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Manganese in PDB 4x4o: Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp

Enzymatic activity of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp

All present enzymatic activity of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp:
2.7.7.72;

Protein crystallography data

The structure of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp, PDB code: 4x4o was solved by C.-D.Kuhn, L.Joshua-Tor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.68 / 3.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.059, 215.602, 58.629, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp (pdb code 4x4o). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp, PDB code: 4x4o:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4x4o

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Manganese binding site 1 out of 8 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:81.9
occ:1.00
 OE1 A:GLU59 2.0 94.3 1.0
O2G A:CTP501 2.2 0.3 1.0
O1A A:CTP501 2.2 89.7 1.0
O1B A:CTP501 2.5 0.7 1.0
OD2 A:ASP61 2.5 0.5 1.0
CD A:GLU59 3.2 0.4 1.0
HB3 A:GLU59 3.3 0.8 1.0
PG A:CTP501 3.4 94.4 1.0
CG A:ASP61 3.4 99.7 1.0
PB A:CTP501 3.5 0.8 1.0
H A:SER47 3.5 0.8 1.0
PA A:CTP501 3.6 91.4 1.0
OD1 A:ASP61 3.7 91.1 1.0
O A:GLU59 3.7 96.3 1.0
O3B A:CTP501 3.7 99.5 1.0
OG A:SER47 3.9 0.4 1.0
O3A A:CTP501 4.0 0.8 1.0
HG A:SER47 4.0 0.3 1.0
OE2 A:GLU59 4.1 0.6 1.0
CB A:GLU59 4.1 95.7 1.0
CG A:GLU59 4.2 99.0 1.0
HA3 A:GLY46 4.2 1.0 1.0
O1G A:CTP501 4.3 0.7 1.0
N A:SER47 4.3 1.0 1.0
O3G A:CTP501 4.4 93.3 1.0
HB3 A:SER47 4.4 0.1 1.0
HG3 A:GLU59 4.4 0.8 1.0
O2A A:CTP501 4.4 94.8 1.0
O5' A:CTP501 4.5 94.8 1.0
C A:GLU59 4.5 92.7 1.0
O2B A:CTP501 4.7 98.9 1.0
CB A:SER47 4.7 0.5 1.0
H A:ASP61 4.7 0.8 1.0
HA2 A:GLY46 4.7 1.0 1.0
H5'2 A:CTP501 4.7 0.0 1.0
HB2 A:GLU59 4.7 0.8 1.0
CB A:ASP61 4.8 0.2 1.0
HB2 A:ASP61 4.8 0.4 1.0
CA A:GLY46 4.9 0.6 1.0
O2 A:CTP501 4.9 99.4 1.0
CA A:GLU59 4.9 91.7 1.0
HG2 A:GLU59 5.0 0.8 1.0

Manganese binding site 2 out of 8 in 4x4o

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Manganese binding site 2 out of 8 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn101

b:94.2
occ:1.00
 O4 B:U14 2.3 98.1 1.0
OP2 B:U13 2.7 0.6 1.0
H5 B:U14 3.2 0.4 1.0
C4 B:U14 3.2 91.9 1.0
C5 B:U14 3.6 91.2 1.0
H5 B:U13 3.9 0.5 1.0
P B:U13 4.1 0.6 1.0
H3' B:G12 4.3 0.1 1.0
N3 B:U14 4.5 83.2 1.0
H3 B:U14 4.7 99.9 1.0
C5 B:U13 4.7 98.8 1.0
O5' B:U13 4.7 89.2 1.0
O5' B:G12 4.8 0.8 1.0
H6 B:U13 4.8 0.9 1.0
OP2 B:G12 4.9 98.8 1.0
OP1 B:U13 4.9 0.8 1.0
C6 B:U14 4.9 84.8 1.0

