Zinc in PDB 8dcd: Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp
Enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp
All present enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp:
6.5.1.8;
Protein crystallography data
The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp, PDB code: 8dcd
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)
|
49.27 /
2.22
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.91,
136.473,
150.065,
90,
90,
90
|
R / Rfree (%)
|
17 /
19.7
|
Other elements in 8dcd:
The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp
(pdb code 8dcd). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp, PDB code: 8dcd:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8dcd
Go back to
Zinc Binding Sites List in 8dcd
Zinc binding site 1 out
of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp
![](/pictures/ZN/pdb/dc/8dcd-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/dc/8dcd-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn513
b:44.2
occ:0.86
|
O
|
A:HOH606
|
2.2
|
43.1
|
1.0
|
O2A
|
A:GTP501
|
2.2
|
34.4
|
0.8
|
NE2
|
A:HIS329
|
2.3
|
40.9
|
1.0
|
NE2
|
A:HIS234
|
2.3
|
34.4
|
1.0
|
O1B
|
A:GTP501
|
2.3
|
39.9
|
0.8
|
SG
|
A:CYS98
|
2.3
|
39.5
|
1.0
|
CE1
|
A:HIS234
|
3.1
|
36.9
|
1.0
|
CE1
|
A:HIS329
|
3.2
|
41.7
|
1.0
|
CD2
|
A:HIS329
|
3.3
|
42.6
|
1.0
|
CD2
|
A:HIS234
|
3.4
|
40.6
|
1.0
|
CB
|
A:CYS98
|
3.5
|
38.4
|
1.0
|
PB
|
A:GTP501
|
3.5
|
40.7
|
0.8
|
PA
|
A:GTP501
|
3.6
|
42.5
|
0.8
|
ZN
|
A:ZN514
|
3.6
|
42.4
|
0.7
|
O3B
|
A:GTP501
|
3.8
|
46.0
|
0.8
|
O3A
|
A:GTP501
|
4.0
|
49.6
|
0.8
|
O1G
|
A:GTP501
|
4.1
|
45.5
|
0.8
|
O5'
|
A:GTP501
|
4.3
|
45.7
|
0.8
|
ND1
|
A:HIS234
|
4.3
|
36.4
|
1.0
|
ND1
|
A:HIS329
|
4.3
|
44.3
|
1.0
|
O
|
A:HOH673
|
4.4
|
46.7
|
0.9
|
PG
|
A:GTP501
|
4.4
|
59.3
|
0.8
|
CG
|
A:HIS329
|
4.4
|
41.0
|
1.0
|
CG
|
A:HIS234
|
4.5
|
34.2
|
1.0
|
C
|
A:CYS98
|
4.5
|
39.3
|
1.0
|
O2G
|
A:GTP501
|
4.5
|
42.3
|
0.8
|
CA
|
A:CYS98
|
4.5
|
38.8
|
1.0
|
C5'
|
A:GTP501
|
4.6
|
45.8
|
0.8
|
N
|
A:GLY99
|
4.6
|
33.8
|
1.0
|
CD2
|
A:HIS404
|
4.7
|
41.9
|
1.0
|
O1A
|
A:GTP501
|
4.7
|
44.1
|
0.8
|
O2B
|
A:GTP501
|
4.8
|
42.7
|
0.8
|
CD2
|
A:HIS203
|
4.9
|
40.4
|
1.0
|
NE2
|
A:HIS203
|
4.9
|
