Calcium in PDB 7l6g: Mbnp From Methylosinus Trichosporium
Protein crystallography data
The structure of Mbnp From Methylosinus Trichosporium, PDB code: 7l6g
was solved by
A.C.Manesis,
A.C.Rosenzweig,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
21.89 /
2.04
|
|
Space group
|
P 61
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.276,
91.276,
383.567,
90,
90,
120
|
|
R / Rfree (%)
|
20.4 /
25.1
|
Other elements in 7l6g:
The structure of Mbnp From Methylosinus Trichosporium also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Mbnp From Methylosinus Trichosporium
(pdb code 7l6g). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Mbnp From Methylosinus Trichosporium, PDB code: 7l6g:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 7l6g
Go back to
Calcium Binding Sites List in 7l6g
Calcium binding site 1 out
of 6 in the Mbnp From Methylosinus Trichosporium
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Mbnp From Methylosinus Trichosporium within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:37.1
occ:1.00
|
O
|
A:ALA265
|
2.3
|
34.0
|
1.0
|
|
OD1
|
A:ASP274
|
2.4
|
40.2
|
1.0
|
|
OD2
|
A:ASP276
|
2.4
|
41.2
|
1.0
|
|
O
|
A:GLY263
|
2.4
|
49.3
|
1.0
|
|
O
|
A:GLY267
|
2.4
|
32.1
|
1.0
|
|
OD1
|
A:ASP261
|
2.5
|
47.6
|
1.0
|
|
OD2
|
A:ASP274
|
2.7
|
39.0
|
1.0
|
|
CG
|
A:ASP274
|
2.9
|
40.9
|
1.0
|
|
OD2
|
A:ASP261
|
3.1
|
45.5
|
1.0
|
|
CG
|
A:ASP261
|
3.2
|
40.9
|
1.0
|
|
CG
|
A:ASP276
|
3.4
|
48.9
|
1.0
|
|
C
|
A:ALA265
|
3.5
|
43.4
|
1.0
|
|
C
|
A:GLY267
|
3.6
|
36.0
|
1.0
|
|
C
|
A:GLY263
|
3.6
|
51.2
|
1.0
|
|
CB
|
A:ASP276
|
3.7
|
38.7
|
1.0
|
|
N
|
A:GLY267
|
3.8
|
38.1
|
1.0
|
|
N
|
A:ALA265
|
4.0
|
43.2
|
1.0
|
|
C
|
A:GLY264
|
4.1
|
51.3
|
1.0
|
|
CA
|
A:GLY267
|
4.2
|
31.5
|
1.0
|
|
N
|
A:GLY263
|
4.3
|
38.1
|
1.0
|
|
CA
|
A:GLY264
|
4.3
|
52.6
|
1.0
|
|
CA
|
A:ALA265
|
4.3
|
48.0
|
1.0
|
|
CB
|
A:ASP274
|
4.4
|
40.6
|
1.0
|
|
N
|
A:GLY264
|
4.4
|
51.5
|
1.0
|
|
N
|
A:ASP276
|
4.4
|
33.4
|
1.0
|
|
C
|
A:VAL266
|
4.5
|
42.0
|
1.0
|
|
OD1
|
A:ASP276
|
4.5
|
40.8
|
1.0
|
|
N
|
A:VAL266
|
4.5
|
39.2
|
1.0
|
|
CA
|
A:GLY263
|
4.5
|
46.4
|
1.0
|
|
O
|
A:GLY264
|
4.6
|
51.8
|
1.0
|
|
CA
|
A:VAL266
|
4.6
|
36.1
|
1.0
|
|
N
|
A:CYS268
|
4.6
|
