Calcium in PDB 4m17: Crystal Structure of Surfactant Protein-D D325A/R343V Mutant

The structure of Crystal Structure of Surfactant Protein-D D325A/R343V Mutant, PDB code: 4m17 was solved by B.C.Goh, M.J.Rynkiewicz, T.R.Cafarella, M.R.White, K.L.Hartshorn, K.Allen, E.C.Crouch, O.Calin, P.H.Seeberger, K.Schulten, B.A.Seaton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.94 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.524, 160.108, 160.073, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 18.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Surfactant Protein-D D325A/R343V Mutant (pdb code 4m17). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 36 binding sites of Calcium where determined in the Crystal Structure of Surfactant Protein-D D325A/R343V Mutant, PDB code: 4m17:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 36 in the Crystal Structure of Surfactant Protein-D D325A/R343V Mutant


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 Surfactant Protein-D D325A/R343V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:26.8 occ:1.00 OD1 A:ASP342 2.3 29.7 1.0 OD1 A:ASN341 2.4 23.0 1.0 OD1 A:ASN323 2.4 29.9 1.0 OE1 A:GLU329 2.4 27.1 1.0 O A:ASP342 2.4 25.8 1.0 OE1 A:GLU321 2.5 28.6 1.0 O A:HOH511 2.9 28.8 1.0 CG A:ASP342 3.2 25.9 1.0 CD A:GLU321 3.3 25.4 1.0 O A:HOH538 3.3 27.5 1.0 CG A:ASN323 3.3 31.1 1.0 CD A:GLU329 3.4 26.2 1.0 CG A:ASN341 3.5 20.3 1.0 C A:ASP342 3.5 23.1 1.0 OE2 A:GLU321 3.5 25.9 1.0 ND2 A:ASN323 3.7 32.8 1.0 OD2 A:ASP342 3.7 26.1 1.0 OE2 A:GLU329 3.8 25.4 1.0 N A:ASP342 3.8 24.1 1.0 ND2 A:ASN341 3.9 21.5 1.0 CA A:ASP342 4.0 21.9 1.0 CB A:ASP342 4.2 26.2 1.0 N A:ASN323 4.2 29.9 1.0 C A:ASN341 4.5 23.4 1.0 CG A:GLU321 4.5 21.8 1.0 N A:ASP324 4.6 29.1 1.0 CB A:ASN323 4.6 24.9 1.0 N A:VAL343 4.7 24.4 1.0 CG A:GLU329 4.7 23.8 1.0 CB A:ASN341 4.7 23.0 1.0 N A:ALA325 4.7 29.7 1.0 CA A:ASN341 4.8 23.8 1.0 CB A:GLU329 4.8 23.3 1.0 CB A:ALA325 4.8 24.0 1.0 CA A:ASN323 4.8 29.5 1.0

Calcium binding site 2 out of 36 in the Crystal Structure of Surfactant Protein-D D325A/R343V Mutant


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 Surfactant Protein-D D325A/R343V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:27.4 occ:1.00 O A:GLU329 2.4 24.0 1.0 OD1 A:ASP324 2.4 27.2 1.0 OD1 A:ASP330 2.4 30.0 1.0 OE1 A:GLU301 2.4 31.5 1.0 OD2 A:ASP297 2.4 25.4 1.0 OE2 A:GLU301 2.4 30.9 1.0 O A:HOH501 2.5 29.3 1.0 OD1 A:ASP297 2.6 25.5 1.0 CD A:GLU301 2.7 28.8 1.0 CG A:ASP297 2.8 24.9 1.0 CG A:ASP324 3.3 25.7 1.0 C A:GLU329 3.3 22.6 1.0 CG A:ASP330 3.5 27.4 1.0 CA A:ASP330 3.7 22.6 1.0 CA A:CA403 3.7 30.5 1.0 N A:ASP330 3.9 23.9 1.0 CB A:ASP324 3.9 26.6 1.0 OD2 A:ASP324 4.1 27.4 1.0 CB A:ASP330 4.1 25.6 1.0 O A:HOH502 4.2 32.3 1.0 CG A:GLU301 4.2 29.2 1.0 CB A:ASP297 4.3 22.9 1.0 CA A:GLU329 4.4 24.4 1.0 OD2 A:ASP330 4.5 32.4 1.0 N A:GLU329 4.5 25.9 1.0 N A:GLY302 4.5 29.5 1.0 CZ A:PHE304 4.5 21.7 1.0 CA A:ASP324 4.6 26.2 1.0 O A:ASP297 4.6 27.6 1.0 CA A:GLU301 4.8 27.7 1.0 OD2 A:ASP342 4.9 26.1 1.0 O A:HOH503 4.9 25.9 1.0 CB A:GLU301 4.9 30.7 1.0 C A:ASP330 4.9 20.0 1.0 CE2 A:PHE304 5.0 21.8 1.0

