Calcium in PDB 3ghg: Crystal Structure of Human Fibrinogen
Protein crystallography data
The structure of Crystal Structure of Human Fibrinogen, PDB code: 3ghg
was solved by
R.F.Doolittle,
J.M.Kollman,
M.R.Sawaya,
L.Pandi,
M.Riley,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.95 /
2.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.238,
94.866,
300.812,
90.00,
94.81,
90.00
|
R / Rfree (%)
|
25.2 /
30.9
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Human Fibrinogen
(pdb code 3ghg). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Crystal Structure of Human Fibrinogen, PDB code: 3ghg:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 3ghg
Go back to
Calcium Binding Sites List in 3ghg
Calcium binding site 1 out
of 8 in the Crystal Structure of Human Fibrinogen
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Human Fibrinogen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca501
b:77.3
occ:1.00
|
O
|
B:TRP385
|
2.4
|
53.8
|
1.0
|
OD1
|
B:ASP381
|
2.5
|
45.0
|
1.0
|
OD1
|
B:ASP383
|
2.5
|
54.8
|
1.0
|
OD2
|
B:ASP381
|
3.0
|
49.8
|
1.0
|
CG
|
B:ASP381
|
3.1
|
47.5
|
1.0
|
C
|
B:TRP385
|
3.4
|
53.4
|
1.0
|
CG
|
B:ASP383
|
3.4
|
58.1
|
1.0
|
OD2
|
B:ASP383
|
3.5
|
58.8
|
1.0
|
CA
|
B:LEU386
|
3.7
|
58.2
|
1.0
|
N
|
B:LEU386
|
4.0
|
55.8
|
1.0
|
N
|
B:THR387
|
4.1
|
65.4
|
1.0
|
CD2
|
B:LEU386
|
4.2
|
64.8
|
1.0
|
N
|
B:TRP385
|
4.4
|
47.4
|
1.0
|
C
|
B:LEU386
|
4.4
|
63.3
|
1.0
|
CA
|
B:TRP385
|
4.5
|
49.8
|
1.0
|
CB
|
B:ASP381
|
4.6
|
48.9
|
1.0
|
O
|
B:ASP383
|
4.7
|
48.5
|
1.0
|
CB
|
B:ASP383
|
4.8
|
50.5
|
1.0
|
CB
|
B:LEU386
|
4.8
|
58.4
|
1.0
|
CB
|
B:TRP385
|
4.8
|
52.8
|
1.0
|
O
|
B:THR387
|
4.9
|
73.6
|
1.0
|
C
|
B:ASP383
|
5.0
|
49.9
|
1.0
|
|
Calcium binding site 2 out
of 8 in 3ghg
Go back to
Calcium Binding Sites List in 3ghg
Calcium binding site 2 out
of 8 in the Crystal Structure of Human Fibrinogen
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Human Fibrinogen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca601
b:49.0
occ:1.00
|
OD2
|
F:ASP318
|
2.1
|
69.6
|
1.0
|
OD2
|
F:ASP320
|
2.3
|
89.6
|
1.0
|
O
|
F:GLY324
|
2.8
|
0.5
|
1.0
|
CG
|
F:ASP318
|
