Chlorine 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:

Copper (Cu) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp, PDB code: 8dcf:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8dcf

Go back to Chlorine Binding Sites List in 8dcf
Chlorine binding site 1 out of 2 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl615

b:63.8
occ:0.87
ND1 A:HIS301 2.7 63.3 0.8
O A:HOH756 3.4 67.3 1.0
CD A:ARG304 3.5 51.2 1.0
N A:GLY161 3.5 55.5 1.0
CA A:GLY161 3.6 53.5 0.6
NH1 A:ARG304 3.6 43.8 0.8
CE1 A:HIS301 3.6 60.6 1.0
CG A:HIS301 3.6 58.4 1.0
CA A:HIS301 3.7 49.5 1.0
CB A:HIS301 3.9 52.9 1.0
NE1 A:TRP162 3.9 53.3 0.9
C A:GLY161 4.2 53.2 1.0
CD1 A:TRP162 4.3 57.6 0.9
CB A:ARG304 4.4 52.0 1.0
NE A:ARG304 4.5 55.8 1.0
CZ A:ARG304 4.5 52.7 1.0
C A:TYR160 4.5 51.0 1.0
O A:HIS301 4.5 48.5 1.0
CG A:ARG304 4.6 55.6 1.0
CE2 A:TRP162 4.6 52.7 1.0
N A:HIS301 4.6 49.7 1.0
C A:HIS301 4.7 50.3 0.8
O A:GLY161 4.7 56.5 1.0
NE2 A:HIS301 4.7 61.3 0.7
CD2 A:HIS301 4.8 52.7 1.0
N A:TRP162 4.9 57.2 1.0

Chlorine binding site 2 out of 2 in 8dcf

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl516

b:55.3
occ:0.81
ND1 B:HIS301 2.9 60.0 1.0
CA B:GLY161 3.4 58.6 1.0
CD B:ARG304 3.4 44.0 1.0
NH1 B:ARG304 3.5 49.1 1.0
NE1 B:TRP162 3.6 55.9 1.0
N B:GLY161 3.7 58.5 1.0
CE1 B:HIS301 3.9 61.4 1.0
CA B:HIS301 3.9 43.5 1.0
CG B:HIS301 3.9 61.9 1.0
CD1 B:TRP162 4.0 54.8 1.0
CB B:HIS301 4.1 47.5 1.0
C B:GLY161 4.3 54.5 1.0
CB B:ARG304 4.3 45.6 1.0
CE2 B:TRP162 4.3 56.0 1.0
NE B:ARG304 4.4 49.0 1.0
CZ B:ARG304 4.4 49.3 1.0
CG B:ARG304 4.5 51.7 1.0
O B:HIS301 4.5 50.4 1.0
C B:TYR160 4.6 53.9 1.0
C B:HIS301 4.7 54.5 1.0
N B:HIS301 4.8 45.9 1.0
O B:GLY161 4.8 52.6 1.0
N B:TRP162 4.9 56.6 1.0
CZ2 B:TRP162 4.9 55.1 1.0
CG B:TRP162 4.9 58.2 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 22:44:21 2023

Last articles

Cl in 3SXS
Cl in 3SWW
Cl in 3SXR
Cl in 3SXQ
Cl in 3SW8
Cl in 3SW2
Cl in 3SVT
Cl in 3SVP
Cl in 3SVK
Cl in 3STG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy