Calcium in PDB 8jxb: Cryo-Em Structure of Rat Megalin Wingac
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
18;
Binding sites:
The binding sites of Calcium atom in the Cryo-Em Structure of Rat Megalin Wingac
(pdb code 8jxb). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the
Cryo-Em Structure of Rat Megalin Wingac, PDB code: 8jxb:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 18 in 8jxb
Go back to
Calcium Binding Sites List in 8jxb
Calcium binding site 1 out
of 18 in the Cryo-Em Structure of Rat Megalin Wingac
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cryo-Em Structure of Rat Megalin Wingac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4704
b:134.8
occ:1.00
|
OD2
|
A:ASP2731
|
2.2
|
128.2
|
1.0
|
O
|
A:ASP2723
|
2.2
|
133.9
|
1.0
|
OD1
|
A:ASP2721
|
2.3
|
125.4
|
1.0
|
OE1
|
A:GLU2732
|
2.3
|
137.7
|
1.0
|
O
|
A:TRP2718
|
2.3
|
122.2
|
1.0
|
OD2
|
A:ASP2725
|
2.4
|
136.3
|
1.0
|
CD
|
A:GLU2732
|
2.6
|
134.5
|
1.0
|
OE2
|
A:GLU2732
|
2.9
|
133.9
|
1.0
|
C
|
A:ASP2723
|
3.4
|
134.0
|
1.0
|
CG
|
A:ASP2721
|
3.4
|
124.1
|
1.0
|
CG
|
A:ASP2731
|
3.5
|
129.4
|
1.0
|
CG
|
A:ASP2725
|
3.5
|
135.5
|
1.0
|
C
|
A:TRP2718
|
3.5
|
121.1
|
1.0
|
CG
|
A:GLU2732
|
3.7
|
133.1
|
1.0
|
N
|
A:ASP2721
|
3.8
|
121.4
|
1.0
|
N
|
A:ASP2723
|
3.8
|
133.8
|
1.0
|
N
|
A:CYS2720
|
3.9
|
118.2
|
1.0
|
CA
|
A:ASP2723
|
3.9
|
133.7
|
1.0
|
CB
|
A:ASP2723
|
4.0
|
131.2
|
1.0
|
N
|
A:ASP2725
|
4.1
|
134.9
|
1.0
|
CB
|
A:ASP2725
|
4.1
|
132.9
|
1.0
|
OD2
|
A:ASP2721
|
4.1
|
125.3
|
1.0
|
OD1
|
A:ASP2731
|
4.3
|
131.4
|
1.0
|
CA
|
A:LYS2719
|
4.3
|
114.6
|
1.0
|
C
|
A:LYS2719
|
4.3
|
114.7
|
1.0
|
N
|
A:LYS2719
|
4.4
|
115.3
|
1.0
|
CB
|
A:ASP2721
|
4.4
|
119.4
|
1.0
|
CB
|
A:ASP2731
|
4.4
|
129.7
|
1.0
|
CA
|
A:ASP2721
|
4.5
|
122.0
|
1.0
|
N
|
A:ASN2724
|
4.5
|
138.1
|
1.0
|
CA
|
A:TRP2718
|
4.5
|
121.5
|
1.0
|
OD1
|
A:ASP2725
|
4.5
|
135.5
|
1.0
|
CB
|
A:TRP2718
|
4.6
|
120.9
|
1.0
|
C
|
A:ASP2721
|
4.6
|
122.3
|
1.0
|
CA
|
A:CYS2720
|
4.7
|
116.8
|
1.0
|
O
|
A:ASP2731
|
4.7
|
133.0
|
1.0
|
N
|
A:ASN2722
|
4.7
|
123.3
|
1.0
|
C
|
A:CYS2720
|
4.7
|
118.1
|
1.0
|
CA
|
A:ASP2725
|
4.8
|
132.2
|
1.0
|
C
|
A:ASP2731
|
4.9
|
131.0
|
1.0
|
CA
|
A:ASN2724
|
4.9
|
137.5
|
1.0
|
C
|
A:ASN2724
|
5.0
|
138.1
|
1.0
|
|
Calcium binding site 2 out
of 18 in 8jxb
Go back to
Calcium Binding Sites List in 8jxb
Calcium binding site 2 out
of 18 in the Cryo-Em Structure of Rat Megalin Wingac
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cryo-Em Structure of Rat Megalin Wingac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4705
b:143.4
occ:1.00
|
OD1
|
A:ASP2766
|
2.2
|
125.1
|
1.0
|
OD1
|
A:ASP2772
|
2.2
|
121.7
|
1.0
|
OD1
|
A:ASP2762
|
2.2
|
122.5
|
1.0
|
O
|
A:TYR2764
|
2.3
|
135.8
|
1.0
|
O
|
A:TYR2759
|
2.4
|
109.0
|
1.0
|
OD2
|
A:ASP2762
|
2.4
|
127.3
|
1.0
|
CG
|
A:ASP2772
|
2.5
|
122.0
|
1.0
|
CG
|
A:ASP2762
|
2.6
|
124.6
|
1.0
|
OD2
|
A:ASP2772
|
2.7
|
121.7
|
1.0
|
CG
|
A:ASP2766
|
3.0
|
124.7
|
1.0
|
OD2
|
A:ASP2766
|
3.3
|
123.8
|
1.0
|
C
|
A:TYR2759
|
3.5
|
103.7
|
1.0
|
C
|
A:TYR2764
|
3.5
|
133.2
|
1.0
|
CB
|
A:ASP2772
|
3.6
|
119.4
|
1.0
|
N
|
A:ASP2766
|
3.7
|
124.3
|
1.0
|
CB
|
A:TYR2759
|
3.8
|
108.0
|
1.0
|
CA
|
A:TYR2759
|
4.0
|
103.0
|
1.0
|
CB
|
A:ASP2762
|
4.1
|
122.2
|
1.0
|
CB
|
A:ASP2766
|
4.2
|
122.7
|
1.0
|
CA
|
A:ASN2765
|
4.3
|
122.0
|
1.0
|
N
|
A:ASN2765
|
4.3
|
121.2
|
1.0
|
C
|
A:ASN2765
|
4.4
|
125.6
|
1.0
|
CA
|
A:TYR2764
|
4.4
|
132.8
|
1.0
|
CA
|
A:ASP2766
|
4.5
|
123.8
|
1.0
|
N
|
A:TYR2764
|
4.5
|
135.4
|
1.0
|
OE2
|
A:GLU2773
|
4.5
|
126.8
|
1.0
|
N
|
A:ASP2762
|
4.6
|
124.5
|
1.0
|
N
|
A:ARG2760
|
4.6
|
102.8
|
1.0
|
CD
|
A:GLU2773
|
4.6
|
125.6
|
1.0
|
CB
|
A:TYR2764
|
4.6
|
134.1
|
1.0
|
CG
|
A:TYR2759
|
4.7
|
107.4
|
1.0
|
CA
|
A:ASP2762
|
4.8
|
124.7
|
1.0
|
CA
|
A:ASP2772
|
4.9
|
120.7
|
1.0
|
CG
|
A:GLU2773
|
4.9
|
124.7
|
1.0
|
CA
|
A:ARG2760
|
4.9
|
108.3
|
1.0
|
C
|
A:ASP2772
|
5.0
|
123.3
|
1.0
|
N
|
A:CYS2767
|
5.0
|
122.3
|
1.0
|
OE1
|
A:GLU2773
|
5.0
|
125.2
|
1.0
|
|
Calcium binding site 3 out
of 18 in 8jxb
Go back to
Calcium Binding Sites List in 8jxb
Calcium binding site 3 out
of 18 in the Cryo-Em Structure of Rat Megalin Wingac
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cryo-Em Structure of Rat Megalin Wingac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4706
b:228.4
occ:1.00
|
OD2
|
A:ASP2814
|
2.4
|
223.9
|
1.0
|
O
|
A:ILE2804
|
2.4
|
228.7
|
1.0
|
O
|
A:TYR2799
|
2.4
|
214.5
|
1.0
|
OE1
|
A:GLU2815
|
2.4
|
236.4
|
1.0
|
OD1
|
A:ASP2814
|
2.4
|
224.0
|
1.0
|
OD1
|
A:ASN2806
|
2.5
|
213.8
|
1.0
|
OD1
|
A:ASN2802
|
2.5
|
228.0
|
1.0
|
CG
|
A:ASP2814
|
2.7
|
224.1
|
1.0
|
CG
|
A:ASN2802
|
3.5
|
226.8
|
1.0
|
C
|
A:ILE2804
|
3.6
|
228.5
|
