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Calcium in PDB 3v4v: Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376

Protein crystallography data

The structure of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376, PDB code: 3v4v was solved by Y.Yu, J.Zhu, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 127.580, 123.530, 154.160, 90.00, 112.63, 90.00
R / Rfree (%) 19.7 / 23.1

Other elements in 3v4v:

The structure of Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 (pdb code 3v4v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376, PDB code: 3v4v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 3v4v

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Calcium binding site 1 out of 10 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376


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 Act-1 and RO0505376 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2005

b:86.8
occ:1.00
 O A:PHE287 2.9 0.5 1.0
OD1 A:ASP285 2.9 0.1 1.0
OD1 A:ASN283 3.0 0.1 1.0
O A:HOH599 3.0 0.5 1.0
OD1 A:ASP289 3.1 0.1 1.0
CG A:ASP289 3.1 0.9 1.0
OD2 A:ASP289 3.2 0.1 1.0
OD1 A:ASP281 3.2 87.1 1.0
N A:ASP289 3.4 89.2 1.0
C A:PHE287 3.6 0.6 1.0
C A:SER288 3.7 89.6 1.0
CG A:ASN283 3.9 1.0 1.0
CA A:SER288 3.9 85.5 1.0
CB A:ASP289 4.0 0.3 1.0
CA A:ASP281 4.0 96.1 1.0
CG A:ASP285 4.0 0.1 1.0
CA A:ASP289 4.1 66.8 1.0
N A:SER288 4.1 92.7 1.0
CG A:ASP281 4.1 0.4 1.0
N A:LEU282 4.2 0.3 1.0
ND2 A:ASN283 4.2 0.1 1.0
CB A:ASP281 4.4 0.2 1.0
O A:ASP285 4.4 1.0 1.0
C A:ASP281 4.4 0.6 1.0
CB A:ASN311 4.4 0.9 1.0
OD2 A:ASP285 4.5 97.6 1.0
O A:SER288 4.5 0.6 1.0
N A:ASN283 4.5 0.1 1.0
N A:ASN311 4.6 0.5 1.0
O A:ASN311 4.7 0.4 1.0
CA A:PHE287 4.7 0.6 1.0
O A:VAL280 4.7 0.6 1.0
CB A:PHE287 4.8 86.7 1.0

Calcium binding site 2 out of 10 in 3v4v

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Calcium binding site 2 out of 10 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376


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 Act-1 and RO0505376 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2006

b:93.0
occ:1.00
 OD1 A:ASP352 2.9 0.8 1.0
OD1 A:ASP348 3.0 1.0 1.0
OD1 A:ASP346 3.0 77.8 1.0
O A:PHE350 3.1 0.8 1.0
OD2 A:ASP352 3.2 96.8 1.0
O A:HOH601 3.2 0.5 1.0
CG A:ASP348 3.3 1.0 1.0
OD2 A:ASP348 3.3 0.5 1.0
CG A:ASP352 3.3 0.2 1.0
C A:PHE350 3.5 0.1 1.0
OD1 A:ASP344 3.5 95.3 1.0
CB A:PHE350 3.6 97.1 1.0
N A:PHE350 3.6 1.0 1.0
CA A:PHE350 3.7 0.5 1.0
O A:GLY372 3.9 99.2 1.0
CG A:ASP346 4.1 0.4 1.0
ND2 A:ASN371 4.2 0.1 1.0
OD2 A:ASP346 4.3 88.4 1.0
N A:GLU351 4.4 96.1 1.0
N A:GLY372 4.4 93.7 1.0
CG A:ASP344 4.4 0.4 1.0
CB A:ASP348 4.5 0.2 1.0
N A:ASP348 4.5 0.6 1.0
CD1 A:PHE350 4.6 0.6 1.0
CG A:PHE350 4.6 0.5 1.0
C A:GLU351 4.6 1.0 1.0
N A:GLY349 4.6 0.6 1.0
CB A:ASP352 4.7 58.4 1.0
N A:ASP352 4.8 90.9 1.0
CA A:ASP348 4.8 91.9 1.0
O A:GLU351 4.8 0.0 1.0
C A:GLY372 4.8 99.6 1.0
C A:GLY349 4.8 0.9 1.0
CB A:ASN371 4.8 62.5 1.0
CA A:GLU351 4.9 0.9 1.0
CA A:GLY372 4.9 0.0 1.0
C A:ASP348 4.9 0.1 1.0

