Cobalt in PDB 6rwf: The Dissociation Mechanism of Processive Cellulases
Protein crystallography data
The structure of The Dissociation Mechanism of Processive Cellulases, PDB code: 6rwf
was solved by
J.Stahlberg,
B.C.Knott,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.52 /
1.64
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.363,
51.632,
65.590,
90.00,
96.31,
90.00
|
R / Rfree (%)
|
12.7 /
16.5
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the The Dissociation Mechanism of Processive Cellulases
(pdb code 6rwf). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the
The Dissociation Mechanism of Processive Cellulases, PDB code: 6rwf:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
Cobalt binding site 1 out
of 5 in 6rwf
Go back to
Cobalt Binding Sites List in 6rwf
Cobalt binding site 1 out
of 5 in the The Dissociation Mechanism of Processive Cellulases
![](/pictures/CO/pdb/rw/6rwf-CO-sphere_01.jpg) Mono view
![](/pictures/CO/pdb/rw/6rwf-CO-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of The Dissociation Mechanism of Processive Cellulases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co501
b:13.5
occ:1.00
|
OD1
|
A:ASP329
|
2.1
|
6.5
|
1.0
|
O
|
A:HOH1017
|
2.1
|
14.8
|
1.0
|
O
|
A:HOH1009
|
2.1
|
14.4
|
1.0
|
O
|
A:HOH734
|
2.2
|
8.3
|
1.0
|
CG
|
A:ASP329
|
3.0
|
5.5
|
1.0
|
OD2
|
A:ASP329
|
3.4
|
5.4
|
1.0
|
O
|
A:HOH1064
|
3.8
|
14.0
|
1.0
|
O
|
A:HOH1124
|
4.1
|
29.6
|
1.0
|
CB
|
A:ASP329
|
4.3
|
4.9
|
1.0
|
O
|
A:HOH962
|
4.5
|
19.3
|
1.0
|
|
Cobalt binding site 2 out
of 5 in 6rwf
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Cobalt Binding Sites List in 6rwf
Cobalt binding site 2 out
of 5 in the The Dissociation Mechanism of Processive Cellulases
![](/pictures/CO/pdb/rw/6rwf-CO-sphere_02.jpg) Mono view
![](/pictures/CO/pdb/rw/6rwf-CO-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of The Dissociation Mechanism of Processive Cellulases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co502
b:25.5
occ:1.00
|
O
|
A:HOH616
|
1.9
|
17.0
|
1.0
|
O
|
A:HOH1078
|
2.0
|
25.4
|
1.0
|
O
|
A:HOH681
|
2.3
|
22.9
|
1.0
|
O
|
A:HOH966
|
2.5
|
21.4
|
1.0
|
O
|
A:PHE280
|
3.9
|
5.5
|
1.0
|
O
|
A:HOH656
|
4.1
|
17.8
|
1.0
|
O
|
A:THR281
|
4.2
|
5.9
|
1.0
|
O
|
A:SER278
|
4.3
|
11.1
|
1.0
|
O
|
A:HOH951
|
4.3
|
20.8
|
1.0
|
CB
|
A:ASP283
|
4.4
|
5.7
|
1.0
|
CA
|
A:SER278
|
4.4
|
11.4
|
1.0
|
C
|
A:SER278
|
4.7
|
10.8
|
1.0
|
OD2
|
A:ASP283
|
4.7
|
7.2
|
1.0
|
O
|
A:GLY277
|
5.0
|
7.6
|
1.0
|
OE1
|
A:GLN306
|
5.0
|
7.2
|
1.0
|
|
Cobalt binding site 3 out
of 5 in 6rwf
Go back to
Cobalt Binding Sites List in 6rwf
Cobalt binding site 3 out
of 5 in the The Dissociation Mechanism of Processive Cellulases
![](/pictures/CO/pdb/rw/6rwf-CO-sphere_03.jpg) Mono view
![](/pictures/CO/pdb/rw/6rwf-CO-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of The Dissociation Mechanism of Processive Cellulases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co503
b:26.5
occ:1.00
|
OD2
|
A:ASP249
|
2.2
|
26.4
|
1.0
|
O
|
A:HOH1041
|
2.3
|
28.0
|
1.0
|
O
|
A:HOH618
|
2.4
|
12.2
|
1.0
|
O
|
A:HOH617
|
2.4
|
21.3
|
1.0
|
CG
|
A:ASP249
|
3.0
|
21.3
|
1.0
|
OD1
|
