Calcium in PDB 3fby: The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein.
Protein crystallography data
The structure of The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein., PDB code: 3fby
was solved by
K.Tan,
J.Lawler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.00 /
3.15
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
192.242,
192.242,
145.681,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.2 /
26.6
|
Calcium Binding Sites:
Calcium binding site 1 out
of 88 in 3fby
Go back to
Calcium Binding Sites List in 3fby
Calcium binding site 1 out
of 88 in the The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca800
b:65.8
occ:1.00
|
OE1
|
A:GLN226
|
2.3
|
38.1
|
1.0
|
OE1
|
B:GLN226
|
2.4
|
17.9
|
1.0
|
OE1
|
C:GLN226
|
2.4
|
41.0
|
1.0
|
OE1
|
A:GLU236
|
2.8
|
40.1
|
1.0
|
CD
|
A:GLN226
|
3.4
|
38.1
|
1.0
|
OE2
|
A:GLU236
|
3.4
|
43.6
|
1.0
|
CD
|
A:GLU236
|
3.4
|
41.6
|
1.0
|
CD
|
B:GLN226
|
3.5
|
19.6
|
1.0
|
CD
|
C:GLN226
|
3.6
|
42.0
|
1.0
|
NE2
|
A:GLN226
|
3.9
|
36.8
|
1.0
|
NE2
|
B:GLN226
|
3.9
|
18.6
|
1.0
|
NE2
|
C:GLN226
|
4.2
|
42.2
|
1.0
|
O
|
A:SER235
|
4.6
|
35.5
|
1.0
|
O
|
B:SER235
|
4.7
|
27.7
|
1.0
|
CG
|
A:GLN226
|
4.7
|
40.1
|
1.0
|
CG
|
B:GLN226
|
4.8
|
23.6
|
1.0
|
CG
|
C:GLN226
|
4.8
|
43.2
|
1.0
|
CG
|
A:GLU236
|
4.9
|
39.5
|
1.0
|
CB
|
A:GLN226
|
4.9
|
42.4
|
1.0
|
CB
|
B:PRO234
|
5.0
|
23.7
|
1.0
|
CB
|
B:GLN226
|
5.0
|
26.6
|
1.0
|
|
Calcium binding site 2 out
of 88 in 3fby
Go back to
Calcium Binding Sites List in 3fby
Calcium binding site 2 out
of 88 in the The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca801
b:56.1
occ:1.00
|
OD1
|
A:ASP271
|
2.1
|
47.2
|
1.0
|
O
|
A:PHE275
|
2.2
|
45.3
|
1.0
|
OD1
|
A:ASP273
|
2.4
|
44.9
|
1.0
|
OD2
|
A:ASP290
|
2.5
|
46.4
|
1.0
|
OD1
|
A:ASP269
|
3.1
|
49.1
|
1.0
|
CG
|
A:ASP271
|
3.2
|
46.0
|
1.0
|
CG
|
A:ASP273
|
3.3
|
44.9
|
1.0
|
C
|
A:PHE275
|
3.4
|
45.8
|
1.0
|
CG
|
A:ASP290
|
3.4
|
47.2
|
1.0
|
CG
|
A:ASP269
|
3.4
|
49.5
|
1.0
|
OD2
|
A:ASP269
|
3.5
|
52.0
|
1.0
|
OD2
|
A:ASP273
|
3.7
|
44.5
|
1.0
|
OD2
|
A:ASP271
|
3.7
|
46.3
|
1.0
|
CB
|
A:ASP290
|
3.8
|
48.7
|
1.0
|
N
|
A:PHE275
|
3.9
|
45.4
|
1.0
|
CA
|
A:PHE275
|
4.0
|
45.4
|
1.0
|
N
|
A:ASP273
|
4.1
|
44.6
|
1.0
|
CA
|
A:CA802
|
4.1
|
58.5
|
1.0
|
N
|
A:ASP271
|
4.1
|
46.5
|
1.0
|
O
|
A:VAL293
|
4.3
|
48.0
|
1.0
|
CB
|
A:ASP273
|
4.4
|
45.0
|
1.0
|
CB
|
A:PHE275
|
4.4
|
45.0
|
1.0
|
N
|
A:THR270
|
4.4
|
47.6
|
1.0
|
OD1
|
A:ASP290
|
4.4
|
44.7
|
1.0
|
C
|
A:ASP271
|
4.5
|
46.1
|
1.0
|
CB
|
A:ASP271
|
4.5
|
45.5
|
1.0
|
N
|
A:PRO276
|
4.5
|
46.6
|
1.0
|
CA
|
A:ASP269
|
4.5
|
48.4
|
1.0
|
CB
|
A:ASP269
|
4.5
|
48.3
|
1.0
|
OD1
|
A:ASP277
|
4.6
|
51.4
|
1.0
|
CA
|
A:ASP273
|
4.6
|
44.8
|
1.0
|
CA
|
A:ASP271
|
4.6
|
46.0
|
1.0
|
N
|
A:LEU272
|
4.6
|
45.3
|
1.0
|
C
|
A:ASP269
|
4.6
|
48.3
|
1.0
|
N
|
A:GLY274
|
4.7
|
44.2
|
1.0
|
O
|
A:ASP271
|
4.7
|
46.9
|
1.0
|
C
|
A:ASP273
|
4.8
|
44.5
|
1.0
|
CA
|
A:PRO276
|
4.8
|
47.5
|
1.0
|
C
|
A:PRO276
|
4.9
|
48.7
|
1.0
|
O
|
A:CYS292
|
5.0
|
49.0
|
1.0
|
|
Calcium binding site 3 out
of 88 in 3fby
Go back to
Calcium Binding Sites List in 3fby
Calcium binding site 3 out
of 88 in the The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca802
b:58.5
occ:1.00
|
O
|
A:CYS292
|
2.3
|
49.0
|
1.0
|
O
|
A:VAL295
|
2.3
|
46.4
|
1.0
|
OD2
|
A:ASP273
|
2.4
|
44.5
|
1.0
|
OD2
|
A:ASP271
|
2.4
|
46.3
|
1.0
|
OD1
|
A:ASN297
|
2.4
|
42.7
|
1.0
|
OD2
|
A:ASP290
|
2.5
|
46.4
|
1.0
|
OD1
|
A:ASP290
|
2.7
|
44.7
|
1.0
|
CG
|
A:ASP290
|
3.0
|
47.2
|
1.0
|
C
|
A:CYS292
|
3.3
|
49.1
|
1.0
|
C
|
A:VAL295
|
3.4
|
46.0
|
1.0
|
CG
|
A:ASP271
|
3.4
|
46.0
|
1.0
|
CG
|
A:ASP273
|
3.5
|
44.9
|
1.0
|
N
|
A:ASN297
|
3.5
|
45.3
|
1.0
|
CB
|
A:CYS292
|
3.6
|
50.4
|
1.0
|
CG
|
A:ASN297
|
3.6
|
43.5
|
1.0
|
OD1
|
A:ASP271
|
3.7
|
47.2
|
1.0
|
CA
|
A:PRO296
|
3.8
|
46.0
|
1.0
|
OD1
|
A:ASP273
|
3.9
|
44.9
|
1.0
|
CA
|
A:CYS292
|
3.9
|
50.2
|
1.0
|
C
|
A:PRO296
|
4.0
|
46.1
|
1.0
|
N
|
A:PRO296
|
4.0
|
46.0
|
1.0
|
CA
|
A:CA801
|
4.1
|
56.1
|
1.0
