Atomistry » Manganese » PDB 8awx-8djy » 8dc9
Atomistry »
  Manganese »
    PDB 8awx-8djy »
      8dc9 »

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: Sun Oct 6 11:30:45 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy