Calcium in PDB 5es4: Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation
Protein crystallography data
The structure of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation, PDB code: 5es4
was solved by
M.Sen,
T.A.Springer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.51 /
3.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
132.030,
163.480,
536.650,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
25.7 /
30.7
|
Other elements in 5es4:
The structure of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Calcium atom in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation
(pdb code 5es4). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the
Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation, PDB code: 5es4:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 16 in 5es4
Go back to
Calcium Binding Sites List in 5es4
Calcium binding site 1 out
of 16 in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2005
b:0.2
occ:1.00
|
OD1
|
A:ASP447
|
2.2
|
0.3
|
1.0
|
OD1
|
A:ASP451
|
2.3
|
0.8
|
1.0
|
OD1
|
A:ASP455
|
2.3
|
0.5
|
1.0
|
OD2
|
A:ASP455
|
2.4
|
0.3
|
1.0
|
OD1
|
A:ASP449
|
2.5
|
0.4
|
1.0
|
O
|
A:SER453
|
2.5
|
0.7
|
1.0
|
CG
|
A:ASP455
|
2.6
|
0.4
|
1.0
|
CG
|
A:ASP451
|
2.8
|
0.9
|
1.0
|
OD2
|
A:ASP451
|
3.1
|
0.9
|
1.0
|
CG
|
A:ASP449
|
3.3
|
0.4
|
1.0
|
CG
|
A:ASP447
|
3.4
|
0.6
|
1.0
|
OD2
|
A:ASP449
|
3.5
|
0.4
|
1.0
|
C
|
A:SER453
|
3.7
|
0.5
|
1.0
|
CB
|
A:ASP455
|
4.0
|
0.7
|
1.0
|
OD2
|
A:ASP447
|
4.0
|
95.7
|
1.0
|
CB
|
A:ASP451
|
4.0
|
0.4
|
1.0
|
N
|
A:ASP451
|
4.1
|
96.8
|
1.0
|
N
|
A:SER453
|
4.2
|
0.3
|
1.0
|
N
|
A:ASP455
|
4.3
|
0.7
|
1.0
|
N
|
A:ASP449
|
4.3
|
0.9
|
1.0
|
CA
|
A:SER453
|
4.3
|
0.8
|
1.0
|
CA
|
A:ASP447
|
4.4
|
0.6
|
1.0
|
N
|
A:VAL448
|
4.4
|
0.0
|
1.0
|
CB
|
A:SER453
|
4.4
|
0.1
|
1.0
|
CB
|
A:ASP447
|
4.5
|
0.0
|
1.0
|
CA
|
A:ASP455
|
4.5
|
0.3
|
1.0
|
C
|
A:ASP447
|
4.5
|
0.3
|
1.0
|
N
|
A:SER450
|
4.5
|
0.1
|
1.0
|
CA
|
A:ASP451
|
4.6
|
0.8
|
1.0
|
CB
|