|
N
|
A:CYS292
|
4.2
|
49.6
|
1.0
|
OE1
|
A:GLN300
|
4.2
|
46.0
|
1.0
|
N
|
A:VAL295
|
4.4
|
46.2
|
1.0
|
CB
|
A:ASN297
|
4.4
|
44.6
|
1.0
|
CA
|
A:ASN297
|
4.4
|
44.6
|
1.0
|
C
|
A:VAL293
|
4.4
|
47.5
|
1.0
|
N
|
A:VAL293
|
4.4
|
48.1
|
1.0
|
CB
|
A:ASP290
|
4.5
|
48.7
|
1.0
|
O
|
A:VAL293
|
4.5
|
48.0
|
1.0
|
CA
|
A:VAL295
|
4.5
|
45.7
|
1.0
|
ND2
|
A:ASN297
|
4.6
|
42.8
|
1.0
|
CA
|
A:VAL293
|
4.7
|
47.2
|
1.0
|
CB
|
A:ASP273
|
4.7
|
45.0
|
1.0
|
CB
|
A:ASP271
|
4.7
|
45.5
|
1.0
|
N
|
A:THR294
|
4.7
|
47.0
|
1.0
|
O
|
A:ASN297
|
4.8
|
44.5
|
1.0
|
C
|
A:THR294
|
4.8
|
46.5
|
1.0
|
C
|
A:ASN297
|
4.9
|
44.5
|
1.0
|
|
Calcium binding site 4 out
of 88 in 3fby
Go back to
Calcium Binding Sites List in 3fby
Calcium binding site 4 out
of 88 in the The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca803
b:76.7
occ:1.00
|
O
|
A:ILE308
|
2.3
|
47.0
|
1.0
|
OD2
|
A:ASP313
|
2.3
|
43.3
|
1.0
|
OD2
|
A:ASP306
|
2.5
|
46.6
|
1.0
|
OD1
|
A:ASP304
|
2.5
|
46.3
|
1.0
|
OD1
|
A:ASP302
|
2.6
|
47.2
|
1.0
|
CG
|
A:ASP304
|
3.3
|
47.1
|
1.0
|
CG
|
A:ASP313
|
3.4
|
46.0
|
1.0
|
C
|
A:ILE308
|
3.4
|
47.4
|
1.0
|
CG
|
A:ASP306
|
3.5
|
46.4
|
1.0
|
OD2
|
A:ASP304
|
3.5
|
46.7
|
1.0
|
O
|
A:ALA316
|
3.6
|
47.0
|
1.0
|
CG
|
A:ASP302
|
3.6
|
46.7
|
1.0
|
CB
|
A:ASP313
|
3.7
|
47.6
|
1.0
|
OD1
|
A:ASP306
|
3.9
|
45.4
|
1.0
|
OD1
|
A:ASP310
|
4.1
|
52.8
|
1.0
|
CB
|
A:ILE308
|
4.2
|
47.5
|
1.0
|
CA
|
A:CA804
|
4.2
|
78.7
|
1.0
|
CA
|
A:ILE308
|
4.2
|
47.6
|
1.0
|
C
|
A:GLY309
|
4.3
|
48.3
|
1.0
|
N
|
A:ASP310
|
4.3
|
48.9
|
1.0
|
OD2
|
A:ASP302
|
4.3
|
49.3
|
1.0
|
N
|
A:ILE308
|
4.4
|
48.3
|
1.0
|
CA
|
A:ASP302
|
4.4
|
45.0
|
1.0
|
C
|
A:ALA316
|
4.4
|
46.2
|
1.0
|
N
|
A:GLY309
|
4.4
|
47.3
|
1.0
|
O
|
A:GLY309
|
4.5
|
48.2
|
1.0
|
OD1
|
A:ASP313
|
4.5
|
43.7
|
1.0
|
CA
|
A:ALA316
|
4.5
|
45.4
|
1.0
|
CB
|
A:ASP302
|
4.5
|
45.0
|
1.0
|
N
|
A:VAL303
|
4.5
|
45.4
|
1.0
|
C
|
A:ASP302
|
4.6
|
45.0
|
1.0
|
N
|
A:ASP306
|
4.6
|
46.7
|
1.0
|
N
|
A:ASP304
|
4.6
|
46.3
|
1.0
|
CA
|
A:GLY309