Calcium binding site 3 out of 36 in the Crystal Structure of Surfactant Protein-D D325A/R343V Mutant


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 Surfactant Protein-D D325A/R343V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:30.5 occ:1.00 OE1 A:GLU301 2.3 31.5 1.0 O A:HOH503 2.3 25.9 1.0 O A:HOH504 2.3 39.2 1.0 O A:HOH502 2.4 32.3 1.0 OD1 A:ASP330 2.4 30.0 1.0 OD2 A:ASP330 2.5 32.4 1.0 O A:HOH581 2.7 40.1 1.0 CG A:ASP330 2.8 27.4 1.0 CD A:GLU301 3.5 28.8 1.0 CA A:CA402 3.7 27.4 1.0 CB A:GLU301 4.0 30.7 1.0 O A:ASP297 4.1 27.6 1.0 CG A:GLU301 4.1 29.2 1.0 CB A:ASP330 4.2 25.6 1.0 OD1 A:ASP324 4.3 27.2 1.0 OD1 A:ASP297 4.3 25.5 1.0 O A:HOH562 4.4 28.3 1.0 OE2 A:GLU301 4.4 30.9 1.0 O A:HOH619 4.5 38.4 1.0 CA A:GLU301 4.5 27.7 1.0 OD2 A:ASP297 4.6 25.4 1.0 CG A:ASP297 4.7 24.9 1.0 O A:HOH552 4.8 32.2 1.0 O A:SER298 4.9 33.1 1.0 OD2 A:ASP324 4.9 27.4 1.0 CA A:SER298 4.9 33.1 1.0 C A:ASP297 4.9 26.9 1.0 CG A:ASP324 5.0 25.7 1.0

Calcium binding site 4 out of 36 in the Crystal Structure of Surfactant Protein-D D325A/R343V Mutant


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 Surfactant Protein-D D325A/R343V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:27.2 occ:1.00 OD1 B:ASP342 2.3 27.9 1.0 OE1 B:GLU329 2.4 31.3 1.0 O B:ASP342 2.4 29.3 1.0 OD1 B:ASN341 2.4 26.9 1.0 OD1 B:ASN323 2.4 31.2 1.0 OE1 B:GLU321 2.4 28.6 1.0 O B:HOH542 2.8 27.6 1.0 CG B:ASP342 3.2 23.9 1.0 CD B:GLU321 3.3 26.1 1.0 CD B:GLU329 3.3 26.9 1.0 CG B:ASN323 3.4 26.9 1.0 O B:HOH558 3.4 25.4 1.0 CG B:ASN341 3.5 25.9 1.0 C B:ASP342 3.5 26.5 1.0 OE2 B:GLU321 3.6 23.9 1.0 OE2 B:GLU329 3.6 25.7 1.0 OD2 B:ASP342 3.8 25.9 1.0 ND2 B:ASN323 3.8 25.3 1.0 N B:ASP342 3.8 24.4 1.0 ND2 B:ASN341 3.9 24.9 1.0 CA B:ASP342 4.1 22.7 1.0 N B:ASN323 4.2 26.7 1.0 CB B:ASP342 4.2 23.0 1.0 C B:ASN341 4.5 23.1 1.0 N B:ASP324 4.6 28.7 1.0 CG B:GLU321 4.6 22.3 1.0 CG B:GLU329 4.6 24.7 1.0 CB B:ASN323 4.6 25.2 1.0 N B:VAL343 4.6 24.4 1.0 N B:ALA325 4.6 26.5 1.0 CB B:ALA325 4.7 26.6 1.0 CB B:ASN341 4.7 24.8 1.0 CB B:GLU329 4.8 24.3 1.0 CA B:ASN323 4.8 26.9 1.0 CA B:ASN341 4.9 23.7 1.0 CA B:VAL343 5.0 22.4 1.0

Calcium binding site 5 out of 36 in the Crystal Structure of Surfactant Protein-D D325A/R343V Mutant


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 Surfactant Protein-D D325A/R343V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:31.2 occ:1.00 OD2 B:ASP297 2.4 27.8 1.0 O B:GLU329 2.4 28.6 1.0 OD1 B:ASP330 2.4 31.2 1.0 OE2 B:GLU301 2.4 32.6 1.0 OD1 B:ASP324 2.4 32.6 1.0 OE1 B:GLU301 2.4 33.1 1.0 O B:HOH501 2.5 30.1 1.0 OD1 B:ASP297 2.5 27.9 1.0 CD B:GLU301 2.7 31.4 1.0 CG B:ASP297 2.8 24.6 1.0 CG B:ASP324 3.3 32.6 1.0 C B:GLU329 3.3 27.8 1.0 CG B:ASP330 3.5 25.6 1.0 CA B:ASP330 3.7 26.0 1.0 CA B:CA403 3.8 34.8 1.0 O B:HOH504 3.9 30.9 1.0 N B:ASP330 3.9 28.9 1.0 CB B:ASP324 3.9 28.7 1.0 OD2 B:ASP324 4.1 33.4 1.0 CB B:ASP330 4.1 27.5 1.0 CG B:GLU301 4.2 30.9 1.0 CB B:ASP297 4.3 26.4 1.0 N B:GLY302 4.4 27.9 1.0 CA B:GLU329 4.5 27.8 1.0 OD2 B:ASP330 4.5 27.9 1.0 CZ B:PHE304 4.5 22.8 1.0 N B:GLU329 4.5 27.0 1.0 CA B:ASP324 4.6 28.3 1.0 O B:ASP297 4.6 27.5 1.0 O B:HOH572 4.7 31.6 1.0 O B:HOH585 4.8 25.9 1.0 CA B:GLU301 4.8 32.6 1.0 O B:HOH503 4.9 30.3 1.0 OD2 B:ASP342 4.9 25.9 1.0 CB B:GLU301 4.9 32.4 1.0 C B:ASP330 4.9 27.3 1.0 CE2 B:PHE304 5.0 22.8 1.0

Calcium binding site 6 out of 36 in the Crystal Structure of Surfactant Protein-D D325A/R343V Mutant


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 Surfactant Protein-D D325A/R343V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:34.8 occ:1.00 O B:HOH504 2.3 30.9 1.0 OE1 B:GLU301 2.3 33.1 1.0 O B:HOH503 2.4 30.3 1.0 O B:HOH502 2.4 29.0 1.0 OD2 B:ASP330 2.4 27.9 1.0 OD1 B:ASP330 2.4 31.2 1.0 O B:HOH505 2.4 31.0 1.0 CG B:ASP330 2.7 25.6 1.0 CD B:GLU301 3.5 31.4 1.0 CA B:CA402 3.8 31.2 1.0 CB B:GLU301 4.0 32.4 1.0 O B:ASP297 4.1 27.5 1.0 CG B:GLU301 4.2 30.9 1.0 CB B:ASP330 4.2 27.5 1.0 OD1 B:ASP324 4.3 32.6 1.0 OD1 B:ASP297 4.4 27.9 1.0 O B:HOH560 4.4 31.7 1.0 OE2 B:GLU301 4.5 32.6 1.0 CA B:GLU301 4.5 32.6 1.0 OD2 B:ASP297 4.7 27.8 1.0 CG B:ASP297 4.8 24.6 1.0 O B:SER298 4.8 35.0 1.0 OD2 B:ASP324 4.9 33.4 1.0 CA B:SER298 4.9 31.5 1.0 C B:ASP297 5.0 27.7 1.0 CG B:ASP324 5.0 32.6 1.0