A:ASP449
|
4.6
|
0.8
|
1.0
|
C
|
A:THR454
|
4.6
|
0.6
|
1.0
|
OG
|
A:SER453
|
4.7
|
0.7
|
1.0
|
N
|
A:THR454
|
4.8
|
0.9
|
1.0
|
CA
|
A:ASP449
|
4.8
|
0.8
|
1.0
|
N
|
A:GLY452
|
4.9
|
0.9
|
1.0
|
C
|
A:ASP449
|
4.9
|
0.6
|
1.0
|
C
|
A:ASP451
|
4.9
|
0.1
|
1.0
|
|
Calcium binding site 2 out
of 16 in 5es4
Go back to
Calcium Binding Sites List in 5es4
Calcium binding site 2 out
of 16 in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2006
b:0.0
occ:1.00
|
OD1
|
A:ASP511
|
2.4
|
0.5
|
1.0
|
OD1
|
A:ASN513
|
2.4
|
0.3
|
1.0
|
OD1
|
A:ASP515
|
2.5
|
0.9
|
1.0
|
OD2
|
A:ASP519
|
2.5
|
0.1
|
1.0
|
O
|
A:LEU517
|
2.5
|
1.0
|
1.0
|
CG
|
A:ASN513
|
3.1
|
0.5
|
1.0
|
N
|
A:VAL512
|
3.2
|
0.7
|
1.0
|
CG
|
A:ASP515
|
3.3
|
0.6
|
1.0
|
N
|
A:ASN513
|
3.3
|
0.8
|
1.0
|
CG
|
A:ASP519
|
3.4
|
0.1
|
1.0
|
CG
|
A:ASP511
|
3.4
|
0.1
|
1.0
|
ND2
|
A:ASN513
|
3.7
|
0.7
|
1.0
|
C
|
A:LEU517
|
3.7
|
0.3
|
1.0
|
OD1
|
A:ASP519
|
3.7
|
0.8
|
1.0
|
OD2
|
A:ASP515
|
3.7
|
0.2
|
1.0
|
CA
|
A:ASP511
|
3.7
|
0.2
|
1.0
|
C
|
A:ASP511
|
3.9
|
0.9
|
1.0
|
CA
|
A:VAL512
|
4.1
|
0.6
|
1.0
|
N
|
A:GLY514
|
4.1
|
0.7
|
1.0
|
N
|
A:ASP515
|
4.1
|
77.7
|
1.0
|
CB
|
A:ASP511
|
4.2
|
0.7
|
1.0
|
CB
|
A:ASN513
|
4.2
|
0.1
|
1.0
|
CA
|
A:ASN513
|
4.2
|
0.9
|
1.0
|
N
|
A:LEU517
|
4.2
|
0.8
|
1.0
|
C
|
A:VAL512
|
4.2
|
0.5
|
1.0
|
OD2
|
A:ASP511
|
4.3
|
0.4
|
1.0
|
CA
|
A:LEU517
|
4.4
|
0.6
|
1.0
|
CB
|
A:ASP515
|
4.5
|
0.2
|
1.0
|
C
|
A:ASN513
|
4.5
|
0.2
|
1.0
|
CB
|
A:VAL512
|
4.5
|
0.4
|
1.0
|
O
|
A:GLY510
|
4.6
|
0.2
|
1.0
|
N
|
A:THR518
|
4.7
|
0.9
|
1.0
|
CB
|
A:ASP519
|
4.7
|
0.1
|
1.0
|
CB
|
A:LEU517
|
4.7
|
0.9
|
1.0
|
CA
|
A:ASP515
|
4.8
|
0.5
|
1.0
|
C
|
A:THR518
|
4.8
|
0.9
|
1.0
|
N
|
A:ASP519
|
4.9
|
0.6
|
1.0
|
N
|
A:LYS516
|
4.9
|
0.1
|
1.0
|
CA
|
A:THR518
|
4.9
|
0.1
|
1.0
|
N
|
A:ASP511
|
5.0
|
0.5
|
1.0
|
|
Calcium binding site 3 out
of 16 in 5es4
Go back to
Calcium Binding Sites List in 5es4
Calcium binding site 3 out
of 16 in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2007
b:0.9
occ:1.00
|
OD1
|
A:ASP578
|
2.4
|
0.5
|
1.0
|
OD1
|
A:ASP574
|
2.4
|
0.9
|
1.0
|
OG1
|
A:THR576
|
2.4
|
0.2
|
1.0
|
OD1
|
A:ASP582
|
2.4
|
0.8
|
1.0
|
O
|
A:LEU580
|
2.5
|
0.6
|
1.0
|
OD2
|
A:ASP582
|
2.9
|
0.6
|
1.0
|
CG
|
A:ASP582
|
3.0
|
0.5
|
1.0
|
CG
|
A:ASP578
|
3.1
|
0.7
|
1.0
|
O
|
A:HOH4020
|
3.1
|
0.9
|
1.0
|
CG
|
A:ASP574
|
3.5
|
0.8
|
1.0
|
C
|
A:LEU580
|
3.6
|
0.9
|
1.0
|
OD2
|
A:ASP578
|
3.6
|
0.7
|
1.0
|
CB
|
A:THR576
|
3.7
|
0.6
|
1.0
|
N
|
A:ASP578
|
3.8
|
0.3
|
1.0
|
N
|
A:LEU580
|
3.9
|
0.2
|
1.0
|
N
|
A:THR576
|
3.9
|
0.4
|
1.0
|
CA
|
A:ASP574
|
4.0
|
0.8
|
1.0
|
N
|
A:GLN577
|
4.1
|
0.4
|
1.0
|
CA
|
A:LEU580
|
4.2
|
0.1
|
1.0
|
CA
|
A:THR576
|
4.2
|
0.4
|
1.0
|
CB
|
A:ASP578
|
4.2
|
0.5
|
1.0
|
CB
|
A:ASP574
|
4.3
|
0.1
|
1.0
|
CG2
|
A:THR576
|
4.3
|
0.1
|
1.0
|
C
|
A:ASP574
|
4.3
|
0.6
|
1.0
|
CA
|
A:ASP578
|
4.3
|
0.1
|
1.0
|
C
|
A:THR576
|
4.3
|
0.8
|
1.0
|
N
|
A:LEU575
|
4.4
|
0.1
|
1.0
|
C
|
A:ASP578
|
4.4
|
0.6
|
1.0
|
C
|
A:VAL581
|
4.4
|
0.1
|
1.0
|
O
|
A:VAL581
|
4.4
|
0.3
|
1.0
|
OD2
|
A:ASP574
|
4.4
|
0.7
|
1.0
|
CB
|
A:ASP582
|
4.5
|
0.3
|
1.0
|
N
|
A:GLY579
|
4.5
|
0.2
|
1.0
|
CB
|
A:LEU580
|
4.5
|
0.1
|
1.0
|
N
|
A:ASP582
|
4.6
|
0.1
|
1.0
|
N
|
A:VAL581
|
4.6
|
0.2
|
1.0
|
CD
|
A:ARG595
|
4.6
|
0.1
|
1.0
|
CG
|
A:ARG595
|
4.7
|
0.5
|
1.0
|
C
|
A:GLN577
|
4.8
|
0.3
|
1.0
|
CA
|
A:VAL581
|
4.9
|
0.7
|
1.0
|
O
|
A:GLN573
|
4.9
|
74.2
|
1.0
|
C
|
A:GLY579
|
4.9
|
1.0
|
1.0
|
CA
|
A:GLN577
|
4.9
|
0.5
|
1.0
|
O
|
A:ASP578
|
5.0
|
0.3
|
1.0
|
O
|
A:ASP574
|
5.0
|
0.7
|
1.0
|
CA
|
A:ASP582
|
5.0
|
99.4
|
1.0
|
|
Calcium binding site 4 out
of 16 in 5es4
Go back to
Calcium Binding Sites List in 5es4
Calcium binding site 4 out
of 16 in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2002
b:0.8
occ:1.00
|
OD2
|
B:ASP120
|
2.4
|
0.6
|
1.0
|
O
|
B:SER116
|
2.4
|
0.3
|
1.0
|
OE2
|
B:GLU325
|
3.0
|
0.3
|
1.0
|
OD2
|
B:ASP242
|
3.2
|
1.0
|
1.0
|
CA
|
B:MET117
|
3.4
|
0.5
|
1.0
|
C
|
B:SER116
|
3.5
|
0.6
|
1.0
|
CG
|
B:ASP120
|
3.5
|
0.1
|
1.0
|
O
|
B:GLU325
|
3.5
|
0.7
|
1.0
|
CD
|
B:GLU325
|
3.7
|
0.3
|
1.0
|
C
|
B:MET117
|
3.8
|
0.5
|
1.0
|
CB
|
B:ASP119
|
3.9
|
1.0
|
1.0
|
N
|
B:MET117
|
3.9
|
0.2
|
1.0
|
N
|
B:ASP120
|
3.9
|
0.3
|
1.0
|
CG
|
B:GLU325
|
4.0
|
0.2
|
1.0
|
N
|
B:ASP119
|
4.0
|
0.8
|
1.0
|
OD1
|
B:ASP120
|
4.2
|
0.5
|
1.0
|
CG
|
B:ASP242
|
4.3
|
0.1
|
1.0
|
N
|
B:LEU118
|
4.3
|
0.3
|
1.0
|
CA
|
B:ASP119
|
4.3
|
0.8
|
1.0
|
O
|
B:MET117
|
4.3
|
0.3
|
1.0
|
SD
|
B:MET117
|
4.4
|
0.7
|
1.0
|
CB
|
B:ASP120
|
4.4
|
0.3
|
1.0
|
C
|
B:ASP119
|
4.4
|
0.4
|
1.0
|
OD1
|
B:ASP242
|
4.5
|
0.3
|
1.0
|
CB
|
B:MET117
|
4.6
|
0.9
|
1.0
|
C
|
B:GLU325
|
4.6
|
0.9
|
1.0
|
OE1
|
B:GLU325
|
4.7
|
0.5
|
1.0
|
CA
|
B:SER116
|
4.8
|
0.4
|
1.0
|
CA
|
B:ASP120
|
4.8
|
0.9
|
1.0
|
CG
|
B:ASP119
|
4.8
|
0.0
|
1.0
|
OD2
|
B:ASP119
|
4.9
|
0.8
|
1.0
|
C
|
B:LEU118
|
5.0
|
0.4
|
1.0
|
CG
|
B:MET117
|
5.0
|
0.5
|
1.0
|
|
Calcium binding site 5 out
of 16 in 5es4
Go back to
Calcium Binding Sites List in 5es4
Calcium binding site 5 out
of 16 in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2005
b:0.9
occ:1.00
|
OD1
|
C:ASP449
|
2.4
|
0.2
|
1.0
|
O
|
C:HOH4003
|
2.4
|
0.5
|
1.0
|
OD1
|
C:ASP455
|
2.5
|
0.1
|
1.0
|
OD1
|
C:ASP451
|
2.5
|
0.2
|
1.0
|
OD2
|
C:ASP451
|
2.6
|
0.7
|
1.0
|
OD2
|
C:ASP455
|
2.6
|
0.5
|
1.0
|
CG
|
C:ASP451
|
2.8
|
0.4
|
1.0
|
CG
|
C:ASP455
|
2.9
|
0.5
|
1.0
|
OD2
|
C:ASP449
|
2.9
|
0.6
|
1.0
|
CG
|
C:ASP449
|
3.0
|
0.7
|
1.0
|
OD1
|
C:ASP447
|
3.1
|
0.7
|
1.0
|
O
|
C:SER453
|
3.3
|
0.2
|
1.0
|
OG
|
C:SER453
|
3.5
|
0.2
|
1.0
|
CG
|
C:ASP447
|
4.1
|
0.3
|
1.0
|
C
|
C:SER453
|
4.2
|
0.5
|
1.0
|
CB
|
C:ASP451
|
4.2
|
0.5
|
1.0
|
CB
|
C:ASP455
|
4.4
|
0.4
|
1.0
|
CB
|
C:ASP449
|
4.4
|
0.3
|
1.0
|
N
|
C:ASP451
|
4.4
|
0.2
|
1.0
|
N
|
C:ASP449
|
4.5
|
0.7
|
1.0
|
N
|
C:SER453
|
4.6
|
0.3
|
1.0
|
OD2
|
C:ASP447
|
4.7
|
1.0
|
1.0
|
CB
|
C:SER453
|
4.7
|
0.4
|
1.0
|
CA
|
C:SER453
|
4.8
|
0.8
|
1.0
|
N
|
