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Cadmium in PDB 4e89: Crystal Structure of Rnaseh From Gammaretrovirus

Enzymatic activity of Crystal Structure of Rnaseh From Gammaretrovirus

All present enzymatic activity of Crystal Structure of Rnaseh From Gammaretrovirus:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Rnaseh From Gammaretrovirus, PDB code: 4e89 was solved by J.H.Kim, S.J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.04 / 2.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 63.700, 63.700, 163.920, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 26

Other elements in 4e89:

The structure of Crystal Structure of Rnaseh From Gammaretrovirus also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Rnaseh From Gammaretrovirus (pdb code 4e89). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Rnaseh From Gammaretrovirus, PDB code: 4e89:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 4e89

Go back to Cadmium Binding Sites List in 4e89
Cadmium binding site 1 out of 4 in the Crystal Structure of Rnaseh From Gammaretrovirus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Rnaseh From Gammaretrovirus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd701

b:17.5
occ:0.50
NE2 A:HIS592 2.1 44.3 1.0
OD2 A:ASP511 2.3 46.0 1.0
CE1 A:HIS592 3.1 47.2 1.0
CD2 A:HIS592 3.1 46.4 1.0
CG A:ASP511 3.1 45.7 1.0
OD1 A:ASP511 3.3 44.5 1.0
ND1 A:HIS592 4.2 45.5 1.0
CG A:HIS592 4.2 46.7 1.0
CB A:ASP511 4.6 44.5 1.0

Cadmium binding site 2 out of 4 in 4e89

Go back to Cadmium Binding Sites List in 4e89
Cadmium binding site 2 out of 4 in the Crystal Structure of Rnaseh From Gammaretrovirus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Rnaseh From Gammaretrovirus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd702

b:53.4
occ:1.00
SG A:CYS635 2.6 52.0 1.0
CB A:CYS635 3.3 56.2 1.0
CD A:CD703 3.6 57.3 1.0
CA A:CYS635 4.2 60.1 1.0

Cadmium binding site 3 out of 4 in 4e89

Go back to Cadmium Binding Sites List in 4e89
Cadmium binding site 3 out of 4 in the Crystal Structure of Rnaseh From Gammaretrovirus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Rnaseh From Gammaretrovirus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd703

b:57.3
occ:1.00
OE1 A:GLU645 2.4 66.4 1.0
ND1 A:HIS638 2.4 78.4 1.0
SG A:CYS635 2.5 52.0 1.0
OE2 A:GLU645 2.9 66.3 1.0
CD A:GLU645 3.0 67.1 1.0
CE1 A:HIS638 3.3 77.7 1.0
CG A:HIS638 3.4 77.0 1.0
CB A:CYS635 3.4 56.2 1.0
CD A:CD702 3.6 53.4 1.0
CB A:HIS638 3.7 76.8 1.0
NE2 A:HIS638 4.4 79.3 1.0
CD2 A:HIS638 4.5 77.7 1.0
CG A:GLU645 4.5 66.4 1.0
O A:CYS635 4.8 65.0 1.0
CA A:CYS635 4.8 60.1 1.0

Cadmium binding site 4 out of 4 in 4e89

Go back to Cadmium Binding Sites List in 4e89
Cadmium binding site 4 out of 4 in the Crystal Structure of Rnaseh From Gammaretrovirus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Rnaseh From Gammaretrovirus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd704

b:67.1
occ:0.60
OE1 A:GLU545 2.1 82.8 1.0
OE2 A:GLU545 2.2 83.2 1.0
CD A:GLU545 2.4 82.1 1.0
CG A:GLU545 3.9 77.5 1.0
CB A:GLU545 4.8 68.4 1.0

Reference:

J.H.Kim, S.Kang, S.K.Jung, K.R.Yu, S.J.Chung, B.H.Chung, R.L.Erikson, B.Y.Kim, S.J.Kim. Crystal Structure of Xenotropic Murine Leukaemia Virus-Related Virus (Xmrv) Ribonuclease H Biosci.Rep. V. 32 455 2012.
ISSN: ISSN 0144-8463
PubMed: 22724525
DOI: 10.1042/BSR20120028
Page generated: Sat Dec 12 08:24:27 2020

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