Calcium in PDB 7jnb: The Structure of CBM32-1 and CBM32-2 Domains From Clostridium Perfringens Zmpb in Complex with Galnac
Protein crystallography data
The structure of The Structure of CBM32-1 and CBM32-2 Domains From Clostridium Perfringens Zmpb in Complex with Galnac, PDB code: 7jnb
was solved by
B.Pluvinage,
A.B.Boraston,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.51 /
2.00
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.61,
89.61,
185.87,
90,
90,
90
|
R / Rfree (%)
|
20.9 /
23.5
|
Calcium Binding Sites:
The binding sites of Calcium atom in the The Structure of CBM32-1 and CBM32-2 Domains From Clostridium Perfringens Zmpb in Complex with Galnac
(pdb code 7jnb). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
The Structure of CBM32-1 and CBM32-2 Domains From Clostridium Perfringens Zmpb in Complex with Galnac, PDB code: 7jnb:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 7jnb
Go back to
Calcium Binding Sites List in 7jnb
Calcium binding site 1 out
of 2 in the The Structure of CBM32-1 and CBM32-2 Domains From Clostridium Perfringens Zmpb in Complex with Galnac
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of The Structure of CBM32-1 and CBM32-2 Domains From Clostridium Perfringens Zmpb in Complex with Galnac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca501
b:43.9
occ:1.00
|
OD1
|
A:ASP321
|
2.2
|
40.0
|
1.0
|
O
|
A:LYS318
|
2.3
|
45.6
|
1.0
|
O
|
A:ASN426
|
2.3
|
35.8
|
1.0
|
OE2
|
A:GLU427
|
2.4
|
38.5
|
1.0
|
O
|
A:THR326
|
2.5
|
51.0
|
1.0
|
O
|
A:ASP323
|
2.5
|
38.5
|
1.0
|
OG1
|
A:THR326
|
2.6
|
46.5
|
1.0
|
CG
|
A:ASP321
|
3.2
|
42.7
|
1.0
|
C
|
A:THR326
|
3.3
|
52.7
|
1.0
|
C
|
A:LYS318
|
3.4
|
47.5
|
1.0
|
C
|
A:ASN426
|
3.5
|
37.9
|
1.0
|
CD
|
A:GLU427
|
3.6
|
38.6
|
1.0
|
C
|
A:ASP323
|
3.6
|
36.1
|
1.0
|
OD2
|
A:ASP321
|
3.7
|
45.7
|
1.0
|
CB
|
A:THR326
|
3.8
|
48.8
|
1.0
|
N
|
A:ASP323
|
3.9
|
37.4
|
1.0
|
CA
|
A:THR326
|
3.9
|
51.9
|
1.0
|
CG
|
A:GLU427
|
4.0
|
36.3
|
1.0
|
CA
|
A:ASP323
|
4.1
|
36.6
|
1.0
|
N
|
A:THR326
|
4.1
|
52.7
|
1.0
|
N
|
A:ASP321
|
4.2
|
38.8
|
1.0
|
CA
|
A:LYS318
|
4.3
|
51.3
|
1.0
|
CB
|
A:ASP323
|
4.3
|
36.9
|
1.0
|
N
|
A:TYR327
|
4.3
|
52.5
|
1.0
|
CA
|
A:ASN426
|
4.3
|
38.5
|
1.0
|
N
|
A:ALA319
|
4.4
|
42.7
|
1.0
|
CA
|
A:ALA319
|
4.5
|
38.8
|
1.0
|
CB
|
A:ASP321
|
4.5
|
40.1
|
1.0
|
C
|
A:ALA319
|
4.5
|
35.7
|
1.0
|
CB
|
A:LYS318
|
4.5
|
53.6
|
1.0
|
N
|
A:GLU427
|
4.6
|
35.7
|
1.0
|
OE1
|
A:GLU427
|
4.6
|
38.4
|
1.0
|
N
|
A:ILE320
|
4.6
|
33.3
|
1.0
|
N
|
A:ASN322
|
4.7