C:ASP455
|
4.8
|
0.5
|
1.0
|
CA
|
C:ASP451
|
4.8
|
0.8
|
1.0
|
CA
|
C:ASP449
|
4.9
|
0.4
|
1.0
|
N
|
C:VAL448
|
4.9
|
0.5
|
1.0
|
N
|
C:SER450
|
4.9
|
0.0
|
1.0
|
CA
|
C:ASP455
|
5.0
|
0.8
|
1.0
|
C
|
C:THR454
|
5.0
|
0.5
|
1.0
|
|
Calcium binding site 6 out
of 16 in 5es4
Go back to
Calcium Binding Sites List in 5es4
Calcium binding site 6 out
of 16 in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2006
b:0.8
occ:1.00
|
O
|
C:LEU517
|
2.3
|
0.8
|
1.0
|
OD1
|
C:ASP511
|
2.4
|
0.8
|
1.0
|
OD1
|
C:ASN513
|
2.4
|
0.4
|
1.0
|
OD1
|
C:ASP515
|
2.4
|
0.0
|
1.0
|
OD2
|
C:ASP519
|
2.4
|
0.6
|
1.0
|
CG
|
C:ASP519
|
3.1
|
0.2
|
1.0
|
OD1
|
C:ASP519
|
3.2
|
0.6
|
1.0
|
CG
|
C:ASP511
|
3.2
|
0.3
|
1.0
|
CG
|
C:ASP515
|
3.3
|
0.5
|
1.0
|
CG
|
C:ASN513
|
3.3
|
0.1
|
1.0
|
C
|
C:LEU517
|
3.4
|
0.3
|
1.0
|
N
|
C:VAL512
|
3.8
|
0.5
|
1.0
|
OD2
|
C:ASP515
|
3.8
|
0.0
|
1.0
|
ND2
|
C:ASN513
|
3.8
|
0.8
|
1.0
|
N
|
C:ASN513
|
3.9
|
0.2
|
1.0
|
OD2
|
C:ASP511
|
3.9
|
0.3
|
1.0
|
CA
|
C:ASP511
|
3.9
|
0.9
|
1.0
|
N
|
C:LEU517
|
4.0
|
0.5
|
1.0
|
CB
|
C:ASP511
|
4.1
|
0.5
|
1.0
|
N
|
C:ASP515
|
4.1
|
0.8
|
1.0
|
CA
|
C:LEU517
|
4.1
|
0.1
|
1.0
|
C
|
C:ASP511
|
4.2
|
0.5
|
1.0
|
N
|
C:GLY514
|
4.4
|
0.4
|
1.0
|
N
|
C:THR518
|
4.4
|
0.7
|
1.0
|
CB
|
C:LEU517
|
4.4
|
0.6
|
1.0
|
CB
|
C:ASP519
|
4.5
|
0.5
|
1.0
|
CB
|
C:ASN513
|
4.5
|
0.0
|
1.0
|
CB
|
C:ASP515
|
4.5
|
0.5
|
1.0
|
C
|
C:THR518
|
4.5
|
0.3
|
1.0
|
CA
|
C:ASN513
|
4.6
|
0.3
|
1.0
|
N
|
C:ASP519
|
4.6
|
0.6
|
1.0
|
ND1
|
C:HIS538
|
4.7
|
0.6
|
1.0
|
CA
|
C:THR518
|
4.7
|
0.3
|
1.0
|
CA
|
C:ASP515
|
4.7
|
0.6
|
1.0
|
CA
|
C:VAL512
|
4.8
|
0.4
|
1.0
|
C
|
C:ASN513
|
4.8
|
0.5
|
1.0
|
N
|
C:LYS516
|
4.8
|
0.4
|
1.0
|
C
|
C:ASP515
|
4.8
|
0.4
|
1.0
|
C
|
C:VAL512
|
4.8
|
0.3
|
1.0
|
O
|
C:THR518
|
4.8
|
0.2
|
1.0
|
O
|
C:GLY510
|
4.9
|
0.6
|
1.0
|
|
Calcium binding site 7 out
of 16 in 5es4
Go back to
Calcium Binding Sites List in 5es4
Calcium binding site 7 out
of 16 in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca2007
