Calcium in PDB 6jwf: Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea
Protein crystallography data
The structure of Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea, PDB code: 6jwf
was solved by
K.Takeda,
T.Ishida,
M.Yoshida,
M.Samejima,
H.Ohno,
K.Igarashi,
N.Nakamura,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
71.07 /
1.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.330,
95.638,
106.204,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16 /
17.7
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea
(pdb code 6jwf). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea, PDB code: 6jwf:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 6jwf
Go back to
Calcium Binding Sites List in 6jwf
Calcium binding site 1 out
of 2 in the Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca701
b:10.3
occ:1.00
|
OD1
|
A:ASP451
|
2.3
|
12.5
|
1.0
|
O
|
A:HOH845
|
2.4
|
11.7
|
1.0
|
O5
|
A:PQQ702
|
2.4
|
10.0
|
1.0
|
O
|
A:HOH1093
|
2.5
|
11.0
|
1.0
|
O7A
|
A:PQQ702
|
2.5
|
9.9
|
1.0
|
N6
|
A:PQQ702
|
2.5
|
9.2
|
1.0
|
O
|
A:SER449
|
2.6
|
10.4
|
1.0
|
C5
|
A:PQQ702
|
3.3
|
9.7
|
1.0
|
C6A
|
A:PQQ702
|
3.3
|
9.3
|
1.0
|
C7X
|
A:PQQ702
|
3.4
|
9.4
|
1.0
|
C7
|
A:PQQ702
|
3.4
|
9.3
|
1.0
|
CG
|
A:ASP451
|
3.5
|
12.3
|
1.0
|
C
|
A:SER449
|
3.7
|
10.8
|
1.0
|
OD2
|
A:ASP451
|
4.1
|
13.9
|
1.0
|
NH1
|
A:ARG430
|
4.2
|
11.5
|
1.0
|
N
|
A:SER449
|
4.2
|
10.7
|
1.0
|
O
|
A:LEU450
|
4.3
|
11.6
|
1.0
|
C
|
A:LEU450
|
4.3
|
11.3
|
1.0
|
ND1
|
A:HIS539
|
4.4
|
10.1
|
1.0
|
O2
|
A:EDO704
|
4.4
|
19.0
|
1.0
|
N
|
A:ASP451
|
4.4
|
11.5
|
1.0
|
NH2
|
A:ARG430
|
4.5
|
12.4
|
1.0
|
CZ
|
A:ARG430
|
4.5
|
11.4
|
1.0
|
CA
|
A:SER449
|
4.6
|
11.0
|
1.0
|
O7B
|
A:PQQ702
|
4.6
|
9.6
|
1.0
|
N
|
A:LEU450
|
4.6
|
11.3
|
1.0
|
C
|
A:ASN448
|
4.6
|
10.8
|
1.0
|
C4
|
A:PQQ702
|
4.7
|
10.1
|
1.0
|
CB
|
A:ASP451
|
4.7
|
12.2
|
1.0
|
CA
|
A:ASP451
|
4.7
|
11.8
|
1.0
|
OE2
|
A:GLU471
|
4.7
|
12.5
|
1.0
|
C8
|
A:PQQ702
|
4.7
|
9.4
|
1.0
|
OD1
|
A:ASN448
|
4.8
|
13.4
|
1.0
|
C9A
|
A:PQQ702
|
4.8
|
9.4
|
1.0
|
CB
|
A:ASN448
|
4.8
|
11.5
|
1.0
|
O
|
A:HOH913
|
4.8
|
12.5
|
1.0
|
CA
|
A:LEU450
|
4.9
|
11.8
|
1.0
|
OE1
|
A:GLU471
|
5.0
|
11.5
|
1.0
|
|
Calcium binding site 2 out
of 2 in 6jwf
Go back to
Calcium Binding Sites List in 6jwf
Calcium binding site 2 out
of 2 in the Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Holo Form of Pyranose Dehydrogenase Pqq Domain From Coprinopsis Cinerea within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca702
b:9.7
occ:1.00
|
OD1
|
B:ASP451
|
2.3
|
10.6
|
1.0
|
O
|
B:HOH824
|
2.4
|
11.1
|
1.0
|
O5
|
B:PQQ703
|
2.4
|
9.8
|
1.0
|
O
|
B:HOH1090
|
2.5
|
10.2
|
1.0
|
O7B
|
B:PQQ703
|
2.5
|
9.9
|
1.0
|
N6
|
B:PQQ703
|
2.5
|
9.3
|
1.0
|
O
|
B:SER449
|
2.6
|
10.3
|
1.0
|
C5
|
B:PQQ703
|
3.3
|
9.6
|
1.0
|
C6A
|
B:PQQ703
|
3.3
|
9.2
|
1.0
|
C7X
|
B:PQQ703
|
3.4
|
9.2
|
1.0
|
C7
|
B:PQQ703
|
3.4
|
9.3
|
1.0
|
CG
|
B:ASP451
|
3.5
|
11.0
|
1.0
|
C
|
B:SER449
|
3.7
|
10.2
|
1.0
|
OD2
|
B:ASP451
|
4.0
|
11.6
|
1.0
|
NH1
|
B:ARG430
|
4.1
|
11.2
|
1.0
|
N
|
B:SER449
|
4.2
|
10.1
|
1.0
|
O
|
B:LEU450
|
4.3
|
10.3
|
1.0
|
C
|
B:LEU450
|
4.3
|
10.5
|
1.0
|
O1
|
B:EDO705
|
4.4
|
17.5
|
1.0
|
ND1
|
B:HIS539
|
4.4
|
9.7
|
1.0
|
NH2
|
B:ARG430
|
4.5
|
11.3
|
1.0
|
N
|
B:ASP451
|
4.5
|
10.4
|
1.0
|
CZ
|
B:ARG430
|
4.5
|
10.5
|
1.0
|
CA
|
B:SER449
|
4.6
|
10.1
|
1.0
|
O7A
|
B:PQQ703
|
4.6
|
9.4
|
1.0
|
C
|
B:ASN448
|
4.6
|
10.1
|
1.0
|
N
|
B:LEU450
|
4.6
|
10.3
|
1.0
|
C4
|
B:PQQ703
|
4.6
|
9.5
|
1.0
|
OE2
|
B:GLU471
|
4.7
|
11.7
|
1.0
|
CB
|
B:ASP451
|
4.7
|
11.0
|
1.0
|
C8
|
B:PQQ703
|
4.7
|
9.2
|
1.0
|
OD1
|
B:ASN448
|
4.7
|
13.4
|
1.0
|
C9A
|
B:PQQ703
|
4.7
|
9.3
|
1.0
|
CA
|
B:ASP451
|
4.8
|
11.1
|
1.0
|
CB
|
B:ASN448
|
4.8
|
11.1
|
1.0
|
O
|
B:HOH920
|
4.8
|
11.7
|
1.0
|
CA
|
B:LEU450
|
4.9
|
10.8
|
1.0
|
OE1
|
B:GLU471
|
5.0
|
11.7
|
1.0
|
CE1
|
B:HIS539
|
5.0
|
10.0
|
1.0
|
|
Reference:
K.Takeda,
T.Ishida,
M.Yoshida,
M.Samejima,
H.Ohno,
K.Igarashi,
N.Nakamura.
The Holo Form Structure of the Catalytic Domain of A Eukaryotic Pqq-Dependent Dehydrogenase To Be Published.
Page generated: Sat Dec 12 06:14:33 2020
|