Calcium binding site 7 out of 36 in the Crystal Structure of Surfactant Protein-D D325A/R343V Mutant


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 Surfactant Protein-D D325A/R343V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:29.9 occ:1.00 OD1 C:ASP342 2.3 29.6 1.0 OD1 C:ASN341 2.4 23.6 1.0 OD1 C:ASN323 2.4 33.4 1.0 OE1 C:GLU329 2.4 27.6 1.0 OE1 C:GLU321 2.4 30.1 1.0 O C:ASP342 2.4 27.6 1.0 O C:HOH585 3.2 29.2 1.0 CD C:GLU321 3.2 25.1 1.0 O C:HOH564 3.2 34.0 1.0 CG C:ASP342 3.3 25.5 1.0 CG C:ASN323 3.3 26.9 1.0 CD C:GLU329 3.3 28.3 1.0 CG C:ASN341 3.4 23.7 1.0 OE2 C:GLU321 3.5 28.0 1.0 C C:ASP342 3.6 24.7 1.0 OE2 C:GLU329 3.6 28.9 1.0 ND2 C:ASN323 3.7 31.7 1.0 ND2 C:ASN341 3.9 24.6 1.0 N C:ASP342 3.9 26.3 1.0 OD2 C:ASP342 3.9 26.1 1.0 CA C:ASP342 4.1 23.4 1.0 N C:ASN323 4.3 26.8 1.0 CB C:ASP342 4.3 24.3 1.0 CG C:GLU321 4.5 21.6 1.0 CB C:ASN323 4.6 25.8 1.0 C C:ASN341 4.6 23.5 1.0 N C:ASP324 4.6 31.7 1.0 CG C:GLU329 4.6 27.5 1.0 N C:VAL343 4.7 26.4 1.0 N C:ALA325 4.7 28.9 1.0 CB C:ALA325 4.7 27.7 1.0 CB C:ASN341 4.7 22.8 1.0 CA C:ASN323 4.9 28.2 1.0 CB C:GLU329 4.9 28.4 1.0 CA C:ASN341 4.9 22.9 1.0

Calcium binding site 8 out of 36 in the Crystal Structure of Surfactant Protein-D D325A/R343V Mutant


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 Surfactant Protein-D D325A/R343V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:31.8 occ:1.00 OD1 C:ASP330 2.4 29.5 1.0 OE2 C:GLU301 2.4 32.7 1.0 OE1 C:GLU301 2.4 35.1 1.0 OD2 C:ASP297 2.4 27.3 1.0 OD1 C:ASP324 2.4 31.6 1.0 O C:GLU329 2.4 29.0 1.0 O C:HOH501 2.4 32.9 1.0 OD1 C:ASP297 2.5 29.3 1.0 CD C:GLU301 2.7 28.9 1.0 CG C:ASP297 2.8 28.5 1.0 CG C:ASP324 3.2 30.1 1.0 C C:GLU329 3.3 26.5 1.0 CG C:ASP330 3.5 28.3 1.0 CA C:CA403 3.7 33.0 1.0 CA C:ASP330 3.7 25.6 1.0 CB C:ASP324 3.9 30.6 1.0 N C:ASP330 3.9 29.9 1.0 O C:HOH503 4.0 28.9 1.0 OD2 C:ASP324 4.1 34.2 1.0 CB C:ASP330 4.2 27.4 1.0 CG C:GLU301 4.2 28.8 1.0 CB C:ASP297 4.3 26.1 1.0 CA C:GLU329 4.4 26.6 1.0 N C:GLY302 4.4 31.4 1.0 OD2 C:ASP330 4.5 32.0 1.0 N C:GLU329 4.5 29.6 1.0 CZ C:PHE304 4.5 22.9 1.0 O C:ASP297 4.6 31.5 1.0 CA C:ASP324 4.6 28.8 1.0 O C:HOH547 4.7 26.4 1.0 CA C:GLU301 4.8 29.3 1.0 CB C:GLU301 4.9 30.0 1.0 OD2 C:ASP342 4.9 26.1 1.0 C C:ASP330 5.0 23.0 1.0 CE2 C:PHE304 5.0 24.0 1.0

