Manganese in PDB 8p5z: Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant
Protein crystallography data
The structure of Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant, PDB code: 8p5z
was solved by
K.Lau,
W.Wang,
F.Pojer,
A.Larabi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.14 /
1.56
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.95,
51.892,
93.367,
90,
117.42,
90
|
R / Rfree (%)
|
18 /
21.8
|
Other elements in 8p5z:
The structure of Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant
(pdb code 8p5z). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant, PDB code: 8p5z:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 8p5z
Go back to
Manganese Binding Sites List in 8p5z
Manganese binding site 1 out
of 4 in the Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn202
b:30.1
occ:0.47
|
H011
|
A:X08201
|
1.3
|
51.8
|
1.0
|
N01
|
A:X08201
|
2.1
|
43.2
|
1.0
|
N08
|
A:X08201
|
2.3
|
43.9
|
1.0
|
C03
|
A:X08201
|
3.0
|
38.0
|
1.0
|
H101
|
A:X08201
|
3.0
|
42.2
|
1.0
|
C10
|
A:X08201
|
3.1
|
35.1
|
1.0
|
C02
|
A:X08201
|
3.1
|
39.8
|
1.0
|
HE3
|
D:MET121
|
3.2
|
56.2
|
1.0
|
C07
|
A:X08201
|
3.2
|
42.9
|
1.0
|
HD11
|
A:LEU124
|
3.3
|
42.9
|
1.0
|
H071
|
A:X08201
|
3.3
|
51.5
|
1.0
|
BR
|
A:BR203
|
3.5
|
74.4
|
0.7
|
H102
|
A:X08201
|
3.5
|
42.2
|
1.0
|
H022
|
A:X08201
|
3.7
|
47.8
|
1.0
|
HD12
|
A:LEU124
|
3.8
|
42.9
|
1.0
|
H021
|
A:X08201
|
3.9
|
47.8
|
1.0
|
HE1
|
D:MET121
|
4.0
|
56.2
|
1.0
|
H091
|
D:X08201
|
4.0
|
55.5
|
1.0
|
CD1
|
A:LEU124
|
4.0
|
35.8
|
1.0
|
CE
|
D:MET121
|
4.0
|
46.8
|
1.0
|
H092
|
D:X08201
|
4.4
|
55.5
|
1.0
|
C04
|
A:X08201
|
4.4
|
43.3
|
1.0
|
C11
|
A:X08201
|
4.4
|
29.8
|
1.0
|
H112
|
A:X08201
|
4.4
|
35.8
|
1.0
|
HE2
|
D:MET121
|
4.5
|
56.2
|
1.0
|
C06
|
A:X08201
|
4.5
|
44.8
|
1.0
|
HG
|
A:LEU124
|
4.6
|
37.9
|
1.0
|
HB2
|
D:MET121
|
4.6
|
35.5
|
1.0
|
C09
|
D:X08201
|
4.7
|
46.2
|
1.0
|
HD13
|
A:LEU124
|
4.7
|
42.9
|
1.0
|
H111
|
A:X08201
|
4.8
|
35.8
|
1.0
|
HD21
|
A:LEU110
|
4.8
|
41.3
|
1.0
|
HD2
|
A:TYR112
|
4.8
|
35.8
|
1.0
|
CG
|
A:LEU124
|
4.9
|
31.6
|
1.0
|
HE2
|
A:TYR112
|
4.9
|
34.0
|
1.0
|
|
Manganese binding site 2 out
of 4 in 8p5z
Go back to
Manganese Binding Sites List in 8p5z
Manganese binding site 2 out
