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Sodium in PDB 8bgj: Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp

Enzymatic activity of Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp

All present enzymatic activity of Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp:
2.7.7.49;

Protein crystallography data

The structure of Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp, PDB code: 8bgj was solved by A.W.H.Li, A.J.Doherty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.46 / 1.63
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 96.92, 96.92, 65.4, 90, 90, 120
R / Rfree (%) 18.3 / 21.9

Other elements in 8bgj:

The structure of Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp (pdb code 8bgj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp, PDB code: 8bgj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8bgj

Go back to Sodium Binding Sites List in 8bgj
Sodium binding site 1 out of 3 in the Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:22.9
occ:1.00
 O A:HOH438 2.3 20.2 1.0
O A:ASN144 2.3 21.6 1.0
O A:HOH464 2.3 22.1 1.0
O A:ILE147 2.5 16.8 1.0
O A:TYR142 2.8 19.8 1.0
C A:ASN144 3.4 22.6 1.0
C A:ILE147 3.5 20.0 1.0
NH1 A:ARG148 3.5 19.6 1.0
O A:PHE141 3.7 20.6 1.0
C A:TYR142 3.7 19.7 1.0
CD A:ARG148 4.0 17.1 1.0
CG1 A:ILE147 4.1 22.0 1.0
N A:ASN144 4.1 22.2 1.0
CA A:ARG148 4.2 13.5 1.0
O A:HOH441 4.2 23.3 1.0
CZ A:ARG148 4.3 23.4 1.0
CA A:ASN144 4.3 22.2 1.0
N A:ARG148 4.3 17.2 1.0
CA A:TYR142 4.3 19.3 1.0
N A:LYS145 4.3 24.2 1.0
N A:ILE147 4.4 18.7 1.0
CA A:LYS145 4.4 24.2 1.0
NE A:ARG148 4.5 17.1 1.0
CA A:ILE147 4.5 17.0 1.0
C A:LYS143 4.5 23.8 1.0
C A:LYS145 4.7 24.9 1.0
CB A:ASN144 4.7 23.0 1.0
N A:LYS143 4.7 20.6 1.0
C A:PHE141 4.7 19.4 1.0
CG A:ARG148 4.9 17.7 1.0
CA A:LYS143 5.0 20.8 1.0
CB A:ILE147 5.0 18.2 1.0
O A:LYS145 5.0 27.6 1.0

Sodium binding site 2 out of 3 in 8bgj

Go back to Sodium Binding Sites List in 8bgj
Sodium binding site 2 out of 3 in the Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:24.2
occ:1.00
 O B:HOH441 2.3 25.2 1.0
O B:ASN144 2.3 23.1 1.0
O B:HOH481 2.4 31.1 1.0
O B:ILE147 2.5 19.9 1.0
O B:TYR142 2.7 22.4 1.0
C B:ASN144 3.4 21.1 1.0
C B:ILE147 3.6 21.3 1.0
C B:TYR142 3.6 21.4 1.0
NH1 B:ARG148 3.6 23.4 1.0
O B:PHE141 3.7 21.6 1.0
N B:ASN144 4.1 22.4 1.0
CG1 B:ILE147 4.1 19.2 1.0
O B:HOH443 4.1 26.1 1.0
CD B:ARG148 4.1 17.6 1.0
CA B:TYR142 4.2 21.1 1.0
N B:LYS145 4.2 25.5 1.0
CA B:LYS145 4.2 26.8 1.0
CA B:ASN144 4.3 25.1 1.0
CA B:ARG148 4.3 16.2 1.0
CZ B:ARG148 4.3 26.2 1.0
N B:ARG148 4.4 17.6 1.0
N B:ILE147 4.4 20.3 1.0
C B:LYS143 4.5 25.5 1.0
CA B:ILE147 4.5 18.0 1.0
NE B:ARG148 4.6 21.2 1.0
C B:LYS145 4.6 25.7 1.0
N B:LYS143 4.6 20.6 1.0
C B:PHE141 4.7 20.8 1.0
CB B:ASN144 4.7 24.8 1.0
CA B:LYS143 4.9 23.2 1.0
O B:LYS145 4.9 28.8 1.0
CD1 B:TYR142 5.0 21.8 1.0
N B:TYR142 5.0 18.0 1.0
CB B:ILE147 5.0 20.2 1.0

Sodium binding site 3 out of 3 in 8bgj

Go back to Sodium Binding Sites List in 8bgj
Sodium binding site 3 out of 3 in the Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Reverse Transcriptase Domain From Caloramator Australicus Cart-Capp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:24.7
occ:1.00
 O C:HOH449 2.2 25.3 1.0
O C:ASN144 2.3 23.3 1.0
O C:HOH469 2.4 27.4 1.0
O C:ILE147 2.4 20.3 1.0
O C:TYR142 2.9 22.2 1.0
C C:ASN144 3.4 25.3 1.0
C C:ILE147 3.5 24.4 1.0
NH1 C:ARG148 3.6 21.9 1.0
O C:PHE141 3.7 23.2 1.0
C C:TYR142 3.8 22.9 1.0
C13 C:1PE302 4.0 37.1 1.0
CD C:ARG148 4.1 19.0 1.0
CG1 C:ILE147 4.1 21.2 1.0
N C:ASN144 4.2 25.6 1.0
O C:HOH440 4.2 21.5 1.0
CA C:ARG148 4.2 18.3 1.0
N C:ILE147 4.3 21.5 1.0
CA C:ASN144 4.3 25.1 1.0
N C:LYS145 4.3 25.7 1.0
N C:ARG148 4.3 19.4 1.0
CA C:LYS145 4.3 27.0 1.0
CZ C:ARG148 4.3 26.3 1.0
CA C:TYR142 4.4 21.0 1.0
CA C:ILE147 4.4 20.1 1.0
C C:LYS145 4.5 27.4 1.0
NE C:ARG148 4.5 20.9 1.0
C C:LYS143 4.6 27.5 1.0
OH3 C:1PE302 4.6 42.6 1.0
CB C:ASN144 4.7 27.0 1.0
N C:LYS143 4.7 22.5 1.0
C24 C:1PE302 4.7 30.7 1.0
C C:PHE141 4.8 22.6 1.0
O C:LYS145 4.8 29.6 1.0
N C:LYS146 4.9 26.7 1.0
CB C:ILE147 4.9 21.4 1.0
OH4 C:1PE302 4.9 38.4 1.0
CG C:ARG148 5.0 20.0 1.0

Reference:

M.Zabrady, K.Zabrady, A.W.H.Li, A.J.Doherty. Reverse Transcriptases Prime Dna Synthesis To Be Published.
Page generated: Wed Oct 9 10:41:25 2024

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