Manganese binding site 3 out of 8 in 4x4o

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Manganese binding site 3 out of 8 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn102

b:80.3
occ:1.00
 N7 B:G1 2.3 80.2 1.0
C8 B:G1 3.2 77.6 1.0
C5 B:G1 3.3 74.0 1.0
H8 B:G1 3.3 93.1 1.0
O6 B:G1 3.5 77.2 1.0
OP2 B:G1 3.6 81.6 1.0
C6 B:G1 3.7 74.3 1.0
N9 B:G1 4.4 69.8 1.0
C4 B:G1 4.4 77.4 1.0
O5' B:G1 4.7 82.6 1.0
P B:G1 4.8 90.5 1.0
O6 B:G2 4.8 69.5 1.0
N7 B:G2 5.0 68.2 1.0

Manganese binding site 4 out of 8 in 4x4o

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Manganese binding site 4 out of 8 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn502

b:46.2
occ:1.00
 OD2 C:ASP61 2.1 50.7 1.0
O1B C:CTP501 2.1 50.2 1.0
O2A C:CTP501 2.3 52.9 1.0
O2G C:CTP501 2.4 51.7 1.0
CG C:ASP61 3.0 50.1 1.0
PB C:CTP501 3.3 50.7 1.0
HB3 C:GLU59 3.3 71.0 1.0
OD1 C:ASP61 3.3 54.2 1.0
OE1 C:GLU59 3.4 67.7 1.0
PG C:CTP501 3.5 47.6 1.0
PA C:CTP501 3.5 52.2 1.0
H C:SER47 3.6 56.4 1.0
O3B C:CTP501 3.7 49.9 1.0
O C:GLU59 3.7 50.5 1.0
O3A C:CTP501 3.8 55.0 1.0
OG C:SER47 4.1 53.9 1.0
HG C:SER47 4.2 64.6 1.0
HA3 C:GLY46 4.2 57.8 1.0
CB C:GLU59 4.2 59.2 1.0
HG2 C:GLU59 4.2 72.8 1.0
CD C:GLU59 4.3 73.9 1.0
CB C:ASP61 4.4 42.5 1.0
O2B C:CTP501 4.4 49.0 1.0
O3G C:CTP501 4.4 43.6 1.0
HB2 C:ASP61 4.4 51.0 1.0
N C:SER47 4.4 47.0 1.0
O5' C:CTP501 4.5 56.7 1.0
CG C:GLU59 4.5 60.7 1.0
O1A C:CTP501 4.5 51.4 1.0
H C:ASP61 4.5 54.6 1.0
C C:GLU59 4.5 50.5 1.0
O1G C:CTP501 4.6 48.5 1.0
H5'1 C:CTP501 4.6 73.7 1.0
HB3 C:SER47 4.8 56.7 1.0
HB2 C:GLU59 4.8 71.0 1.0
HA2 C:GLY46 4.9 57.8 1.0
N C:ASP61 4.9 45.5 1.0
CA C:GLY46 4.9 48.1 1.0
CB C:SER47 4.9 47.3 1.0
H C:TYR48 4.9 44.8 1.0
CA C:GLU59 5.0 58.7 1.0
HB3 C:ASP61 5.0 51.0 1.0

Manganese binding site 5 out of 8 in 4x4o

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Manganese binding site 5 out of 8 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn102

b:92.1
occ:1.00
 N7 D:G11 2.7 74.5 1.0
H8 D:G11 3.4 94.2 1.0
C8 D:G11 3.5 78.5 1.0
C5 D:G11 3.9 79.0 1.0
O6 D:G11 4.2 79.6 1.0
OP2 D:G11 4.3 79.8 1.0
C6 D:G11 4.5 78.7 1.0
N9 D:G11 4.7 81.9 1.0
O6 D:G12 4.9 92.8 1.0
H5'' D:G11 4.9 94.8 1.0
C4 D:G11 5.0 82.4 1.0