1.0
|
CD
|
A:GLU2815
|
3.6
|
236.6
|
1.0
|
C
|
A:TYR2799
|
3.6
|
214.4
|
1.0
|
CG
|
A:ASN2806
|
3.6
|
212.8
|
1.0
|
N
|
A:ASN2806
|
3.7
|
213.7
|
1.0
|
N
|
A:CYS2801
|
3.9
|
232.3
|
1.0
|
N
|
A:ASN2802
|
3.9
|
227.2
|
1.0
|
CA
|
A:VAL2800
|
3.9
|
219.1
|
1.0
|
OE2
|
A:GLU2815
|
4.1
|
236.1
|
1.0
|
C
|
A:VAL2800
|
4.2
|
219.9
|
1.0
|
CB
|
A:ASN2806
|
4.2
|
212.4
|
1.0
|
CB
|
A:ASP2814
|
4.2
|
224.1
|
1.0
|
ND2
|
A:ASN2802
|
4.2
|
225.4
|
1.0
|
N
|
A:VAL2800
|
4.2
|
219.6
|
1.0
|
N
|
A:ILE2804
|
4.3
|
228.3
|
1.0
|
CA
|
A:ASN2805
|
4.3
|
222.0
|
1.0
|
O
|
A:ASP2814
|
4.3
|
223.1
|
1.0
|
CB
|
A:ASN2802
|
4.3
|
226.8
|
1.0
|
N
|
A:ASN2805
|
4.3
|
222.1
|
1.0
|
C
|
A:ASP2814
|
4.5
|
223.6
|
1.0
|
C
|
A:ASN2805
|
4.6
|
221.7
|
1.0
|
CA
|
A:ILE2804
|
4.6
|
228.7
|
1.0
|
N
|
A:GLY2803
|
4.6
|
233.9
|
1.0
|
CA
|
A:ASN2802
|
4.6
|
227.6
|
1.0
|
CA
|
A:ASN2806
|
4.6
|
212.5
|
1.0
|
CA
|
A:CYS2801
|
4.7
|
232.5
|
1.0
|
C
|
A:CYS2801
|
4.7
|
232.2
|
1.0
|
ND2
|
A:ASN2806
|
4.7
|
212.0
|
1.0
|
CA
|
A:TYR2799
|
4.8
|
214.2
|
1.0
|
CG
|
A:GLU2815
|
4.8
|
236.7
|
1.0
|
N
|
A:GLU2815
|
4.8
|
235.2
|
1.0
|
CB
|
A:TYR2799
|
4.9
|
213.8
|
1.0
|
CA
|
A:GLU2815
|
4.9
|
236.3
|
1.0
|
CB
|
A:GLU2815
|
4.9
|
236.2
|
1.0
|
CG2
|
A:ILE2804
|
4.9
|
227.2
|
1.0
|
CA
|
A:ASP2814
|
5.0
|
223.4
|
1.0
|
|
Calcium binding site 4 out
of 18 in 8jxb
Go back to
Calcium Binding Sites List in 8jxb
Calcium binding site 4 out
of 18 in the Cryo-Em Structure of Rat Megalin Wingac
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Cryo-Em Structure of Rat Megalin Wingac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4707
b:304.2
occ:1.00
|
OD1
|
A:ASP2854
|
2.2
|
295.9
|
1.0
|
OD1
|
A:ASP2844
|
2.3
|
296.5
|
1.0
|
OD2
|
A:ASP2848
|
2.3
|
294.2
|
1.0
|
O
|
A:ASP2846
|
2.3
|
298.4
|
1.0
|
OE1
|
A:GLU2855
|
2.4
|
295.8
|
1.0
|
O
|
A:PHE2841
|
2.6
|
294.5
|
1.0
|
CG
|
A:ASP2854
|
3.0
|
295.7
|
1.0
|
CG
|
A:ASP2844
|
3.0
|
295.9
|
1.0
|
OD2
|
A:ASP2844
|
3.1
|
295.8
|
1.0
|
N
|
A:GLU2855
|
3.4
|
295.7
|
1.0
|
CG
|
A:ASP2848
|
3.4
|
293.7
|
1.0
|
CD
|
A:GLU2855
|
3.5
|
295.2
|
1.0
|
C
|
A:ASP2846
|
3.5
|
297.8
|
1.0
|
C
|
A:PHE2841
|
3.6
|
294.5
|
1.0
|
OD2
|
A:ASP2854
|
3.7
|
296.1
|
1.0
|
N
|
A:ASP2848
|
3.7
|
294.4
|
1.0
|
CB
|
A:ASP2854
|
3.8
|
295.4
|
1.0
|
CB
|
A:GLU2855
|
3.8
|
295.6
|
1.0
|
C
|
A:ASP2854
|
3.9
|
295.6
|
1.0
|
CA
|
A:ASP2854
|
