Calcium in PDB 4irz: Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab

The structure of Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab, PDB code: 4irz was solved by Y.Yu, T.Schurpf, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.62 / 2.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.610, 77.890, 217.740, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 28.7

The structure of Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab (pdb code 4irz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab, PDB code: 4irz:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab


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 A4B7 Headpiece Complexed with Fab Natalizumab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:55.4 occ:1.00 O A:PHE287 2.0 73.7 1.0 OD1 A:ASP281 2.3 70.1 1.0 OD1 A:ASN283 2.3 62.1 1.0 OD2 A:ASP289 2.4 47.0 1.0 OD1 A:ASP285 2.4 64.5 1.0 O A:HOH701 2.4 29.3 1.0 OD1 A:ASP289 2.4 44.2 1.0 CG A:ASP289 2.6 45.5 1.0 HA A:ASP281 3.2 78.5 1.0 C A:PHE287 3.2 72.4 1.0 CG A:ASP285 3.3 66.2 1.0 CG A:ASN283 3.4 63.5 1.0 HD22 A:ASN283 3.4 77.5 1.0 H A:ASN283 3.4 71.6 1.0 OD2 A:ASP285 3.4 65.8 1.0 CG A:ASP281 3.5 69.3 1.0 H A:LEU282 3.6 49.6 1.0 HA A:SER288 3.7 55.2 1.0 H A:ASP289 3.8 51.0 1.0 N A:ASP289 3.8 42.5 1.0 ND2 A:ASN283 3.8 64.6 1.0 H A:ASP285 3.8 79.3 1.0 C A:SER288 3.9 44.8 1.0 CB A:ASP289 3.9 43.5 1.0 HB2 A:PHE287 3.9 94.0 1.0 CA A:ASP281 4.0 65.5 1.0 CA A:SER288 4.1 46.0 1.0 N A:SER288 4.1 49.4 1.0 HB3 A:ASN311 4.2 81.1 1.0 N A:LEU282 4.2 41.4 1.0 H A:PHE287 4.2 94.7 1.0 CA A:PHE287 4.2 76.5 1.0 HB2 A:ASP289 4.2 52.2 1.0 H A:GLY286 4.3 90.4 1.0 N A:ASN283 4.3 59.7 1.0 CB A:ASP281 4.3 67.0 1.0 N A:PHE287 4.3 78.9 1.0 H A:ASN311 4.3 77.3 1.0 CA A:ASP289 4.4 42.5 1.0 O A:SER288 4.4 47.7 1.0 OD2 A:ASP281 4.4 70.5 1.0 C A:ASP281 4.5 66.3 1.0 HG23 A:ILE310 4.5 59.0 1.0 CB A:PHE287 4.5 78.3 1.0 HA A:ASP289 4.5 51.0 1.0 HB2 A:ASP281 4.6 80.5 1.0 HB3 A:ASP289 4.6 52.2 1.0 N A:ASP285 4.6 66.1 1.0 HD21 A:ASN283 4.6 77.5 1.0 CB A:ASP285 4.7 69.1 1.0 CB A:ASN283 4.7 64.2 1.0 H A:ALA284 4.8 66.6 1.0 N A:GLY286 4.8 75.3 1.0 HB3 A:PHE287 4.8 94.0 1.0 O A:VAL280 4.8 42.7 1.0 CA A:ASN283 4.9 62.6 1.0 H A:SER288 4.9 59.2 1.0 N A:ALA284 5.0 55.5 1.0 CB A:ASN311 5.0 67.6 1.0 HB2 A:ASN311 5.0 81.1 1.0 HB3 A:ASP285 5.0 82.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab


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 A4B7 Headpiece Complexed with Fab Natalizumab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:57.7 occ:1.00 OD1 A:ASP348 2.3 64.2 1.0 OD1 A:ASP346 2.3 59.8 1.0 OD1 A:ASP352 2.3 44.8 1.0 O A:PHE350 2.4 68.6 1.0 OD1 A:ASP344 2.4 73.7 1.0 OD2 A:ASP352 2.4 42.9 1.0 O A:HOH702 2.4 56.0 1.0 CG A:ASP352 2.7 42.3 1.0 CG A:ASP348 3.1 64.8 1.0 CG A:ASP346 3.3 62.4 1.0 H A:PHE350 3.3 79.6 1.0 HB2 A:PHE350 3.4 79.6 1.0 C A:PHE350 3.4 66.1 1.0 OD2 A:ASP348 3.5 65.4 1.0 HD21 A:ASN371 3.6 78.5 1.0 CG A:ASP344 3.6 74.6 1.0 H A:ASP348 3.6 74.2 1.0 H A:GLY372 3.7 59.8 1.0 H A:ASP346 3.7 79.1 1.0 OD2 A:ASP346 3.8 64.4 1.0 HA A:ASP344 3.8 84.1 1.0 N A:PHE350 3.9 66.3 1.0 HB3 A:ASN371 3.9 75.9 1.0 CA A:PHE350 4.0 66.5 1.0 CB A:PHE350 4.2 66.4 1.0 HB3 A:ASP348 4.2 78.6 1.0 CB A:ASP352 4.2 39.4 1.0 CB A:ASP348 4.2 65.5 1.0 H A:ILE345 4.2 79.5 1.0 H A:GLY349 4.2 72.7 1.0 N A:ASP348 4.3 61.8 1.0 OD2 A:ASP344 4.3 77.5 1.0 ND2 A:ASN371 4.4 65.4 1.0 HD1 A:PHE350 4.4 83.0 1.0 N A:ASP352 4.5 39.1 1.0 N A:ASP346 4.5 66.0 1.0 N A:GLU351 4.5 57.7 1.0 N A:GLY372 4.5 49.9 1.0 C A:GLU351 4.5 54.8 1.0 HA A:GLU351 4.5 67.7 1.0 H A:ASP352 4.5 46.9 1.0 HB2 A:ASP352 4.6 47.3 1.0 CA A:ASP344 4.6 70.1 1.0 CB A:ASP344 4.6 73.1 1.0 CB A:ASP346 4.6 62.8 1.0 N A:GLY349 4.6 60.6 1.0 HB3 A:ASP352 4.7 47.3 1.0 H A:ASN347 4.7 60.7 1.0 CA A:ASP348 4.7 64.5 1.0 HB3 A:PHE350 4.7 79.6 1.0 N A:ILE345 4.7 66.2 1.0 N A:ASN347 4.8 50.6 1.0 CA A:GLU351 4.8 56.4 1.0 HB2 A:ASP344 4.8 87.8 1.0 HA A:ASN371 4.8 72.6 1.0 CB A:ASN371 4.8 63.2 1.0 CA A:ASP352 4.8 38.2 1.0 C A:ASP346 4.8 66.1 1.0 O A:GLY372 4.8 57.1 1.0 HG22 A:ILE345 4.9 76.7 1.0 HB3 A:ASP346 4.9 75.3 1.0 CA A:ASP346 4.9 64.3 1.0 O A:GLU351 4.9 54.6 1.0 HD22 A:ASN371 4.9 78.5 1.0 HA3 A:GLY372 5.0 60.4 1.0 HA A:ASP352 5.0 45.8 1.0 C A:ASP348 5.0 64.2 1.0 HB2 A:ASP348 5.0 78.6 1.0 C A:ASP344 5.0 72.4 1.0 HA A:PHE350 5.0 79.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Natalizumab


