Calcium in PDB 7qqm: The Pdz Domain of LRRC7 Fused with ANXA2
Protein crystallography data
The structure of The Pdz Domain of LRRC7 Fused with ANXA2, PDB code: 7qqm
was solved by
A.Cousido-Siah,
G.Trave,
G.Gogl,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.48 /
1.60
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
59.78,
70.08,
102.44,
90,
90,
90
|
R / Rfree (%)
|
17 /
19.8
|
Calcium Binding Sites:
The binding sites of Calcium atom in the The Pdz Domain of LRRC7 Fused with ANXA2
(pdb code 7qqm). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
The Pdz Domain of LRRC7 Fused with ANXA2, PDB code: 7qqm:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 7qqm
Go back to
Calcium Binding Sites List in 7qqm
Calcium binding site 1 out
of 4 in the The Pdz Domain of LRRC7 Fused with ANXA2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of The Pdz Domain of LRRC7 Fused with ANXA2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1901
b:36.0
occ:1.00
|
OE1
|
A:GLU1569
|
2.4
|
35.5
|
1.0
|
O
|
A:HOH2254
|
2.5
|
45.8
|
1.0
|
O
|
A:GLY1566
|
2.5
|
27.8
|
1.0
|
O
|
A:HOH2203
|
2.5
|
53.2
|
1.0
|
OE2
|
A:GLU1569
|
2.5
|
36.9
|
1.0
|
O
|
A:VAL1567
|
2.5
|
26.1
|
1.0
|
O
|
A:HOH2386
|
2.6
|
45.7
|
1.0
|
CD
|
A:GLU1569
|
2.8
|
33.9
|
1.0
|
C
|
A:GLY1566
|
3.4
|
25.9
|
1.0
|
C
|
A:VAL1567
|
3.7
|
26.9
|
1.0
|
N
|
A:VAL1567
|
4.2
|
25.0
|
1.0
|
CA
|
A:VAL1567
|
4.3
|
22.4
|
1.0
|
CG
|
A:GLU1569
|
4.3
|
22.4
|
1.0
|
CA
|
A:GLY1566
|
4.3
|
30.0
|
1.0
|
CB
|
A:VAL1567
|
4.4
|
22.5
|
1.0
|
N
|
A:GLU1569
|
4.7
|
20.6
|
1.0
|
N
|
A:ASP1568
|
4.8
|
22.8
|
1.0
|
O
|
A:HOH2245
|
4.8
|
29.7
|
1.0
|
|
Calcium binding site 2 out
of 4 in 7qqm
Go back to
Calcium Binding Sites List in 7qqm
Calcium binding site 2 out
of 4 in the The Pdz Domain of LRRC7 Fused with ANXA2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of The Pdz Domain of LRRC7 Fused with ANXA2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1902
b:28.4
occ:1.00
|
O
|
A:LYS1604
|
2.3
|
28.2
|
1.0
|
OE1
|
A:GLU1612
|
2.4
|
34.1
|
1.0
|
O
|
A:HOH2217
|
2.5
|
39.0
|
1.0
|
O
|
A:HOH2369
|
2.5
|
46.1
|
1.0
|
O
|
A:HOH2127
|
2.5
|
39.9
|
1.0
|
O
|
A:HOH2339
|
2.5
|
43.2
|
1.0
|
O
|
A:LEU1607
|
2.5
|
26.1
|
1.0
|
CD
|
A:GLU1612
|
3.3
|
33.0
|
1.0
|
C
|
A:LYS1604
|
3.6
|
28.2
|
1.0
|
OE2
|
A:GLU1612
|
3.6
|
34.3
|
1.0
|
C
|
A:LEU1607
|
3.7
|
23.0
|
1.0
|
CA
|
A:SER1608
|
4.2
|
21.6
|
1.0
|
N
|
A:SER1608
|
4.4
|
20.6
|
1.0
|
CA
|
A:LYS1604
|
4.4
|
28.5
|
1.0
|
CG
|
A:LYS1604
|
4.4
|
43.2
|
1.0
|
CB
|
A:SER1608
|
4.5
|
25.7
|
1.0
|
N
|
A:SER1605
|
4.5
|
27.2
|
0.3
|
N
|
A:SER1605
|
4.5
|
27.0
|
0.7
|
CG
|
A:GLU1612
|
4.5
|
22.0
|
1.0
|
CA
|
A:SER1605
|
4.6
|
28.3
|
0.3
|
CA
|
A:SER1605
|
4.6
|
27.9
|
0.7
|
O
|
A:SER1605
|
4.6
|
31.9
|
0.7
|
C
|
A:SER1605
|
4.7
|
27.9
|
0.7
|
C
|
A:SER1605
|
4.7
|
28.4
|
0.3
|
N
|
A:LEU1607
|
4.7
|
23.2
|
1.0
|
O
|
A:SER1605
|
4.8
|
31.2
|
0.3
|
CA
|
A:LEU1607
|
4.8
|
18.8
|
1.0
|
|
Calcium binding site 3 out
of 4 in 7qqm
Go back to
Calcium Binding Sites List in 7qqm
Calcium binding site 3 out