2.9
|
69.3
|
1.0
|
OD1
|
F:ASP318
|
3.1
|
70.4
|
1.0
|
O
|
F:GLU323
|
3.3
|
93.5
|
1.0
|
CG
|
F:ASP320
|
3.3
|
86.6
|
1.0
|
C
|
F:GLY324
|
3.4
|
0.5
|
1.0
|
C
|
F:GLU323
|
3.4
|
96.1
|
1.0
|
C
|
F:PHE322
|
3.5
|
93.0
|
1.0
|
O
|
F:ASP320
|
3.6
|
88.7
|
1.0
|
O
|
F:PHE322
|
3.6
|
92.5
|
1.0
|
CB
|
F:PHE322
|
3.6
|
93.5
|
1.0
|
N
|
F:GLU323
|
3.7
|
96.0
|
1.0
|
OD1
|
F:ASP320
|
3.8
|
86.0
|
1.0
|
CA
|
F:PHE322
|
3.9
|
91.0
|
1.0
|
N
|
F:PHE322
|
3.9
|
88.7
|
1.0
|
N
|
F:GLY324
|
3.9
|
0.0
|
1.0
|
CA
|
F:GLU323
|
3.9
|
97.7
|
1.0
|
N
|
F:ASN325
|
4.0
|
96.9
|
1.0
|
CA
|
F:ASN325
|
4.2
|
93.0
|
1.0
|
CA
|
F:GLY324
|
4.2
|
99.5
|
1.0
|
C
|
F:ASP320
|
4.3
|
89.5
|
1.0
|
CB
|
F:ASP318
|
4.4
|
72.3
|
1.0
|
CB
|
F:ASP320
|
4.6
|
85.5
|
1.0
|
CG
|
F:PHE322
|
4.7
|
97.7
|
1.0
|
CD1
|
F:PHE322
|
4.8
|
99.7
|
1.0
|
N
|
F:ASP320
|
4.8
|
84.9
|
1.0
|
CA
|
F:ASP320
|
4.8
|
86.5
|
1.0
|
C
|
F:LYS321
|
4.9
|
85.2
|
1.0
|
|
Calcium binding site 3 out
of 8 in 3ghg
Go back to
Calcium Binding Sites List in 3ghg
Calcium binding site 3 out
of 8 in the Crystal Structure of Human Fibrinogen
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Human Fibrinogen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca601
b:31.8
occ:1.00
|
OD1
|
C:ASP318
|
2.0
|
32.4
|
1.0
|
OD1
|
C:ASP320
|
2.3
|
46.5
|
1.0
|
O
|
C:PHE322
|
2.7
|
40.0
|
1.0
|
CG
|
C:ASP318
|
3.0
|
39.5
|
1.0
|
O
|
C:GLY324
|
3.1
|
25.6
|
1.0
|
CB
|
C:ASP318
|
3.2
|
42.6
|
1.0
|
CG
|
C:ASP320
|
3.5
|
44.7
|
1.0
|
O
|
C:ASP320
|
3.6
|
40.6
|
1.0
|
C
|
C:PHE322
|
3.8
|
43.1
|
1.0
|
O
|
C:ASP318
|
3.8
|
46.7
|
1.0
|
C
|
C:ASP318
|
4.0
|
40.8
|
1.0
|
CA
|
C:ASP318
|
4.1
|
39.7
|
1.0
|
OD2
|
C:ASP320
|
4.1
|
36.4
|
1.0
|
OD2
|
C:ASP318
|
4.2
|
44.8
|
1.0
|
C
|
C:GLY324
|
4.2
|
27.8
|
1.0
|
N
|
C:ASP320
|
4.2
|
36.6
|
1.0
|
C
|
C:ASP320
|
4.3
|
39.6
|
1.0
|
N
|
C:PHE322
|
4.3
|
43.3
|
1.0
|
O
|
C:GLU323
|
4.4
|
35.0
|
1.0
|
CA
|
C:PHE322
|
4.5
|
41.9
|
1.0
|
CB
|
C:PHE322
|
4.6
|
39.4
|
1.0
|
CB
|
C:ASP320
|
4.6
|
41.0
|
1.0
|
CA
|
C:ASP320
|
4.6
|
38.5
|
1.0
|
C
|
C:GLU323
|
4.6
|
37.7
|
1.0
|
N
|
C:ASN319
|
4.8
|
38.4
|
1.0
|
N
|
C:GLU323
|
4.9
|
46.3
|
1.0
|
N
|
C:GLY324
