Copper in PDB 8dcf: Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp

Enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp

All present enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp:
6.5.1.8;

Protein crystallography data

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp, PDB code: 8dcf 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) 49.56 / 2.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.105, 137.828, 149.755, 90, 90, 90
R / Rfree (%) 16.5 / 20.4

Other elements in 8dcf:

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp (pdb code 8dcf). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp, PDB code: 8dcf:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 8dcf

Go back to Copper Binding Sites List in 8dcf
Copper binding site 1 out of 6 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu612

b:70.0
occ:0.46
 O A:HOH735 2.1 71.9 1.0
NE2 A:HIS301 2.3 61.3 0.7
OE2 A:GLU305 2.5 74.5 1.0
O A:HOH754 2.5 76.4 1.0
CE1 A:HIS301 3.2 60.6 1.0
CD2 A:HIS301 3.2 52.7 1.0
CD A:GLU305 3.7 72.1 0.5
ND1 A:HIS301 4.3 63.3 0.8
CG A:HIS301 4.4 58.4 1.0
OE1 A:GLU305 4.4 78.0 0.6
CG A:GLU305 4.7 63.4 0.9
O A:GLY159 4.7 59.5 0.7

Copper binding site 2 out of 6 in 8dcf

Go back to Copper Binding Sites List in 8dcf
Copper binding site 2 out of 6 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu613

b:45.1
occ:0.78
 SG A:CYS98 1.9 66.8 1.0
NE2 A:HIS234 2.0 46.8 1.0
NE2 A:HIS329 2.1 44.8 1.0
O2A A:GTP601 2.8 65.4 0.9
CE1 A:HIS329 2.8 46.1 0.7
CE1 A:HIS234 2.9 48.3 1.0
CD2 A:HIS234 3.0 47.8 1.0
CU A:CU614 3.2 63.7 0.9
CD2 A:HIS329 3.3 44.0 0.7
CB A:CYS98 3.4 48.0 1.0
O1B A:GTP601 3.8 60.4 0.7
N A:GLY99 3.9 45.3 0.8
C A:CYS98 3.9 44.7 0.8
ND1 A:HIS329 4.0 46.9 1.0
O3G A:GTP601 4.0 57.3 0.0
ND1 A:HIS234 4.1 52.4 1.0
PA A:GTP601 4.1 56.2 0.6
CG A:HIS234 4.1 48.1 1.0
O3B A:GTP601 4.2 65.6 0.5
CA A:CYS98 4.2 44.5 0.7
CG A:HIS329 4.3 46.0 0.8
O5' A:GTP601 4.4 59.2 0.5
O A:CYS98 4.4 43.5 0.9
C5' A:GTP601 4.4 54.6 0.7
PB A:GTP601 4.5 56.4 0.6
CA A:GLY99 4.6 36.8 1.0
PG A:GTP601 4.6 79.6 0.8
O3A A:GTP601 4.8 62.7 0.3
O A:GLY99 4.8 36.6 0.8
NE2 A:HIS203 4.9 49.2 1.0
CD2 A:HIS203 4.9 48.3 1.0
C A:GLY99 5.0 44.4 1.0

Copper binding site 3 out of 6 in 8dcf

Go back to Copper Binding Sites List in 8dcf
Copper binding site 3 out of 6 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu614

b:63.7
occ:0.86
 SG A:CYS98 2.1 66.8 1.0
NE2 A:HIS203 2.2 49.2 1.0
O3G A:GTP601 2.3 57.3 0.0
OD2 A:ASP95 2.9 48.8 0.7
O1B A:GTP601 3.0 60.4 0.7
CD2 A:HIS203 3.0 48.3 1.0
CB A:CYS98 3.1 48.0 1.0
CU A:CU613 3.2 45.1 0.8
CE1 A:HIS203 3.3 50.3 1.0
PG A:GTP601 3.7 79.6 0.8
CG A:ASP95 3.7 44.2 0.7
NE2 A:HIS234 3.9 46.8 1.0
CA A:CYS98 4.0 44.5 0.7
O3B A:GTP601 4.0 65.6 0.5
PB A:GTP601 4.1 56.4 0.6
CG A:HIS203 4.2 52.1 1.0
CE1 A:HIS234 4.2 48.3 1.0
ND1 A:HIS203 4.3 51.4 0.5
CB A:ASP95 4.4 41.0 1.0
N A:GLY236 4.4 38.2 0.8
O A:HOH708 4.4 43.5 0.8
C A:THR235 4.4 38.5 1.0
OD1 A:ASP95 4.5 42.7 0.9
O1G A:GTP601 4.5 62.2 0.6
CA A:THR235 4.6 41.6 0.8
O2G A:GTP601 4.6 48.5 0.6
CD2 A:HIS234 4.6 47.8 1.0
CA A:GLY236 4.7 39.8 1.0
O2A A:GTP601 4.7 65.4 0.9
C A:CYS98 4.8 44.7 0.8
O A:THR235 4.9 39.2 0.8
N A:GLY99 4.9 45.3 0.8