3.9
|
295.5
|
1.0
|
CB
|
A:ASP2848
|
4.0
|
293.6
|
1.0
|
CA
|
A:GLU2855
|
4.1
|
295.4
|
1.0
|
C
|
A:ASN2847
|
4.1
|
294.9
|
1.0
|
CA
|
A:ASN2847
|
4.2
|
294.9
|
1.0
|
CG
|
A:GLU2855
|
4.3
|
295.3
|
1.0
|
N
|
A:ASN2847
|
4.3
|
295.1
|
1.0
|
CA
|
A:LEU2842
|
4.4
|
293.7
|
1.0
|
N
|
A:ASP2846
|
4.4
|
297.4
|
1.0
|
N
|
A:LEU2842
|
4.4
|
293.9
|
1.0
|
OE2
|
A:GLU2855
|
4.4
|
294.9
|
1.0
|
OD1
|
A:ASP2848
|
4.4
|
293.4
|
1.0
|
CA
|
A:ASP2848
|
4.4
|
293.7
|
1.0
|
CB
|
A:ASP2844
|
4.5
|
295.7
|
1.0
|
CA
|
A:PHE2841
|
4.6
|
294.5
|
1.0
|
CA
|
A:ASP2846
|
4.6
|
297.4
|
1.0
|
N
|
A:ASP2844
|
4.8
|
296.3
|
1.0
|
CB
|
A:PHE2841
|
4.8
|
294.3
|
1.0
|
O
|
A:ASP2854
|
4.8
|
295.2
|
1.0
|
O
|
A:ASN2847
|
4.9
|
294.7
|
1.0
|
N
|
A:GLY2845
|
5.0
|
297.6
|
1.0
|
C
|
A:ASP2844
|
5.0
|
296.2
|
1.0
|
CA
|
A:ASP2844
|
5.0
|
296.0
|
1.0
|
|
Calcium binding site 5 out
of 18 in 8jxb
Go back to
Calcium Binding Sites List in 8jxb
Calcium binding site 5 out
of 18 in the Cryo-Em Structure of Rat Megalin Wingac
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Cryo-Em Structure of Rat Megalin Wingac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4708
b:304.9
occ:1.00
|
OD1
|
A:ASP2886
|
2.4
|
295.3
|
1.0
|
OD2
|
A:ASP2896
|
2.4
|
300.3
|
1.0
|
O
|
A:TRP2883
|
2.4
|
294.3
|
1.0
|
O
|
A:GLU2888
|
2.5
|
289.9
|
1.0
|
OD2
|
A:ASP2890
|
2.5
|
294.5
|
1.0
|
OE2
|
A:GLU2897
|
2.6
|
299.3
|
1.0
|
CG
|
A:ASP2886
|
3.1
|
294.6
|
1.0
|
CG
|
A:ASP2896
|
3.3
|
300.0
|
1.0
|
CG
|
A:ASP2890
|
3.3
|
294.1
|
1.0
|
OD2
|
A:ASP2886
|
3.6
|
293.9
|
1.0
|
C
|
A:TRP2883
|
3.6
|
293.9
|
1.0
|
CB
|
A:ASP2896
|
3.6
|
299.9
|
1.0
|
CD
|
A:GLU2897
|
3.7
|
298.8
|
1.0
|
C
|
A:GLU2888
|
3.7
|
289.4
|
1.0
|
N
|
A:ASP2890
|
3.8
|
294.6
|
1.0
|
CD1
|
A:ILE2879
|
3.9
|
292.6
|
1.0
|
N
|
A:ASP2886
|
4.0
|
295.5
|
1.0
|
OD1
|
A:ASP2890
|
4.1
|
293.5
|
1.0
|
CB
|
A:ASP2890
|
4.1
|
294.2
|
1.0
|
CB
|
A:ASP2886
|
4.2
|
294.7
|
1.0
|
CG
|
A:GLU2897
|
4.3
|
298.6
|
1.0
|
N
|
A:CYS2885
|
4.3
|
299.9
|
1.0
|
CA
|
A:PHE2884
|
4.5
|
294.7
|
1.0
|
OD1
|
A:ASP2896
|
4.5
|
300.2
|
1.0
|
O
|
A:ASP2896
|
4.5
|
300.3
|
1.0
|
N
|
A:GLU2888
|
4.5
|
289.3
|
1.0
|
N
|
A:PHE2884
|
4.5
|
294.8
|
1.0
|
CA
|
A:TRP2883
|
4.6
|
293.8
|
1.0
|
CA
|
A:ASP2890
|
4.6
|
294.2
|
1.0
|
CA
|
A:ASP2886
|
4.6
|
295.1
|
1.0
|
N
|
A:ALA2889
|
4.6
|
290.5
|
1.0
|
CA
|
A:ALA2889
|
4.6
|
290.3
|
1.0
|
C
