Atomistry » Chlorine » PDB 2c5u-2chw » 2c5u
Atomistry »
  Chlorine »
    PDB 2c5u-2chw »
      2c5u »

Chlorine in PDB 2c5u: T4 Rna Ligase (RNL1) Crystal Structure

Enzymatic activity of T4 Rna Ligase (RNL1) Crystal Structure

All present enzymatic activity of T4 Rna Ligase (RNL1) Crystal Structure:
6.5.1.3;

Protein crystallography data

The structure of T4 Rna Ligase (RNL1) Crystal Structure, PDB code: 2c5u was solved by K.El Omari, J.Ren, L.E.Bird, M.K.Bona, G.Klarmann, S.F.J.Legrice, D.K.Stammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.78 / 2.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.050, 39.870, 108.540, 90.00, 117.27, 90.00
R / Rfree (%) 19.8 / 25.8

Other elements in 2c5u:

The structure of T4 Rna Ligase (RNL1) Crystal Structure also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Calcium (Ca) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the T4 Rna Ligase (RNL1) Crystal Structure (pdb code 2c5u). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the T4 Rna Ligase (RNL1) Crystal Structure, PDB code: 2c5u:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 2c5u

Go back to Chlorine Binding Sites List in 2c5u
Chlorine binding site 1 out of 3 in the T4 Rna Ligase (RNL1) Crystal Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of T4 Rna Ligase (RNL1) Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1378

b:24.6
occ:1.00
O A:HOH2369 3.1 18.4 1.0
O3' A:APC1375 3.1 17.4 1.0
N A:LEU104 3.3 14.8 1.0
O A:HOH2193 3.4 13.3 1.0
NH2 A:ARG54 3.5 19.0 1.0
O2' A:APC1375 3.5 15.1 1.0
CB A:LEU104 3.5 11.7 1.0
O A:HOH2148 3.8 27.0 1.0
CA A:LEU104 4.0 12.4 1.0
C3' A:APC1375 4.1 18.3 1.0
CA A:SER103 4.2 14.9 1.0
C A:SER103 4.2 16.0 1.0
C4' A:APC1375 4.3 22.1 1.0
C2' A:APC1375 4.4 16.6 1.0
CZ A:ARG54 4.5 28.2 1.0
NH1 A:ARG54 4.7 23.3 1.0
O A:GLY102 4.7 19.0 1.0
CA A:CA1376 4.8 22.2 1.0
O A:HOH2371 4.8 26.0 1.0
CG A:LEU104 4.9 16.9 1.0

Chlorine binding site 2 out of 3 in 2c5u

Go back to Chlorine Binding Sites List in 2c5u
Chlorine binding site 2 out of 3 in the T4 Rna Ligase (RNL1) Crystal Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of T4 Rna Ligase (RNL1) Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1379

b:55.5
occ:1.00
N A:ALA27 3.7 31.1 1.0
CD2 A:LEU115 3.8 38.1 1.0
O A:HOH2154 4.0 41.4 1.0
O A:HOH2162 4.0 21.7 1.0
OH A:TYR108 4.0 24.3 1.0
CB A:ALA27 4.1 33.4 1.0
CB A:SER26 4.1 25.0 1.0
CA A:SER26 4.3 35.4 1.0
O A:ILE122 4.5 23.1 1.0
C A:SER26 4.5 36.5 1.0
CA A:ALA27 4.5 33.5 1.0
CD1 A:ILE122 4.7 19.9 1.0
CG A:LEU115 4.7 37.1 1.0
ND2 A:ASN131 4.9 22.8 1.0
O A:HOH2170 5.0 28.8 1.0

Chlorine binding site 3 out of 3 in 2c5u

Go back to Chlorine Binding Sites List in 2c5u
Chlorine binding site 3 out of 3 in the T4 Rna Ligase (RNL1) Crystal Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of T4 Rna Ligase (RNL1) Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1380

b:20.3
occ:1.00
O B:HOH2354 3.0 23.4 1.0
O3' B:APC1375 3.1 17.2 1.0
NH2 B:ARG54 3.4 19.1 1.0
O B:HOH2197 3.4 20.6 1.0
N B:LEU104 3.5 16.8 1.0
O2' B:APC1375 3.7 18.1 1.0
CB B:LEU104 3.7 5.7 1.0
O B:HOH2155 4.0 18.5 1.0
C3' B:APC1375 4.2 8.3 1.0
CA B:LEU104 4.3 14.5 1.0
CA B:SER103 4.3 17.6 1.0
CZ B:ARG54 4.4 25.1 1.0
C4' B:APC1375 4.4 15.5 1.0
C B:SER103 4.4 29.3 1.0
C2' B:APC1375 4.5 12.6 1.0
NH1 B:ARG54 4.5 13.7 1.0
O B:HOH2153 4.6 37.7 1.0
CA B:CA1377 4.8 20.7 1.0
O B:GLY102 4.8 13.9 1.0
C3A B:APC1375 4.9 21.8 1.0

Reference:

K.El Omari, J.Ren, L.E.Bird, M.K.Bona, G.Klarmann, S.F.J.Legrice, D.K.Stammers. Molecular Architecture and Ligand Recognition Determinants For T4 Rna Ligase J.Biol.Chem. V. 281 1573 2006.
ISSN: ISSN 0021-9258
PubMed: 16263720
DOI: 10.1074/JBC.M509658200
Page generated: Sat Dec 12 09:01:51 2020

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