41.0
|
1.0
|
O
|
A:CYS98
|
4.9
|
36.5
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8dcd
Go back to
Zinc Binding Sites List in 8dcd
Zinc binding site 2 out
of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp
![](/pictures/ZN/pdb/dc/8dcd-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/dc/8dcd-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn514
b:42.4
occ:0.73
|
O1G
|
A:GTP501
|
1.8
|
45.5
|
0.8
|
OD2
|
A:ASP95
|
2.0
|
42.9
|
1.0
|
NE2
|
A:HIS203
|
2.2
|
41.0
|
1.0
|
SG
|
A:CYS98
|
2.3
|
39.5
|
1.0
|
O1B
|
A:GTP501
|
2.7
|
39.9
|
0.8
|
CG
|
A:ASP95
|
3.0
|
40.1
|
1.0
|
CB
|
A:CYS98
|
3.1
|
38.4
|
1.0
|
CE1
|
A:HIS203
|
3.2
|
39.1
|
1.0
|
CD2
|
A:HIS203
|
3.2
|
40.4
|
1.0
|
PG
|
A:GTP501
|
3.2
|
59.3
|
0.8
|
CB
|
A:ASP95
|
3.6
|
36.0
|
1.0
|
ZN
|
A:ZN513
|
3.6
|
44.2
|
0.9
|
O
|
A:HOH606
|
3.6
|
43.1
|
1.0
|
PB
|
A:GTP501
|
3.6
|
40.7
|
0.8
|
O3B
|
A:GTP501
|
3.9
|
46.0
|
0.8
|
O2B
|
A:GTP501
|
3.9
|
42.7
|
0.8
|
O2G
|
A:GTP501
|
3.9
|
42.3
|
0.8
|
OD1
|
A:ASP95
|
4.0
|
41.2
|
1.0
|
O3G
|
A:GTP501
|
4.3
|
56.4
|
0.8
|
O
|
A:HOH652
|
4.3
|
36.4
|
1.0
|
ND1
|
A:HIS203
|
4.3
|
45.2
|
1.0
|
CA
|
A:CYS98
|
4.3
|
38.8
|
1.0
|
CG
|
A:HIS203
|
4.4
|
40.8
|
1.0
|
N
|
A:GLY236
|
4.5
|
36.4
|
1.0
|
O2
|
A:SO4504
|
4.5
|
55.7
|
0.8
|
NE2
|
A:HIS234
|
4.5
|
34.4
|
1.0
|
CA
|
A:GLY236
|
4.8
|
31.1
|
1.0
|
C
|
A:THR235
|
4.8
|
39.0
|
1.0
|
CA
|
A:THR235
|
5.0
|
40.7
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8dcd
Go back to
Zinc Binding Sites List in 8dcd
Zinc binding site 3 out
of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp
![](/pictures/ZN/pdb/dc/8dcd-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/dc/8dcd-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn509
b:44.4
occ:0.78
|
O2B
|
B:GTP501
|
1.8
|
51.6
|
0.9
|
NE2
|
B:HIS234
|
2.2
|
42.2
|
1.0
|
NE2
|
B:HIS329
|
2.3
|
39.0
|
1.0
|
SG
|
B:CYS98
|
2.3
|
38.5
|
1.0
|
PB
|
B:GTP501
|
2.5
|
71.2
|
0.9
|
O1B
|
B:GTP501
|
2.9
|
70.4
|
0.9
|
O3B
|
B:GTP501
|
2.9
|
63.1
|
0.9
|
CE1
|
B:HIS234
|
3.0
|
38.3
|
1.0
|
CD2
|
B:HIS329
|
3.2
|
38.5
|
1.0
|
CD2
|
B:HIS234
|
3.3
|
36.6
|
1.0
|
ZN
|
B:ZN510
|
3.3
|
42.5
|
0.7
|
CE1
|
B:HIS329
|
3.3
|
47.0
|
1.0
|
CB
|
B:CYS98
|
3.3
|
30.1
|
1.0
|