38.9
|
1.0
|
|
CB
|
A:ASP261
|
4.6
|
38.8
|
1.0
|
|
CA
|
A:ASP276
|
4.7
|
35.3
|
1.0
|
|
N
|
A:LYS262
|
4.8
|
33.0
|
1.0
|
|
CD
|
A:PRO275
|
4.9
|
31.4
|
1.0
|
|
CA
|
A:CYS268
|
4.9
|
35.1
|
1.0
|
|
Calcium binding site 2 out
of 6 in 7l6g
Go back to
Calcium Binding Sites List in 7l6g
Calcium binding site 2 out
of 6 in the Mbnp From Methylosinus Trichosporium
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Mbnp From Methylosinus Trichosporium within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca402
b:54.7
occ:1.00
|
O
|
B:GLY267
|
2.3
|
49.3
|
1.0
|
|
O
|
B:ALA265
|
2.3
|
52.3
|
1.0
|
|
O
|
B:GLY263
|
2.4
|
58.3
|
1.0
|
|
OD2
|
B:ASP276
|
2.4
|
51.5
|
1.0
|
|
OD1
|
B:ASP274
|
2.5
|
56.0
|
1.0
|
|
OD1
|
B:ASP261
|
2.6
|
67.5
|
1.0
|
|
OD2
|
B:ASP274
|
2.6
|
57.8
|
1.0
|
|
CG
|
B:ASP274
|
2.9
|
55.0
|
1.0
|
|
CG
|
B:ASP276
|
3.3
|
53.8
|
1.0
|
|
CG
|
B:ASP261
|
3.4
|
63.2
|
1.0
|
|
C
|
B:GLY267
|
3.4
|
47.6
|
1.0
|
|
OD2
|
B:ASP261
|
3.5
|
68.6
|
1.0
|
|
C
|
B:ALA265
|
3.5
|
51.4
|
1.0
|
|
CB
|
B:ASP276
|
3.6
|
45.6
|
1.0
|
|
C
|
B:GLY263
|
3.6
|
63.9
|
1.0
|
|
N
|
B:GLY267
|
3.6
|
50.8
|
1.0
|
|
CA
|
B:GLY267
|
4.0
|
44.4
|
1.0
|
|
N
|
B:ALA265
|
4.1
|
55.6
|
1.0
|
|
C
|
B:GLY264
|
4.2
|
53.6
|
1.0
|
|
N
|
B:GLY263
|
4.2
|
50.6
|
1.0
|
|
C
|
B:VAL266
|
4.4
|
56.8
|
1.0
|
|
CA
|
B:ALA265
|
4.4
|
54.1
|
1.0
|
|
CB
|
B:ASP274
|
4.4
|
52.5
|
1.0
|
|
N
|
B:CYS268
|
4.4
|
43.3
|
1.0
|
|
CA
|
B:GLY264
|
4.5
|
60.3
|
1.0
|
|
N
|
B:ASP276
|
4.5
|
37.3
|
1.0
|
|
N
|
B:GLY264
|
4.5
|
68.4
|
1.0
|
|
N
|
B:VAL266
|
4.5
|
52.1
|
1.0
|
|
OD1
|
B:ASP276
|
4.5
|
58.9
|
1.0
|
|
CA
|
B:GLY263
|
4.5
|
55.6
|
1.0
|
|
CA
|
B:VAL266
|
4.6
|
56.9
|
1.0
|
|
CA
|
B:ASP276
|
4.6
|
41.7
|
1.0
|
|
O
|
B:GLY264
|
4.7
|
48.5
|
1.0
|
|
CA
|
B:CYS268
|
4.7
|
42.8
|
1.0
|
|
CD
|
B:PRO275
|
4.7
|
37.8
|
1.0
|
|
CB
|
B:ASP261
|
4.8
|
59.0
|
1.0
|
|
N
|
B:LYS262
|
4.8
|
64.6
|
1.0
|
|
Calcium binding site 3 out
of 6 in 7l6g
Go back to
Calcium Binding Sites List in 7l6g
Calcium binding site 3 out
of 6 in the Mbnp From Methylosinus Trichosporium
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Mbnp From Methylosinus Trichosporium within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca402
