Calcium in PDB 3gn9: Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus
Protein crystallography data
The structure of Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus, PDB code: 3gn9
was solved by
K.V.Korotkov,
M.D.Gray,
A.Kreger,
S.Turley,
M.Sandkvist,
W.G.J.Hol,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.90 /
1.86
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
100.180,
104.510,
55.410,
90.00,
106.16,
90.00
|
R / Rfree (%)
|
17.8 /
20.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus
(pdb code 3gn9). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the
Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus, PDB code: 3gn9:
Jump to Calcium binding site number:
1;
2;
3;
Calcium binding site 1 out
of 3 in 3gn9
Go back to
Calcium Binding Sites List in 3gn9
Calcium binding site 1 out
of 3 in the Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus
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 the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca201
b:65.9
occ:1.00
|
O
|
A:ALA125
|
2.2
|
30.2
|
1.0
|
O
|
A:GLN118
|
2.2
|
40.9
|
1.0
|
O
|
A:LEU113
|
2.3
|
34.2
|
1.0
|
O
|
A:GLY120
|
2.4
|
38.5
|
1.0
|
OD1
|
A:ASP127
|
2.4
|
35.3
|
1.0
|
OD1
|
A:ASP116
|
2.6
|
33.7
|
1.0
|
CG
|
A:ASP116
|
3.3
|
35.4
|
1.0
|
OD2
|
A:ASP116
|
3.3
|
36.4
|
1.0
|
C
|
A:LEU113
|
3.4
|
33.3
|
1.0
|
C
|
A:ALA125
|
3.4
|
29.9
|
1.0
|
C
|
A:GLN118
|
3.5
|
41.1
|
1.0
|
CG
|
A:ASP127
|
3.5
|
33.1
|
1.0
|
C
|
A:GLY120
|
3.5
|
38.2
|
1.0
|
N
|
A:GLY120
|
3.9
|
39.8
|
1.0
|
OD2
|
A:ASP127
|
4.0
|
36.5
|
1.0
|
N
|
A:ASP127
|
4.1
|
29.1
|
1.0
|
C
|
A:GLU119
|
4.1
|
40.5
|
1.0
|
C
|
A:ALA126
|
4.1
|
29.0
|
1.0
|
CA
|
A:LEU113
|
4.1
|
33.4
|
1.0
|
O
|
A:HOH211
|
4.2
|
36.9
|
1.0
|
N
|
A:GLN118
|
4.2
|
40.3
|
1.0
|
CA
|
A:ALA125
|
4.3
|
30.8
|
1.0
|
CA
|
A:GLY120
|
4.3
|
39.0
|
1.0
|
N
|
A:GLU119
|
4.3
|
41.1
|
1.0
|
CB
|
A:LEU113
|
4.3
|
33.9
|
1.0
|
CA
|
A:GLU119
|
4.3
|
41.1
|
1.0
|
N
|
A:GLY114
|
4.3
|
33.4
|
1.0
|
N
|
A:ALA126
|
4.3
|
29.1
|
1.0
|
CA
|
A:ALA126
|
4.4
|
28.9
|
1.0
|
O
|
A:ALA126
|
4.4
|
29.0
|
1.0
|
CB
|
A:ALA125
|
4.4
|
30.5
|
1.0
|
CA
|
A:GLN118
|
4.4
|
41.0
|
1.0
|
N
|
A:GLY121
|
4.5
|
37.1
|
1.0
|
CA
|
A:GLY114
|
4.5
|
33.4
|
1.0
|
CA
|
A:ASP127
|
4.5
|
29.7
|
1.0
|
O
|
A:GLU119
|
4.6
|
41.0
|
1.0
|
CB
|
A:ASP127
|
4.6
|
30.2
|
1.0
|
CA
|
A:GLY121
|
4.7
|
36.4
|
1.0
|
CB
|
A:ASP116
|
4.8
|
35.8
|
1.0
|
C
|
A:GLY114
|
4.9
|
33.8
|
1.0
|
|
Calcium binding site 2 out
of 3 in 3gn9
Go back to
Calcium Binding Sites List in 3gn9
Calcium binding site 2 out
of 3 in the Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus
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 the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca201
b:71.3
occ:1.00
|
O
|
B:LEU113
|
2.1
|
36.6
|
1.0
|
O
|
B:GLN118
|
2.2
|
45.5
|
1.0
|
OD1
|
B:ASP127
|
2.3
|
39.5
|
1.0
|
O
|
B:ALA125
|
2.3
|
36.2
|
1.0
|
O
|
B:GLY120
|
2.5
|
44.4
|
1.0
|
OD1
|
B:ASP116
|
2.5
|
42.5
|
1.0
|
C
|
B:LEU113
|
3.2
|
36.5
|
1.0
|
CG
|
B:ASP116
|
3.3
|
43.0
|
1.0
|
C
|
B:GLN118
