Manganese in PDB 8dc9: Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp

Enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp

All present enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp:
6.5.1.8;

Protein crystallography data

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp, PDB code: 8dc9 was solved by A.Jacewicz, S.Dantuluri, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 2.47
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.741, 137.284, 150.157, 90, 90, 90
R / Rfree (%) 18.3 / 21.8

Other elements in 8dc9:

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp (pdb code 8dc9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp, PDB code: 8dc9:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 8dc9

Go back to Manganese Binding Sites List in 8dc9
Manganese binding site 1 out of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn513

b:64.0
occ:0.91
 OD2 A:ASP95 2.0 53.7 1.0
NE2 A:HIS203 2.4 56.4 1.0
SG A:CYS98 2.5 57.8 1.0
O3B A:GTP501 2.9 76.3 0.8
O3G A:GTP501 2.9 57.2 0.8
CG A:ASP95 3.0 54.2 1.0
CE1 A:HIS203 3.0 44.8 1.0
CB A:CYS98 3.1 48.5 1.0
O1G A:GTP501 3.1 60.9 0.8
PG A:GTP501 3.1 78.8 0.8
CB A:ASP95 3.5 41.8 1.0
CD2 A:HIS203 3.5 55.9 1.0
O1B A:GTP501 3.5 69.4 0.8
MN A:MN514 3.6 66.9 1.0
PB A:GTP501 3.6 72.0 0.8
OD1 A:ASP95 4.0 50.6 1.0
O2B A:GTP501 4.1 80.1 0.8
ND1 A:HIS203 4.2 52.3 1.0
CA A:CYS98 4.3 53.1 1.0
CG A:HIS203 4.4 55.7 1.0
O2 A:SO4503 4.5 76.7 1.0
O2G A:GTP501 4.6 74.4 0.8
NE2 A:HIS234 4.9 59.1 1.0
N A:GLY236 4.9 41.6 1.0
CA A:ASP95 5.0 51.0 1.0

Manganese binding site 2 out of 4 in 8dc9

Go back to Manganese Binding Sites List in 8dc9
Manganese binding site 2 out of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn514

b:66.9
occ:1.00
 SG A:CYS98 2.3 57.8 1.0
O2A A:GTP501 2.5 54.6 0.8
NE2 A:HIS234 2.5 59.1 1.0
O3B A:GTP501 2.6 76.3 0.8
NE2 A:HIS329 2.6 61.3 1.0
CE1 A:HIS234 3.1 52.6 1.0
CD2 A:HIS329 3.3 58.4 1.0
CB A:CYS98 3.4 48.5 1.0
O1B A:GTP501 3.5 69.4 0.8
O1G A:GTP501 3.6 60.9 0.8
PB A:GTP501 3.6 72.0 0.8
MN A:MN513 3.6 64.0 0.9
CD2 A:HIS234 3.7 53.6 1.0
PA A:GTP501 3.7 69.6 0.8
PG A:GTP501 3.7 78.8 0.8
CE1 A:HIS329 3.8 63.5 1.0
O3A A:GTP501 4.0 73.0 0.8
OD1 A:ASN330 4.2 64.9 1.0
C5' A:GTP501 4.3 70.4 0.8
O5' A:GTP501 4.3 73.6 0.8
ND1 A:HIS234 4.3 60.3 1.0
C A:CYS98 4.4 51.9 1.0
CA A:CYS98 4.5 53.1 1.0
O2G A:GTP501 4.6 74.4 0.8
CG A:HIS329 4.6 54.1 1.0
CG A:HIS234 4.6 51.5 1.0
N A:GLY99 4.7 51.3 1.0
CD2 A:HIS404 4.7 55.2 1.0
O A:CYS98 4.8 49.7 1.0
ND1 A:HIS329 4.8 52.8 1.0
O3G A:GTP501 4.8 57.2 0.8
NE2 A:HIS203 4.8 56.4 1.0
O2B A:GTP501 4.9 80.1 0.8
O1A A:GTP501 5.0 57.6 0.8
NE2 A:HIS404 5.0 57.8 1.0