b:43.4
occ:1.00
|
O
|
C:ALA265
|
2.3
|
54.4
|
1.0
|
|
OD2
|
C:ASP276
|
2.3
|
38.0
|
1.0
|
|
O
|
C:GLY267
|
2.4
|
51.8
|
1.0
|
|
O
|
C:GLY263
|
2.5
|
52.1
|
1.0
|
|
OD1
|
C:ASP274
|
2.6
|
41.7
|
1.0
|
|
OD1
|
C:ASP261
|
2.6
|
62.1
|
1.0
|
|
OD2
|
C:ASP274
|
2.7
|
45.6
|
1.0
|
|
CG
|
C:ASP274
|
3.0
|
46.3
|
1.0
|
|
CG
|
C:ASP276
|
3.4
|
38.8
|
1.0
|
|
C
|
C:GLY267
|
3.5
|
43.1
|
1.0
|
|
C
|
C:ALA265
|
3.5
|
51.9
|
1.0
|
|
CG
|
C:ASP261
|
3.6
|
63.6
|
1.0
|
|
C
|
C:GLY263
|
3.6
|
45.3
|
1.0
|
|
N
|
C:GLY267
|
3.7
|
42.1
|
1.0
|
|
CB
|
C:ASP276
|
3.8
|
46.0
|
1.0
|
|
OD2
|
C:ASP261
|
3.8
|
61.3
|
1.0
|
|
N
|
C:ALA265
|
4.1
|
53.5
|
1.0
|
|
CA
|
C:GLY267
|
4.2
|
34.6
|
1.0
|
|
C
|
C:GLY264
|
4.2
|
53.1
|
1.0
|
|
N
|
C:GLY263
|
4.3
|
51.2
|
1.0
|
|
CA
|
C:ALA265
|
4.4
|
52.7
|
1.0
|
|
OD1
|
C:ASP276
|
4.5
|
40.4
|
1.0
|
|
CB
|
C:ASP274
|
4.5
|
38.0
|
1.0
|
|
N
|
C:ASP276
|
4.5
|
43.5
|
1.0
|
|
N
|
C:VAL266
|
4.5
|
52.5
|
1.0
|
|
CA
|
C:GLY264
|
4.5
|
41.4
|
1.0
|
|
C
|
C:VAL266
|
4.5
|
55.0
|
1.0
|
|
N
|
C:GLY264
|
4.5
|
44.1
|
1.0
|
|
CA
|
C:GLY263
|
4.6
|
51.6
|
1.0
|
|
CA
|
C:VAL266
|
4.6
|
55.8
|
1.0
|
|
N
|
C:CYS268
|
4.6
|
45.3
|
1.0
|
|
O
|
C:GLY264
|
4.6
|
64.5
|
1.0
|
|
N
|
C:LYS262
|
4.7
|
50.4
|
1.0
|
|
CD
|
C:PRO275
|
4.7
|
45.5
|
1.0
|
|
CA
|
C:ASP276
|
4.8
|
48.9
|
1.0
|
|
CA
|
C:CYS268
|
4.9
|
40.1
|
1.0
|
|
CB
|
C:ASP261
|
4.9
|
60.8
|
1.0
|
|
Calcium binding site 4 out
of 6 in 7l6g
Go back to
Calcium Binding Sites List in 7l6g
Calcium binding site 4 out
of 6 in the Mbnp From Methylosinus Trichosporium
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Mbnp From Methylosinus Trichosporium within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca402
b:52.8
occ:1.00
|
OD2
|
D:ASP276
|
2.3
|
62.2
|
1.0
|
|
O
|
D:ALA265
|
2.3
|
67.2
|
1.0
|
|
O
|
D:GLY267
|
2.5
|
54.9
|
1.0
|
|
OD1
|
D:ASP274
|
2.5
|
47.1
|
1.0
|
|
O
|
D:GLY263
|
2.5
|
64.8
|
1.0
|
|
OD2
|
D:ASP274
|
2.6
|
53.3
|
1.0
|
|
OD1
|
D:ASP261
|
2.7
|
85.5
|
1.0
|
|
CG
|
D:ASP274
|
2.9
|
52.7
|
1.0
|
|
CG
|
D:ASP276
|
3.3
|
63.5
|
1.0
|
|
C
|
D:ALA265
|
3.5
|
73.7
|
1.0
|
|
CG
|
D:ASP261
|
3.5
|
87.6
|
1.0
|
|
C
|
D:GLY263
|
3.5
|
67.6
|
1.0
|
|
OD2
|
D:ASP261
|
3.5
|
86.5
|
1.0
|
|
C
|
D:GLY267
|
3.7
|
53.9
|
1.0
|
|
CB
|
D:ASP276
|
3.8
|
59.1
|
1.0
|
|
N
|
D:ALA265
|
3.8
|
74.8
|
1.0
|
|
C
|
D:GLY264
|
3.9
|
71.6
|
1.0
|
|
N
|
D:GLY267
|
4.0
|
50.0
|
1.0
|
|
CA
|
D:GLY264
|
4.1
|
59.8
|
1.0
|
|
N
|
D:GLY264
|
4.2
|
66.6
|
1.0
|
|
CA
|
D:ALA265
|
4.2
|
76.6
|
1.0
|
|
OD1
|
D:ASP276
|
4.3
|
65.9
|
1.0
|
|
N
|
D:GLY263
|
4.4
|
59.7
|
1.0
|
|
O
|
D:GLY264
|
4.4
|
79.5
|
1.0
|
|
CA
|
D:GLY267
|
4.4
|
51.4
|
1.0
|
|
CB
|
D:ASP274
|
4.4
|
59.9
|
1.0
|
|
N
|
D:VAL266
|
4.5
|
68.7
|
1.0
|
|
C
|
D:VAL266
|
4.5
|
59.4
|
1.0
|
|
CA
|
D:GLY263
|
4.6
|
67.6
|
1.0
|
|
N
|
D:ASP276
|
4.6
|
59.1
|
1.0
|
|
N
|
D:CYS268
|
4.7
|
51.5
|
1.0
|
|
CA
|
D:VAL266
|
4.7
|
60.8
|
1.0
|
|
CD
|
D:PRO275
|
4.8
|
54.2
|
1.0
|
|
CA
|
D:ASP276
|
4.9
|
61.1
|
1.0
|
|
CA
|
D:CYS268
|
4.9
|
49.6
|
1.0
|
|
N
|
D:LYS262
|
4.9
|
71.7
|
1.0
|
|
CB
|
D:ASP261
|
4.9
|
85.2
|
1.0
|
|
Calcium binding site 5 out
of 6 in 7l6g
Go back to
Calcium Binding Sites List in 7l6g
Calcium binding site 5 out
of 6 in the Mbnp From Methylosinus Trichosporium
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Mbnp From Methylosinus Trichosporium within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca403
b:58.5
occ:1.00
|
O
|
E:GLY263
|
2.4
|
72.0
|
1.0
|
|
O
|
E:ALA265
|
2.4
|
57.9
|
1.0
|
|
OD1
|
E:ASP274
|
2.4
|
41.6
|
1.0
|
|
OD1
|
E:ASP261
|
2.5
|
69.4
|
1.0
|
|
OD2
|
E:ASP276
|
2.5
|
52.8
|
1.0
|
|
O
|
E:GLY267
|
2.5
|
47.6
|
1.0
|
|
OD2
|
E:ASP274
|
2.7
|
51.8
|
1.0
|
|
CG
|
E:ASP274
|
2.9
|
49.5
|
1.0
|
|
CG
|
E:ASP261
|
3.3
|
71.7
|
1.0
|
|
CG
|
E:ASP276
|
3.4
|
53.9
|
1.0
|
|
C
|
E:GLY263
|
3.5
|
60.8
|
1.0
|
|
OD2
|
E:ASP261
|
3.5
|
70.8
|
1.0
|
|
C
|
E:ALA265
|
3.6
|
57.3
|
1.0
|
|
C
|
E:GLY267
|
3.6
|
46.8
|
1.0
|
|
CB
|
E:ASP276
|
3.7
|
59.3
|
1.0
|
|
N
|
E:GLY267
|
3.9
|
59.1
|
1.0
|
|
C
|
E:GLY264
|
4.1
|
57.2
|
1.0
|
|
N
|
E:GLY263
|
4.1
|
55.4
|
1.0
|
|
N
|
E:ALA265
|
4.2
|
57.8
|
1.0
|
|
O
|
E:GLY264
|
4.3
|
58.2
|
1.0
|
|
CA
|
E:GLY267
|
4.4
|
50.2
|
1.0
|
|
CA
|
E:GLY264
|
4.4
|
47.5
|
1.0
|
|
N
|
E:GLY264
|
4.4
|
58.9
|
1.0
|
|
N
|
E:ASP276
|
4.4
|
50.2
|
1.0
|
|
CA
|
E:GLY263
|
4.4
|
54.2
|
1.0
|
|
CB
|
E:ASP274
|
4.4
|
53.0
|
1.0
|
|
CA
|
E:ALA265
|
4.5
|
57.4
|
1.0
|
|
C
|
E:VAL266
|
4.5
|
59.3