of 4 in the Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn203
b:41.4
occ:0.53
|
H011
|
B:X08201
|
1.3
|
63.5
|
1.0
|
N01
|
B:X08201
|
2.1
|
52.9
|
1.0
|
N08
|
B:X08201
|
2.6
|
46.9
|
1.0
|
H101
|
B:X08201
|
2.8
|
50.1
|
1.0
|
C10
|
B:X08201
|
3.0
|
41.7
|
1.0
|
C02
|
B:X08201
|
3.2
|
43.4
|
1.0
|
BR
|
C:BR203
|
3.2
|
97.9
|
1.0
|
C03
|
B:X08201
|
3.2
|
42.5
|
1.0
|
HE2
|
C:MET121
|
3.3
|
76.0
|
1.0
|
HE1
|
C:MET121
|
3.3
|
76.0
|
1.0
|
HE3
|
C:MET121
|
3.3
|
76.0
|
1.0
|
H102
|
B:X08201
|
3.5
|
50.1
|
1.0
|
CE
|
C:MET121
|
3.5
|
63.3
|
1.0
|
HD11
|
B:LEU124
|
3.6
|
48.9
|
1.0
|
C07
|
B:X08201
|
3.6
|
48.4
|
1.0
|
H022
|
B:X08201
|
3.7
|
52.0
|
1.0
|
H071
|
B:X08201
|
3.7
|
58.1
|
1.0
|
H093
|
C:X08201
|
3.8
|
67.8
|
1.0
|
H021
|
B:X08201
|
4.0
|
52.0
|
1.0
|
H112
|
B:X08201
|
4.2
|
49.9
|
1.0
|
HD12
|
B:LEU124
|
4.2
|
48.9
|
1.0
|
C11
|
B:X08201
|
4.2
|
41.5
|
1.0
|
CD1
|
B:LEU124
|
4.3
|
40.7
|
1.0
|
HG
|
B:LEU124
|
4.4
|
40.4
|
1.0
|
HB2
|
C:MET121
|
4.5
|
51.1
|
1.0
|
H091
|
C:X08201
|
4.6
|
67.8
|
1.0
|
C04
|
B:X08201
|
4.6
|
49.3
|
1.0
|
C09
|
C:X08201
|
4.7
|
56.5
|
1.0
|
H111
|
B:X08201
|
4.7
|
49.9
|
1.0
|
CG
|
B:LEU124
|
4.9
|
33.6
|
1.0
|
C06
|
B:X08201
|
4.9
|
54.2
|
1.0
|
HD21
|
B:LEU124
|
4.9
|
45.0
|
1.0
|
HD21
|
B:LEU110
|
5.0
|
46.0
|
1.0
|
|
Manganese binding site 3 out
of 4 in 8p5z
Go back to
Manganese Binding Sites List in 8p5z
Manganese binding site 3 out
of 4 in the Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn202
b:43.8
occ:0.45
|
H011
|
C:X08201
|
2.2
|
55.8
|
1.0
|
N08
|
C:X08201
|
2.6
|
56.9
|
1.0
|
N01
|
C:X08201
|
2.8
|
46.5
|
1.0
|
H112
|
C:X08201
|
3.2
|
54.1
|
1.0
|
H071
|
C:X08201
|
3.2
|
68.7
|
1.0
|
C07
|
C:X08201
|
3.3
|
57.3
|
1.0
|
BR
|
C:BR204
|
3.4
|
104.1
|
1.0
|
HE3
|
B:MET121
|
3.5
|
65.1
|
1.0
|
C03
|
C:X08201
|
3.5
|
57.8
|
1.0
|
C02
|
C:X08201
|
3.7
|
56.5
|
1.0
|
HD11
|
C:LEU124
|
3.9
|
52.3
|
1.0
|
C10
|
C:X08201
|
3.9
|
55.6
|
1.0
|
C11
|
C:X08201
|
4.0
|
45.0
|
1.0
|
HE1
|
B:MET121
|
4.1
|
65.1
|
1.0
|
H111
|
C:X08201
|
4.1
|
54.1
|
1.0
|
CE
|
B:MET121
|
4.2
|
54.2
|
1.0
|
HG
|
C:LEU124
|
4.3
|
41.6
|
1.0
|
H021
|
C:X08201
|
4.3
|
67.8
|
1.0
|
H022
|
C:X08201
|
4.4
|
67.8
|
1.0
|
H101
|
C:X08201
|
4.5
|
66.7
|
1.0
|
CD1
|
C:LEU124
