Cobalt in PDB 7emr: Crystal Structure of Hasap Capturing Cobalt Tetraphenylporphyrin
Protein crystallography data
The structure of Crystal Structure of Hasap Capturing Cobalt Tetraphenylporphyrin, PDB code: 7emr
was solved by
Y.Shisaka,
E.Sakakibara,
H.Sugimoto,
O.Shoji,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.55
|
Space group
|
P 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.06,
85.06,
84.087,
90,
90,
90
|
R / Rfree (%)
|
13.2 /
16.4
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of Hasap Capturing Cobalt Tetraphenylporphyrin
(pdb code 7emr). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the
Crystal Structure of Hasap Capturing Cobalt Tetraphenylporphyrin, PDB code: 7emr:
Jump to Cobalt binding site number:
1;
2;
3;
Cobalt binding site 1 out
of 3 in 7emr
Go back to
Cobalt Binding Sites List in 7emr
Cobalt binding site 1 out
of 3 in the Crystal Structure of Hasap Capturing Cobalt Tetraphenylporphyrin
![](/pictures/CO/pdb/em/7emr-CO-sphere_01.jpg) Mono view
![](/pictures/CO/pdb/em/7emr-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 Crystal Structure of Hasap Capturing Cobalt Tetraphenylporphyrin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co201
b:19.2
occ:1.00
|
CO
|
A:J83201
|
0.0
|
19.2
|
1.0
|
NAS
|
A:J83201
|
2.0
|
19.5
|
1.0
|
NAI
|
A:J83201
|
2.0
|
19.2
|
1.0
|
NAX
|
A:J83201
|
2.0
|
20.3
|
1.0
|
NAN
|
A:J83201
|
2.1
|
19.8
|
1.0
|
NE2
|
A:HIS32
|
2.1
|
18.5
|
1.0
|
OH
|
A:TYR75
|
2.3
|
22.3
|
1.0
|
CAR
|
A:J83201
|
3.0
|
19.3
|
1.0
|
CAO
|
A:J83201
|
3.0
|
20.2
|
1.0
|
CAW
|
A:J83201
|
3.0
|
19.9
|
1.0
|
CAT
|
A:J83201
|
3.0
|
19.5
|
1.0
|
CAE
|
A:J83201
|
3.0
|
20.2
|
1.0
|
CAM
|
A:J83201
|
3.1
|
19.9
|
1.0
|
CAJ
|
A:J83201
|
3.1
|
19.3
|
1.0
|
CAH
|
A:J83201
|
3.1
|
20.6
|
1.0
|
CD2
|
A:HIS32
|
3.1
|
19.3
|
1.0
|
CE1
|
A:HIS32
|
3.1
|
22.3
|
1.0
|
CZ
|
A:TYR75
|
3.2
|
21.5
|
1.0
|
CAC
|
A:J83201
|
3.4
|
18.0
|
1.0
|
CAD
|
A:J83201
|
3.4
|
19.7
|
1.0
|
CAB
|
A:J83201
|
3.4
|
18.9
|
1.0
|
CAA
|
A:J83201
|
3.4
|
18.6
|
1.0
|
CE1
|
A:TYR75
|
3.9
|
20.2
|
1.0
|
CE2
|
A:TYR75
|
3.9
|
19.7
|
1.0
|
ND1
|
A:HIS83
|
4.0
|
21.9
|
1.0
|
CAQ
|
A:J83201
|
4.2
|
21.3
|
1.0
|
CAP
|
A:J83201
|
4.2
|
20.3
|
1.0
|
CAV
|
A:J83201
|
4.2
|
20.1
|
1.0
|
CAF
|
A:J83201
|
4.2
|
19.8
|
1.0
|
CAU
|
A:J83201
|
4.2
|
19.4
|
1.0
|
ND1
|
A:HIS32
|
4.2
|
21.2