A:ASP249
|
3.4
|
28.6
|
1.0
|
O
|
A:HOH736
|
3.8
|
33.4
|
1.0
|
OD2
|
A:ASP241
|
4.0
|
7.5
|
1.0
|
O
|
A:HOH666
|
4.2
|
26.3
|
1.0
|
OD1
|
A:ASP241
|
4.2
|
9.8
|
1.0
|
CB
|
A:ASP249
|
4.3
|
16.9
|
1.0
|
OE2
|
A:GLU193
|
4.5
|
18.6
|
0.5
|
CG
|
A:ASP241
|
4.5
|
8.4
|
1.0
|
|
Cobalt binding site 4 out
of 5 in 6rwf
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Cobalt Binding Sites List in 6rwf
Cobalt binding site 4 out
of 5 in the The Dissociation Mechanism of Processive Cellulases
![](/pictures/CO/pdb/rw/6rwf-CO-sphere_04.jpg) Mono view
![](/pictures/CO/pdb/rw/6rwf-CO-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of The Dissociation Mechanism of Processive Cellulases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co504
b:21.3
occ:1.00
|
O
|
A:HOH604
|
1.7
|
15.9
|
1.0
|
OE2
|
A:GLU239
|
2.0
|
17.9
|
1.0
|
O
|
A:HOH884
|
2.0
|
28.1
|
1.0
|
O
|
A:HOH676
|
2.1
|
29.9
|
1.0
|
NE2
|
A:HIS206
|
2.3
|
5.2
|
0.3
|
NE2
|
A:HIS206
|
2.3
|
8.8
|
0.7
|
CD
|
A:GLU239
|
2.9
|
14.9
|
1.0
|
CE1
|
A:HIS206
|
3.0
|
7.8
|
0.7
|
CE1
|
A:HIS206
|
3.1
|
5.1
|
0.3
|
OE1
|
A:GLU239
|
3.2
|
20.0
|
1.0
|
CD2
|
A:HIS206
|
3.4
|
5.0
|
0.3
|
CD2
|
A:HIS206
|
3.4
|
7.1
|
0.7
|
ND1
|
A:HIS206
|
4.2
|
7.3
|
0.7
|
O
|
A:HOH1113
|
4.2
|
37.3
|
1.0
|
O
|
A:HOH1123
|
4.2
|
27.6
|
1.0
|
ND1
|
A:HIS206
|
4.2
|
5.0
|
0.3
|
CG
|
A:GLU239
|
4.3
|
13.0
|
1.0
|
CG
|
A:HIS206
|
4.4
|
6.4
|
0.7
|
CG
|
A:HIS206
|
4.4
|
4.8
|
0.3
|
O
|
A:HOH752
|
4.4
|
25.1
|
1.0
|
O
|
A:HOH686
|
4.5
|
25.7
|
1.0
|
O
|
A:HOH782
|
4.5
|
27.7
|
1.0
|
CB
|
A:GLU239
|
4.8
|
9.8
|
1.0
|
|
Cobalt binding site 5 out
of 5 in 6rwf
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Cobalt Binding Sites List in 6rwf
Cobalt binding site 5 out
of 5 in the The Dissociation Mechanism of Processive Cellulases
![](/pictures/CO/pdb/rw/6rwf-CO-sphere_05.jpg) Mono view
![](/pictures/CO/pdb/rw/6rwf-CO-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of The Dissociation Mechanism of Processive Cellulases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co506
b:91.0
occ:1.00
|
O
|
A:HOH1056
|
1.9
|
37.4
|
1.0
|
O
|
A:HOH860
|
1.9
|
16.2
|
1.0
|
O
|
A:HOH1214
|
2.4
|
29.5
|
1.0
|
O
|
A:HOH876
|
2.4
|
22.8
|
1.0
|
O
|
A:HOH1006
|
2.6
|
17.6
|
1.0
|
O
|
A:HOH628
|
2.7
|
26.6
|
1.0
|
O
|
A:HOH1101
|
3.4
|
25.1
|
1.0
|
O
|
A:HOH1106
|
3.7
|
23.7
|
1.0
|
O
|
A:HOH639
|
3.8
|
9.3
|
1.0
|
OE1
|
A:GLU217
|
3.8
|
8.2
|
1.0
|
OE2
|
A:GLU212
|
3.9
|
3.3
|
1.0
|
CZ2
|
A:TRP367
|
4.2
|
7.0
|
1.0
|
CG
|
A:GLN175
|
4.2
|
6.9
|
1.0
|
NE2
|
A:GLN175
|
4.5
|
7.8
|
1.0
|
CH2
|
A:TRP367
|
4.5
|
7.6
|
1.0
|
CD
|
A:GLN175
|
4.6
|
7.5
|
1.0
|
OE1
|
A:GLU212
|
4.7
|
3.0
|
1.0
|
CD
|
A:GLU217
|
4.7
|
6.3
|
1.0
|
CD
|
A:GLU212
|
4.7
|
2.9
|
1.0
|
OD2
|
A:ASP214
|
4.8
|
3.9
|
1.0
|
OD2
|
A:ASP173
|
4.9
|
3.0
|
1.0
|
OE2
|
A:GLU217
|
5.0
|
6.7
|
1.0
|
|
Reference:
J.V.Vermaas,
R.Kont,
G.T.Beckham,
M.F.Crowley,
M.Gudmundsson,
M.Sandgren,
J.Stahlberg,
P.Valjamae,
B.C.Knott.
The Dissociation Mechanism of Processive Cellulases. Proc.Natl.Acad.Sci.Usa V. 116 23061 2019.
ISSN: ESSN 1091-6490
PubMed: 31666327
DOI: 10.1073/PNAS.1913398116
Page generated: Tue Jul 30 18:58:43 2024
|