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Calcium in PDB 1pw9: High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D

Protein crystallography data

The structure of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D, PDB code: 1pw9 was solved by A.K.Shrive, H.A.Tharia, P.Strong, U.Kishore, I.Burns, P.J.Rizkallah, K.B.Reid, T.J.Greenhough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.50 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.550, 108.520, 55.690, 90.00, 91.20, 90.00
R / Rfree (%) 22.7 / 24.9

Calcium Binding Sites:

The binding sites of Calcium atom in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D (pdb code 1pw9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D, PDB code: 1pw9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1pw9

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Calcium binding site 1 out of 10 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:16.6
occ:1.00
 OD1 A:ASP342 2.3 17.1 1.0
OD1 A:ASN341 2.4 16.4 1.0
OD1 A:ASN323 2.4 21.0 1.0
OE1 A:GLU329 2.4 18.2 1.0
OE1 A:GLU321 2.5 21.8 1.0
O A:HOH447 2.6 22.2 1.0
O A:HOH416 2.6 17.2 1.0
O A:ASP342 2.8 19.2 1.0
CG A:ASN323 3.3 22.1 1.0
CG A:ASP342 3.3 18.1 1.0
CG A:ASN341 3.4 16.8 1.0
CD A:GLU329 3.4 18.0 1.0
CD A:GLU321 3.5 23.3 1.0
ND2 A:ASN323 3.7 22.9 1.0
OE2 A:GLU329 3.8 17.6 1.0
OE2 A:GLU321 3.8 24.1 1.0
C A:ASP342 3.8 19.2 1.0
ND2 A:ASN341 3.9 16.0 1.0
N A:ASP342 3.9 17.7 1.0
OD2 A:ASP342 4.0 17.2 1.0
N A:ASN323 4.2 19.2 1.0
CA A:ASP342 4.2 18.2 1.0
CB A:ASP342 4.4 17.7 1.0
CB A:ASN323 4.5 20.4 1.0
C A:ASN341 4.6 17.3 1.0
CB A:ASP325 4.7 23.7 1.0
N A:ASP324 4.7 18.1 1.0
CB A:ASN341 4.7 16.3 1.0
CG A:GLU321 4.7 22.6 1.0
N A:ASP325 4.7 21.1 1.0
CG A:GLU329 4.7 18.1 1.0
CA A:ASN323 4.8 19.2 1.0
CA A:ASN341 4.9 17.3 1.0
CB A:GLU329 4.9 17.8 1.0
N A:ARG343 5.0 20.1 1.0

Calcium binding site 2 out of 10 in 1pw9

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Calcium binding site 2 out of 10 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:16.2
occ:1.00
 O A:HOH425 2.3 17.4 1.0
OD1 A:ASP324 2.5 16.6 1.0
OD1 A:ASP330 2.5 16.5 1.0
O A:GLU329 2.5 16.9 1.0
OD2 A:ASP297 2.5 16.6 1.0
OE1 A:GLU301 2.6 18.5 1.0
OE2 A:GLU301 2.7 18.5 1.0
OD1 A:ASP297 2.8 16.1 1.0
CD A:GLU301 3.0 20.3 1.0
CG A:ASP297 3.0 16.4 1.0
CG A:ASP324 3.3 17.4 1.0
C A:GLU329 3.4 18.0 1.0
CG A:ASP330 3.6 16.7 1.0
CA A:ASP330 3.7 16.5 1.0
N A:ASP330 3.9 17.0 1.0
CB A:ASP324 4.0 17.5 1.0
CA A:CA403 4.0 19.2 1.0
OD2 A:ASP324 4.1 16.5 1.0
CB A:ASP330 4.2 16.7 1.0
O A:HOH437 4.3 22.4 1.0
N A:GLU329 4.3 20.2 1.0
CZ A:PHE304 4.4 17.6 1.0
CA A:GLU329 4.4 18.7 1.0
CG A:GLU301 4.5 19.6 1.0
CA A:ASP324 4.5 19.0 1.0
CB A:ASP297 4.5 16.3 1.0
OD2 A:ASP342 4.6 17.2 1.0
O A:HOH408 4.6 18.0 1.0
OD2 A:ASP330 4.6 17.8 1.0
N A:GLY302 4.7 20.1 1.0
CE1 A:PHE304 4.8 17.3 1.0
O A:ASP297 4.9 19.3 1.0
CB A:GLU329 4.9 17.8 1.0
C A:ASP330 4.9 17.1 1.0
O A:HOH423 5.0 21.9 1.0
O A:HOH421 5.0 19.0 1.0