|
38.9
|
1.0
|
N
|
A:VAL324
|
4.7
|
36.7
|
1.0
|
CA
|
A:TYR327
|
4.7
|
55.9
|
1.0
|
CA
|
A:ASP321
|
4.7
|
40.3
|
1.0
|
CA
|
A:GLU427
|
4.8
|
35.9
|
1.0
|
O
|
A:ALA319
|
4.9
|
34.9
|
1.0
|
C
|
A:ASP321
|
4.9
|
40.7
|
1.0
|
CG2
|
A:THR326
|
4.9
|
48.4
|
1.0
|
CB
|
A:ASN426
|
4.9
|
38.8
|
1.0
|
CA
|
A:VAL324
|
5.0
|
41.6
|
1.0
|
|
Calcium binding site 2 out
of 2 in 7jnb
Go back to
Calcium Binding Sites List in 7jnb
Calcium binding site 2 out
of 2 in the The Structure of CBM32-1 and CBM32-2 Domains From Clostridium Perfringens Zmpb in Complex with Galnac
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of The Structure of CBM32-1 and CBM32-2 Domains From Clostridium Perfringens Zmpb in Complex with Galnac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca502
b:30.8
occ:1.00
|
O
|
A:LYS93
|
2.2
|
28.2
|
1.0
|
O
|
A:ASN98
|
2.2
|
34.7
|
1.0
|
O
|
A:THR101
|
2.3
|
31.2
|
1.0
|
OE2
|
A:GLU205
|
2.3
|
30.6
|
1.0
|
O
|
A:ALA204
|
2.4
|
25.4
|
1.0
|
OG1
|
A:THR101
|
2.6
|
30.3
|
1.0
|
OD1
|
A:ASP96
|
2.6
|
32.6
|
1.0
|
C
|
A:THR101
|
3.2
|
29.9
|
1.0
|
C
|
A:ASN98
|
3.4
|
35.3
|
1.0
|
C
|
A:LYS93
|
3.4
|
29.1
|
1.0
|
CD
|
A:GLU205
|
3.4
|
30.6
|
1.0
|
CG
|
A:ASP96
|
3.5
|
33.0
|
1.0
|
C
|
A:ALA204
|
3.6
|
24.9
|
1.0
|
CB
|
A:THR101
|
3.7
|
30.9
|
1.0
|
CA
|
A:THR101
|
3.8
|
31.2
|
1.0
|
OD2
|
A:ASP96
|
3.8
|
33.8
|
1.0
|
CG
|
A:GLU205
|
3.9
|
30.3
|
1.0
|
N
|
A:ASN98
|
4.0
|
35.6
|
1.0
|
N
|
A:THR101
|
4.0
|
32.6
|
1.0
|
CA
|
A:ASN98
|
4.1
|
34.9
|
1.0
|
N
|
A:HIS102
|
4.2
|
26.7
|
1.0
|
CA
|
A:LYS93
|
4.3
|
28.6
|
1.0
|
CA
|
A:ALA204
|
4.3
|
23.8
|
1.0
|
CB
|
A:ASN98
|
4.3
|
35.7
|
1.0
|
N
|
A:ALA94
|
4.4
|
27.7
|
1.0
|
N
|
A:ASP96
|
4.4
|
30.4
|
1.0
|
N
|
A:LEU99
|
4.4
|
31.8
|
1.0
|
CA
|
A:ALA94
|
4.4
|
29.7
|
1.0
|
C
|
A:ALA94
|
4.5
|
31.1
|
1.0
|
OE1
|
A:GLU205
|
4.5
|
31.2
|
1.0
|
CA
|
A:HIS102
|
4.6
|
26.4
|
1.0
|
N
|
A:GLU205
|
4.6
|
25.2
|
1.0
|
CA
|
A:LEU99
|
4.7
|
34.0
|
1.0
|
CB
|
A:LYS93
|
4.7
|
29.0
|
1.0
|
CA
|
A:GLU205
|
4.7
|
26.2
|
1.0
|
CB
|
A:ASP96
|
4.8
|
34.1
|
1.0
|
N
|
A:ILE95
|
4.8
|
29.7
|
1.0
|
O
|
A:ALA94
|
4.8
|
34.3
|
1.0
|
N
|
A:GLY97
|
4.8
|
34.9
|
1.0
|
C
|
A:LEU99
|
4.9
|
34.3
|
1.0
|
CG2
|
A:THR101
|
4.9
|
31.7
|
1.0
|
CB
|
A:GLU205
|
4.9
|
27.8
|
1.0
|
CA
|
A:ASP96
|
4.9
|
33.8
|
1.0
|
|
Reference:
B.Pluvinage,
E.Ficko-Blean,
I.Noach,
C.Stuart,
N.Thompson,
H.Mcclure,
N.Buenbrazo,
W.Wakarchuck,
A.B.Boraston.
Molecular Insights Into Architecturally Complex Glycopeptidases To Be Published.
Page generated: Sat Apr 17 14:08:55 2021
|