Calcium in PDB 4z20: Crystal Structure of Meganuclease I-Smami Bound to Uncleaveable Dna with A Ttgt Central Four

Protein crystallography data

The structure of Crystal Structure of Meganuclease I-Smami Bound to Uncleaveable Dna with A Ttgt Central Four, PDB code: 4z20 was solved by J.P.Hallinan, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.13 / 3.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.690, 172.262, 59.994, 90.00, 92.36, 90.00
R / Rfree (%) 23.3 / 29.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Meganuclease I-Smami Bound to Uncleaveable Dna with A Ttgt Central Four (pdb code 4z20). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Meganuclease I-Smami Bound to Uncleaveable Dna with A Ttgt Central Four, PDB code: 4z20:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4z20

Go back to Calcium Binding Sites List in 4z20
Calcium binding site 1 out of 2 in the Crystal Structure of Meganuclease I-Smami Bound to Uncleaveable Dna with A Ttgt Central Four


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 Meganuclease I-Smami Bound to Uncleaveable Dna with A Ttgt Central Four within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:0.1
occ:1.00
OP2 B:DT16 1.9 0.9 1.0
O A:ALA19 2.9 0.6 1.0
OD1 A:ASP179 3.2 0.2 1.0
P B:DT16 3.2 1.0 1.0
OD2 A:ASP179 3.2 0.7 1.0
OE2 A:GLU20 3.5 0.1 1.0
CG A:ASP179 3.6 0.1 1.0
OP1 B:DT16 3.7 0.8 1.0
O5' B:DT16 3.9 0.3 1.0
OP1 C:DT14 4.1 0.4 1.0
C A:ALA19 4.1 0.5 1.0
O C:HOH201 4.4 0.1 1.0
O3' B:DA15 4.4 0.8 1.0
O3' C:DT14 4.4 0.8 1.0
CD A:GLU20 4.5 0.4 1.0
OP2 C:DC15 4.6 0.1 1.0
CA A:GLU20 4.7 0.6 1.0
N A:GLU20 4.9 0.7 1.0

Calcium binding site 2 out of 2 in 4z20

Go back to Calcium Binding Sites List in 4z20
Calcium binding site 2 out of 2 in the Crystal Structure of Meganuclease I-Smami Bound to Uncleaveable Dna with A Ttgt Central Four


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Meganuclease I-Smami Bound to Uncleaveable Dna with A Ttgt Central Four within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:0.3
occ:1.00
O F:HOH202 2.3 0.8 1.0
OP2 E:DT16 2.3 0.3 1.0
OD1 D:ASP179 2.5 0.3 1.0
O3' F:DT14 3.1 0.3 1.0
O F:HOH201 3.1 0.2 1.0
OE2 D:GLU20 3.1 0.2 1.0
O D:HOH503 3.3 0.3 1.0
CG D:ASP179 3.3 0.6 1.0
OP2 F:DC15 3.3 0.4 1.0
OD2 D:ASP179 3.3 0.6 1.0
P E:DT16 3.5 0.4 1.0
O D:ALA19 3.6 0.4 1.0
P F:DC15 3.8 0.1 1.0
OP1 E:DT16 3.8 0.8 1.0
OP1 F:DT14 4.2 0.7 1.0
C3' F:DT14 4.2 0.9 1.0
CD D:GLU20 4.3 0.6 1.0
C4' F:DT14 4.3 0.2 1.0
O3' E:DA15 4.5 0.1 1.0
OP1 F:DC15 4.6 0.5 1.0
CB D:ASP179 4.7 0.8 1.0
O5' E:DT16 4.7 0.6 1.0
C D:ALA19 4.7 0.5 1.0
OE1 D:GLU20 4.8 0.9 1.0
C4' E:DA15 4.9 1.0 1.0
O4' F:DT14 5.0 0.3 1.0

Reference:

A.R.Lambert, J.P.Hallinan, B.W.Shen, J.K.Chik, J.M.Bolduc, N.Kulshina, L.I.Robins, B.K.Kaiser, J.Jarjour, K.Havens, A.M.Scharenberg, B.L.Stoddard. Indirect Dna Sequence Recognition and Its Impact on Nuclease Cleavage Activity. Structure V. 24 862 2016.
ISSN: ISSN 0969-2126
PubMed: 27133026
DOI: 10.1016/J.STR.2016.03.024
Page generated: Sat Dec 12 05:14:35 2020

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