Calcium binding site 3 out of 10 in 3v4v

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Calcium binding site 3 out of 10 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376


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 Act-1 and RO0505376 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2007

b:79.2
occ:1.00
 O A:TYR412 2.6 68.4 1.0
OD1 A:ASP408 2.7 0.9 1.0
OD1 A:ASN410 2.9 86.5 1.0
O A:HOH602 3.0 66.8 1.0
OD1 A:ASP406 3.0 76.2 1.0
OD2 A:ASP414 3.0 0.5 1.0
OD1 A:ASP414 3.0 80.7 1.0
CG A:ASP414 3.3 0.3 1.0
CG A:ASP408 3.6 0.3 1.0
C A:TYR412 3.6 0.8 1.0
CG A:ASN410 3.7 0.5 1.0
N A:TYR412 3.7 87.7 1.0
OG1 A:THR430 3.9 0.9 1.0
CG A:ASP406 3.9 0.5 1.0
OD2 A:ASP408 3.9 0.8 1.0
N A:ASN410 4.0 0.8 1.0
CA A:TYR412 4.1 81.1 1.0
CB A:TYR412 4.2 68.5 1.0
ND2 A:ASN410 4.3 0.7 1.0
N A:GLY411 4.4 86.3 1.0
N A:ALA407 4.5 73.3 1.0
CB A:ASN410 4.5 0.2 1.0
N A:ASP408 4.5 88.3 1.0
N A:ASN409 4.6 0.5 1.0
CA A:ASP406 4.6 64.4 1.0
CA A:ASN410 4.6 81.5 1.0
OD2 A:ASP406 4.6 0.3 1.0
N A:ASP414 4.7 94.2 1.0
C A:ASN410 4.7 0.8 1.0
CB A:ASP414 4.7 74.7 1.0
N A:THR430 4.7 98.7 1.0
CB A:ASP406 4.7 0.4 1.0
O A:THR430 4.8 0.4 1.0
N A:VAL413 4.8 0.4 1.0
C A:VAL413 4.8 66.4 1.0
CB A:ASP408 4.9 0.2 1.0
C A:ASP406 4.9 97.2 1.0
C A:GLY411 4.9 1.0 1.0

Calcium binding site 4 out of 10 in 3v4v

Go back to Calcium Binding Sites List in 3v4v
Calcium binding site 4 out of 10 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376


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 A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2002

b:0.3
occ:1.00
 O B:GLU354 2.9 0.1 1.0
O B:SER144 2.9 0.1 1.0
OD1 B:ASP147 3.0 0.8 1.0
O B:HOH506 3.0 0.8 1.0
O B:HOH507 3.1 0.4 1.0
OD1 B:ASP148 3.2 0.1 1.0
OD2 B:ASP147 3.7 0.7 1.0
CG B:ASP147 3.7 0.6 1.0
C B:GLU354 3.9 0.7 1.0
C B:SER144 4.1 0.8 1.0
CB B:GLU354 4.1 0.8 1.0
CG B:ASP148 4.2 0.8 1.0
CA B:GLU354 4.3 0.4 1.0
OD2 B:ASP148 4.5 0.1 1.0
OD2 B:ASP270 4.6 0.5 1.0
CA B:MET145 4.8 68.5 1.0
N B:MET145 5.0 1.0 1.0
CG B:GLU354 5.0 0.7 1.0
OG B:SER144 5.0 0.0 1.0

Calcium binding site 5 out of 10 in 3v4v

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Calcium binding site 5 out of 10 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376