b:0.5
occ:1.00
|
O
|
C:LEU580
|
2.1
|
0.6
|
1.0
|
OG1
|
C:THR576
|
2.3
|
0.3
|
1.0
|
OD1
|
C:ASP578
|
2.4
|
0.6
|
1.0
|
OD1
|
C:ASP574
|
2.4
|
0.9
|
1.0
|
OD1
|
C:ASP582
|
2.4
|
0.9
|
1.0
|
O
|
C:HOH4007
|
2.5
|
0.7
|
1.0
|
OD2
|
C:ASP582
|
2.8
|
0.6
|
1.0
|
CG
|
C:ASP582
|
2.9
|
0.8
|
1.0
|
C
|
C:LEU580
|
3.1
|
0.5
|
1.0
|
CG
|
C:ASP578
|
3.2
|
0.1
|
1.0
|
CG
|
C:ASP574
|
3.4
|
0.9
|
1.0
|
OD2
|
C:ASP578
|
3.5
|
0.2
|
1.0
|
N
|
C:LEU580
|
3.6
|
0.9
|
1.0
|
CB
|
C:THR576
|
3.7
|
0.1
|
1.0
|
CA
|
C:LEU580
|
3.7
|
0.0
|
1.0
|
CA
|
C:ASP574
|
4.0
|
0.6
|
1.0
|
CB
|
C:ASP574
|
4.1
|
0.4
|
1.0
|
CB
|
C:LEU580
|
4.1
|
0.6
|
1.0
|
N
|
C:ASP578
|
4.1
|
0.6
|
1.0
|
C
|
C:VAL581
|
4.1
|
0.1
|
1.0
|
N
|
C:THR576
|
4.2
|
0.7
|
1.0
|
N
|
C:VAL581
|
4.2
|
0.2
|
1.0
|
OD2
|
C:ASP574
|
4.2
|
0.8
|
1.0
|
O
|
C:VAL581
|
4.2
|
0.4
|
1.0
|
CB
|
C:ASP582
|
4.3
|
0.6
|
1.0
|
N
|
C:ASP582
|
4.4
|
0.9
|
1.0
|
CG2
|
C:THR576
|
4.4
|
0.1
|
1.0
|
CA
|
C:THR576
|
4.4
|
0.3
|
1.0
|
CB
|
C:ASP578
|
4.4
|
0.9
|
1.0
|
N
|
C:GLN577
|
4.4
|
0.8
|
1.0
|
N
|
C:GLY579
|
4.5
|
0.8
|
1.0
|
CA
|
C:VAL581
|
4.5
|
0.5
|
1.0
|
C
|
C:ASP574
|
4.6
|
0.6
|
1.0
|
CA
|
C:ASP578
|
4.6
|
0.3
|
1.0
|
C
|
C:THR576
|
4.6
|
0.9
|
1.0
|
N
|
C:LEU575
|
4.7
|
0.8
|
1.0
|
C
|
C:GLY579
|
4.7
|
0.8
|
1.0
|
C
|
C:ASP578
|
4.7
|
0.5
|
1.0
|
CA
|
C:ASP582
|
4.7
|
0.2
|
1.0
|
O
|
C:GLN573
|
4.9
|
0.9
|
1.0
|
|
Calcium binding site 8 out
of 16 in 5es4
Go back to
Calcium Binding Sites List in 5es4
Calcium binding site 8 out
of 16 in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca2002
b:0.1
occ:1.01
|
OE2
|
D:GLU325
|
2.4
|
1.0
|
1.0
|
O
|
D:SER116
|
2.4
|
0.9
|
1.0
|
OD2
|
D:ASP120
|
3.3
|
0.1
|
1.0
|
CD
|
D:GLU325
|
3.3
|
0.5
|
1.0
|
C
|
D:SER116
|
3.6
|
0.8
|
1.0
|
CG
|
D:GLU325
|
3.6
|
0.4
|
1.0
|
O
|
D:GLU325
|
3.6
|
0.6
|
1.0
|
CG
|
D:ASP120
|
3.7
|
0.0
|
1.0
|
CA
|
D:MET117
|
3.9
|
0.7
|
1.0
|
OD1
|
D:ASP120
|
3.9
|
0.3
|
1.0
|
N
|
D:MET117
|
4.2
|
0.7
|
1.0
