Calcium in PDB 8xmk: Local Refinement of SRCR5-9 Domains
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
17;
Binding sites:
The binding sites of Calcium atom in the Local Refinement of SRCR5-9 Domains
(pdb code 8xmk). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 17 binding sites of Calcium where determined in the
Local Refinement of SRCR5-9 Domains, PDB code: 8xmk:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 17 in 8xmk
Go back to
Calcium Binding Sites List in 8xmk
Calcium binding site 1 out
of 17 in the Local Refinement of SRCR5-9 Domains
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Local Refinement of SRCR5-9 Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca1103
b:24.0
occ:1.00
|
OD1
|
D:ASP955
|
2.3
|
24.7
|
1.0
|
OE1
|
D:GLU1022
|
2.5
|
20.6
|
1.0
|
OD1
|
D:ASP956
|
2.6
|
20.1
|
1.0
|
CG
|
D:ASP955
|
3.2
|
19.8
|
1.0
|
OD2
|
D:ASP955
|
3.5
|
20.9
|
1.0
|
CD
|
D:GLU1022
|
3.6
|
22.2
|
1.0
|
CG
|
D:ASP956
|
3.8
|
21.0
|
1.0
|
N
|
D:ASP956
|
4.1
|
18.9
|
1.0
|
CG
|
D:GLU1022
|
4.2
|
13.6
|
1.0
|
CB
|
D:GLU1022
|
4.2
|
11.7
|
1.0
|
CA
|
D:ASP956
|
4.3
|
14.8
|
1.0
|
C
|
D:ASP955
|
4.3
|
16.1
|
1.0
|
CE
|
F:LYS811
|
4.5
|
44.4
|
1.0
|
CB
|
D:ASP955
|
4.5
|
15.5
|
1.0
|
OD2
|
D:ASP956
|
4.6
|
24.4
|
1.0
|
O
|
D:ASP955
|
4.6
|
22.6
|
1.0
|
CB
|
D:ASP956
|
4.7
|
16.6
|
1.0
|
OE2
|
D:GLU1022
|
4.7
|
24.9
|
1.0
|
SG
|
D:CYS954
|
4.8
|
22.7
|
1.0
|
CA
|
D:ASP955
|
4.9
|
11.1
|
1.0
|
NZ
|
F:LYS811
|
5.0
|
50.3
|
1.0
|
|
Calcium binding site 2 out
of 17 in 8xmk
Go back to
Calcium Binding Sites List in 8xmk
Calcium binding site 2 out
of 17 in the Local Refinement of SRCR5-9 Domains
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Local Refinement of SRCR5-9 Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca1104
b:18.3
occ:1.00
|
OD2
|
D:ASP616
|
2.2
|
24.5
|
1.0
|
O
|
D:PHE650
|
2.4
|
27.6
|
1.0
|
OD2
|
D:ASP613
|
2.4
|
36.6
|
1.0
|
O
|
D:HIS611
|
2.5
|
30.4
|
1.0
|
CG
|
D:ASP616
|
3.0
|
23.6
|
1.0
|
OD1
|
D:ASP616
|
3.1
|
28.7
|
1.0
|
CG
|
D:ASP613
|
3.4
|
30.9
|
1.0
|
N
|
D:ASP613
|
3.6
|
28.9
|
1.0
|
C
|
D:PHE650
|
3.6
|
16.6
|
1.0
|
CB
|
D:ASP613
|
3.7
|
30.0
|
1.0
|
C
|
D:HIS611
|
3.7
|
31.2
|
1.0
|
CA
|
D:ASP613
|
4.3
|
31.3
|
1.0
|
CA
|
D:HIS651
|
4.3
|
13.8
|
1.0
|
N
|
D:HIS651
|
4.4
|
11.3
|
1.0
|
CB
|
D:ASP616
|
4.4
|
19.8
|
1.0
|
CA
|
D:TRP612
|
4.4
|
27.9
|
1.0
|
C
|
D:TRP612
|
4.5
|
28.3
|
1.0
|
N
|
D:TRP612
|
4.5
|
28.2
|
1.0
|
OD1
|
D:ASP613
|
4.5
|
29.0