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 A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:69.5
occ:1.00
 OD1 B:ASN235 2.8 89.0 1.0
OD2 B:ASP179 2.9 44.2 1.0
O B:ASP237 3.0 88.4 1.0
O B:PRO239 3.0 0.4 1.0
OD1 B:ASP237 3.1 64.2 1.0
C B:PRO239 3.4 39.2 1.0
OE1 B:GLU240 3.4 0.5 1.0
CA B:GLU240 3.5 38.1 1.0
CD B:GLU240 3.5 0.4 1.0
O B:SER238 3.6 73.5 1.0
N B:GLU240 3.6 0.3 1.0
CG B:ASN235 3.6 98.0 1.0
C B:ASP237 3.7 89.5 1.0
ND2 B:ASN235 3.8 66.3 1.0
CG B:ASP179 3.8 91.9 1.0
OE2 B:GLU240 3.8 51.9 1.0
CG B:ASP237 3.8 0.4 1.0
C B:SER238 3.9 58.7 1.0
CB B:ASP179 4.1 73.8 1.0
N B:PRO239 4.1 58.7 1.0
CG B:GLU240 4.2 0.6 1.0
NE2 B:HIS274 4.2 72.2 1.0
CB B:GLU240 4.3 0.3 1.0
CA B:PRO239 4.3 84.5 1.0
N B:ASP237 4.4 81.8 1.0
CA B:ASP237 4.4 81.3 1.0
OD2 B:ASP237 4.4 68.5 1.0
N B:SER238 4.5 0.7 1.0
C B:GLU240 4.6 83.4 1.0
CB B:ASP237 4.6 0.3 1.0
CA B:SER238 4.6 70.0 1.0
CD2 B:HIS274 4.7 0.9 1.0
O B:VAL178 4.7 0.0 1.0
OD1 B:ASP179 4.8 83.0 1.0
N B:GLY241 4.8 68.8 1.0
CD B:PRO239 5.0 0.8 1.0

Calcium binding site 6 out of 10 in 3v4v

Go back to Calcium Binding Sites List in 3v4v
Calcium binding site 6 out of 10 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376


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 A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2005

b:96.1
occ:1.00
 O C:PHE287 2.9 0.1 1.0
OD1 C:ASP285 2.9 99.6 1.0
OD1 C:ASN283 3.0 0.1 1.0
OD1 C:ASP289 3.1 0.8 1.0
CG C:ASP289 3.1 0.9 1.0
O C:HOH600 3.2 0.8 1.0
OD2 C:ASP289 3.2 0.1 1.0
OD1 C:ASP281 3.3 0.2 1.0
N C:ASP289 3.4 0.5 1.0
C C:PHE287 3.6 0.8 1.0
C C:SER288 3.7 0.9 1.0
CG C:ASN283 3.9 0.4 1.0
CA C:SER288 3.9 86.2 1.0
CB C:ASP289 4.0 0.4 1.0
CA C:ASP281 4.0 0.0 1.0
CG C:ASP285 4.0 0.5 1.0
CA C:ASP289 4.1 76.1 1.0
N C:SER288 4.1 99.0 1.0
CG C:ASP281 4.1 0.6 1.0
N C:LEU282 4.2 0.5 1.0
ND2 C:ASN283 4.2 0.8 1.0
CB C:ASP281 4.4 88.3 1.0
O C:ASP285 4.4 0.2 1.0
CB C:ASN311 4.4 0.8 1.0
C C:ASP281 4.4 0.5 1.0
OD2 C:ASP285 4.5 0.6 1.0
O C:SER288 4.5 0.4 1.0
N C:ASN283 4.5 0.0 1.0
N C:ASN311 4.6 0.5 1.0
O C:ASN311 4.6 1.0 1.0
CA C:PHE287 4.7 0.6 1.0
O C:VAL280 4.7 0.7 1.0
CB C:PHE287 4.8 85.4 1.0

Calcium binding site 7 out of 10 in 3v4v

Go back to Calcium Binding Sites List in 3v4v
Calcium binding site 7 out of 10 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376


