Manganese in PDB 6sa1: Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp
Protein crystallography data
The structure of Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp, PDB code: 6sa1
was solved by
N.C.Brissett,
A.J.Doherty,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
88.66 /
2.01
|
Space group
|
P 4 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
198.250,
198.250,
85.300,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.5 /
20.4
|
Other elements in 6sa1:
The structure of Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp
(pdb code 6sa1). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp, PDB code: 6sa1:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 6sa1
Go back to
Manganese Binding Sites List in 6sa1
Manganese binding site 1 out
of 4 in the Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn401
b:99.4
occ:1.00
|
O1A
|
A:U3H403
|
2.5
|
99.6
|
0.8
|
OD2
|
A:ASP142
|
2.7
|
0.9
|
1.0
|
OD2
|
A:ASP231
|
2.7
|
53.2
|
1.0
|
OD2
|
A:ASP140
|
2.8
|
50.6
|
1.0
|
PA
|
A:U3H403
|
3.6
|
91.1
|
0.8
|
CG
|
A:ASP231
|
3.6
|
55.3
|
1.0
|
O2A
|
A:U3H403
|
3.6
|
91.5
|
0.8
|
CB
|
A:ASP231
|
3.6
|
49.1
|
1.0
|
CG
|
A:ASP140
|
3.8
|
50.8
|
1.0
|
MN
|
A:MN402
|
3.8
|
93.9
|
1.0
|
CG
|
A:ASP142
|
3.8
|
91.4
|
1.0
|
H5'1
|
A:U3H403
|
4.1
|
0.7
|
0.8
|
OD1
|
A:ASP140
|
4.3
|
56.2
|
1.0
|
CG
|
A:GLN234
|
4.4
|
59.8
|
1.0
|
CB
|
A:ASP142
|
4.4
|
70.6
|
1.0
|
CD
|
A:GLN234
|
4.4
|
73.7
|
1.0
|
O5'
|
A:U3H403
|
4.5
|
0.2
|
0.8
|
NE2
|
A:GLN234
|
4.6
|
92.2
|
1.0
|
OD1
|
A:ASP142
|
4.8
|
99.9
|
1.0
|
O3A
|
A:U3H403
|
4.8
|
73.0
|
0.8
|
OD1
|
A:ASP231
|
4.8
|
55.6
|
1.0
|
C5'
|
A:U3H403
|
4.8
|
98.1
|
0.8
|
CB
|
A:ASP140
|
4.9
|
45.8
|
1.0
|
OE1
|
A:GLN234
|
4.9
|
80.9
|
1.0
|
|
Manganese binding site 2 out
of 4 in 6sa1
Go back to
Manganese Binding Sites List in 6sa1
Manganese binding site 2 out
of 4 in the Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn402
b:93.9
occ:1.00
|
OD1
|
A:ASP140
|
2.3
|
56.2
|
1.0
|
O1A
|
A:U3H403
|
2.6
|
99.6
|
0.8
|
O2G
|
A:U3H403
|
2.7
|
81.0
|
0.8
|
CG
|
A:ASP140
|
3.0
|
50.8
|
1.0
|
O2B
|
A:U3H403
|
3.0
|
57.8
|
0.8
|
OD2
|
A:ASP140
|
3.0
|
50.6
|
1.0
|
O1G
|
A:U3H403
|
3.4
|
58.8
|
0.8
|
PG
|
A:U3H403
|
3.5
|
77.0
|
0.8
|
OD2
|
A:ASP142
|
3.7
|
0.9
|
1.0
|
PA
|
A:U3H403
|
3.8
|
91.1
|
0.8
|
MN
|
A:MN401
|
3.8
|
99.4
|
1.0
|
CG
|
A:ASP142
|
3.8
|
91.4
|
1.0
|
PB
|
A:U3H403
|
3.8
|
64.1
|
0.8
|
O3A
|
A:U3H403
|
3.8
|
73.0
|
0.8
|
NE2
|
A:HIS182
|
3.8
|
45.9
|
1.0
|
CB
|
A:ASP142
|
4.1
|
70.6
|
1.0
|
O3B
|
A:U3H403
|
4.1
|
70.3
|
0.8
|
CD2
|
A:HIS182
|
4.3
|
42.9
|
1.0
|
OD1
|
A:ASP142
|
4.3
|
99.9
|
1.0
|
O
|
A:LEU141
|
4.3
|
48.0
|
1.0
|
CA
|
A:ASP142
|
4.3
|
55.5
|
1.0
|
CB
|
A:ASP140