|
4.6
|
47.5
|
1.0
|
CB
|
A:ASP306
|
4.7
|
46.4
|
1.0
|
CB
|
A:ASP304
|
4.7
|
46.4
|
1.0
|
CA
|
A:ASP310
|
4.8
|
49.5
|
1.0
|
O
|
A:ASP315
|
4.8
|
46.4
|
1.0
|
CG2
|
A:ILE308
|
4.9
|
47.5
|
1.0
|
N
|
A:ARG305
|
5.0
|
47.2
|
1.0
|
|
Calcium binding site 5 out
of 88 in 3fby
Go back to
Calcium Binding Sites List in 3fby
Calcium binding site 5 out
of 88 in the The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca804
b:78.7
occ:1.00
|
OD2
|
A:ASP313
|
2.5
|
43.3
|
1.0
|
OD2
|
A:ASP304
|
2.6
|
46.7
|
1.0
|
O
|
A:ASP315
|
2.6
|
46.4
|
1.0
|
OD1
|
A:ASP313
|
2.8
|
43.7
|
1.0
|
CG
|
A:ASP313
|
3.0
|
46.0
|
1.0
|
OD1
|
A:ASP306
|
3.1
|
45.4
|
1.0
|
C
|
A:ASP315
|
3.6
|
46.1
|
1.0
|
CG
|
A:ASP304
|
3.7
|
47.1
|
1.0
|
CG
|
A:ASP306
|
3.8
|
46.4
|
1.0
|
CA
|
A:CA803
|
4.2
|
76.7
|
1.0
|
OD2
|
A:ASP306
|
4.2
|
46.6
|
1.0
|
CA
|
A:GLY318
|
4.2
|
45.1
|
1.0
|
CB
|
A:ASP315
|
4.3
|
46.2
|
1.0
|
OD1
|
A:ASP304
|
4.3
|
46.3
|
1.0
|
N
|
A:GLY318
|
4.3
|
45.4
|
1.0
|
CA
|
A:ASP315
|
4.3
|
46.5
|
1.0
|
N
|
A:ASP315
|
4.4
|
47.1
|
1.0
|
CB
|
A:ASP313
|
4.5
|
47.6
|
1.0
|
N
|
A:ALA316
|
4.6
|
45.5
|
1.0
|
C
|
A:ALA316
|
4.7
|
46.2
|
1.0
|
O
|
A:ALA316
|
4.7
|
47.0
|
1.0
|
CB
|
A:ASP306
|
4.7
|
46.4
|
1.0
|
CA
|
A:ALA316
|
4.8
|
45.4
|
1.0
|
CB
|
A:ASP304
|
4.9
|
46.4
|
1.0
|
|
Calcium binding site 6 out
of 88 in 3fby
Go back to
Calcium Binding Sites List in 3fby
Calcium binding site 6 out
of 88 in the The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca805
b:60.9
occ:1.00
|
OD1
|
A:ASP319
|
2.2
|
42.8
|
1.0
|
OD2
|
A:ASP315
|
2.3
|
50.0
|
1.0
|
O
|
A:VAL321
|
2.3
|
43.6
|
1.0
|
OD1
|
A:ASP317
|
2.4
|
45.8
|
1.0
|
OD2
|
A:ASP326
|
2.5
|
39.6
|
1.0
|
CG
|
A:ASP319
|
3.2
|
43.9
|
1.0
|
CG
|
A:ASP317
|
3.3
|
45.9
|
1.0
|
CG
|
A:ASP315
|
3.4
|
47.0
|
1.0
|
C
|
A:VAL321
|
3.4
|
43.3
|
1.0
|
CG
|
A:ASP326
|
3.5
|
40.4
|
1.0
|
OD2
|
A:ASP317
|
3.6
|
44.6
|
1.0
|
CA
|
A:CA806
|
3.8
|
54.9
|
1.0
|
OD2
|
A:ASP319
|
3.8
|
43.9
|
1.0
|
N
|
A:VAL321
|
3.8
|
43.4
|
1.0
|
OD1
|
A:ASP315