Manganese binding site 6 out of 8 in 4x4o

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Manganese binding site 6 out of 8 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn103

b:0.8
occ:1.00
 O4 D:U14 2.5 1.0 1.0
OP2 D:U13 2.8 89.0 1.0
H5 D:U14 3.2 0.4 1.0
C4 D:U14 3.3 97.0 1.0
H5 D:U13 3.3 0.7 1.0
C5 D:U14 3.6 92.8 1.0
H3' D:G12 4.1 0.1 1.0
C5 D:U13 4.2 83.9 1.0
OP2 D:G12 4.2 65.4 1.0
P D:U13 4.3 90.5 1.0
O5' D:G12 4.5 73.4 1.0
H6 D:U13 4.6 99.2 1.0
N3 D:U14 4.6 92.4 1.0
P D:G12 4.8 69.4 1.0
C6 D:U13 4.8 82.7 1.0
O5' D:U13 4.8 90.8 1.0
H3 D:U14 4.8 0.8 1.0
C6 D:U14 4.9 90.4 1.0
OP1 D:G12 5.0 78.3 1.0
C3' D:G12 5.0 86.0 1.0

Manganese binding site 7 out of 8 in 4x4o

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Manganese binding site 7 out of 8 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn104

b:99.8
occ:1.00
 HD2 C:TYR94 2.9 0.2 1.0
O2 D:CTP101 3.1 98.8 1.0
HB3 C:TYR94 3.1 82.3 1.0
H1' D:G1 3.3 82.2 1.0
N9 D:G1 3.5 66.8 1.0
CD2 C:TYR94 3.6 86.8 1.0
C1' D:G1 3.7 68.5 1.0
C4 D:G1 3.8 69.7 1.0
C2 D:CTP101 3.8 0.5 1.0
O4' D:G1 3.9 74.2 1.0
CB C:TYR94 3.9 68.6 1.0
C8 D:G1 3.9 75.9 1.0
HB2 C:TYR94 4.1 82.3 1.0
N3 D:G1 4.1 69.8 1.0
H1' D:CTP101 4.1 0.6 1.0
CG C:TYR94 4.2 76.1 1.0
C5 D:G1 4.2 74.4 1.0
H8 D:G1 4.3 91.0 1.0
N3 D:CTP101 4.3 99.1 1.0
N7 D:G1 4.4 77.6 1.0
N1 D:CTP101 4.6 0.1 1.0
CE2 C:TYR94 4.6 87.1 1.0
HE2 C:TYR94 4.6 0.5 1.0
C1' D:CTP101 4.8 0.5 1.0
O1B D:CTP101 4.8 95.5 1.0
HD21 C:ASN292 4.9 79.7 1.0
C2 D:G1 4.9 63.7 1.0
H C:GLU96 5.0 95.8 1.0

Manganese binding site 8 out of 8 in 4x4o

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Manganese binding site 8 out of 8 in the Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of the A.Fulgidus Cca-Adding Enzyme in Complex with A G70A Arginyl-Trna Minihelix and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn105

b:0.6
occ:1.00
 H5'1 D:CTP101 2.5 0.9 1.0
H6 D:CTP101 3.1 0.7 1.0
H5'2 D:CTP101 3.2 0.9 1.0
C5' D:CTP101 3.2 0.3 1.0
H5 D:CTP101 3.7 0.1 1.0
O5' D:CTP101 3.7 0.1 1.0
C6 D:CTP101 3.9 0.1 1.0
O1A D:CTP101 4.0 0.5 1.0
OP2 D:G1 4.0 88.8 1.0
C5 D:CTP101 4.2 0.9 1.0
PA D:CTP101 4.3 0.5 1.0
C4' D:CTP101 4.5 0.4 1.0
O3A D:CTP101 4.6 0.8 1.0
O4' D:CTP101 4.7 1.0 1.0
H3' D:CTP101 4.9 0.3 1.0

Reference:

C.-D.Kuhn, J.E.Wilusz, Y.Zheng, P.A.Beal, L.Joshua-Tor. On-Enzyme Refolding Permits Small Rna and Trna Surveillance By the Cca-Adding Enzyme To Be Published.
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