|
4.5
|
45.8
|
1.0
|
O5'
|
A:U3H403
|
4.6
|
0.2
|
0.8
|
C
|
A:LEU141
|
4.6
|
49.4
|
1.0
|
N
|
A:ASP142
|
4.7
|
43.8
|
1.0
|
C
|
A:ASP140
|
5.0
|
47.5
|
1.0
|
N
|
A:LEU141
|
5.0
|
43.5
|
1.0
|
|
Manganese binding site 3 out
of 4 in 6sa1
Go back to
Manganese Binding Sites List in 6sa1
Manganese binding site 3 out
of 4 in the Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn401
b:0.5
occ:1.00
|
OD2
|
D:ASP142
|
2.7
|
92.0
|
1.0
|
OD2
|
D:ASP140
|
2.7
|
58.2
|
1.0
|
OD2
|
D:ASP231
|
3.0
|
59.6
|
1.0
|
CG
|
D:ASP140
|
3.7
|
61.3
|
1.0
|
CG
|
D:ASP142
|
3.8
|
81.2
|
1.0
|
MN
|
D:MN402
|
3.8
|
0.9
|
1.0
|
CG
|
D:ASP231
|
3.9
|
56.5
|
1.0
|
CB
|
D:ASP231
|
3.9
|
49.7
|
1.0
|
OD1
|
D:ASP140
|
4.1
|
65.2
|
1.0
|
O31
|
D:PPV403
|
4.1
|
0.3
|
1.0
|
CB
|
D:ASP142
|
4.3
|
75.6
|
1.0
|
CD
|
D:GLN234
|
4.4
|
73.9
|
1.0
|
NE2
|
D:GLN234
|
4.5
|
80.5
|
1.0
|
CG
|
D:GLN234
|
4.5
|
60.9
|
1.0
|
OD1
|
D:ASP142
|
4.7
|
86.5
|
1.0
|
O21
|
D:PPV403
|
4.8
|
99.3
|
1.0
|
CB
|
D:ASP140
|
4.8
|
52.8
|
1.0
|
OE1
|
D:GLN234
|
4.8
|
68.3
|
1.0
|
|
Manganese binding site 4 out
of 4 in 6sa1
Go back to
Manganese Binding Sites List in 6sa1
Manganese binding site 4 out
of 4 in the Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Post Catalytic Complex of Prim-Polc From Mycobacterium Smegmatis with Gapped Dna and 3'-Dutp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn402
b:0.9
occ:1.00
|
OD1
|
D:ASP140
|
2.6
|
65.2
|
1.0
|
O21
|
D:PPV403
|
2.7
|
99.3
|
1.0
|
O22
|
D:PPV403
|
3.3
|
0.2
|
1.0
|
O32
|
D:PPV403
|
3.3
|
0.6
|
1.0
|
CG
|
D:ASP140
|
3.4
|
61.3
|
1.0
|
OD2
|
D:ASP140
|
3.5
|
58.2
|
1.0
|
P1
|
D:PPV403
|
3.6
|
0.3
|
1.0
|
OD2
|
D:ASP142
|
3.7
|
92.0
|
1.0
|
CG
|
D:ASP142
|
3.7
|
81.2
|
1.0
|
O31
|
D:PPV403
|
3.7
|
0.3
|
1.0
|
P2
|
D:PPV403
|
3.8
|
0.2
|
1.0
|
MN
|
D:MN401
|
3.8
|
0.5
|
1.0
|
NE2
|
D:HIS182
|
3.9
|
44.5
|
1.0
|
CB
|
D:ASP142
|
4.0
|
75.6
|
1.0
|
OD1
|
D:ASP142
|
4.1
|
86.5
|
1.0
|
CA
|
D:ASP142
|
4.1
|
58.4
|
1.0
|
O
|
D:LEU141
|
4.1
|
54.4
|
1.0
|
OPP
|
D:PPV403
|
4.2
|
98.8
|
1.0
|
CD2
|
D:HIS182
|
4.4
|
46.1
|
1.0
|
C
|
D:LEU141
|
4.5
|
51.9
|
1.0
|
N
|
D:ASP142
|
4.6
|
49.9
|
1.0
|
CA
|
D:GLY180
|
4.7
|
53.3
|
1.0
|
CB
|
D:SER176
|
4.8
|
50.6
|
1.0
|
NH2
|
D:ARG179
|
4.8
|
0.2
|
1.0
|
CB
|
D:ASP140
|
4.8
|
52.8
|
1.0
|
OG
|
D:SER176
|
4.9
|
46.2
|
1.0
|
O11
|
D:PPV403
|
5.0
|
0.5
|
1.0
|
|
Reference:
N.C.Brissett,
K.Zabrady,
P.Plocinski,
J.Bianchi,
M.Korycka-Machala,
A.Brzostek,
J.Dziadek,
A.J.Doherty.
Molecular Basis For Dna Repair Synthesis on Short Gaps By Mycobacterial Primase-Polymerase C. Nat Commun V. 11 4196 2020.
ISSN: ESSN 2041-1723
PubMed: 32826907
DOI: 10.1038/S41467-020-18012-8
Page generated: Sun Oct 6 07:06:37 2024
|