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 A4B7 Headpiece Complexed with Fab Natalizumab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:44.9 occ:1.00 O A:TYR412 2.2 42.7 1.0 OD1 A:ASN410 2.3 60.6 1.0 OD1 A:ASP408 2.3 57.1 1.0 OD1 A:ASP406 2.3 56.0 1.0 OD1 A:ASP414 2.4 45.0 1.0 OD2 A:ASP414 2.4 46.2 1.0 O A:HOH703 2.4 88.5 1.0 CG A:ASP414 2.6 43.6 1.0 H A:TYR412 3.0 58.6 1.0 HG1 A:THR430 3.1 59.3 1.0 CG A:ASP408 3.3 61.0 1.0 C A:TYR412 3.3 43.5 1.0 CG A:ASP406 3.3 55.6 1.0 CG A:ASN410 3.3 61.4 1.0 H A:ASN410 3.3 78.3 1.0 HB2 A:TYR412 3.4 56.1 1.0 OD2 A:ASP408 3.5 63.0 1.0 N A:TYR412 3.6 48.8 1.0 HA A:ASP406 3.7 58.6 1.0 HD22 A:ASN410 3.7 72.7 1.0 OG1 A:THR430 3.8 49.4 1.0 H A:ASP408 3.8 71.8 1.0 CA A:TYR412 3.8 46.5 1.0 H A:ALA407 3.9 50.7 1.0 OD2 A:ASP406 4.0 58.2 1.0 ND2 A:ASN410 4.0 60.5 1.0 CB A:TYR412 4.1 46.7 1.0 H A:THR430 4.1 50.0 1.0 CB A:ASP414 4.1 40.7 1.0 H A:ASN409 4.1 72.2 1.0 H A:GLY411 4.1 65.6 1.0 N A:ASN410 4.2 65.3 1.0 CB A:ASP406 4.3 52.5 1.0 N A:ASP414 4.3 36.7 1.0 HB3 A:TYR412 4.3 56.1 1.0 H A:ASP414 4.4 44.1 1.0 CA A:ASP406 4.4 48.8 1.0 HB2 A:ASP406 4.4 63.0 1.0 N A:VAL413 4.4 42.0 1.0 C A:VAL413 4.4 37.9 1.0 N A:GLY411 4.5 54.6 1.0 CB A:ASN410 4.5 64.4 1.0 N A:ASP408 4.5 59.9 1.0 N A:ALA407 4.5 42.2 1.0 HA A:ASP414 4.5 42.8 1.0 HB2 A:ASP414 4.5 48.8 1.0 N A:ASN409 4.5 60.1 1.0 CA A:ASP414 4.6 35.7 1.0 CB A:ASP408 4.6 62.4 1.0 HB3 A:ASP414 4.6 48.8 1.0 HA A:VAL413 4.7 47.1 1.0 CA A:ASN410 4.7 66.9 1.0 HB3 A:ASN410 4.7 77.3 1.0 C A:ASN410 4.7 68.0 1.0 HA A:TYR412 4.8 55.8 1.0 HD21 A:ASN410 4.8 72.7 1.0 CA A:VAL413 4.8 39.3 1.0 C A:GLY411 4.8 52.5 1.0 C A:ASP406 4.8 50.5 1.0 O A:VAL413 4.8 38.0 1.0 N A:THR430 4.9 41.6 1.0 CA A:ASP408 4.9 62.0 1.0 O A:THR430 5.0 47.1 1.0

Y.Yu, T.Schurpf, T.A.Springer. How Natalizumab Binds and Antagonizes Alpha 4 Integrins. J.Biol.Chem. V. 288 32314 2013.
ISSN: ISSN 0021-9258
PubMed: 24047894
DOI: 10.1074/JBC.M113.501668