Copper binding site 4 out of 6 in 8dcf

Go back to Copper Binding Sites List in 8dcf
Copper binding site 4 out of 6 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu513

b:53.9
occ:1.00
 NE2 B:HIS329 2.1 53.3 1.0
SG B:CYS98 2.1 66.6 1.0
NE2 B:HIS234 2.1 52.7 1.0
O2A B:GTP501 2.7 60.6 0.9
CE1 B:HIS329 3.0 56.4 1.0
CE1 B:HIS234 3.1 46.8 1.0
CD2 B:HIS234 3.1 42.8 1.0
CD2 B:HIS329 3.2 47.6 1.0
O3B B:GTP501 3.2 75.8 0.9
CB B:CYS98 3.3 45.5 1.0
CU B:CU514 3.3 65.2 0.9
O3G B:GTP501 3.6 65.1 0.7
PA B:GTP501 4.1 61.3 0.7
C B:CYS98 4.1 49.8 1.0
PG B:GTP501 4.1 70.4 0.4
ND1 B:HIS329 4.1 55.3 1.0
N B:GLY99 4.1 51.7 1.0
CA B:CYS98 4.2 46.9 1.0
ND1 B:HIS234 4.2 51.3 1.0
CG B:HIS329 4.3 55.0 1.0
CG B:HIS234 4.3 49.7 1.0
PB B:GTP501 4.3 62.8 0.9
C5' B:GTP501 4.4 61.6 1.0
O2B B:GTP501 4.4 67.2 0.5
O5' B:GTP501 4.5 66.5 0.8
O B:CYS98 4.5 50.9 1.0
O3A B:GTP501 4.7 72.0 0.5
NE2 B:HIS203 4.8 53.9 1.0
CD2 B:HIS203 4.8 50.3 1.0
O1G B:GTP501 4.9 75.1 1.0
CA B:GLY99 4.9 46.7 1.0
CD2 B:HIS404 4.9 49.2 1.0
O B:GLY99 5.0 44.5 1.0

Copper binding site 5 out of 6 in 8dcf

Go back to Copper Binding Sites List in 8dcf
Copper binding site 5 out of 6 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu514

b:65.2
occ:0.90
 NE2 B:HIS203 1.9 53.9 1.0
SG B:CYS98 2.0 66.6 1.0
O3B B:GTP501 2.7 75.8 0.9
CD2 B:HIS203 2.9 50.3 1.0
OD2 B:ASP95 2.9 56.6 1.0
CE1 B:HIS203 3.0 42.5 1.0
CB B:CYS98 3.2 45.5 1.0
O3G B:GTP501 3.3 65.1 0.7
CU B:CU513 3.3 53.9 1.0
PG B:GTP501 3.4 70.4 0.4
O2G B:GTP501 3.5 78.3 1.0
O2B B:GTP501 3.6 67.2 0.5
PB B:GTP501 3.7 62.8 0.9
CG B:ASP95 3.8 52.1 1.0
NE2 B:HIS234 4.0 52.7 1.0
CG B:HIS203 4.0 58.7 1.0
ND1 B:HIS203 4.1 57.6 1.0
CA B:CYS98 4.3 46.9 1.0
O1B B:GTP501 4.4 73.2 0.4
CB B:ASP95 4.4 40.3 1.0
N B:GLY236 4.5 41.4 1.0
CE1 B:HIS234 4.5 46.8 1.0
O B:HOH607 4.5 44.8 0.9
OD1 B:ASP95 4.5 51.5 1.0
C B:THR235 4.5 44.8 1.0
CA B:THR235 4.7 43.0 1.0
CA B:GLY236 4.7 35.7 1.0
CD2 B:HIS234 4.7 42.8 1.0
O2A B:GTP501 4.7 60.6 0.9
O1G B:GTP501 4.8 75.1 1.0
O1 B:SO4504 5.0 68.9 1.0

Copper binding site 6 out of 6 in 8dcf

Go back to Copper Binding Sites List in 8dcf
Copper binding site 6 out of 6 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu515

b:65.8
occ:0.65
 NE2 B:HIS301 2.1 68.8 1.0
O B:HOH629 2.2 80.8 1.0
OE2 B:GLU305 2.3 79.2 1.0
O B:HOH643 2.4 83.7 1.0
O B:HOH646 2.4 76.2 1.0
CD2 B:HIS301 3.0 53.4 1.0
CE1 B:HIS301 3.1 61.4 1.0
CD B:GLU305 3.1 80.9 1.0
OE1 B:GLU305 3.5 87.4 1.0
ND1 B:HIS301 4.2 60.0 1.0
CG B:HIS301 4.2 61.9 1.0
CG B:GLU305 4.3 61.7 1.0
O B:HOH649 4.7 65.3 1.0
O B:HOH638 4.8 79.4 1.0
NE1 B:TRP302 4.9 62.9 1.0
O B:GLY159 4.9 66.6 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: Tue Apr 4 23:33:48 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy