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Zinc in PDB 5z42: Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions.

Protein crystallography data

The structure of Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions., PDB code: 5z42 was solved by K.Fukui, T.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.79 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 35.623, 35.623, 167.918, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 20.4

Other elements in 5z42:

The structure of Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions. (pdb code 5z42). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions., PDB code: 5z42:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5z42

Go back to Zinc Binding Sites List in 5z42
Zinc binding site 1 out of 5 in the Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:14.1
occ:1.00
O A:HOH372 2.3 19.6 1.0
OE2 A:GLU34 2.3 17.6 1.0
NE2 A:HIS30 2.3 18.1 1.0
O A:HOH379 2.4 22.4 1.0
SG A:CYS48 2.6 20.4 1.0
O A:HOH399 2.7 19.8 1.0
CE1 A:HIS30 3.2 18.2 1.0
CD A:GLU34 3.4 17.4 1.0
CD2 A:HIS30 3.4 16.6 1.0
CB A:CYS48 3.5 18.1 1.0
ZN A:ZN203 3.8 22.2 0.9
OE1 A:GLU34 3.9 18.1 1.0
ZN A:ZN202 4.0 14.8 1.0
O A:HOH382 4.2 23.3 1.0
CA A:CYS48 4.2 18.5 1.0
O A:HOH425 4.3 30.9 1.0
CE1 A:HIS81 4.3 30.0 1.0
ND1 A:HIS30 4.4 16.8 1.0
CG A:GLU34 4.4 18.2 1.0
CG A:HIS30 4.5 16.3 1.0
O A:HOH408 4.6 27.1 1.0
ND1 A:HIS81 4.6 23.4 1.0
CB A:GLU34 4.9 15.8 1.0
C A:CYS48 4.9 17.2 1.0
O A:CYS48 5.0 17.6 1.0

Zinc binding site 2 out of 5 in 5z42

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Zinc binding site 2 out of 5 in the Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:14.8
occ:1.00
OE1 A:GLU34 2.2 18.1 1.0
O A:HOH382 2.3 23.3 1.0
ND1 A:HIS81 2.3 23.4 1.0
O A:HOH372 2.4 19.6 1.0
SG A:CYS79 2.5 19.1 1.0
CD A:GLU34 3.0 17.4 1.0
OE2 A:GLU34 3.2 17.6 1.0
CG A:HIS81 3.3 25.8 1.0
CE1 A:HIS81 3.3 30.0 1.0
CB A:CYS79 3.4 18.6 1.0
CB A:HIS81 3.5 24.3 1.0
CD2 A:LEU31 3.7 17.3 1.0
ZN A:ZN201 4.0 14.1 1.0
N A:HIS81 4.0 22.5 1.0
O A:HOH399 4.3 19.8 1.0
CA A:HIS81 4.3 24.1 1.0
NE2 A:HIS81 4.4 28.0 1.0
CD2 A:HIS81 4.4 27.5 1.0
CG A:GLU34 4.4 18.2 1.0
CD A:PRO80 4.4 20.1 1.0
N A:PRO80 4.6 21.4 1.0
CG A:PRO80 4.6 25.0 1.0
CA A:CYS79 4.7 18.4 1.0
C A:CYS79 4.8 21.8 1.0

Zinc binding site 3 out of 5 in 5z42

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Zinc binding site 3 out of 5 in the Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:22.2
occ:0.93
O A:HOH406 2.2 26.2 1.0
O A:HOH399 2.5 19.8 1.0
O A:HOH425 2.5 30.9 1.0
SG A:CYS48 2.6 20.4 1.0
O A:HOH422 2.8 23.4 1.0
O A:HOH373 3.0 25.6 1.0
CB A:CYS48 3.5 18.1 1.0
ZN A:ZN201 3.8 14.1 1.0
O A:HOH379 3.9 22.4 1.0
O A:HOH341 4.4 25.0 1.0
CE1 A:HIS81 4.6 30.0 1.0
OE2 A:GLU34 4.8 17.6 1.0
NE2 A:HIS81 4.8 28.0 1.0
CA A:CYS48 4.9 18.5 1.0

Zinc binding site 4 out of 5 in 5z42

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Zinc binding site 4 out of 5 in the Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:29.5
occ:0.74
OE1 A:GLU96 2.1 36.5 1.0
OE2 A:GLU93 2.1 45.5 1.0
O A:HOH390 2.3 38.3 1.0
O A:HOH384 2.5 33.5 1.0
O A:HOH310 2.5 40.2 1.0
CD A:GLU96 2.9 37.3 1.0
CD A:GLU93 2.9 43.8 1.0
OE2 A:GLU96 3.0 39.5 1.0
OE1 A:GLU93 3.0 48.8 1.0
O A:HOH302 4.1 37.2 1.0
O A:HOH424 4.3 39.9 1.0
CG A:GLU93 4.3 35.1 1.0
CG A:GLU96 4.3 29.9 1.0
CD A:ARG92 4.4 38.9 1.0
O A:HOH423 4.5 40.2 1.0
NH1 A:ARG92 4.5 37.9 1.0
O A:HOH328 4.7 27.6 1.0
CA A:GLU93 4.9 18.6 1.0

Zinc binding site 5 out of 5 in 5z42

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Zinc binding site 5 out of 5 in the Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Aquifex Aeolicus Mutl Endonuclease Domain with Three Zinc Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:13.6
occ:1.00
OE1 A:GLU61 2.3 19.0 1.0
OE2 A:GLU61 2.4 19.0 1.0
O A:HOH387 2.5 13.5 1.0
O A:HOH395 2.5 12.6 1.0
CD A:GLU61 2.7 18.1 1.0
NE A:ARG64 4.3 22.8 1.0
CG A:GLU61 4.3 21.3 1.0
CG A:GLU65 4.5 21.0 1.0
O A:GLU61 4.8 17.8 1.0
NH2 A:ARG64 4.8 20.7 1.0
CB A:ARG64 4.8 18.7 1.0
OE2 A:GLU65 4.9 20.7 1.0

Reference:

K.Fukui, S.Baba, T.Kumasaka, T.Yano. Multiple Zinc Ions Maintain the Open Conformation of the Catalytic Site in the Dna Mismatch Repair Endonuclease Mutl From Aquifex Aeolicus Febs Lett. V. 592 1611 2018.
ISSN: ISSN 1873-3468
PubMed: 29645090
DOI: 10.1002/1873-3468.13050
Page generated: Wed Dec 16 11:25:00 2020

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