|
5.0
|
35.6
|
1.0
|
|
Calcium binding site 4 out
of 8 in 3ghg
Go back to
Calcium Binding Sites List in 3ghg
Calcium binding site 4 out
of 8 in the Crystal Structure of Human Fibrinogen
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Human Fibrinogen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca501
b:47.7
occ:1.00
|
OD1
|
E:ASP383
|
2.0
|
49.9
|
1.0
|
O
|
E:TRP385
|
2.6
|
66.4
|
1.0
|
OD1
|
E:ASP381
|
2.9
|
58.4
|
1.0
|
C
|
E:TRP385
|
3.0
|
61.9
|
1.0
|
OD2
|
E:ASP381
|
3.0
|
59.7
|
1.0
|
CG
|
E:ASP383
|
3.0
|
48.9
|
1.0
|
OD2
|
E:ASP383
|
3.3
|
51.2
|
1.0
|
CG
|
E:ASP381
|
3.3
|
57.0
|
1.0
|
N
|
E:LEU386
|
3.6
|
63.7
|
1.0
|
N
|
E:TRP385
|
3.6
|
56.7
|
1.0
|
CA
|
E:TRP385
|
3.7
|
59.3
|
1.0
|
CA
|
E:LEU386
|
3.7
|
65.3
|
1.0
|
CB
|
E:TRP385
|
3.8
|
59.8
|
1.0
|
O
|
E:ASP383
|
3.8
|
56.5
|
1.0
|
N
|
E:THR387
|
4.0
|
70.8
|
1.0
|
CD2
|
E:LEU386
|
4.0
|
72.4
|
1.0
|
CB
|
E:ASP383
|
4.3
|
55.9
|
1.0
|
C
|
E:ASP383
|
4.3
|
59.0
|
1.0
|
C
|
E:LEU386
|
4.4
|
70.5
|
1.0
|
O
|
E:LYS392
|
4.4
|
68.4
|
1.0
|
O
|
E:THR387
|
4.5
|
66.7
|
1.0
|
CA
|
E:ASP383
|
4.8
|
60.0
|
1.0
|
C
|
E:GLY384
|
4.8
|
56.5
|
1.0
|
N
|
E:ASP383
|
4.8
|
62.4
|
1.0
|
CB
|
E:LEU386
|
4.8
|
66.7
|
1.0
|
CB
|
E:ASP381
|
4.8
|
58.0
|
1.0
|
CG
|
E:TRP385
|
4.9
|
59.2
|
1.0
|
|
Calcium binding site 5 out
of 8 in 3ghg
Go back to
Calcium Binding Sites List in 3ghg
Calcium binding site 5 out
of 8 in the Crystal Structure of Human Fibrinogen
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Human Fibrinogen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca501
b:51.0
occ:1.00
|
O
|
H:TRP385
|
2.1
|
57.0
|
1.0
|
OD1
|
H:ASP383
|
2.1
|
53.2
|
1.0
|
OD1
|
H:ASP381
|
2.6
|
51.5
|
1.0
|
OD2
|
H:ASP381
|
2.6
|
51.6
|
1.0
|
CG
|
H:ASP381
|
3.0
|
53.3
|
1.0
|
CG
|
H:ASP383
|
3.1
|
53.1
|
1.0
|
C
|
H:TRP385
|
3.2
|
57.8
|
1.0
|
OD2
|
H:ASP383
|
3.5
|
56.1
|
1.0
|
CA
|
H:TRP385
|
4.0
|
56.0
|
1.0
|
CB
|
H:TRP385
|
4.1
|
56.1
|
1.0
|
N
|
H:TRP385
|
4.1
|
55.5
|
1.0
|
N
|
H:LEU386
|
4.2
|
58.9
|
1.0
|
O
|
H:ASP383
|
4.2
|
57.3
|
1.0
|
CA
|
H:LEU386
|
4.3
|
62.4
|
1.0
|
O
|
H:LYS392
|
4.4
|
65.5
|
1.0
|
CB
|
H:ASP383
|
4.5
|
52.2
|