|
1.0
|
CA
|
D:PHE650
|
4.6
|
6.0
|
1.0
|
N
|
D:CYS652
|
4.7
|
18.8
|
1.0
|
CB
|
D:HIS611
|
4.7
|
34.8
|
1.0
|
CA
|
D:HIS611
|
4.8
|
34.6
|
1.0
|
N
|
D:PHE650
|
4.8
|
6.8
|
1.0
|
CB
|
D:PHE650
|
4.9
|
8.9
|
1.0
|
ND1
|
D:HIS651
|
4.9
|
16.5
|
1.0
|
C
|
D:HIS651
|
5.0
|
17.2
|
1.0
|
|
Calcium binding site 3 out
of 17 in 8xmk
Go back to
Calcium Binding Sites List in 8xmk
Calcium binding site 3 out
of 17 in the Local Refinement of SRCR5-9 Domains
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Local Refinement of SRCR5-9 Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca1105
b:21.8
occ:1.00
|
OD2
|
D:ASP962
|
2.3
|
26.8
|
1.0
|
O
|
D:SER957
|
2.4
|
20.1
|
1.0
|
O
|
D:VAL996
|
2.4
|
37.4
|
1.0
|
OD1
|
D:ASP959
|
2.6
|
30.1
|
1.0
|
CG
|
D:ASP962
|
3.1
|
26.8
|
1.0
|
OD1
|
D:ASP962
|
3.2
|
33.6
|
1.0
|
CG
|
D:ASP959
|
3.3
|
28.8
|
1.0
|
OD2
|
D:ASP959
|
3.6
|
30.9
|
1.0
|
C
|
D:SER957
|
3.6
|
19.2
|
1.0
|
C
|
D:VAL996
|
3.6
|
33.7
|
1.0
|
N
|
D:ASP959
|
3.9
|
21.5
|
1.0
|
OG
|
D:SER957
|
3.9
|
23.8
|
1.0
|
CA
|
D:LYS997
|
4.2
|
40.3
|
1.0
|
N
|
D:CYS998
|
4.3
|
41.5
|
1.0
|
CB
|
D:SER957
|
4.3
|
19.9
|
1.0
|
N
|
D:LYS997
|
4.4
|
38.7
|
1.0
|
CB
|
D:ASP959
|
4.4
|
21.2
|
1.0
|
CB
|
D:ASP962
|
4.4
|
22.5
|
1.0
|
CA
|
D:TRP958
|
4.5
|
15.7
|
1.0
|
N
|
D:TRP958
|
4.5
|
17.7
|
1.0
|
CG2
|
D:VAL996
|
4.6
|
28.6
|
1.0
|
CA
|
D:SER957
|
4.6
|
18.5
|
1.0
|
CA
|
D:ASP959
|
4.7
|
20.2
|
1.0
|
C
|
D:TRP958
|
4.7
|
20.7
|
1.0
|
C
|
D:LYS997
|
4.7
|
43.7
|
1.0
|
CA
|
D:VAL996
|
4.8
|
32.9
|
1.0
|
N
|
D:VAL996
|
4.9
|
29.3
|
1.0
|
N
|
D:ASP962
|
5.0
|
33.4
|
1.0
|
|
Calcium binding site 4 out
of 17 in 8xmk
Go back to
Calcium Binding Sites List in 8xmk
Calcium binding site 4 out
of 17 in the Local Refinement of SRCR5-9 Domains
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Local Refinement of SRCR5-9 Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca1106
b:54.0
occ:1.00
|
OE2
|
D:GLU812
|
2.3
|
50.5
|
1.0
|
OD1
|
D:ASP746
|
2.3
|
55.6
|
1.0
|
OD2
|
D:ASP745
|
2.5
|
53.3
|
1.0
|
CD
|
D:GLU812
|
3.4
|
54.7
|
1.0
|
CG
|
D:ASP746
|
3.5
|
55.6
|
1.0
|
CG
|
D:ASP745
|
3.6
|
53.0
|
1.0
|
CA
|
D:ASP746
|
4.0
|
53.0
|
1.0
|
CG
|
D:GLU812
|
4.1
|
53.4
|
1.0
|
OD1
|
D:ASP745
|
4.2
|
58.3
|
1.0
|
N
|
D:ASP746
|
4.3
|
55.2
|
1.0
|
OE1
|
D:GLU812
|
4.3
|
55.0
|
1.0
|
O
|
D:ASP745
|
4.3
|
45.8
|
1.0
|
CB
|
D:ASP746
|
4.3
|
53.0
|
1.0
|
C
|
D:ASP745
|
4.4
|
49.0
|
1.0
|
OD2
|
D:ASP746
|
4.4
|
58.1
|
1.0
|
CB
|
D:ASP745
|
4.8
|
48.0
|
1.0
|
O
|
D:CYS744
|
4.8
|
55.1
|
1.0
|
|
Calcium binding site 5 out
of 17 in 8xmk
Go back to
Calcium Binding Sites List in 8xmk
Calcium binding site 5 out
of 17 in the Local Refinement of SRCR5-9 Domains
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Local Refinement of SRCR5-9 Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca1107
b:57.7
occ:1.00
|
OD2
|
D:ASP752
|
2.3
|
57.2
|
1.0
|
O
|
D:MET786
|
2.4
|
61.5
|
1.0
|
O
|
D:SER747
|
2.4
|
57.1
|
1.0
|
CG
|
D:ASP752
|
3.1
|
57.9
|
1.0
|
OD1
|
D:ASP752
|
3.3
|
58.0
|
1.0
|
C
|
D:MET786
|
3.5
|
63.4
|
1.0
|
C
|
D:SER747
|
3.5
|
57.5
|
1.0
|
CA
|
D:LYS787
|
3.7
|
68.7
|
1.0
|
CB
|
D:SER747
|
4.0
|
52.2
|
1.0
|
N
|
D:LYS787
|
4.1
|
69.1
|
1.0
|
N
|
D:ASP749
|
4.1
|
55.3
|
1.0
|
CB
|
D:ASP749
|
4.1
|
56.8
|
1.0
|
OG
|
D:SER747
|
4.2
|
54.5
|
1.0
|
CA
|
D:SER747
|
4.3
|
53.2
|
1.0
|
CG
|
D:LYS787
|
4.4
|
68.4
|
1.0
|
C
|
D:LYS787
|
4.5
|
69.0
|
1.0
|
N
|
D:TRP748
|
4.5
|
54.4
|
1.0
|
CB
|
D:ASP752
|
4.6
|
55.4
|
1.0
|
OG
|
D:SER751
|
4.6
|
53.9
|
1.0
|
N
|
D:CYS788
|
4.6
|
64.1
|
1.0
|
CB
|
D:LYS787
|
4.6
|
69.1
|
1.0
|
CA
|
D:TRP748
|
4.7
|
49.5
|
1.0
|
CA
|
D:ASP749
|
4.8
|
55.4
|
1.0
|
CA
|
D:MET786
|
4.8
|
61.7
|
1.0
|
C
|
D:TRP748
|
4.9
|
53.3
|
1.0
|
|
Calcium binding site 6 out
of 17 in 8xmk
Go back to
Calcium Binding Sites List in 8xmk
Calcium binding site 6 out
of 17 in the Local Refinement of SRCR5-9 Domains
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Local Refinement of SRCR5-9 Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca1108
b:66.5
occ:1.00
|
OD2
|
D:ASP784
|
2.3
|
60.2
|
1.0
|
OD2
|
D:ASP746
|
2.4
|
58.1
|
1.0
|
OD1
|
D:ASN807
|
2.4
|
60.5
|
1.0
|
OE2
|
D:GLU785
|
2.4
|
59.5
|
1.0
|
OD1
|
D:ASP784
|
2.8
|
61.7
|
1.0
|
CG
|
D:ASP784
|
2.9
|
61.6
|
1.0
|
NZ
|
E:LYS977
|
2.9
|
75.1
|
1.0
|
CG
|
D:ASP746
|
3.4
|
55.6
|
1.0
|
SG
|
D:CYS808
|
3.5
|
67.5
|
1.0
|
CG
|
D:ASN807
|
3.5
|
60.4
|
1.0
|
CD
|
D:GLU785
|
3.6
|
60.0
|
1.0
|
CB
|
D:ASP746
|
3.6
|
53.0
|
1.0
|
SG
|
D:CYS744
|
3.8
|
61.6
|
1.0
|
CE
|
E:LYS977
|
3.8
|
77.4
|
1.0
|
ND2
|
D:ASN807
|
4.0
|
59.2
|
1.0
|
CG
|
D:GLU785
|
4.2
|
60.3
|
1.0
|
O
|
D:ASN807
|
4.3
|
57.0
|
1.0
|
CB
|
D:ASP784
|
4.3
|
60.7
|
1.0
|
OD1
|
D:ASP746
|
4.5
|
55.6
|
1.0
|
OE1
|
D:GLU785
|
4.6
|
60.2
|
1.0
|
CB
|
D:ASN807
|
4.8
|
60.4
|
1.0
|
CB
|
D:CYS744
|
4.9
|
52.6
|
1.0
|
|
Calcium binding site 7 out
of 17 in 8xmk
Go back to
Calcium Binding Sites List in 8xmk
Calcium binding site 7 out
of 17 in the Local Refinement of SRCR5-9 Domains
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Local Refinement of SRCR5-9 Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca1103
b:29.6
occ:1.00
|
O
|
E:PHE650
|
2.3
|
30.3
|
1.0
|
OD2
|
E:ASP616
|
2.4
|
37.2
|
1.0
|
O
|
E:HIS611
|
2.4
|
42.4
|
1.0
|
CG
|
E:ASP616
|
3.1
|
33.5
|
1.0
|
OD1
|
E:ASP616
|
3.2
|
33.3
|
1.0
|
C
|
E:PHE650
|
3.6
|
10.2
|
1.0
|
C
|
E:HIS611
|
3.6
|
39.6
|
1.0
|
N
|
E:ASP613
|
3.7
|
43.1
|
1.0
|
CB
|
E:ASP613
|
3.8
|
43.1
|
1.0
|
OD2
|
E:ASP613
|
3.8
|
53.0
|
1.0
|
CG
|
E:ASP613
|
4.1
|
51.1
|
1.0
|
CA
|
E:HIS651
|
4.3
|
12.6
|
1.0
|
CB
|
E:HIS611
|
4.4
|
38.4
|
1.0
|
N
|
E:HIS651
|
4.4
|
1.5
|
1.0
|
CA
|
E:ASP613
|
4.4
|
42.5
|
1.0
|
CA
|
E:HIS611
|
4.5
|
40.0
|
1.0
|
N
|
E:TRP612
|
4.5
|
37.7
|
1.0
|
CA
|
E:PHE650
|
4.6
|
8.5
|
1.0
|
CA
|
E:TRP612
|
4.6
|
39.4
|
1.0
|
CB
|
E:ASP616
|
4.6
|
32.0
|
1.0
|
N
|
E:PHE650
|
4.6
|
7.5
|
1.0
|
C
|
E:TRP612
|
4.6
|
42.0
|
1.0
|
N
|
E:CYS652
|
4.8
|
36.2
|
1.0
|
ND1
|
E:HIS651
|
4.8
|
22.4
|
1.0
|
CB
|
E:PHE650
|
4.9
|
15.1
|
1.0
|
C
|
E:HIS651
|
5.0
|
27.0
|
1.0
|
|
Calcium binding site 8 out
of 17 in 8xmk
Go back to
Calcium Binding Sites List in 8xmk
Calcium binding site 8 out
of 17 in the Local Refinement of SRCR5-9 Domains
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Local Refinement of SRCR5-9 Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca1104
b:37.7
occ:1.00
|
OD1
|
E:ASP746
|
2.3
|
40.4
|
1.0
|
OE1
|
E:GLU812
|
2.4
|
39.3
|
1.0
|
OD1
|
E:ASP745
|
2.5
|
42.6
|
1.0
|
CG
|
E:ASP745
|
3.4
|
35.8
|
1.0
|
CD
|
E:GLU812
|
3.5
|
41.5
|
1.0
|
CG
|
E:ASP746
|
3.5
|
40.7
|
1.0
|
OD2
|
E:ASP745
|
3.8
|
39.8
|
1.0
|
N
|
E:ASP746
|
4.0
|
35.5
|
1.0
|
CB
|
E:GLU812
|
4.0
|
39.9
|
1.0
|
C
|
E:ASP745
|
4.1
|
32.1
|
1.0
|
NZ
|
F:LYS1021
|
4.2
|
37.7
|
1.0
|
OE2
|
F:GLU981
|
4.2
|
44.4
|
1.0
|
CA
|
E:ASP746
|
4.2
|
35.1
|
1.0
|
CG
|
E:GLU812
|
4.3
|
37.6
|
1.0
|
OE2
|
E:GLU812
|
4.3
|
49.1
|
1.0
|
O
|
E:ASP745
|
4.3
|
39.2
|
1.0
|
OD2
|
E:ASP746
|
4.3
|
36.3
|
1.0
|
SG
|
E:CYS744
|
4.4
|
56.2
|
1.0
|
CB
|
E:ASP746
|
4.5
|
33.7
|
1.0
|
CB
|
E:ASP745
|
4.6
|
28.7
|
1.0
|
CE
|
F:LYS1021
|
4.7
|
28.9
|
1.0
|
CA
|
E:ASP745
|
4.7
|
23.1
|
1.0
|
N
|
E:ASP745
|
4.8
|
34.5
|
1.0
|
CD
|
F:GLU981
|
4.9
|
45.2
|
1.0
|
|
Calcium binding site 9 out
of 17 in 8xmk
Go back to
Calcium Binding Sites List in 8xmk
Calcium binding site 9 out
of 17 in the Local Refinement of SRCR5-9 Domains