Calcium binding site 3 out of 10 in 1pw9

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Calcium binding site 3 out of 10 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:19.2
occ:1.00
 O A:HOH421 2.2 19.0 1.0
O A:HOH469 2.3 32.0 1.0
O A:HOH437 2.4 22.4 1.0
OD2 A:ASP330 2.5 17.8 1.0
OD1 A:ASP330 2.5 16.5 1.0
O A:HOH524 2.6 37.2 1.0
OE1 A:GLU301 2.6 18.5 1.0
CG A:ASP330 2.9 16.7 1.0
CD A:GLU301 3.7 20.3 1.0
CA A:CA402 4.0 16.2 1.0
OD1 A:ASP324 4.3 16.6 1.0
CB A:GLU301 4.3 19.7 1.0
CB A:ASP330 4.4 16.7 1.0
CG A:GLU301 4.4 19.6 1.0
O A:ASP297 4.5 19.3 1.0
OE2 A:GLU301 4.7 18.5 1.0
OD2 A:ASP324 4.7 16.5 1.0
OD1 A:ASP297 4.7 16.1 1.0
CA A:GLU301 4.8 20.6 1.0
O A:GLY327 4.9 26.2 1.0
O A:HOH441 4.9 23.4 1.0
CG A:ASP324 4.9 17.4 1.0
OD2 A:ASP297 5.0 16.6 1.0

Calcium binding site 4 out of 10 in 1pw9

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Calcium binding site 4 out of 10 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:27.6
occ:1.00
 OE1 C:GLU232 2.2 18.7 1.0
O B:HOH428 2.2 18.1 1.0
OE1 B:GLU232 2.3 25.4 1.0
O A:HOH455 2.3 22.3 1.0
OE1 A:GLU232 2.4 21.9 1.0
O A:HOH449 2.4 27.1 1.0
CD A:GLU232 3.0 20.6 1.0
CD C:GLU232 3.2 17.7 1.0
OE2 A:GLU232 3.2 22.4 1.0
CD B:GLU232 3.3 24.3 1.0
OE2 C:GLU232 3.6 18.6 1.0
OE2 B:GLU232 3.8 25.8 1.0
NZ C:LYS246 4.1 14.4 1.0
CA B:GLU232 4.2 16.7 1.0
CA C:GLU232 4.3 14.7 1.0
O B:GLU232 4.3 15.5 1.0
CG A:GLU232 4.3 19.0 1.0
CA A:GLU232 4.3 15.1 1.0
CB B:GLU232 4.4 18.7 1.0
NZ A:LYS246 4.4 13.7 1.0
CG C:GLU232 4.4 17.0 1.0
O A:GLU232 4.4 13.7 1.0
O C:GLU232 4.4 14.9 1.0
CG B:GLU232 4.4 22.4 1.0
CB C:GLU232 4.4 15.8 1.0
CB A:GLU232 4.4 16.1 1.0
NZ B:LYS246 4.5 18.4 1.0
C B:GLU232 4.7 16.2 1.0
O B:HOH414 4.8 19.9 1.0
O C:HOH524 4.8 22.4 1.0
O A:HOH435 4.8 21.2 1.0
C A:GLU232 4.8 14.2 1.0
C C:GLU232 4.9 15.5 1.0

Calcium binding site 5 out of 10 in 1pw9

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Calcium binding site 5 out of 10 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:13.3
occ:1.00
 OD1 B:ASP342 2.3 13.9 1.0
OD1 B:ASN341 2.4 14.7 1.0
OE1 B:GLU329 2.4 17.5 1.0
OD1 B:ASN323 2.5 15.5 1.0
O B:HOH418 2.5 14.3 1.0
O B:HOH406 2.6 17.0 1.0
OE1 B:GLU321 2.6 16.0 1.0
O B:ASP342 2.7 13.0 1.0
CG B:ASN341 3.4 15.4 1.0
CD B:GLU329 3.4 17.8 1.0
CG B:ASP342 3.4 14.3 1.0
CG B:ASN323 3.5 16.3 1.0
CD B:GLU321 3.5 15.9 1.0
OE2 B:GLU329 3.7 17.8 1.0
C B:ASP342 3.7 14.0 1.0
ND2 B:ASN341 3.8 15.1 1.0
N B:ASP342 3.8 13.9 1.0
OE2 B:GLU321 3.9 16.1 1.0
ND2 B:ASN323 4.0 15.8 1.0
OD2 B:ASP342 4.1 13.1 1.0
CA B:ASP342 4.2 13.9 1.0
N B:ASN323 4.2 15.4 1.0
CB B:ASP342 4.4 14.1 1.0
C B:ASN341 4.5 14.6 1.0
CB B:ASN323 4.6 15.7 1.0
CB B:ASN341 4.7 14.9 1.0
CB B:ASP325 4.7 22.0 1.0
CG B:GLU329 4.7 16.4 1.0
CG B:GLU321 4.7 16.0 1.0
N B:ASP325 4.8 18.7 1.0
N B:ASP324 4.8 16.3 1.0
CA B:ASN323 4.8 15.9 1.0
CA B:ASN341 4.8 14.9 1.0
N B:ARG343 4.9 14.7 1.0
CB B:GLU329 4.9 16.9 1.0

Calcium binding site 6 out of 10 in 1pw9

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Calcium binding site 6 out of 10 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:13.7
occ:1.00
 O B:HOH422 2.2 17.5 1.0
O B:GLU329 2.4 16.0 1.0
OD2 B:ASP297 2.4 19.3 1.0
OD1 B:ASP330 2.5 18.8 1.0
OD1 B:ASP324 2.6 17.2 1.0
OD1 B:ASP297 2.6 16.6 1.0
OE2 B:GLU301 2.6 17.6 1.0
OE1 B:GLU301 2.6 17.0 1.0
CG B:ASP297 2.9 19.1 1.0
CD B:GLU301 2.9 18.8 1.0
C B:GLU329 3.3 16.2 1.0
CG B:ASP324 3.4 18.6 1.0
CG B:ASP330 3.6 19.1 1.0
CA B:ASP330 3.7 17.1 1.0
CA B:CA403 3.9 19.2 1.0
N B:ASP330 3.9 16.8 1.0
CB B:ASP324 4.0 17.0 1.0
O B:HOH439 4.1 23.1 1.0
CB B:ASP330 4.3 17.7 1.0
OD2 B:ASP324 4.3 18.0 1.0
O B:HOH460 4.4 23.3 1.0
CB B:ASP297 4.4 19.2 1.0
CG B:GLU301 4.4 19.7 1.0
CA B:GLU329 4.4 17.2 1.0
CZ B:PHE304 4.5 19.1 1.0
N B:GLU329 4.5 18.1 1.0
CA B:ASP324 4.5 17.7 1.0
OD2 B:ASP342 4.5 13.1 1.0
OD2 B:ASP330 4.5 18.4 1.0
N B:GLY302 4.7 22.2 1.0
O B:ASP297 4.8 20.7 1.0
C B:ASP330 4.9 17.6 1.0
O B:HOH445 4.9 18.6 1.0
CA B:GLU301 4.9 22.0 1.0
CB B:GLU329 4.9 16.9 1.0
O B:HOH450 5.0 26.8 1.0

