 2.6 46.5 1.0
OE1 C:GLU366 2.6 45.1 1.0
CG C:ASP378 3.2 41.5 1.0
CD C:GLU359 3.3 58.6 1.0
C4 C:FUC13 3.3 79.2 1.0
C3 C:FUC13 3.3 79.3 1.0
CD C:GLU366 3.5 47.0 1.0
CG C:ASN377 3.5 43.6 1.0
CG C:ASN361 3.5 48.3 1.0
OE2 C:GLU359 3.6 59.1 1.0
C C:ASP378 3.6 44.5 1.0
N C:ASP378 3.7 42.9 1.0
OE2 C:GLU366 3.8 50.5 1.0
C2 C:FUC13 3.9 82.2 1.0
ND2 C:ASN361 3.9 47.4 1.0
ND2 C:ASN377 3.9 41.4 1.0
OD2 C:ASP378 4.0 42.3 1.0
CA C:ASP378 4.1 42.7 1.0
CB C:ASP378 4.3 41.8 1.0
N C:ASN361 4.3 49.8 1.0
CG C:GLU359 4.5 56.9 1.0
C C:ASN377 4.6 43.0 1.0
O2 C:FUC13 4.6 80.4 1.0
C5 C:FUC13 4.7 80.7 1.0
CG C:GLU366 4.7 44.2 1.0
N C:ASN379 4.7 46.6 1.0
CB C:ASN377 4.8 43.1 1.0
N C:ASN362 4.8 51.1 1.0
CB C:ASN361 4.8 48.0 1.0
CB C:GLU366 4.8 42.9 1.0
CA C:ASN377 4.9 44.1 1.0
N C:SER363 4.9 53.0 1.0
CA C:ASN361 4.9 50.0 1.0
O5 C:FUC13 5.0 82.1 1.0

Reference:

Y.Guo, H.Feinberg, E.Conroy, D.A.Mitchell, R.Alvarez, O.Blixt, M.E.Taylor, W.I.Weis, K.Drickamer. Structural Basis For Distinct Ligand-Binding and Targeting Properties of the Receptors Dc-Sign and Dc-Signr Nat.Struct.Mol.Biol. V. 11 591 2004.
ISSN: ISSN 1545-9993
PubMed: 15195147
DOI: 10.1038/NSMB784
Page generated: Sat Dec 12 03:19:30 2020

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