|
N
|
D:ASP120
|
4.4
|
0.1
|
1.0
|
SD
|
D:MET117
|
4.4
|
0.7
|
1.0
|
C
|
D:MET117
|
4.4
|
0.8
|
1.0
|
OE1
|
D:GLU325
|
4.5
|
0.4
|
1.0
|
CB
|
D:ASP119
|
4.5
|
0.9
|
1.0
|
N
|
D:ASP119
|
4.6
|
0.5
|
1.0
|
CB
|
D:ASP120
|
4.6
|
0.4
|
1.0
|
C
|
D:GLU325
|
4.6
|
0.4
|
1.0
|
N
|
D:LEU118
|
4.7
|
0.9
|
1.0
|
OD2
|
D:ASP242
|
4.8
|
0.4
|
1.0
|
CA
|
D:SER116
|
4.8
|
0.2
|
1.0
|
CB
|
D:GLU325
|
4.8
|
0.6
|
1.0
|
C
|
D:ASP119
|
4.8
|
0.3
|
1.0
|
CA
|
D:ASP119
|
4.9
|
0.5
|
1.0
|
CB
|
D:SER116
|
5.0
|
0.9
|
1.0
|
|
Calcium binding site 9 out
of 16 in 5es4
Go back to
Calcium Binding Sites List in 5es4
Calcium binding site 9 out
of 16 in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca2005
b:0.2
occ:1.00
|
O
|
E:HOH4001
|
2.1
|
0.4
|
1.0
|
OD1
|
E:ASP451
|
2.3
|
0.3
|
1.0
|
O
|
E:SER453
|
2.5
|
0.5
|
1.0
|
OD1
|
E:ASP455
|
2.5
|
0.9
|
1.0
|
OD2
|
E:ASP455
|
2.5
|
0.1
|
1.0
|
OD2
|
E:ASP451
|
2.7
|
0.1
|
1.0
|
CG
|
E:ASP451
|
2.8
|
0.3
|
1.0
|
CG
|
E:ASP455
|
2.8
|
0.2
|
1.0
|
OD1
|
E:ASP447
|
2.9
|
0.2
|
1.0
|
O
|
E:ASP449
|
3.2
|
0.7
|
1.0
|
OD1
|
E:ASP449
|
3.4
|
1.0
|
1.0
|
C
|
E:SER453
|
3.6
|
0.3
|
1.0
|
CG
|
E:ASP449
|
3.8
|
0.8
|
1.0
|
OD2
|
E:ASP449
|
3.9
|
0.4
|
1.0
|
CG
|
E:ASP447
|
4.0
|
0.3
|
1.0
|
CB
|
E:ASP451
|
4.2
|
0.3
|
1.0
|
CB
|
E:SER453
|
4.2
|
0.1
|
1.0
|
CA
|
E:SER453
|
4.2
|
1.0
|
1.0
|
CB
|
E:ASP455
|
4.3
|
0.7
|
1.0
|
N
|
E:SER453
|
4.3
|
0.8
|
1.0
|
C
|
E:ASP449
|
4.4
|
0.4
|
1.0
|
N
|
E:ASP455
|
4.4
|
0.1
|
1.0
|
C
|
E:THR454
|
4.5
|
0.7
|
1.0
|
N
|
E:ASP451
|
4.5
|
0.1
|
1.0
|
N
|
E:THR454
|
4.6
|
0.4
|
1.0
|
OG
|
E:SER453
|
4.7
|
1.0
|
1.0
|
CA
|
E:ASP455
|
4.7
|
0.2
|
1.0
|
OD2
|
E:ASP447
|
4.7
|
0.1
|
1.0
|
N
|
E:VAL448
|
4.8
|
0.4
|
1.0
|
N
|
E:ASP449
|
4.8
|
0.5
|
1.0
|
O
|
E:THR454
|
4.8
|
0.5
|
1.0
|
CA
|
E:ASP447
|
4.8
|
0.1
|
1.0
|
CA
|
E:ASP451
|
4.9
|
0.9
|
1.0
|
CB
|
E:ASP447
|
4.9
|
0.0
|
1.0
|
CA
|
E:THR454
|
4.9
|
0.0
|
1.0
|
CA
|
E:ASP449
|
5.0
|
0.1
|
1.0
|
|
Calcium binding site 10 out
of 16 in 5es4
