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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: Wed Jul 31 09:37:15 2024

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