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 A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2006

b:0.0
occ:1.00
 OD1 C:ASP346 2.8 76.0 1.0
O C:PHE350 2.8 75.3 1.0
OD1 C:ASP344 2.9 0.7 1.0
OD1 C:ASP348 3.0 0.8 1.0
OD2 C:ASP352 3.0 70.7 1.0
OD1 C:ASP352 3.1 0.5 1.0
O C:HOH599 3.2 0.2 1.0
CG C:ASP348 3.3 0.6 1.0
CG C:ASP352 3.4 0.4 1.0
C C:PHE350 3.4 0.2 1.0
OD2 C:ASP348 3.5 0.1 1.0
N C:PHE350 3.6 0.9 1.0
CA C:PHE350 3.8 1.0 1.0
CB C:PHE350 3.8 97.5 1.0
CG C:ASP344 3.9 0.5 1.0
CG C:ASP346 3.9 0.5 1.0
N C:ASP348 4.1 0.4 1.0
N C:GLY349 4.3 0.5 1.0
OD2 C:ASP346 4.3 0.3 1.0
CB C:ASP348 4.3 0.5 1.0
ND2 C:ASN371 4.4 92.0 1.0
N C:GLU351 4.4 1.0 1.0
O C:GLY372 4.5 77.8 1.0
CA C:ASP348 4.5 99.8 1.0
OD2 C:ASP344 4.6 0.1 1.0
C C:GLY349 4.6 95.0 1.0
C C:GLU351 4.7 0.1 1.0
C C:ASP348 4.7 0.4 1.0
CA C:ASP344 4.7 0.8 1.0
CB C:ASP344 4.7 0.1 1.0
CB C:ASP352 4.7 66.9 1.0
N C:ASP352 4.7 67.9 1.0
N C:ASN347 4.8 77.8 1.0
CA C:GLU351 4.8 92.2 1.0
CD1 C:PHE350 4.9 84.4 1.0
N C:GLY372 4.9 72.0 1.0
CG C:PHE350 4.9 0.1 1.0
N C:ASP346 4.9 0.3 1.0
N C:ILE345 5.0 0.5 1.0

Calcium binding site 8 out of 10 in 3v4v

Go back to Calcium Binding Sites List in 3v4v
Calcium binding site 8 out of 10 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376


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 A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2007

b:99.5
occ:1.00
 O C:TYR412 2.6 89.2 1.0
OD1 C:ASP408 2.7 0.4 1.0
OD1 C:ASN410 2.9 0.7 1.0
O C:HOH601 2.9 0.6 1.0
OD1 C:ASP414 3.0 0.6 1.0
OD2 C:ASP414 3.1 99.5 1.0
OD1 C:ASP406 3.1 89.6 1.0
CG C:ASP414 3.3 0.0 1.0
CG C:ASP408 3.6 0.0 1.0
CG C:ASN410 3.6 0.7 1.0
C C:TYR412 3.7 98.8 1.0
N C:TYR412 3.8 0.4 1.0
OG1 C:THR430 3.8 0.4 1.0
OD2 C:ASP408 3.9 0.5 1.0
CG C:ASP406 4.0 0.4 1.0
CA C:TYR412 4.1 78.7 1.0
N C:ASN410 4.1 0.7 1.0
CB C:TYR412 4.1 74.1 1.0
ND2 C:ASN410 4.2 0.7 1.0
CB C:ASN410 4.4 0.7 1.0
N C:GLY411 4.5 0.1 1.0
N C:ASP408 4.5 87.6 1.0
O C:THR430 4.5 0.2 1.0
N C:ALA407 4.6 0.9 1.0
CA C:ASN410 4.6 79.6 1.0
N C:ASN409 4.6 0.1 1.0
N C:THR430 4.6 89.9 1.0
CA C:ASP406 4.7 89.3 1.0
OD2 C:ASP406 4.7 0.4 1.0
C C:ASN410 4.7 0.1 1.0
CB C:ASP414 4.7 93.6 1.0
N C:ASP414 4.7 0.0 1.0
N C:VAL413 4.8 0.3 1.0
C C:VAL413 4.8 76.9 1.0
CB C:ASP406 4.9 0.6 1.0
CB C:ASP408 4.9 1.0 1.0
C C:GLY411 4.9 0.5 1.0
C C:ASP406 5.0 0.4 1.0