|
A:ASP2896
|
4.7
|
300.2
|
1.0
|
CA
|
A:GLU2888
|
4.7
|
289.2
|
1.0
|
OE1
|
A:GLU2897
|
4.7
|
298.6
|
1.0
|
C
|
A:PHE2884
|
4.7
|
295.2
|
1.0
|
C
|
A:ALA2889
|
4.7
|
290.6
|
1.0
|
CB
|
A:TRP2883
|
4.8
|
293.5
|
1.0
|
CA
|
A:ASP2896
|
4.8
|
300.0
|
1.0
|
CA
|
A:CYS2885
|
5.0
|
299.5
|
1.0
|
|
Calcium binding site 6 out
of 18 in 8jxb
Go back to
Calcium Binding Sites List in 8jxb
Calcium binding site 6 out
of 18 in the Cryo-Em Structure of Rat Megalin Wingac
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Cryo-Em Structure of Rat Megalin Wingac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca4709
b:322.3
occ:1.00
|
OE2
|
A:GLU2939
|
2.2
|
314.9
|
1.0
|
OD1
|
A:ASP2928
|
2.3
|
315.3
|
1.0
|
OD2
|
A:ASP2938
|
2.3
|
313.9
|
1.0
|
O
|
A:TRP2925
|
2.3
|
310.7
|
1.0
|
OD2
|
A:ASP2932
|
2.4
|
309.7
|
1.0
|
O
|
A:ASP2930
|
2.7
|
310.8
|
1.0
|
CG
|
A:ASP2928
|
3.2
|
314.7
|
1.0
|
CG
|
A:ASP2938
|
3.3
|
313.6
|
1.0
|
CD
|
A:GLU2939
|
3.3
|
314.4
|
1.0
|
CG
|
A:ASP2932
|
3.3
|
309.1
|
1.0
|
C
|
A:TRP2925
|
3.5
|
310.4
|
1.0
|
CB
|
A:ASP2938
|
3.7
|
313.4
|
1.0
|
N
|
A:ASP2928
|
3.8
|
315.0
|
1.0
|
CB
|
A:ASP2932
|
3.8
|
308.9
|
1.0
|
OD2
|
A:ASP2928
|
3.9
|
314.5
|
1.0
|
C
|
A:ASP2930
|
3.9
|
310.5
|
1.0
|
N
|
A:CYS2927
|
3.9
|
314.9
|
1.0
|
N
|
A:ASP2932
|
4.1
|
309.4
|
1.0
|
CG
|
A:GLU2939
|
4.1
|
314.0
|
1.0
|
OE1
|
A:GLU2939
|
4.1
|
314.4
|
1.0
|
N
|
A:ASP2930
|
4.3
|
310.4
|
1.0
|
CB
|
A:ASP2928
|
4.3
|
314.6
|
1.0
|
C
|
A:VAL2926
|
4.3
|
312.0
|
1.0
|
CA
|
A:VAL2926
|
4.3
|
311.6
|
1.0
|
OD1
|
A:ASP2938
|
4.3
|
313.6
|
1.0
|
N
|
A:VAL2926
|
4.4
|
311.7
|
1.0
|
OD1
|
A:ASP2932
|
4.4
|
308.8
|
1.0
|
CA
|
A:TRP2925
|
4.5
|
310.4
|
1.0
|
CA
|
A:ASP2928
|
4.5
|
314.6
|
1.0
|
N
|
A:GLY2929
|
4.5
|
310.5
|
1.0
|
CA
|
A:ASP2932
|
4.6
|
308.9
|
1.0
|
CA
|
A:ASP2930
|
4.6
|
310.4
|
1.0
|
CA
|
A:CYS2927
|
4.6
|
314.7
|
1.0
|
C
|
A:CYS2927
|
4.7
|
314.6
|
1.0
|
CB
|
A:TRP2925
|
4.7
|
310.1
|
1.0
|
CD1
|
A:ILE2921
|
4.7
|
306.6
|
1.0
|
C
|
A:ASN2931
|
4.8
|
306.7
|
1.0
|
N
|
A:ASN2931
|
4.9
|
307.1
|
1.0
|
C
|
A:ASP2928
|
4.9
|
314.4
|
1.0
|
C
|
A:ASP2938
|
5.0
|
313.8
|
1.0
|
|
Calcium binding site 7 out
of 18 in 8jxb
Go back to
Calcium Binding Sites List in 8jxb
Calcium binding site 7 out
of 18 in the Cryo-Em Structure of Rat Megalin Wingac