O1G
|
B:GTP501
|
3.7
|
45.5
|
0.9
|
PG
|
B:GTP501
|
4.0
|
63.3
|
0.9
|
O3A
|
B:GTP501
|
4.0
|
61.0
|
0.9
|
O5'
|
B:GTP501
|
4.1
|
56.3
|
0.9
|
ND1
|
B:HIS234
|
4.2
|
42.1
|
1.0
|
C
|
B:CYS98
|
4.3
|
39.9
|
1.0
|
CG
|
B:HIS329
|
4.4
|
42.9
|
1.0
|
CG
|
B:HIS234
|
4.4
|
40.8
|
1.0
|
ND1
|
B:HIS329
|
4.4
|
43.8
|
1.0
|
CA
|
B:CYS98
|
4.4
|
33.9
|
1.0
|
N
|
B:GLY99
|
4.5
|
34.2
|
1.0
|
CD2
|
B:HIS203
|
4.6
|
41.5
|
1.0
|
NE2
|
B:HIS203
|
4.6
|
42.0
|
1.0
|
C5'
|
B:GTP501
|
4.6
|
48.7
|
0.9
|
O
|
B:CYS98
|
4.7
|
38.5
|
1.0
|
PA
|
B:GTP501
|
4.7
|
55.1
|
0.9
|
O2G
|
B:GTP501
|
4.7
|
69.6
|
0.9
|
CD2
|
B:HIS404
|
4.8
|
48.6
|
1.0
|
ND2
|
B:ASN330
|
4.9
|
39.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8dcd
Go back to
Zinc Binding Sites List in 8dcd
Zinc binding site 4 out
of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp
![](/pictures/ZN/pdb/dc/8dcd-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/dc/8dcd-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn510
b:42.5
occ:0.71
|
O1G
|
B:GTP501
|
1.9
|
45.5
|
0.9
|
OD2
|
B:ASP95
|
2.1
|
42.5
|
1.0
|
NE2
|
B:HIS203
|
2.2
|
42.0
|
1.0
|
SG
|
B:CYS98
|
2.3
|
38.5
|
1.0
|
CG
|
B:ASP95
|
3.0
|
41.1
|
1.0
|
CB
|
B:CYS98
|
3.1
|
30.1
|
1.0
|
CE1
|
B:HIS203
|
3.2
|
39.7
|
1.0
|
CD2
|
B:HIS203
|
3.2
|
41.5
|
1.0
|
PG
|
B:GTP501
|
3.2
|
63.3
|
0.9
|
ZN
|
B:ZN509
|
3.3
|
44.4
|
0.8
|
O1B
|
B:GTP501
|
3.6
|
70.4
|
0.9
|
CB
|
B:ASP95
|
3.6
|
38.9
|
1.0
|
O3B
|
B:GTP501
|
3.6
|
63.1
|
0.9
|
OD1
|
B:ASP95
|
4.0
|
38.2
|
1.0
|
PB
|
B:GTP501
|
4.1
|
71.2
|
0.9
|
O2G
|
B:GTP501
|
4.2
|
69.6
|
0.9
|
O3G
|
B:GTP501
|
4.2
|
69.5
|
0.9
|
ND1
|
B:HIS203
|
4.3
|
40.8
|
1.0
|
CG
|
B:HIS203
|
4.3
|
42.5
|
1.0
|
O
|
B:HOH648
|
4.3
|
37.9
|
1.0
|
CA
|
B:CYS98
|
4.4
|
33.9
|
1.0
|
N
|
B:GLY236
|
4.4
|
41.9
|
1.0
|
ND2
|
B:ASN202
|
4.5
|
54.8
|
1.0
|
NE2
|
B:HIS234
|
4.5
|
42.2
|
1.0
|
O2B
|
B:GTP501
|
4.6
|
51.6
|
0.9
|
O4
|
B:SO4503
|
4.6
|
48.5
|
0.9
|
CA
|
B:GLY236
|
4.7
|
31.8
|
1.0
|
C
|
B:THR235
|
4.7
|
37.9
|
1.0
|
CE1
|
B:HIS234
|
4.9
|
38.3
|
1.0
|
CA
|
B:THR235
|
4.9
|
36.7
|
1.0
|
ND2
|
B:ASN330
|
4.9
|
39.6
|
1.0
|
O
|
B:ASP95
|
5.0
|
43.1
|
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: Sat Apr 8 08:11:38 2023
|