Go back to
Calcium Binding Sites List in 5es4
Calcium binding site 10 out
of 16 in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca2006
b:0.1
occ:1.00
|
OD1
|
E:ASN513
|
2.4
|
0.1
|
1.0
|
OD1
|
E:ASP511
|
2.4
|
0.3
|
1.0
|
O
|
E:LEU517
|
2.4
|
0.9
|
1.0
|
OD1
|
E:ASP515
|
2.4
|
0.2
|
1.0
|
OD2
|
E:ASP519
|
2.5
|
0.7
|
1.0
|
CG
|
E:ASN513
|
3.1
|
0.0
|
1.0
|
OD1
|
E:ASP519
|
3.2
|
0.3
|
1.0
|
CG
|
E:ASP519
|
3.2
|
0.5
|
1.0
|
CG
|
E:ASP515
|
3.2
|
0.8
|
1.0
|
CG
|
E:ASP511
|
3.3
|
0.1
|
1.0
|
OD2
|
E:ASP515
|
3.5
|
0.8
|
1.0
|
C
|
E:LEU517
|
3.5
|
0.8
|
1.0
|
ND2
|
E:ASN513
|
3.5
|
0.1
|
1.0
|
CA
|
E:ASP511
|
3.6
|
0.4
|
1.0
|
N
|
E:VAL512
|
3.7
|
0.7
|
1.0
|
N
|
E:ASN513
|
3.8
|
0.2
|
1.0
|
CB
|
E:ASP511
|
3.9
|
0.9
|
1.0
|
N
|
E:LEU517
|
4.0
|
0.1
|
1.0
|
C
|
E:ASP511
|
4.1
|
0.6
|
1.0
|
CA
|
E:LEU517
|
4.2
|
0.2
|
1.0
|
OD2
|
E:ASP511
|
4.2
|
0.2
|
1.0
|
CB
|
E:ASN513
|
4.3
|
0.7
|
1.0
|
N
|
E:ASP515
|
4.3
|
0.8
|
1.0
|
CB
|
E:LEU517
|
4.3
|
0.4
|
1.0
|
O
|
E:GLY510
|
4.3
|
0.3
|
1.0
|
N
|
E:GLY514
|
4.4
|
0.2
|
1.0
|
CA
|
E:ASN513
|
4.5
|
0.1
|
1.0
|
CB
|
E:ASP515
|
4.5
|
0.3
|
1.0
|
N
|
E:THR518
|
4.5
|
0.5
|
1.0
|
CB
|
E:ASP519
|
4.6
|
0.7
|
1.0
|
ND1
|
E:HIS538
|
4.6
|
0.8
|
1.0
|
C
|
E:THR518
|
4.6
|
0.8
|
1.0
|
N
|
E:ASP511
|
4.7
|
0.2
|
1.0
|
C
|
E:VAL512
|
4.7
|
0.3
|
1.0
|
C
|
E:ASN513
|
4.8
|
0.8
|
1.0
|
CA
|
E:VAL512
|
4.8
|
0.1
|
1.0
|
N
|
E:ASP519
|
4.8
|
0.5
|
1.0
|
CA
|
E:ASP515
|
4.8
|
0.3
|
1.0
|
O
|
E:THR518
|
4.8
|
0.9
|
1.0
|
CA
|
E:THR518
|
4.8
|
0.5
|
1.0
|
N
|
E:LYS516
|
4.9
|
0.0
|
1.0
|
C
|
E:GLY510
|
5.0
|
0.3
|
1.0
|
|
Reference:
M.Sen,
T.A.Springer.
Leukocyte Integrin Alpha L Beta 2 Headpiece Structures: the Alpha I Domain, the Pocket For the Internal Ligand, and Concerted Movements of Its Loops. Proc.Natl.Acad.Sci.Usa V. 113 2940 2016.
ISSN: ESSN 1091-6490
PubMed: 26936951
DOI: 10.1073/PNAS.1601379113
Page generated: Sun Jul 14 18:48:12 2024
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