|
1.0
|
CAK
|
A:J83201
|
4.2
|
19.2
|
1.0
|
CAG
|
A:J83201
|
4.2
|
19.3
|
1.0
|
CAL
|
A:J83201
|
4.2
|
18.9
|
1.0
|
CG
|
A:HIS32
|
4.2
|
18.8
|
1.0
|
CE1
|
A:HIS83
|
4.6
|
23.5
|
1.0
|
CBK
|
A:J83201
|
4.9
|
19.9
|
1.0
|
CG
|
A:HIS83
|
4.9
|
21.5
|
1.0
|
CBQ
|
A:J83201
|
4.9
|
20.4
|
1.0
|
CBE
|
A:J83201
|
4.9
|
21.4
|
1.0
|
CAY
|
A:J83201
|
4.9
|
19.5
|
1.0
|
|
Cobalt binding site 2 out
of 3 in 7emr
Go back to
Cobalt Binding Sites List in 7emr
Cobalt binding site 2 out
of 3 in the Crystal Structure of Hasap Capturing Cobalt Tetraphenylporphyrin
![](/pictures/CO/pdb/em/7emr-CO-sphere_02.jpg) Mono view
![](/pictures/CO/pdb/em/7emr-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 Crystal Structure of Hasap Capturing Cobalt Tetraphenylporphyrin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co201
b:19.4
occ:1.00
|
CO
|
B:J83201
|
0.0
|
19.4
|
1.0
|
NAX
|
B:J83201
|
2.0
|
17.9
|
1.0
|
NAS
|
B:J83201
|
2.0
|
19.6
|
1.0
|
NAN
|
B:J83201
|
2.1
|
19.6
|
1.0
|
NAI
|
B:J83201
|
2.1
|
19.0
|
1.0
|
NE2
|
B:HIS32
|
2.1
|
18.0
|
1.0
|
OH
|
B:TYR75
|
2.3
|
19.7
|
1.0
|
CAR
|
B:J83201
|
3.0
|
20.4
|
1.0
|
CAT
|
B:J83201
|
3.0
|
19.8
|
1.0
|
CAO
|
B:J83201
|
3.0
|
22.2
|
1.0
|
CAW
|
B:J83201
|
3.0
|
19.7
|
1.0
|
CAM
|
B:J83201
|
3.0
|
19.9
|
1.0
|
CAJ
|
B:J83201
|
3.0
|
20.4
|
1.0
|
CAE
|
B:J83201
|
3.1
|
19.4
|
1.0
|
CD2
|
B:HIS32
|
3.1
|
19.3
|
1.0
|
CAH
|
B:J83201
|
3.1
|
20.6
|
1.0
|
CE1
|
B:HIS32
|
3.1
|
20.5
|
1.0
|
CZ
|
B:TYR75
|
3.1
|
20.4
|
1.0
|
CAC
|
B:J83201
|
3.4
|
18.0
|
1.0
|
CAB
|
B:J83201
|
3.4
|
21.1
|
1.0
|
CAD
|
B:J83201
|
3.4
|
18.8
|
1.0
|
CAA
|
B:J83201
|
3.4
|
19.5
|
1.0
|
CE2
|
B:TYR75
|
3.9
|
18.8
|
1.0
|
CE1
|
B:TYR75
|
3.9
|
19.8
|
1.0
|
ND1
|
B:HIS83
|
4.0
|
21.7
|
1.0
|
CAP
|
B:J83201
|
4.2
|
22.2
|
1.0
|
CAQ
|
B:J83201
|
4.2
|
21.8
|
1.0
|
CAU
|
B:J83201
|
4.2
|
18.6
|
1.0
|
CAV
|
B:J83201
|
4.2
|
19.2
|
1.0
|
CAK
|
B:J83201
|
4.2
|
20.3
|
1.0
|
CAL
|
B:J83201
|
4.2
|
20.0
|
1.0
|
ND1
|
B:HIS32
|
4.2
|
21.8
|
1.0
|
CAF
|
B:J83201
|
4.2
|
20.8
|
1.0
|
CG
|
B:HIS32
|
4.2
|
18.5
|
1.0
|
CAG
|
B:J83201
|
4.2
|
19.3
|
1.0
|
CG
|
B:HIS83
|
4.7
|
21.1
|
1.0
|
CB
|
B:HIS83
|
4.8
|
21.2
|
1.0
|
CE1
|
B:HIS83
|
4.8
|
24.3
|
1.0
|
CBK
|
B:J83201
|
4.8
|
18.6
|
1.0
|
CBQ
|
B:J83201
|
4.9
|
19.8
|
1.0
|
CBE
|
B:J83201
|
4.9
|
23.9
|
1.0
|
CAY
|
B:J83201
|
4.9
|
20.4
|
1.0
|