1.0
|
N
|
H:ASP383
|
4.5
|
52.5
|
1.0
|
CB
|
H:ASP381
|
4.5
|
55.0
|
1.0
|
C
|
H:ASP383
|
4.5
|
59.5
|
1.0
|
CD2
|
H:LEU386
|
4.6
|
65.0
|
1.0
|
N
|
H:THR387
|
4.7
|
63.3
|
1.0
|
CA
|
H:ASP383
|
4.7
|
54.2
|
1.0
|
C
|
H:GLY384
|
4.9
|
54.5
|
1.0
|
|
Calcium binding site 6 out
of 8 in 3ghg
Go back to
Calcium Binding Sites List in 3ghg
Calcium binding site 6 out
of 8 in the Crystal Structure of Human Fibrinogen
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Human Fibrinogen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ca601
b:56.9
occ:1.00
|
OD2
|
I:ASP318
|
1.9
|
41.1
|
1.0
|
OD2
|
I:ASP320
|
2.0
|
41.6
|
1.0
|
O
|
I:PHE322
|
2.5
|
52.4
|
1.0
|
CG
|
I:ASP318
|
2.7
|
43.6
|
1.0
|
O
|
I:GLY324
|
2.8
|
69.1
|
1.0
|
OD1
|
I:ASP318
|
2.9
|
43.6
|
1.0
|
CG
|
I:ASP320
|
2.9
|
43.2
|
1.0
|
OD1
|
I:ASP320
|
3.3
|
47.5
|
1.0
|
O
|
I:ASP320
|
3.5
|
44.8
|
1.0
|
O
|
I:GLU323
|
3.7
|
53.7
|
1.0
|
C
|
I:PHE322
|
3.7
|
49.8
|
1.0
|
C
|
I:GLY324
|
3.9
|
69.3
|
1.0
|
C
|
I:GLU323
|
3.9
|
55.7
|
1.0
|
CB
|
I:ASP318
|
4.1
|
44.1
|
1.0
|
C
|
I:ASP320
|
4.2
|
40.4
|
1.0
|
CB
|
I:ASP320
|
4.2
|
39.0
|
1.0
|
N
|
I:ASP320
|
4.2
|
42.8
|
1.0
|
CA
|
I:GLU323
|
4.3
|
59.6
|
1.0
|
CA
|
I:ASP320
|
4.4
|
40.4
|
1.0
|
N
|
I:GLY324
|
4.5
|
64.4
|
1.0
|
N
|
I:GLU323
|
4.5
|
53.7
|
1.0
|
N
|
I:PHE322
|
4.6
|
52.0
|
1.0
|
CA
|
I:ASN325
|
4.7
|
67.0
|
1.0
|
CA
|
I:PHE322
|
4.7
|
49.0
|
1.0
|
N
|
I:ASN325
|
4.7
|
70.3
|
1.0
|
CA
|
I:GLY324
|
4.8
|
67.9
|
1.0
|
O
|
I:ASP318
|
4.9
|
40.4
|
1.0
|
C
|
I:ASP318
|
4.9
|
40.5
|
1.0
|
|
Calcium binding site 7 out
of 8 in 3ghg
Go back to
Calcium Binding Sites List in 3ghg
Calcium binding site 7 out
of 8 in the Crystal Structure of Human Fibrinogen
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Human Fibrinogen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Ca501
b:68.6
occ:1.00
|
OD1
|
K:ASP381
|
2.4
|
59.0
|
1.0
|
O
|
K:TRP385
|
2.4
|
63.0
|
1.0
|
OD2
|
K:ASP381
|
2.5
|
62.0
|
1.0
|
CG
|
K:ASP381
|
2.8
|
58.5
|
1.0
|
OD1
|
K:ASP383
|
2.9
|
58.1
|
1.0
|
C
|
K:TRP385
|
3.4
|
62.6
|
1.0
|
CG
|
K:ASP383
|
3.6
|
58.7
|
1.0
|
OD2
|
K:ASP383
|
3.8
|
65.4
|
1.0
|
CA
|
K:LEU386
|