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Cryo-Em Structure of Rat Megalin Wingac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca4711
b:246.5
occ:1.00
|
OD1
|
B:ASP203
|
2.2
|
231.4
|
1.0
|
OD1
|
B:ASP213
|
2.2
|
240.5
|
1.0
|
O
|
B:ASP205
|
2.3
|
232.2
|
1.0
|
OD2
|
B:ASP207
|
2.3
|
242.9
|
1.0
|
OD2
|
B:ASP213
|
2.4
|
239.5
|
1.0
|
OE2
|
B:GLU214
|
2.5
|
233.0
|
1.0
|
CG
|
B:ASP213
|
2.5
|
239.9
|
1.0
|
O
|
B:TYR200
|
2.7
|
249.3
|
1.0
|
CG
|
B:ASP207
|
3.0
|
243.2
|
1.0
|
OD1
|
B:ASP207
|
3.2
|
243.5
|
1.0
|
C
|
B:ASP205
|
3.3
|
231.5
|
1.0
|
CG
|
B:ASP203
|
3.3
|
230.7
|
1.0
|
N
|
B:ASP205
|
3.5
|
230.5
|
1.0
|
N
|
B:ASP203
|
3.6
|
230.3
|
1.0
|
CD
|
B:GLU214
|
3.6
|
232.3
|
1.0
|
CA
|
B:ASP205
|
3.9
|
230.5
|
1.0
|
C
|
B:TYR200
|
3.9
|
249.1
|
1.0
|
N
|
B:CYS202
|
3.9
|
235.2
|
1.0
|
CG
|
B:GLU214
|
3.9
|
232.5
|
1.0
|
CB
|
B:ASP213
|
4.0
|
239.8
|
1.0
|
OD2
|
B:ASP203
|
4.0
|
230.1
|
1.0
|
N
|
B:HIS204
|
4.2
|
206.8
|
1.0
|
CB
|
B:ASP207
|
4.2
|
243.7
|
1.0
|
CB
|
B:ASP205
|
4.2
|
230.6
|
1.0
|
CA
|
B:ASP203
|
4.3
|
229.8
|
1.0
|
O
|
B:ASN206
|
4.3
|
237.6
|
1.0
|
CB
|
B:ASP203
|
4.3
|
229.9
|
1.0
|
CA
|
B:CYS202
|
4.3
|
234.5
|
1.0
|
C
|
B:ASN206
|
4.4
|
238.5
|
1.0
|
C
|
B:ASP203
|
4.4
|
229.2
|
1.0
|
N
|
B:ASN206
|
4.4
|
238.2
|
1.0
|
C
|
B:CYS202
|
4.4
|
233.9
|
1.0
|
CB
|
B:TYR200
|
4.6
|
248.8
|
1.0
|
C
|
B:HIS204
|
4.6
|
206.8
|
1.0
|
OE1
|
B:GLU214
|
4.7
|
231.6
|
1.0
|
C
|
B:VAL201
|
4.7
|
243.8
|
1.0
|
CA
|
B:TYR200
|
4.7
|
249.3
|
1.0
|
CA
|
B:VAL201
|
4.8
|
243.4
|
1.0
|
CA
|
B:ASN206
|
4.8
|
238.0
|
1.0
|
N
|
B:VAL201
|
4.8
|
243.6
|
1.0
|
N
|
B:ASP207
|
4.8
|
244.3
|
1.0
|
CA
|
B:HIS204
|
4.9
|
206.0
|
1.0
|
C
|
B:ASP213
|
4.9
|
240.3
|
1.0
|
|
Calcium binding site 8 out
of 18 in 8jxb
Go back to
Calcium Binding Sites List in 8jxb
Calcium binding site 8 out
of 18 in the Cryo-Em Structure of Rat Megalin Wingac
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Cryo-Em Structure of Rat Megalin Wingac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca4712
b:141.1
occ:1.00
|
O
|
B:ASP244
|
2.3
|
132.9
|
1.0
|
OD1
|
B:ASP242
|
2.3
|
125.8
|
1.0
|
OE1
|
B:GLU253
|
2.3
|
127.5
|
1.0
|
OD1
|
B:ASP252
|
2.5
|
131.5
|
1.0
|
O
|
B:TRP239
|
2.9
|
117.6
|
1.0
|
OD2
|
B:ASP246
|
3.1
|
132.5
|
1.0
|
C
|
B:ASP244
|
3.2
|
133.7
|
1.0
|
CD
|
B:GLU253
|
3.3
|
124.4
|
1.0
|
CG
|
B:ASP242
|
3.3
|
128.0
|
1.0
|
N
|
B:ASP244
|
3.4
|
135.0
|
1.0
|
CG
|
B:ASP252