|
Cobalt binding site 3 out
of 3 in 7emr
Go back to
Cobalt Binding Sites List in 7emr
Cobalt binding site 3 out
of 3 in the Crystal Structure of Hasap Capturing Cobalt Tetraphenylporphyrin
![](/pictures/CO/pdb/em/7emr-CO-sphere_03.jpg) Mono view
![](/pictures/CO/pdb/em/7emr-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 Crystal Structure of Hasap Capturing Cobalt Tetraphenylporphyrin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co201
b:26.1
occ:1.00
|
CO
|
C:J83201
|
0.0
|
26.1
|
1.0
|
NAI
|
C:J83201
|
2.0
|
26.4
|
1.0
|
NAX
|
C:J83201
|
2.0
|
25.5
|
1.0
|
NAS
|
C:J83201
|
2.1
|
26.8
|
1.0
|
NAN
|
C:J83201
|
2.1
|
27.7
|
1.0
|
NE2
|
C:HIS32
|
2.1
|
24.3
|
1.0
|
OH
|
C:TYR75
|
2.3
|
30.6
|
1.0
|
CAH
|
C:J83201
|
3.0
|
29.9
|
1.0
|
CAE
|
C:J83201
|
3.0
|
26.0
|
1.0
|
CAW
|
C:J83201
|
3.0
|
23.8
|
1.0
|
CAT
|
C:J83201
|
3.0
|
25.3
|
1.0
|
CAR
|
C:J83201
|
3.0
|
25.8
|
1.0
|
CAJ
|
C:J83201
|
3.0
|
29.2
|
1.0
|
CAO
|
C:J83201
|
3.0
|
26.6
|
1.0
|
CAM
|
C:J83201
|
3.1
|
29.9
|
1.0
|
CD2
|
C:HIS32
|
3.1
|
27.1
|
1.0
|
CE1
|
C:HIS32
|
3.1
|
28.5
|
1.0
|
CZ
|
C:TYR75
|
3.1
|
25.8
|
1.0
|
CAD
|
C:J83201
|
3.4
|
24.4
|
1.0
|
CAA
|
C:J83201
|
3.4
|
27.0
|
1.0
|
CAC
|
C:J83201
|
3.4
|
23.5
|
1.0
|
CAB
|
C:J83201
|
3.4
|
27.9
|
1.0
|
CE1
|
C:TYR75
|
3.8
|
23.7
|
1.0
|
CE2
|
C:TYR75
|
3.9
|
27.1
|
1.0
|
ND1
|
C:HIS83
|
4.1
|
23.3
|
1.0
|
CAG
|
C:J83201
|
4.1
|
29.0
|
1.0
|
CAF
|
C:J83201
|
4.1
|
28.4
|
1.0
|
CAV
|
C:J83201
|
4.2
|
23.7
|
1.0
|
CAQ
|
C:J83201
|
4.2
|
27.0
|
1.0
|
CAP
|
C:J83201
|
4.2
|
26.5
|
1.0
|
CAU
|
C:J83201
|
4.2
|
24.8
|
1.0
|
CAK
|
C:J83201
|
4.2
|
30.8
|
1.0
|
CAL
|
C:J83201
|
4.2
|
29.3
|
1.0
|
ND1
|
C:HIS32
|
4.2
|
27.8
|
1.0
|
CG
|
C:HIS32
|
4.2
|
27.8
|
1.0
|
CE1
|
C:HIS83
|
4.8
|
25.6
|
1.0
|
CBQ
|
C:J83201
|
4.8
|
23.4
|
1.0
|
CBK
|
C:J83201
|
4.9
|
25.4
|
1.0
|
CAY
|
C:J83201
|
4.9
|
29.7
|
1.0
|
CG
|
C:HIS83
|
4.9
|
24.6
|
1.0
|
CBE
|
C:J83201
|
4.9
|
33.5
|
1.0
|
CD1
|
C:TYR75
|
5.0
|
21.5
|
1.0
|
|
Reference:
Y.Shisaka,
E.Sakakibara,
K.Suzuki,
J.K.Stanfield,
H.Onoda,
G.Ueda,
M.Hatano,
H.Sugimoto,
O.Shoji.
Tetraphenylporphyrin Enters the Ring: First Example of A Complex Between Highly Bulky Porphyrins and A Protein. Chembiochem V. 23 00095 2022.
ISSN: ESSN 1439-7633
PubMed: 35352458
DOI: 10.1002/CBIC.202200095
Page generated: Tue Jul 30 19:15:09 2024
|