|
1.0
|
|
N
|
E:VAL266
|
4.5
|
53.7
|
1.0
|
|
CA
|
E:VAL266
|
4.5
|
51.2
|
1.0
|
|
OD1
|
E:ASP276
|
4.6
|
60.5
|
1.0
|
|
N
|
E:CYS268
|
4.7
|
45.3
|
1.0
|
|
CA
|
E:ASP276
|
4.7
|
56.0
|
1.0
|
|
CD
|
E:PRO275
|
4.7
|
61.0
|
1.0
|
|
CB
|
E:ASP261
|
4.7
|
65.5
|
1.0
|
|
N
|
E:LYS262
|
4.8
|
64.7
|
1.0
|
|
CA
|
E:CYS268
|
4.8
|
41.6
|
1.0
|
|
Calcium binding site 6 out
of 6 in 7l6g
Go back to
Calcium Binding Sites List in 7l6g
Calcium binding site 6 out
of 6 in the Mbnp From Methylosinus Trichosporium
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Mbnp From Methylosinus Trichosporium within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca402
b:52.0
occ:1.00
|
O
|
F:ALA265
|
2.3
|
55.7
|
1.0
|
|
O
|
F:GLY263
|
2.4
|
58.1
|
1.0
|
|
O
|
F:GLY267
|
2.4
|
46.2
|
1.0
|
|
OD1
|
F:ASP274
|
2.4
|
45.7
|
1.0
|
|
OD2
|
F:ASP276
|
2.5
|
53.4
|
1.0
|
|
OD2
|
F:ASP274
|
2.5
|
49.9
|
1.0
|
|
OD1
|
F:ASP261
|
2.7
|
79.8
|
1.0
|
|
CG
|
F:ASP274
|
2.8
|
51.0
|
1.0
|
|
CG
|
F:ASP276
|
3.4
|
58.6
|
1.0
|
|
OD2
|
F:ASP261
|
3.4
|
70.3
|
1.0
|
|
CG
|
F:ASP261
|
3.4
|
75.4
|
1.0
|
|
C
|
F:GLY267
|
3.5
|
49.5
|
1.0
|
|
C
|
F:ALA265
|
3.5
|
58.8
|
1.0
|
|
C
|
F:GLY263
|
3.6
|
57.8
|
1.0
|
|
CB
|
F:ASP276
|
3.7
|
59.1
|
1.0
|
|
N
|
F:GLY267
|
3.9
|
57.3
|
1.0
|
|
N
|
F:ALA265
|
4.1
|
65.8
|
1.0
|
|
C
|
F:GLY264
|
4.2
|
61.8
|
1.0
|
|
N
|
F:GLY263
|
4.2
|
57.9
|
1.0
|
|
CA
|
F:GLY267
|
4.3
|
48.9
|
1.0
|
|
CB
|
F:ASP274
|
4.3
|
55.1
|
1.0
|
|
C
|
F:VAL266
|
4.4
|
61.8
|
1.0
|
|
CA
|
F:ALA265
|
4.4
|
63.0
|
1.0
|
|
OD1
|
F:ASP276
|
4.5
|
64.0
|
1.0
|
|
N
|
F:VAL266
|
4.5
|
55.7
|
1.0
|
|
CA
|
F:GLY263
|
4.5
|
61.1
|
1.0
|
|
N
|
F:CYS268
|
4.5
|
55.0
|
1.0
|
|
CA
|
F:GLY264
|
4.5
|
67.7
|
1.0
|
|
N
|
F:GLY264
|
4.5
|
66.8
|
1.0
|
|
N
|
F:ASP276
|
4.6
|
57.7
|
1.0
|
|
O
|
F:GLY264
|
4.6
|
59.5
|
1.0
|
|
CA
|
F:VAL266
|
4.6
|
60.3
|
1.0
|
|
CA
|
F:ASP276
|
4.7
|
56.8
|
1.0
|
|
CA
|
F:CYS268
|
4.8
|
45.6
|
1.0
|
|
CB
|
F:ASP261
|
4.9
|
74.0
|
1.0
|
|
N
|
F:LYS262
|
4.9
|
67.9
|
1.0
|
|
Reference:
A.C.Manesis,
R.J.Jodts,
B.M.Hoffman,
A.C.Rosenzweig.
Copper Binding By A Unique Family of Metalloproteins Is Dependent on Kynurenine Formation To Be Published.
Page generated: Fri Jul 19 01:29:23 2024
|