|
3.9
|
48.1
|
1.0
|
CA
|
A:VAL321
|
4.0
|
43.2
|
1.0
|
CB
|
A:ASP326
|
4.0
|
41.4
|
1.0
|
CB
|
A:VAL321
|
4.1
|
43.2
|
1.0
|
N
|
A:ASP319
|
4.1
|
44.3
|
1.0
|
CB
|
A:ASP319
|
4.2
|
44.4
|
1.0
|
O
|
A:PRO329
|
4.2
|
40.5
|
1.0
|
OD1
|
A:ASP326
|
4.4
|
40.1
|
1.0
|
N
|
A:ASP317
|
4.5
|
46.2
|
1.0
|
N
|
A:PRO322
|
4.5
|
43.3
|
1.0
|
N
|
A:GLY318
|
4.5
|
45.4
|
1.0
|
N
|
A:GLY320
|
4.5
|
43.3
|
1.0
|
CA
|
A:ASP319
|
4.6
|
44.1
|
1.0
|
CB
|
A:ASP315
|
4.6
|
46.2
|
1.0
|
C
|
A:ASP319
|
4.6
|
43.6
|
1.0
|
CB
|
A:ASP317
|
4.6
|
46.1
|
1.0
|
OD1
|
A:ASN323
|
4.7
|
47.0
|
1.0
|
CA
|
A:ASP315
|
4.7
|
46.5
|
1.0
|
C
|
A:GLY320
|
4.8
|
43.4
|
1.0
|
C
|
A:PRO322
|
4.9
|
43.7
|
1.0
|
C
|
A:PRO329
|
4.9
|
40.0
|
1.0
|
C
|
A:ASP315
|
4.9
|
46.1
|
1.0
|
CA
|
A:PRO322
|
4.9
|
43.5
|
1.0
|
CA
|
A:ASP317
|
4.9
|
45.9
|
1.0
|
C
|
A:ASP317
|
4.9
|
45.8
|
1.0
|
CG2
|
A:VAL321
|
4.9
|
42.8
|
1.0
|
O
|
A:CYS328
|
4.9
|
41.2
|
1.0
|
CA
|
A:PRO329
|
4.9
|
40.4
|
1.0
|
N
|
A:ALA316
|
5.0
|
45.5
|
1.0
|
|
Calcium binding site 7 out
of 88 in 3fby
Go back to
Calcium Binding Sites List in 3fby
Calcium binding site 7 out
of 88 in the The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca806
b:54.9
occ:1.00
|
OD1
|
A:ASN333
|
2.2
|
39.1
|
1.0
|
OD2
|
A:ASP326
|
2.3
|
39.6
|
1.0
|
O
|
A:CYS328
|
2.3
|
41.2
|
1.0
|
OD2
|
A:ASP317
|
2.4
|
44.6
|
1.0
|
O
|
A:VAL331
|
2.5
|
41.1
|
1.0
|
OD2
|
A:ASP319
|
2.5
|
43.9
|
1.0
|
OD1
|
A:ASP326
|
2.8
|
40.1
|
1.0
|
CG
|
A:ASP326
|
2.9
|
40.4
|
1.0
|
CG
|
A:ASP319
|
3.3
|
43.9
|
1.0
|
CG
|
A:ASP317
|
3.4
|
45.9
|
1.0
|
CG
|
A:ASN333
|
3.5
|
41.4
|
1.0
|
C
|
A:CYS328
|
3.5
|
41.1
|
1.0
|
N
|
A:ASN333
|
3.6
|
42.1
|
1.0
|
C
|
A:VAL331
|
3.6
|
40.6
|
1.0
|
OD1
|
A:ASP319
|
3.7
|
42.8
|
1.0
|
CA
|
A:ARG332
|
3.7
|
42.5
|
1.0
|
OD1
|
A:ASP317
|
3.7
|
45.8
|
1.0
|
CA
|
A:CA805
|
3.8
|
60.9
|
1.0
|
C
|
A:ARG332
|
4.0
|
42.2
|
1.0
|
CB
|
A:CYS328
|
4.0
|
41.1
|
1.0
|
N
|
A:ARG332
|
4.1
|
41.7
|
1.0
|
NE2
|
A:GLN336
|
4.2
|
38.2
|
1.0
|
ND2
|
A:ASN333
|
4.3
|
42.4