Calcium binding site 9 out of 36 in the Crystal Structure of Surfactant Protein-D D325A/R343V Mutant


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 Surfactant Protein-D D325A/R343V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:33.0 occ:1.00 O C:HOH503 2.1 28.9 1.0 OE1 C:GLU301 2.3 35.1 1.0 OD1 C:ASP330 2.3 29.5 1.0 OD2 C:ASP330 2.4 32.0 1.0 O C:HOH504 2.5 37.2 1.0 CG C:ASP330 2.7 28.3 1.0 O C:HOH502 2.8 26.3 1.0 O C:HOH513 2.8 31.9 1.0 CD C:GLU301 3.5 28.9 1.0 CA C:CA402 3.7 31.8 1.0 OD1 C:ASP324 4.1 31.6 1.0 CB C:ASP330 4.2 27.4 1.0 CB C:GLU301 4.2 30.0 1.0 CG C:GLU301 4.3 28.8 1.0 O C:ASP297 4.3 31.5 1.0 O C:HOH551 4.3 30.8 1.0 OD1 C:ASP297 4.4 29.3 1.0 OE2 C:GLU301 4.5 32.7 1.0 OD2 C:ASP324 4.8 34.2 1.0 CA C:GLU301 4.8 29.3 1.0 O C:GLY327 4.8 34.4 1.0 OD2 C:ASP297 4.8 27.3 1.0 CG C:ASP324 4.8 30.1 1.0 CG C:ASP297 4.9 28.5 1.0 CA C:ASP330 5.0 25.6 1.0

Calcium binding site 10 out of 36 in the Crystal Structure of Surfactant Protein-D D325A/R343V Mutant


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 Surfactant Protein-D D325A/R343V Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:29.6 occ:1.00 OD1 D:ASP342 2.3 28.7 1.0 OE1 D:GLU329 2.4 28.6 1.0 OE1 D:GLU321 2.4 28.7 1.0 OD1 D:ASN341 2.4 29.6 1.0 O D:ASP342 2.4 30.7 1.0 OD1 D:ASN323 2.4 28.9 1.0 CG D:ASP342 3.2 28.8 1.0 O D:HOH562 3.2 30.0 1.0 CD D:GLU321 3.3 26.0 1.0 CG D:ASN323 3.3 29.1 1.0 CD D:GLU329 3.4 28.5 1.0 CG D:ASN341 3.5 25.2 1.0 C D:ASP342 3.5 26.8 1.0 OE2 D:GLU321 3.5 28.4 1.0 OD2 D:ASP342 3.7 30.6 1.0 OE2 D:GLU329 3.7 28.1 1.0 ND2 D:ASN323 3.8 29.6 1.0 N D:ASP342 3.8 27.4 1.0 ND2 D:ASN341 4.0 25.8 1.0 CA D:ASP342 4.0 24.2 1.0 N D:ASN323 4.1 27.6 1.0 CB D:ASP342 4.2 27.6 1.0 N D:ASP324 4.5 31.6 1.0 C D:ASN341 4.5 24.1 1.0 CG D:GLU321 4.5 23.2 1.0 CB D:ASN323 4.6 25.4 1.0 CG D:GLU329 4.6 27.2 1.0 N D:VAL343 4.6 28.1 1.0 N D:ALA325 4.7 32.5 1.0 CA D:ASN323 4.7 28.7 1.0 CB D:ASN341 4.7 24.0 1.0 CB D:ALA325 4.8 27.7 1.0 CB D:GLU329 4.8 27.5 1.0 CA D:ASN341 4.9 24.8 1.0 C D:ASN323 5.0 32.5 1.0 CB D:GLU321 5.0 25.5 1.0

B.C.Goh, M.J.Rynkiewicz, T.R.Cafarella, M.R.White, K.L.Hartshorn, K.Allen, E.C.Crouch, O.Calin, P.H.Seeberger, K.Schulten, B.A.Seaton. Molecular Mechanisms of Inhibition of Influenza By Surfactant Protein D Revealed By Large-Scale Molecular Dynamics Simulation. Biochemistry V. 52 8527 2013.
ISSN: ISSN 0006-2960
PubMed: 24224757
DOI: 10.1021/BI4010683