Calcium binding site 9 out of 10 in 3v4v

Go back to Calcium Binding Sites List in 3v4v
Calcium binding site 9 out of 10 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376


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 A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2002

b:0.2
occ:1.00
 O D:GLU354 2.9 0.1 1.0
O D:SER144 2.9 0.5 1.0
OD1 D:ASP147 3.1 0.6 1.0
O D:HOH508 3.1 80.7 1.0
OD1 D:ASP148 3.2 0.6 1.0
O D:HOH507 3.2 0.9 1.0
C D:GLU354 3.9 0.5 1.0
CG D:ASP147 3.9 0.1 1.0
OD2 D:ASP147 3.9 0.1 1.0
CB D:GLU354 4.1 0.3 1.0
C D:SER144 4.1 0.8 1.0
CG D:ASP148 4.2 0.9 1.0
CA D:GLU354 4.2 0.0 1.0
OD2 D:ASP148 4.4 0.6 1.0
OD2 D:ASP270 4.4 0.3 1.0
CA D:MET145 4.8 74.8 1.0
CG D:GLU354 4.9 0.4 1.0
OG D:SER144 4.9 0.9 1.0
N D:MET145 5.0 0.2 1.0

Calcium binding site 10 out of 10 in 3v4v

Go back to Calcium Binding Sites List in 3v4v
Calcium binding site 10 out of 10 in the Crystal Structure of A4B7 Headpiece Complexed with Fab Act-1 and RO0505376


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 A4B7 Headpiece Complexed with Fab Act-1 and RO0505376 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2003

b:83.3
occ:1.00
 OD1 D:ASN235 2.9 0.3 1.0
O D:ASP237 3.0 93.3 1.0
OD2 D:ASP179 3.0 65.5 1.0
O D:PRO239 3.0 0.6 1.0
OD1 D:ASP237 3.1 86.3 1.0
C D:PRO239 3.3 61.5 1.0
OE1 D:GLU240 3.4 0.7 1.0
CA D:GLU240 3.5 61.0 1.0
CD D:GLU240 3.5 0.8 1.0
O D:SER238 3.6 87.4 1.0
N D:GLU240 3.6 0.2 1.0
CG D:ASN235 3.7 0.8 1.0
C D:ASP237 3.7 87.6 1.0
OE2 D:GLU240 3.7 64.7 1.0
ND2 D:ASN235 3.8 98.4 1.0
CG D:ASP179 3.8 91.8 1.0
CG D:ASP237 3.8 0.9 1.0
C D:SER238 3.8 67.7 1.0
N D:PRO239 4.1 71.3 1.0
CB D:ASP179 4.1 78.9 1.0
CG D:GLU240 4.1 0.5 1.0
CB D:GLU240 4.2 1.0 1.0
NE2 D:HIS274 4.3 69.9 1.0
CA D:PRO239 4.3 99.6 1.0
CA D:ASP237 4.4 90.4 1.0
OD2 D:ASP237 4.4 73.9 1.0
N D:ASP237 4.4 97.0 1.0
N D:SER238 4.5 0.5 1.0
C D:GLU240 4.6 89.3 1.0
CA D:SER238 4.6 88.7 1.0
CB D:ASP237 4.6 0.2 1.0
O D:VAL178 4.7 0.9 1.0
CD2 D:HIS274 4.7 0.2 1.0
OD1 D:ASP179 4.8 0.3 1.0
N D:GLY241 4.8 65.8 1.0
CD D:PRO239 5.0 0.5 1.0

Reference:

Y.Yu, J.Zhu, L.Z.Mi, T.Walz, H.Sun, J.Chen, T.A.Springer. Structural Specializations of A4B7, An Integrin That Mediates Rolling Adhesion J.Cell Biol. V. 196 131 2012.
ISSN: ISSN 0021-9525
PubMed: 22232704
DOI: 10.1083/JCB.201110023
Page generated: Sat Jul 13 20:33:50 2024

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