|
3.4
|
131.8
|
1.0
|
N
|
B:ASP242
|
3.6
|
125.3
|
1.0
|
CG
|
B:GLU253
|
3.7
|
122.0
|
1.0
|
N
|
B:CYS241
|
3.7
|
115.8
|
1.0
|
N
|
B:GLY243
|
3.8
|
131.6
|
1.0
|
CA
|
B:ASP244
|
3.9
|
134.2
|
1.0
|
OD2
|
B:ASP242
|
4.0
|
130.7
|
1.0
|
OD2
|
B:ASP252
|
4.0
|
133.8
|
1.0
|
CG
|
B:ASP246
|
4.1
|
131.6
|
1.0
|
C
|
B:TRP239
|
4.1
|
115.7
|
1.0
|
CA
|
B:CYS241
|
4.2
|
115.5
|
1.0
|
N
|
B:ASP245
|
4.2
|
131.9
|
1.0
|
O
|
B:ASP252
|
4.3
|
130.1
|
1.0
|
CA
|
B:ASP242
|
4.3
|
126.3
|
1.0
|
N
|
B:ASP246
|
4.3
|
130.3
|
1.0
|
C
|
B:GLY243
|
4.3
|
134.4
|
1.0
|
C
|
B:CYS241
|
4.3
|
118.0
|
1.0
|
CB
|
B:ASP242
|
4.4
|
125.4
|
1.0
|
C
|
B:VAL240
|
4.4
|
116.5
|
1.0
|
OE2
|
B:GLU253
|
4.4
|
123.3
|
1.0
|
CB
|
B:ASP252
|
4.4
|
131.4
|
1.0
|
C
|
B:ASP242
|
4.5
|
127.3
|
1.0
|
CA
|
B:ASP245
|
4.5
|
132.9
|
1.0
|
CA
|
B:VAL240
|
4.6
|
113.5
|
1.0
|
CA
|
B:GLY243
|
4.6
|
133.2
|
1.0
|
C
|
B:ASP252
|
4.6
|
129.4
|
1.0
|
CB
|
B:ASP244
|
4.6
|
134.3
|
1.0
|
OD1
|
B:ASP246
|
4.8
|
130.6
|
1.0
|
N
|
B:VAL240
|
4.9
|
111.7
|
1.0
|
CB
|
B:ASP246
|
4.9
|
132.5
|
1.0
|
C
|
B:ASP245
|
5.0
|
132.3
|
1.0
|
CB
|
B:GLU253
|
5.0
|
117.8
|
1.0
|
|
Calcium binding site 9 out
of 18 in 8jxb
Go back to
Calcium Binding Sites List in 8jxb
Calcium binding site 9 out
of 18 in the Cryo-Em Structure of Rat Megalin Wingac
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Cryo-Em Structure of Rat Megalin Wingac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca4713
b:302.3
occ:1.00
|
O
|
B:ASP296
|
2.3
|
288.8
|
1.0
|
OD1
|
B:ASP286
|
2.4
|
291.9
|
1.0
|
O
|
B:LYS283
|
2.4
|
278.2
|
1.0
|
OE1
|
B:GLU297
|
2.5
|
293.8
|
1.0
|
OD2
|
B:ASP296
|
2.6
|
288.6
|
1.0
|
O
|
B:VAL288
|
2.9
|
292.4
|
1.0
|
N
|
B:CYS285
|
2.9
|
288.9
|
1.0
|
N
|
B:ASP286
|
3.1
|
290.9
|
1.0
|
CG
|
B:ASP296
|
3.4
|
288.4
|
1.0
|
CG
|
B:ASP286
|
3.4
|
290.8
|
1.0
|
C
|
B:ASP296
|
3.5
|
288.3
|
1.0
|
C
|
B:LYS283
|
3.5
|
277.7
|
1.0
|
C
|
B:VAL284
|
3.6
|
283.7
|
1.0
|
CA
|
B:CYS285
|
3.6
|
288.4
|
1.0
|
CD
|
B:GLU297
|
3.6
|
293.2
|
1.0
|
CA
|
B:VAL284
|
3.7
|
283.8
|
1.0
|
CB
|
B:ASP296
|
3.8
|
288.4
|
1.0
|
C
|
B:CYS285
|
3.8
|
288.1
|
1.0
|
C
|
B:VAL288
|
3.9
|
291.6
|
1.0
|
N
|
B:VAL288
|
4.0
|
291.7
|
1.0
|
CA
|
B:ASP286
|
4.0
|
290.9
|
1.0
|
N
|
B:VAL284
|
4.1
|
283.7
|
1.0
|
N
|
B:GLY287
|
4.1
|
291.9
|
1.0
|
CB
|
B:ASP286
|
4.2
|
290.8
|
1.0
|
OD2
|
B:ASP286
|
4.2
|
