Calcium in PDB 6doh: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C, PDB code: 6doh was solved by N.L.Samara, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 1.36
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.194, 37.843, 61.829, 90.00, 96.15, 90.00
R / Rfree (%) 16.8 / 20

Other elements in 6doh:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C also contains other interesting chemical elements:

Potassium (K) 3 atoms
Iodine (I) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C (pdb code 6doh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C, PDB code: 6doh:

Calcium binding site 1 out of 1 in 6doh

Go back to Calcium Binding Sites List in 6doh
Calcium binding site 1 out of 1 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Soak in 0.5 Mm Egta and 200 Mm K+ at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:15.8
occ:0.30
 K A:K202 1.8 25.3 0.7
OD1 A:ASP192 2.3 60.4 1.0
OP1 b:C5 2.3 23.1 1.0
O A:HOH333 2.4 41.5 1.0
O A:HOH403 2.5 26.4 0.4
OD2 A:ASP71 2.6 34.2 1.0
OD1 A:ASP71 2.8 24.7 1.0
CG A:ASP71 3.0 34.0 1.0
HA A:ASP192 3.5 53.7 1.0
CG A:ASP192 3.6 94.2 1.0
P b:C5 3.6 19.9 1.0
H A:TYR193 3.8 58.3 1.0
K A:K203 3.9 21.9 0.7
OP2 b:G6 4.0 27.5 1.0
O A:VAL72 4.1 19.6 1.0
OP2 b:C5 4.1 23.2 1.0
HG22 A:ILE189 4.1 37.9 1.0
CA A:ASP192 4.4 44.8 1.0
OE2 A:GLU188 4.4 0.4 1.0
OD2 A:ASP192 4.4 93.7 1.0
CB A:ASP192 4.4 47.4 1.0
O5' b:C5 4.5 18.3 1.0
CB A:ASP71 4.5 21.6 1.0
O b:HOH101 4.6 45.4 1.0
N A:TYR193 4.6 48.6 1.0
HD1 A:TYR193 4.6 48.4 1.0
HB2 A:ASP192 4.6 56.9 1.0
HG21 A:ILE189 4.6 37.9 1.0
OD2 A:ASP132 4.7 26.1 1.0
O3' B:U4 4.7 18.7 1.0
HB2 A:ASP71 4.7 25.9 1.0
CG2 A:ILE189 4.8 31.6 1.0
HB2 A:TYR193 4.8 93.6 1.0
C5' b:C5 4.8 15.4 1.0
H A:VAL72 4.8 21.2 1.0
O A:HOH406 4.9 32.3 0.6
HG23 A:ILE189 4.9 37.9 1.0
HB3 A:ASP71 4.9 25.9 1.0
OE1 A:GLU188 4.9 85.7 1.0

Reference:

N.L.Samara, W.Yang. Cation Trafficking Propels Rna Hydrolysis. Nat. Struct. Mol. Biol. V. 25 715 2018.
ISSN: ESSN 1545-9985
PubMed: 30076410
DOI: 10.1038/S41594-018-0099-4
Page generated: Sat Dec 12 06:03:35 2020

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