4.0
|
65.2
|
1.0
|
N
|
K:LEU386
|
4.1
|
63.6
|
1.0
|
N
|
K:THR387
|
4.3
|
70.0
|
1.0
|
O
|
K:ASP383
|
4.3
|
61.2
|
1.0
|
CA
|
K:TRP385
|
4.3
|
61.2
|
1.0
|
CB
|
K:ASP381
|
4.3
|
56.7
|
1.0
|
N
|
K:TRP385
|
4.4
|
61.7
|
1.0
|
CG
|
K:GLN393
|
4.4
|
62.9
|
1.0
|
CD2
|
K:LEU386
|
4.6
|
74.9
|
1.0
|
CB
|
K:TRP385
|
4.6
|
60.6
|
1.0
|
C
|
K:LEU386
|
4.7
|
66.9
|
1.0
|
O
|
K:LYS392
|
4.8
|
71.3
|
1.0
|
C
|
K:ASP383
|
4.8
|
60.5
|
1.0
|
N
|
K:ASP383
|
4.9
|
60.0
|
1.0
|
CB
|
K:ASP383
|
4.9
|
60.4
|
1.0
|
OG1
|
K:THR387
|
5.0
|
68.6
|
1.0
|
|
Calcium binding site 8 out
of 8 in 3ghg
Go back to
Calcium Binding Sites List in 3ghg
Calcium binding site 8 out
of 8 in the Crystal Structure of Human Fibrinogen
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Human Fibrinogen within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ca601
b:51.4
occ:1.00
|
OD2
|
L:ASP320
|
2.0
|
62.8
|
1.0
|
OD2
|
L:ASP318
|
2.1
|
66.4
|
1.0
|
CG
|
L:ASP318
|
2.7
|
64.9
|
1.0
|
O
|
L:PHE322
|
2.7
|
81.9
|
1.0
|
OD1
|
L:ASP318
|
2.9
|
66.8
|
1.0
|
O
|
L:ASP320
|
3.0
|
66.5
|
1.0
|
CG
|
L:ASP320
|
3.0
|
63.0
|
1.0
|
O
|
L:GLY324
|
3.1
|
64.6
|
1.0
|
OD1
|
L:ASP320
|
3.6
|
65.3
|
1.0
|
N
|
L:ASP320
|
3.8
|
68.0
|
1.0
|
C
|
L:PHE322
|
3.8
|
82.7
|
1.0
|
C
|
L:ASP320
|
3.8
|
68.8
|
1.0
|
CB
|
L:ASP318
|
3.9
|
63.0
|
1.0
|
O
|
L:ASP318
|
4.1
|
56.2
|
1.0
|
CA
|
L:ASP320
|
4.1
|
66.2
|
1.0
|
N
|
L:PHE322
|
4.1
|
80.7
|
1.0
|
CB
|
L:ASP320
|
4.2
|
63.9
|
1.0
|
C
|
L:ASP318
|
4.2
|
57.5
|
1.0
|
C
|
L:GLY324
|
4.4
|
68.6
|
1.0
|
CA
|
L:PHE322
|
4.4
|
79.8
|
1.0
|
O
|
L:GLU323
|
4.5
|
91.4
|
1.0
|
CA
|
L:ASP318
|
4.6
|
62.0
|
1.0
|
CB
|
L:PHE322
|
4.6
|
78.4
|
1.0
|
N
|
L:ASN319
|
4.7
|
55.9
|
1.0
|
C
|
L:GLU323
|
4.8
|
88.7
|
1.0
|
C
|
L:ASN319
|
4.8
|
65.2
|
1.0
|
N
|
L:GLU323
|
4.9
|
84.9
|
1.0
|
N
|
L:LYS321
|
4.9
|
71.5
|
1.0
|
CA
|
L:ASN325
|
4.9
|
74.9
|
1.0
|
ND2
|
L:ASN325
|
4.9
|
65.6
|
1.0
|
|
Reference:
J.M.Kollman,
L.Pandi,
M.R.Sawaya,
M.Riley,
R.F.Doolittle.
Crystal Structure of Human Fibrinogen. Biochemistry V. 48 3877 2009.
ISSN: ISSN 0006-2960
PubMed: 19296670
DOI: 10.1021/BI802205G
Page generated: Sat Jul 13 10:37:27 2024
|