Calcium binding site 7 out of 10 in 1pw9

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Calcium binding site 7 out of 10 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:19.2
occ:1.00
 O B:HOH445 2.2 18.6 1.0
O B:HOH470 2.3 23.1 1.0
OE1 B:GLU301 2.4 17.0 1.0
O B:HOH439 2.4 23.1 1.0
OD1 B:ASP330 2.5 18.8 1.0
O B:HOH417 2.5 19.4 1.0
OD2 B:ASP330 2.5 18.4 1.0
CG B:ASP330 2.8 19.1 1.0
CD B:GLU301 3.6 18.8 1.0
CA B:CA402 3.9 13.7 1.0
CB B:GLU301 4.2 21.3 1.0
O B:HOH421 4.2 23.1 1.0
OD1 B:ASP324 4.3 17.2 1.0
O B:ASP297 4.3 20.7 1.0
CG B:GLU301 4.3 19.7 1.0
CB B:ASP330 4.3 17.7 1.0
O B:HOH494 4.4 39.8 1.0
OD1 B:ASP297 4.5 16.6 1.0
OE2 B:GLU301 4.5 17.6 1.0
O B:HOH491 4.6 30.4 1.0
CA B:GLU301 4.6 22.0 1.0
O B:HOH518 4.7 31.8 1.0
OD2 B:ASP297 4.8 19.3 1.0
CG B:ASP297 4.9 19.1 1.0
OD2 B:ASP324 4.9 18.0 1.0
O B:HOH427 5.0 20.3 1.0
CG B:ASP324 5.0 18.6 1.0
O B:GLY327 5.0 19.9 1.0

Calcium binding site 8 out of 10 in 1pw9

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Calcium binding site 8 out of 10 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:16.5
occ:1.00
 OD1 C:ASP342 2.2 14.6 1.0
OE1 C:GLU329 2.3 17.3 1.0
OD1 C:ASN341 2.4 16.3 1.0
OD1 C:ASN323 2.4 16.7 1.0
O C:HOH411 2.6 17.1 1.0
O C:ASP342 2.7 16.8 1.0
O C:HOH422 2.7 16.8 1.0
OE1 C:GLU321 2.7 17.2 1.0
CD C:GLU329 3.3 18.3 1.0
CG C:ASP342 3.3 15.0 1.0
CG C:ASN341 3.4 17.8 1.0
CG C:ASN323 3.5 17.6 1.0
CD C:GLU321 3.5 17.3 1.0
OE2 C:GLU329 3.6 18.6 1.0
C C:ASP342 3.7 17.4 1.0
ND2 C:ASN341 3.8 16.4 1.0
OE2 C:GLU321 3.8 18.3 1.0
N C:ASP342 3.8 16.7 1.0
ND2 C:ASN323 4.0 17.9 1.0
OD2 C:ASP342 4.0 13.9 1.0
CA C:ASP342 4.2 17.1 1.0
N C:ASN323 4.2 15.4 1.0
CB C:ASP342 4.3 16.0 1.0
O C:HOH513 4.3 38.8 1.0
C C:ASN341 4.5 17.1 1.0
CG C:GLU329 4.6 18.1 1.0
CB C:ASP325 4.6 21.4 1.0
N C:ASP325 4.6 17.2 1.0
CB C:ASN323 4.6 16.6 1.0
CB C:ASN341 4.7 16.8 1.0
N C:ASP324 4.7 16.1 1.0
CG C:GLU321 4.8 15.2 1.0
CB C:GLU329 4.8 18.7 1.0
CA C:ASN323 4.8 15.7 1.0
CA C:ASN341 4.9 17.4 1.0
N C:ARG343 4.9 18.6 1.0
C C:ASN323 5.0 16.2 1.0

Calcium binding site 9 out of 10 in 1pw9

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Calcium binding site 9 out of 10 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:18.4
occ:1.00
 O C:HOH409 2.4 14.2 1.0
O C:GLU329 2.4 18.6 1.0
OD2 C:ASP297 2.5 19.6 1.0
OE2 C:GLU301 2.5 19.5 1.0
OD1 C:ASP324 2.6 17.0 1.0
OD1 C:ASP330 2.6 17.6 1.0
OE1 C:GLU301 2.6 18.9 1.0
OD1 C:ASP297 2.7 19.1 1.0
CD C:GLU301 2.9 19.9 1.0
CG C:ASP297 3.0 20.5 1.0
C C:GLU329 3.4 19.0 1.0
CG C:ASP324 3.4 18.9 1.0
CG C:ASP330 3.7 19.9 1.0
CA C:ASP330 3.8 19.0 1.0
CB C:ASP324 3.9 17.7 1.0
O C:HOH421 3.9 18.4 1.0
N C:ASP330 4.0 18.9 1.0
CA C:CA403 4.0 19.3 1.0
OD2 C:ASP324 4.2 18.2 1.0
CB C:ASP330 4.3 19.2 1.0
CG C:GLU301 4.4 20.6 1.0
CZ C:PHE304 4.4 18.6 1.0
CA C:GLU329 4.4 19.3 1.0
N C:GLU329 4.5 20.7 1.0
CA C:ASP324 4.5 16.6 1.0
CB C:ASP297 4.5 21.0 1.0
OD2 C:ASP342 4.5 13.9 1.0
N C:GLY302 4.6 21.4 1.0
OD2 C:ASP330 4.7 18.1 1.0
CE1 C:PHE304 4.7 18.6 1.0
O C:HOH431 4.8 22.8 1.0
O C:ASP297 4.8 22.8 1.0
CB C:GLU329 5.0 18.7 1.0
O C:HOH450 5.0 20.8 1.0
CA C:GLU301 5.0 22.3 1.0
O C:HOH407 5.0 19.5 1.0
C C:ASP330 5.0 18.6 1.0

Calcium binding site 10 out of 10 in 1pw9

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Calcium binding site 10 out of 10 in the High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of High Resolution Crystal Structure of An Active Recombinant Fragment of Human Lung Surfactant Protein D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:19.3
occ:1.00
 O C:HOH450 2.2 20.8 1.0
O C:HOH421 2.3 18.4 1.0
OE1 C:GLU301 2.4 18.9 1.0
O C:HOH454 2.4 27.6 1.0
OD2 C:ASP330 2.6 18.1 1.0
O C:HOH500 2.6 30.4 1.0
OD1 C:ASP330 2.6 17.6 1.0
CG C:ASP330 2.9 19.9 1.0
CD C:GLU301 3.6 19.9 1.0
CA C:CA402 4.0 18.4 1.0
O C:HOH448 4.1 25.2 1.0
CB C:GLU301 4.2 21.6 1.0
CG C:GLU301 4.3 20.6 1.0
O C:ASP297 4.3 22.8 1.0
OD1 C:ASP324 4.4 17.0 1.0
CB C:ASP330 4.4 19.2 1.0
OE2 C:GLU301 4.5 19.5 1.0
O C:HOH515 4.6 34.3 1.0
CA C:GLU301 4.7 22.3 1.0
OD1 C:ASP297 4.7 19.1 1.0
OD2 C:ASP324 4.9 18.2 1.0
O C:HOH444 4.9 21.3 1.0
OD2 C:ASP297 5.0 19.6 1.0
O C:GLY327 5.0 20.9 1.0

Reference:

A.K.Shrive, H.A.Tharia, P.Strong, U.Kishore, I.Burns, P.J.Rizkallah, K.B.Reid, T.J.Greenhough. High Resolution Structural Insights Into Ligand Binding and Immune Cell Recognition By Human Lung Surfactant Protein D J.Mol.Biol. V. 331 509 2003.
ISSN: ISSN 0022-2836
PubMed: 12888356
DOI: 10.1016/S0022-2836(03)00761-7
Page generated: Thu Jul 11 13:54:12 2024

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