289.9
|
1.0
|
CA
|
B:ASP296
|
4.2
|
288.1
|
1.0
|
OD1
|
B:ASP296
|
4.3
|
288.3
|
1.0
|
OE2
|
B:GLU297
|
4.3
|
292.7
|
1.0
|
N
|
B:GLU297
|
4.4
|
292.7
|
1.0
|
CA
|
B:VAL288
|
4.5
|
291.2
|
1.0
|
C
|
B:ASP286
|
4.5
|
291.1
|
1.0
|
O
|
B:VAL284
|
4.5
|
283.2
|
1.0
|
CA
|
B:GLU297
|
4.5
|
293.3
|
1.0
|
CB
|
B:GLU297
|
4.6
|
293.0
|
1.0
|
CG
|
B:GLU297
|
4.7
|
293.1
|
1.0
|
CA
|
B:LYS283
|
4.7
|
277.1
|
1.0
|
CB
|
B:VAL288
|
4.9
|
290.4
|
1.0
|
C
|
B:GLY287
|
4.9
|
291.7
|
1.0
|
N
|
B:ASP290
|
4.9
|
289.4
|
1.0
|
N
|
B:PRO289
|
4.9
|
292.4
|
1.0
|
O
|
B:CYS285
|
5.0
|
287.7
|
1.0
|
|
Calcium binding site 10 out
of 18 in 8jxb
Go back to
Calcium Binding Sites List in 8jxb
Calcium binding site 10 out
of 18 in the Cryo-Em Structure of Rat Megalin Wingac
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Cryo-Em Structure of Rat Megalin Wingac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca4714
b:62.4
occ:1.00
|
OD1
|
B:ASP578
|
2.4
|
83.3
|
1.0
|
OD2
|
B:ASP578
|
2.4
|
78.7
|
1.0
|
O
|
B:PRO601
|
2.4
|
75.6
|
1.0
|
O
|
B:SER575
|
2.6
|
74.5
|
1.0
|
OG1
|
B:THR1131
|
2.6
|
85.9
|
1.0
|
CG
|
B:ASP578
|
2.7
|
79.5
|
1.0
|
O
|
B:THR1131
|
3.0
|
89.0
|
1.0
|
CB
|
B:THR1131
|
3.4
|
83.6
|
1.0
|
OD1
|
B:ASP1132
|
3.5
|
98.8
|
1.0
|
C
|
B:PRO601
|
3.6
|
67.8
|
1.0
|
C
|
B:SER575
|
3.6
|
75.4
|
1.0
|
C
|
B:THR1131
|
3.9
|
85.2
|
1.0
|
CB
|
B:ASP578
|
4.2
|
65.4
|
1.0
|
O
|
B:ARG576
|
4.2
|
84.2
|
1.0
|
CA
|
B:THR1131
|
4.3
|
86.2
|
1.0
|
CA
|
B:ARG576
|
4.4
|
78.2
|
1.0
|
N
|
B:ARG576
|
4.4
|
82.1
|
1.0
|
CA
|
B:HIS602
|
4.5
|
67.4
|
1.0
|
N
|
B:HIS602
|
4.5
|
64.2
|
1.0
|
CA
|
B:PRO601
|
4.5
|
65.8
|
1.0
|
CA
|
B:SER575
|
4.5
|
70.2
|
1.0
|
CG2
|
B:THR1131
|
4.5
|
81.4
|
1.0
|
CB
|
B:HIS602
|
4.6
|
65.2
|
1.0
|
C
|
B:ARG576
|
4.6
|
78.5
|
1.0
|
ND1
|
B:HIS602
|
4.6
|
69.0
|
1.0
|
CG
|
B:ASP1132
|
4.7
|
98.6
|
1.0
|
CG
|
B:HIS602
|
4.8
|
64.7
|
1.0
|
O
|
B:ASP1130
|
4.8
|
94.5
|
1.0
|
N
|
B:ASP1132
|
4.9
|
87.5
|
1.0
|
CA
|
B:ASP578
|
4.9
|
71.3
|
1.0
|
|
Reference:
S.Goto,
A.Tsutsumi,
Y.Lee,
M.Hosojima,
H.Kabasawa,
K.Komochi,
S.Nagatoishi,
K.Takemoto,
K.Tsumoto,
T.Nishizawa,
M.Kikkawa,
A.Saito.
Cryo-Em Structures Elucidate the Multiligand Receptor Nature of Megalin. Proc.Natl.Acad.Sci.Usa V. 121 59121 2024.
ISSN: ESSN 1091-6490
PubMed: 38771880
DOI: 10.1073/PNAS.2318859121
Page generated: Fri Jul 19 10:21:27 2024
|