|
1.0
|
CA
|
A:CYS328
|
4.3
|
41.2
|
1.0
|
CB
|
A:ASP326
|
4.4
|
41.4
|
1.0
|
C
|
A:PRO329
|
4.4
|
40.0
|
1.0
|
N
|
A:PRO329
|
4.4
|
40.9
|
1.0
|
CA
|
A:PRO329
|
4.4
|
40.4
|
1.0
|
CA
|
A:ASN333
|
4.4
|
42.0
|
1.0
|
CB
|
A:ASP319
|
4.5
|
44.4
|
1.0
|
CB
|
A:ASN333
|
4.5
|
41.8
|
1.0
|
N
|
A:CYS328
|
4.6
|
41.1
|
1.0
|
O
|
A:PRO329
|
4.6
|
40.5
|
1.0
|
N
|
A:VAL331
|
4.6
|
39.5
|
1.0
|
O
|
A:ASN333
|
4.6
|
42.4
|
1.0
|
N
|
A:LEU330
|
4.7
|
39.8
|
1.0
|
C
|
A:ASN333
|
4.7
|
42.4
|
1.0
|
CB
|
A:ASP317
|
4.8
|
46.1
|
1.0
|
CA
|
A:VAL331
|
4.8
|
39.5
|
1.0
|
CB
|
A:ARG332
|
4.9
|
42.8
|
1.0
|
|
Calcium binding site 8 out
of 88 in 3fby
Go back to
Calcium Binding Sites List in 3fby
Calcium binding site 8 out
of 88 in the The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca807
b:61.8
occ:1.00
|
O
|
A:TRP344
|
2.2
|
40.8
|
1.0
|
OD2
|
A:ASP340
|
2.4
|
39.9
|
1.0
|
OD2
|
A:ASP342
|
2.4
|
42.5
|
1.0
|
OD2
|
A:ASP349
|
2.4
|
41.2
|
1.0
|
OD1
|
A:ASN338
|
2.5
|
39.3
|
1.0
|
CG
|
A:ASP340
|
3.3
|
39.1
|
1.0
|
CG
|
A:ASP342
|
3.3
|
42.7
|
1.0
|
CG
|
A:ASN338
|
3.4
|
36.2
|
1.0
|
C
|
A:TRP344
|
3.5
|
41.0
|
1.0
|
CG
|
A:ASP349
|
3.5
|
40.8
|
1.0
|
OD1
|
A:ASP340
|
3.6
|
41.2
|
1.0
|
OD1
|
A:ASP342
|
3.7
|
43.5
|
1.0
|
OD2
|
A:ASP346
|
3.8
|
39.8
|
1.0
|
CB
|
A:ASP349
|
4.0
|
40.0
|
1.0
|
CA
|
A:CA808
|
4.0
|
56.7
|
1.0
|
ND2
|
A:ASN338
|
4.0
|
37.5
|
1.0
|
N
|
A:ASP342
|
4.1
|
40.5
|
1.0
|
O
|
A:ARG352
|
4.1
|
39.0
|
1.0
|
C
|
A:GLY345
|
4.2
|
39.3
|
1.0
|
O
|
A:GLY345
|
4.3
|
38.1
|
1.0
|
O
|
A:ASP342
|
4.3
|
41.2
|
1.0
|
N
|
A:ASP340
|
4.3
|
37.6
|
1.0
|
N
|
A:GLU341
|
4.4
|
39.2
|
1.0
|
CA
|
A:TRP344
|
4.4
|
41.5
|
1.0
|
N
|
A:GLY345
|
4.4
|
40.5
|
1.0
|
N
|
A:ASP346
|
4.4
|
39.4
|
1.0
|
CA
|
A:ASN338
|
4.4
|
35.5
|
1.0
|
CB
|
A:ASN338
|
4.4
|
35.1
|
1.0
|
CA
|
A:GLY345
|
4.5
|
39.9
|
1.0
|
C
|
A:ASN338
|
4.5
|
35.4
|
1.0
|
N
|
A:THR339
|
4.5
|
35.5
|
1.0
|
CB
|
A:ASP342
|
4.5
|
41.8
|
1.0
|
CB
|
A:ASP340
|
4.5
|
38.3
|
1.0
|
N
|
A:TRP344
|
4.5
|
42.0
|
1.0
|
OD1
|
A:ASP349
|
4.6
|
42.1
|
1.0
|
CB
|
A:TRP344
|
4.6
|
42.0
|
1.0
|
CA
|
A:ASP342
|
4.6
|
41.5
|
1.0
|
C
|
A:ASP342
|
4.7
|
41.5
|
1.0
|
CA
|
A:ASP340
|
4.8
|
38.6
|
1.0
|
O
|
A:CYS351
|
4.9
|
41.0
|
1.0
|
CA
|
A:ASP346
|
4.9
|
39.5
|
1.0
|
C
|
A:ASP340
|
4.9
|
38.9
|
1.0
|
O
|
A:ASN338
|
4.9
|
35.1
|
1.0
|
|
Calcium binding site 9 out
of 88 in 3fby
Go back to
Calcium Binding Sites List in 3fby
Calcium binding site 9 out
of 88 in the The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca808
b:56.7
occ:1.00
|
OD1
|
A:ASP342
|
2.2
|
43.5
|
1.0
|
O
|
A:CYS351
|
2.3
|
41.0
|
1.0
|
O
|
A:GLN354
|
2.3
|
40.5
|
1.0
|
OD2
|
A:ASP349
|
2.4
|
41.2
|
1.0
|
OD1
|
A:ASN356
|
2.5
|
43.1
|
1.0
|
OD1
|
A:ASP340
|
2.5
|
41.2
|
1.0
|
OD1
|
A:ASP349
|
2.5
|
42.1
|
1.0
|
CG
|
A:ASP349
|
2.8
|
40.8
|
1.0
|
CG
|
A:ASP342
|
3.3
|
42.7
|
1.0
|
C
|
A:GLN354
|
3.3
|
40.7
|
1.0
|
C
|
A:CYS351
|
3.4
|
40.9
|
1.0
|
CG
|
A:ASP340
|
3.6
|
39.1
|
1.0
|
CG
|
A:ASN356
|
3.6
|
41.0
|
1.0
|
CB
|
A:CYS351
|
3.7
|
42.3
|
1.0
|
OD2
|
A:ASP342
|
3.7
|
42.5
|
1.0
|
CA
|
A:CA807
|
4.0
|
61.8
|
1.0
|
OD2
|
A:ASP340
|
4.0
|
39.9
|
1.0
|
CA
|
A:CYS351
|
4.0
|
41.6
|
1.0
|
N
|
A:ASN356
|
4.0
|
41.4
|
1.0
|
O
|
A:ARG352
|
4.0
|
39.0
|
1.0
|
CA
|
A:LYS355
|
4.0
|
41.2
|
1.0
|
N
|
A:GLN354
|
4.1
|
40.2
|
1.0
|
N
|
A:LYS355
|
4.1
|
41.0
|
1.0
|
NE2
|
A:GLN359
|
4.2
|
43.5
|
1.0
|
C
|
A:LYS355
|
4.2
|
41.3
|
1.0
|
CA
|
A:GLN354
|
4.2
|
40.7
|
1.0
|
ND2
|
A:ASN356
|
4.3
|
42.3
|
1.0
|
N
|
A:CYS351
|
4.3
|
40.9
|
1.0
|
CB
|
A:ASP349
|
4.3
|
40.0
|
1.0
|
C
|
A:ARG352
|
4.4
|
39.5
|
1.0
|
N
|
A:ARG352
|
4.5
|
40.2
|
1.0
|
CB
|
A:ASP342
|
4.5
|
41.8
|
1.0
|
CA
|
A:ARG352
|
4.7
|
39.9
|
1.0
|
CB
|
A:ASN356
|
4.7
|
41.1
|
1.0
|
CB
|
A:GLN354
|
4.7
|
41.1
|
1.0
|
CB
|
A:ASP340
|
4.8
|
38.3
|
1.0
|
CA
|
A:ASN356
|
4.9
|
41.7
|
1.0
|
|
Calcium binding site 10 out
of 88 in 3fby
Go back to
Calcium Binding Sites List in 3fby
Calcium binding site 10 out
of 88 in the The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein.