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Local Refinement of SRCR5-9 Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca1105
b:49.8
occ:1.00
|
OD1
|
E:ASP784
|
2.3
|
47.7
|
1.0
|
OD1
|
E:ASN807
|
2.3
|
44.5
|
1.0
|
OE2
|
E:GLU785
|
2.4
|
47.1
|
1.0
|
OD2
|
E:ASP746
|
2.5
|
36.3
|
1.0
|
CG
|
E:ASN807
|
3.2
|
42.6
|
1.0
|
CG
|
E:ASP784
|
3.3
|
44.4
|
1.0
|
ND2
|
E:ASN807
|
3.4
|
45.8
|
1.0
|
CG
|
E:ASP746
|
3.5
|
40.7
|
1.0
|
OD2
|
E:ASP784
|
3.5
|
42.9
|
1.0
|
CD
|
E:GLU785
|
3.5
|
43.4
|
1.0
|
CB
|
E:ASP746
|
3.8
|
33.7
|
1.0
|
CG
|
E:GLU785
|
4.1
|
41.2
|
1.0
|
NZ
|
F:LYS1021
|
4.1
|
37.7
|
1.0
|
CD
|
F:LYS1021
|
4.3
|
26.3
|
1.0
|
SG
|
E:CYS808
|
4.4
|
62.1
|
1.0
|
OE1
|
E:GLU785
|
4.6
|
44.7
|
1.0
|
OD1
|
E:ASP746
|
4.6
|
40.4
|
1.0
|
CB
|
E:ASP784
|
4.6
|
42.7
|
1.0
|
CB
|
E:ASN807
|
4.6
|
41.6
|
1.0
|
CE
|
F:LYS1021
|
4.8
|
28.9
|
1.0
|
N
|
E:ASN807
|
4.8
|
46.6
|
1.0
|
CE1
|
E:HIS801
|
4.9
|
45.8
|
1.0
|
|
Calcium binding site 10 out
of 17 in 8xmk
Go back to
Calcium Binding Sites List in 8xmk
Calcium binding site 10 out
of 17 in the Local Refinement of SRCR5-9 Domains
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Local Refinement of SRCR5-9 Domains within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca1106
b:31.4
occ:1.00
|
OD1
|
E:ASP749
|
2.2
|
36.3
|
1.0
|
O
|
E:MET786
|
2.2
|
41.2
|
1.0
|
OD2
|
E:ASP752
|
2.5
|
44.9
|
1.0
|
O
|
E:SER747
|
2.6
|
34.1
|
1.0
|
OD1
|
E:ASP752
|
2.9
|
44.0
|
1.0
|
CG
|
E:ASP752
|
3.1
|
39.1
|
1.0
|
CG
|
E:ASP749
|
3.3
|
36.0
|
1.0
|
C
|
E:MET786
|
3.3
|
43.1
|
1.0
|
C
|
E:SER747
|
3.8
|
36.5
|
1.0
|
OD2
|
E:ASP749
|
3.8
|
35.0
|
1.0
|
CA
|
E:LYS787
|
3.8
|
51.4
|
1.0
|
N
|
E:LYS787
|
4.0
|
47.0
|
1.0
|
N
|
E:ASP749
|
4.0
|
32.0
|
1.0
|
N
|
E:CYS788
|
4.1
|
52.7
|
1.0
|
OG
|
E:SER747
|
4.3
|
45.6
|
1.0
|
C
|
E:LYS787
|
4.4
|
53.8
|
1.0
|
CA
|
E:MET786
|
4.4
|
37.7
|
1.0
|
CB
|
E:MET786
|
4.5
|
36.3
|
1.0
|
CB
|
E:ASP749
|
4.5
|
31.7
|
1.0
|
CB
|
E:SER747
|
4.5
|
36.9
|
1.0
|
CB
|
E:ASP752
|
4.5
|
32.3
|
1.0
|
CA
|
E:TRP748
|
4.6
|
22.8
|
1.0
|
N
|
E:TRP748
|
4.6
|
29.9
|
1.0
|
CA
|
E:SER747
|
4.7
|
37.8
|
1.0
|
CD
|
E:LYS787
|
4.8
|
55.3
|
1.0
|
O
|
E:CYS788
|
4.8
|
56.2
|
1.0
|
CA
|
E:ASP749
|
4.8
|
27.2
|
1.0
|
C
|
E:TRP748
|
4.8
|
30.9
|
1.0
|
N
|
E:MET786
|
4.9
|
37.8
|
1.0
|
N
|
E:ASP752
|
4.9
|
33.0
|
1.0
|
|
Reference:
H.Xu,
X.D.Su.
Local Refinement of SRCR5-9 Domains To Be Published.
Page generated: Sat Feb 8 16:11:43 2025
|