|
4.6
|
43.5
|
1.0
|
HD12
|
C:LEU124
|
4.6
|
52.3
|
1.0
|
HB2
|
B:MET121
|
4.6
|
62.0
|
1.0
|
C06
|
C:X08201
|
4.7
|
59.0
|
1.0
|
H102
|
C:X08201
|
4.7
|
66.7
|
1.0
|
HD21
|
C:LEU124
|
4.7
|
52.2
|
1.0
|
HE1
|
C:TYR112
|
4.8
|
50.7
|
1.0
|
HD1
|
C:TYR112
|
4.8
|
49.4
|
1.0
|
HE2
|
B:MET121
|
4.8
|
65.1
|
1.0
|
C04
|
C:X08201
|
4.8
|
60.6
|
1.0
|
H093
|
B:X08201
|
4.8
|
56.1
|
1.0
|
CG
|
C:LEU124
|
4.9
|
34.6
|
1.0
|
H071
|
B:X08201
|
4.9
|
58.1
|
1.0
|
CE1
|
C:TYR112
|
4.9
|
44.9
|
1.0
|
CD1
|
C:TYR112
|
4.9
|
48.0
|
1.0
|
|
Manganese binding site 4 out
of 4 in 8p5z
Go back to
Manganese Binding Sites List in 8p5z
Manganese binding site 4 out
of 4 in the Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Artificial Transfer Hydrogenase with A Mn-5 Cofactor and Streptavidin S112Y-K121M Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn202
b:34.7
occ:0.49
|
H011
|
D:X08201
|
2.3
|
51.2
|
1.0
|
N08
|
D:X08201
|
2.4
|
45.4
|
1.0
|
N01
|
D:X08201
|
2.4
|
42.7
|
1.0
|
H071
|
D:X08201
|
3.2
|
63.5
|
1.0
|
C07
|
D:X08201
|
3.3
|
52.9
|
1.0
|
C03
|
D:X08201
|
3.3
|
44.4
|
1.0
|
HD11
|
D:LEU124
|
3.3
|
45.2
|
1.0
|
C02
|
D:X08201
|
3.4
|
49.7
|
1.0
|
C10
|
D:X08201
|
3.6
|
50.6
|
1.0
|
H101
|
D:X08201
|
3.6
|
60.7
|
1.0
|
BR
|
D:BR203
|
3.6
|
81.5
|
0.7
|
H111
|
D:X08201
|
3.7
|
40.3
|
1.0
|
HD12
|
D:LEU124
|
3.9
|
45.2
|
1.0
|
O
|
D:HOH342
|
4.0
|
43.5
|
1.0
|
CD1
|
D:LEU124
|
4.0
|
37.6
|
1.0
|
H021
|
D:X08201
|
4.1
|
59.6
|
1.0
|
H022
|
D:X08201
|
4.1
|
59.6
|
1.0
|
H092
|
A:X08201
|
4.2
|
46.0
|
1.0
|
C11
|
D:X08201
|
4.2
|
33.6
|
1.0
|
H102
|
D:X08201
|
4.4
|
60.7
|
1.0
|
HG
|
D:LEU124
|
4.4
|
41.1
|
1.0
|
HB2
|
A:MET121
|
4.5
|
33.4
|
1.0
|
C04
|
D:X08201
|
4.6
|
47.1
|
1.0
|
C06
|
D:X08201
|
4.6
|
47.9
|
1.0
|
H112
|
D:X08201
|
4.8
|
40.3
|
1.0
|
HD13
|
D:LEU124
|
4.8
|
45.2
|
1.0
|
CG
|
D:LEU124
|
4.8
|
34.3
|
1.0
|
HD21
|
D:LEU110
|
4.9
|
38.2
|
1.0
|
SD
|
A:MET121
|
4.9
|
39.0
|
1.0
|
|
Reference:
W.Wang,
R.Tachibana,
Z.Zou,
D.Chen,
X.Zhang,
K.Lau,
F.Pojer,
T.Ward,
X.Hu.
Manganese Transfer Hydrogenases Based on the Biotin-Streptavidin Technology. Angew.Chem.Int.Ed.Engl. 11896 2023.
ISSN: ESSN 1521-3773
PubMed: 37671593
DOI: 10.1002/ANIE.202311896
Page generated: Sun Oct 6 13:31:18 2024
|