|
3.4
|
45.6
|
1.0
|
OD2
|
B:ASP116
|
3.4
|
43.4
|
1.0
|
C
|
B:ALA125
|
3.5
|
36.5
|
1.0
|
CG
|
B:ASP127
|
3.5
|
37.3
|
1.0
|
C
|
B:GLY120
|
3.7
|
44.0
|
1.0
|
CA
|
B:LEU113
|
3.9
|
36.2
|
1.0
|
N
|
B:GLN118
|
4.0
|
45.1
|
1.0
|
N
|
B:GLY120
|
4.1
|
44.7
|
1.0
|
CB
|
B:LEU113
|
4.1
|
36.5
|
1.0
|
C
|
B:GLU119
|
4.1
|
45.2
|
1.0
|
OD2
|
B:ASP127
|
4.1
|
40.4
|
1.0
|
N
|
B:ASP127
|
4.2
|
35.8
|
1.0
|
N
|
B:GLY114
|
4.2
|
37.1
|
1.0
|
C
|
B:ALA126
|
4.3
|
36.0
|
1.0
|
CA
|
B:GLN118
|
4.3
|
45.5
|
1.0
|
N
|
B:GLU119
|
4.3
|
45.6
|
1.0
|
CA
|
B:ALA125
|
4.4
|
36.9
|
1.0
|
CA
|
B:GLY114
|
4.4
|
37.5
|
1.0
|
CA
|
B:GLU119
|
4.5
|
45.6
|
1.0
|
CA
|
B:GLY120
|
4.5
|
44.4
|
1.0
|
O
|
B:GLU119
|
4.5
|
45.5
|
1.0
|
N
|
B:ALA126
|
4.5
|
36.2
|
1.0
|
CB
|
B:ALA125
|
4.5
|
36.9
|
1.0
|
CA
|
B:ASP127
|
4.6
|
35.7
|
1.0
|
O
|
B:ALA126
|
4.6
|
35.8
|
1.0
|
CA
|
B:ALA126
|
4.6
|
36.1
|
1.0
|
N
|
B:GLY121
|
4.6
|
43.4
|
1.0
|
CB
|
B:ASP127
|
4.7
|
36.2
|
1.0
|
CA
|
B:GLY121
|
4.8
|
43.0
|
1.0
|
CB
|
B:ASP116
|
4.8
|
42.5
|
1.0
|
N
|
B:GLY117
|
4.8
|
43.6
|
1.0
|
C
|
B:GLY114
|
4.8
|
38.4
|
1.0
|
CD2
|
B:LEU113
|
4.9
|
37.3
|
1.0
|
|
Calcium binding site 3 out
of 3 in 3gn9
Go back to
Calcium Binding Sites List in 3gn9
Calcium binding site 3 out
of 3 in the Crystal Structure of the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus
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 the Major Pseudopilin From the Type 2 Secretion System of Vibrio Vulnificus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca201
b:60.1
occ:0.50
|
O
|
C:ALA125
|
2.1
|
26.7
|
1.0
|
O
|
C:GLN118
|
2.3
|
21.1
|
1.0
|
O
|
C:GLY120
|
2.4
|
27.4
|
1.0
|
O
|
C:LEU113
|
2.4
|
28.1
|
1.0
|
OD1
|
C:ASP127
|
2.5
|
26.8
|
1.0
|
C
|
C:ALA125
|
3.3
|
26.4
|
1.0
|
C
|
C:LEU113
|
3.4
|
28.8
|
1.0
|
C
|
C:GLY120
|
3.5
|
26.8
|
1.0
|
C
|
C:GLN118
|
3.5
|
22.3
|
1.0
|
N
|
C:GLY120
|
3.7
|
25.6
|
1.0
|
CG
|
C:ASP127
|
3.7
|
25.1
|
1.0
|
C
|
C:GLU119
|
3.7
|
24.8
|
1.0
|
N
|
C:ASP127
|
4.0
|
24.5
|
1.0
|
O
|
C:GLU119
|
4.1
|
24.9
|
1.0
|
CA
|
C:GLY120
|
4.1
|
26.2
|
1.0
|
C
|
C:ALA126
|
4.1
|
25.0
|
1.0
|
CA
|
C:GLU119
|
4.2
|
24.0
|
1.0
|
CA
|
C:LEU113
|
4.2
|
29.2
|
1.0
|
CA
|
C:ALA125
|
4.2
|
26.8
|
1.0
|
N
|
C:GLU119
|
4.3
|
23.2
|
1.0
|
N
|
C:ALA126
|
4.3
|
26.0
|
1.0
|
CB
|
C:ALA125
|
4.3
|
26.9
|
1.0
|
OD2
|
C:ASP127
|
4.3
|
26.2
|
1.0
|
N
|
C:GLY114
|
4.4
|
28.6
|
1.0
|
CA
|
C:ALA126
|
4.4
|
25.2
|
1.0
|
CA
|
C:GLY114
|
4.5
|
28.1
|
1.0
|
CB
|
C:LEU113
|
4.5
|
29.5
|
1.0
|
CA
|
C:ASP127
|
4.6
|
24.4
|
1.0
|
N
|
C:GLY121
|
4.6
|
26.9
|
1.0
|
N
|
C:GLN118
|
4.6
|
22.5
|
1.0
|
O
|
C:ALA126
|
4.6
|
24.6
|
1.0
|
CA
|
C:GLN118
|
4.6
|
22.1
|
1.0
|
CB
|
C:ASP127
|
4.7
|
24.7
|
1.0
|
CA
|
C:GLY121
|
4.9
|
27.2
|
1.0
|
|
Reference:
K.V.Korotkov,
M.D.Gray,
A.Kreger,
S.Turley,
M.Sandkvist,
W.G.Hol.
Calcium Is Essential For the Major Pseudopilin in the Type 2 Secretion System. J.Biol.Chem. V. 284 25466 2009.
ISSN: ISSN 0021-9258
PubMed: 19640838
DOI: 10.1074/JBC.C109.037655
Page generated: Sat Jul 13 10:43:58 2024
|