Manganese binding site 3 out of 4 in 8dc9

Go back to Manganese Binding Sites List in 8dc9
Manganese binding site 3 out of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn510

b:61.5
occ:1.00
 O2A B:GTP501 2.2 58.1 0.4
O1B B:GTP501 2.3 54.2 0.3
O3G B:GTP501 2.3 55.2 0.8
SG B:CYS98 2.3 52.0 1.0
NE2 B:HIS329 2.3 60.0 1.0
NE2 B:HIS234 2.5 52.5 1.0
PA B:GTP501 3.0 57.8 0.7
PB B:GTP501 3.2 57.8 0.7
CE1 B:HIS234 3.2 57.1 1.0
O3A B:GTP501 3.2 60.1 0.8
CE1 B:HIS329 3.3 60.2 1.0
CD2 B:HIS329 3.3 58.0 1.0
PG B:GTP501 3.5 55.3 0.5
O5' B:GTP501 3.5 66.1 0.7
CB B:CYS98 3.5 46.5 1.0
MN B:MN511 3.5 54.7 0.8
CD2 B:HIS234 3.6 53.0 1.0
O3B B:GTP501 3.7 60.8 0.6
O2G B:GTP501 4.1 57.7 1.0
ND1 B:HIS329 4.4 54.7 1.0
ND1 B:HIS234 4.4 57.2 1.0
CG B:HIS329 4.4 52.7 1.0
O1A B:GTP501 4.4 70.1 1.0
O2B B:GTP501 4.5 68.2 0.8
C5' B:GTP501 4.5 65.8 0.9
C B:CYS98 4.6 44.8 1.0
CD2 B:HIS404 4.6 61.0 1.0
CG B:HIS234 4.6 49.4 1.0
CA B:CYS98 4.7 45.2 1.0
O1G B:GTP501 4.7 54.5 0.7
NE2 B:HIS203 4.8 57.0 1.0
CD2 B:HIS203 4.8 51.3 1.0
NE2 B:HIS404 4.9 61.0 1.0
N B:GLY99 4.9 46.0 1.0
O B:CYS98 4.9 52.8 1.0

Manganese binding site 4 out of 4 in 8dc9

Go back to Manganese Binding Sites List in 8dc9
Manganese binding site 4 out of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn511

b:54.7
occ:0.77
 O2G B:GTP501 2.2 57.7 1.0
OD2 B:ASP95 2.2 58.2 1.0
NE2 B:HIS203 2.3 57.0 1.0
O1B B:GTP501 2.3 54.2 0.3
SG B:CYS98 2.3 52.0 1.0
CB B:CYS98 2.9 46.5 1.0
CG B:ASP95 3.0 54.1 1.0
O3G B:GTP501 3.1 55.2 0.8
PG B:GTP501 3.1 55.3 0.5
CE1 B:HIS203 3.2 44.6 1.0
CD2 B:HIS203 3.3 51.3 1.0
MN B:MN510 3.5 61.5 1.0
PB B:GTP501 3.5 57.8 0.7
CB B:ASP95 3.6 41.4 1.0
O3B B:GTP501 3.9 60.8 0.6
OD1 B:ASP95 3.9 48.3 1.0
O2B B:GTP501 4.1 68.2 0.8
CA B:CYS98 4.1 45.2 1.0
ND1 B:HIS203 4.3 57.2 1.0
O1G B:GTP501 4.4 54.5 0.7
CG B:HIS203 4.4 61.0 1.0
NE2 B:HIS234 4.6 52.5 1.0
N B:GLY236 4.6 40.6 1.0
O3 B:SO4502 4.8 57.8 0.9
CA B:GLY236 4.8 43.6 1.0
O3A B:GTP501 4.8 60.1 0.8
C B:THR235 4.9 49.3 1.0
O2A B:GTP501 4.9 58.1 0.4
O B:ASP95 4.9 50.5 1.0

Reference:

A.Jacewicz, S.Dantuluri, S.Shuman. Structures of Rna Ligase Rtcb in Complexes with Divalent Cations and Gtp. Rna V. 28 1509 2022.
ISSN: ESSN 1469-9001
PubMed: 36130078
DOI: 10.1261/RNA.079327.122
Page generated: Fri Apr 7 13:25:20 2023

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