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca809
b:65.8
occ:1.00
|
OD1
|
A:ASP363
|
2.2
|
48.6
|
1.0
|
OD1
|
A:ASP361
|
2.3
|
44.3
|
1.0
|
O
|
A:ARG367
|
2.4
|
46.7
|
1.0
|
OD2
|
A:ASP365
|
2.4
|
38.9
|
1.0
|
OD1
|
A:ASP372
|
2.7
|
48.8
|
1.0
|
CG
|
A:ASP365
|
3.3
|
42.8
|
1.0
|
CG
|
A:ASP361
|
3.3
|
45.1
|
1.0
|
CG
|
A:ASP363
|
3.5
|
47.0
|
1.0
|
CG
|
A:ASP372
|
3.6
|
49.2
|
1.0
|
C
|
A:ARG367
|
3.6
|
46.4
|
1.0
|
O
|
A:ILE375
|
3.7
|
44.4
|
1.0
|
OD1
|
A:ASP365
|
3.7
|
41.6
|
1.0
|
OD1
|
A:ASP369
|
3.8
|
51.6
|
1.0
|
N
|
A:ASP363
|
3.8
|
45.6
|
1.0
|
CB
|
A:ASP372
|
3.9
|
49.2
|
1.0
|
CA
|
A:ASP361
|
3.9
|
45.9
|
1.0
|
C
|
A:ASP361
|
4.0
|
46.2
|
1.0
|
N
|
A:THR362
|
4.1
|
46.0
|
1.0
|
OD2
|
A:ASP361
|
4.2
|
43.4
|
1.0
|
C
|
A:GLY368
|
4.2
|
47.1
|
1.0
|
CB
|
A:ASP361
|
4.2
|
45.9
|
1.0
|
OD2
|
A:ASP363
|
4.2
|
48.4
|
1.0
|
O
|
A:GLY368
|
4.2
|
47.4
|
1.0
|
CB
|
A:ASP363
|
4.4
|
46.1
|
1.0
|
N
|
A:ASP365
|
4.4
|
46.4
|
1.0
|
CA
|
A:ASP363
|
4.4
|
45.9
|
1.0
|
O
|
A:ASP361
|
4.4
|
46.6
|
1.0
|
CA
|
A:GLY368
|
4.4
|
46.7
|
1.0
|
CB
|
A:ASP365
|
4.5
|
45.4
|
1.0
|
N
|
A:GLY368
|
4.5
|
46.3
|
1.0
|
N
|
A:ASP369
|
4.5
|
47.0
|
1.0
|
C
|
A:ASP363
|
4.5
|
46.0
|
1.0
|
N
|
A:GLN364
|
4.6
|
46.2
|
1.0
|
C
|
A:ILE375
|
4.6
|
44.5
|
1.0
|
CA
|
A:ARG367
|
4.6
|
46.6
|
1.0
|
CB
|
A:ARG367
|
4.7
|
46.5
|
1.0
|
CA
|
A:CA810
|
4.7
|
0.6
|
1.0
|
OD2
|
A:ASP372
|
4.7
|
50.0
|
1.0
|
N
|
A:ARG367
|
4.7
|
46.5
|
1.0
|
CA
|
A:ILE375
|
4.8
|
44.6
|
1.0
|
CA
|
A:ASP369
|
4.8
|
47.2
|
1.0
|
C
|
A:THR362
|
4.9
|
45.4
|
1.0
|
CA
|
A:ASP365
|
5.0
|
46.0
|
1.0
|
|
Reference:
K.Tan,
M.Duquette,
A.Joachimiak,
J.Lawler.
The Crystal Structure of the Signature Domain of Cartilage Oligomeric Matrix Protein: Implications For Collagen, Glycosaminoglycan and Integrin Binding. Faseb J. V. 23 2490 2009.
ISSN: ISSN 0892-6638
PubMed: 19276170
DOI: 10.1096/FJ.08-128090
Page generated: Sat Jul 13 09:45:10 2024
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