of 4 in the The Pdz Domain of LRRC7 Fused with ANXA2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of The Pdz Domain of LRRC7 Fused with ANXA2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1903
b:26.2
occ:1.00
|
O
|
A:ARG1721
|
2.4
|
27.0
|
1.0
|
O
|
A:GLY1718
|
2.4
|
23.2
|
1.0
|
OE1
|
A:GLU1763
|
2.4
|
21.3
|
1.0
|
O
|
A:GLY1723
|
2.4
|
26.6
|
1.0
|
O
|
A:HOH2356
|
2.4
|
28.1
|
1.0
|
O
|
A:HOH2289
|
2.5
|
36.6
|
1.0
|
OE2
|
A:GLU1763
|
2.6
|
25.4
|
1.0
|
CD
|
A:GLU1763
|
2.8
|
22.2
|
1.0
|
C
|
A:GLY1718
|
3.3
|
22.8
|
1.0
|
C
|
A:GLY1723
|
3.5
|
30.8
|
1.0
|
C
|
A:ARG1721
|
3.6
|
32.1
|
1.0
|
N
|
A:GLY1723
|
3.8
|
29.3
|
1.0
|
CA
|
A:GLY1718
|
4.1
|
21.6
|
1.0
|
C
|
A:LYS1722
|
4.1
|
28.5
|
1.0
|
CA
|
A:GLY1723
|
4.1
|
30.6
|
1.0
|
N
|
A:VAL1719
|
4.2
|
22.5
|
1.0
|
OG1
|
A:THR1724
|
4.2
|
29.1
|
1.0
|
CA
|
A:VAL1719
|
4.2
|
22.6
|
1.0
|
O
|
A:HOH2063
|
4.2
|
29.4
|
1.0
|
CG
|
A:GLU1763
|
4.3
|
24.5
|
1.0
|
N
|
A:ARG1721
|
4.4
|
27.4
|
1.0
|
O
|
A:HOH2408
|
4.4
|
58.9
|
1.0
|
CA
|
A:LYS1722
|
4.4
|
33.2
|
1.0
|
O
|
A:HOH2081
|
4.4
|
33.9
|
1.0
|
N
|
A:LYS1722
|
4.4
|
33.1
|
1.0
|
C
|
A:VAL1719
|
4.4
|
25.1
|
1.0
|
CG
|
A:ARG1721
|
4.5
|
29.9
|
1.0
|
CA
|
A:ARG1721
|
4.5
|
31.1
|
1.0
|
O
|
A:VAL1719
|
4.5
|
27.2
|
1.0
|
N
|
A:THR1724
|
4.6
|
28.0
|
1.0
|
O
|
A:HOH2367
|
4.6
|
51.6
|
1.0
|
O
|
A:LYS1722
|
4.8
|
33.9
|
1.0
|
O
|
A:HOH2228
|
4.8
|
51.5
|
1.0
|
CA
|
A:THR1724
|
4.8
|
27.8
|
1.0
|
O
|
A:HOH2155
|
4.9
|
43.3
|
1.0
|
|
Calcium binding site 4 out
of 4 in 7qqm
Go back to
Calcium Binding Sites List in 7qqm
Calcium binding site 4 out
of 4 in the The Pdz Domain of LRRC7 Fused with ANXA2
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of The Pdz Domain of LRRC7 Fused with ANXA2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1904
b:17.7
occ:1.00
|
O
|
A:GLY1798
|
2.4
|
19.1
|
1.0
|
O
|
A:GLY1796
|
2.4
|
18.0
|
1.0
|
O
|
A:MET1794
|
2.4
|
19.6
|
1.0
|
OD1
|
A:ASP1838
|
2.5
|
18.1
|
1.0
|
OD2
|
A:ASP1838
|
2.5
|
17.9
|
1.0
|
CG
|
A:ASP1838
|
2.8
|
19.6
|
1.0
|
C
|
A:MET1794
|
3.4
|
17.6
|
1.0
|
C
|
A:GLY1798
|
3.5
|
22.1
|
1.0
|
C
|
A:GLY1796
|
3.6
|
21.4
|
1.0
|
N
|
A:GLY1798
|
4.0
|
19.5
|
1.0
|
CA
|
A:MET1794
|
4.0
|
17.4
|
1.0
|
N
|
A:GLY1796
|
4.1
|
19.7
|
1.0
|
CA
|
A:GLY1798
|
4.2
|
21.2
|
1.0
|
C
|
A:LYS1797
|
4.2
|
20.9
|
1.0
|
C
|
A:LYS1795
|
4.3
|
19.4
|
1.0
|
CB
|
A:ASP1838
|
4.3
|
14.8
|
1.0
|
OG1
|
A:THR1799
|
4.3
|
20.6
|
1.0
|
O
|
A:HOH2096
|
4.3
|
27.0
|
1.0
|
CA
|
A:GLY1796
|
4.4
|
21.7
|
1.0
|
N
|
A:LYS1795
|
4.5
|
18.9
|
1.0
|
N
|
A:THR1799
|
4.5
|
18.8
|
1.0
|
N
|
A:LYS1797
|
4.6
|
19.7
|
1.0
|
O
|
A:LYS1795
|
4.6
|
20.6
|
1.0
|
CB
|
A:MET1794
|
4.6
|
15.4
|
1.0
|
O
|
A:LYS1797
|
4.7
|
23.3
|
1.0
|
CA
|
A:LYS1797
|
4.7
|
18.1
|
1.0
|
CA
|
A:THR1799
|
4.8
|
19.5
|
1.0
|
O
|
A:HOH2118
|
4.8
|
17.4
|
1.0
|
CA
|
A:LYS1795
|
4.9
|
16.1
|
1.0
|
CA
|
A:ASP1838
|
5.0
|
17.4
|
1.0
|
|
Reference:
A.Cousido-Siah,
L.Carneiro,
C.Kostmann,
P.Ecsedi,
L.Nyitray,
G.Trave,
G.Gogl.
A Scalable Strategy to Solve Structures of Pdz Domains and Their Complexes. Acta Crystallogr D Struct V. 78 509 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35362473
DOI: 10.1107/S2059798322001784
Page generated: Fri Jul 19 03:30:05 2024
|