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Zinc in PDB 1a74: I-Ppol Homing Endonuclease/Dna Complex

Protein crystallography data

The structure of I-Ppol Homing Endonuclease/Dna Complex, PDB code: 1a74 was solved by B.L.Jurica, K.E.Flick, R.J.Monnat Junior, M.S.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.400, 113.400, 88.200, 90.00, 90.00, 120.00
R / Rfree (%) 21.6 / 26.5

Zinc Binding Sites:

The binding sites of Zinc atom in the I-Ppol Homing Endonuclease/Dna Complex (pdb code 1a74). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the I-Ppol Homing Endonuclease/Dna Complex, PDB code: 1a74:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1a74

Go back to Zinc Binding Sites List in 1a74
Zinc binding site 1 out of 4 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:20.2
occ:1.00
ND1 A:HIS134 2.2 13.3 1.0
SG A:CYS125 2.4 14.4 1.0
SG A:CYS138 2.4 16.9 1.0
SG A:CYS132 2.5 16.9 1.0
CE1 A:HIS134 3.1 11.8 1.0
CB A:CYS132 3.2 14.6 1.0
CG A:HIS134 3.3 15.7 1.0
CB A:CYS138 3.3 15.2 1.0
CB A:CYS125 3.4 15.3 1.0
CB A:HIS134 3.6 14.7 1.0
O A:HOH621 4.0 19.9 1.0
CA A:CYS132 4.0 16.4 1.0
N A:CYS138 4.1 15.8 1.0
NE2 A:HIS134 4.2 11.7 1.0
CA A:CYS138 4.3 13.9 1.0
N A:HIS134 4.3 15.9 1.0
CD2 A:HIS134 4.3 14.1 1.0
N A:VAL133 4.5 17.5 1.0
NH2 A:ARG122 4.6 17.0 1.0
C A:CYS132 4.6 17.1 1.0
CA A:HIS134 4.6 14.8 1.0
CA A:CYS125 4.8 15.1 1.0
NE A:ARG122 4.9 19.4 1.0

Zinc binding site 2 out of 4 in 1a74

Go back to Zinc Binding Sites List in 1a74
Zinc binding site 2 out of 4 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:21.0
occ:1.00
ND1 A:HIS110 2.2 12.2 1.0
SG A:CYS41 2.4 13.8 1.0
SG A:CYS100 2.4 15.2 1.0
SG A:CYS105 2.4 15.6 1.0
CB A:CYS100 3.1 15.3 1.0
CE1 A:HIS110 3.1 11.2 1.0
CB A:CYS105 3.1 12.1 1.0
CG A:HIS110 3.2 14.3 1.0
CB A:CYS41 3.3 13.0 1.0
CB A:HIS110 3.5 10.7 1.0
CA A:CYS41 3.7 14.3 1.0
NE2 A:HIS110 4.2 12.3 1.0
CD2 A:HIS110 4.3 11.1 1.0
N A:CYS41 4.5 13.6 1.0
CB A:ASN102 4.5 13.6 1.0
CA A:CYS100 4.5 17.5 1.0
CA A:CYS105 4.6 14.9 1.0
CB A:ASN107 4.6 6.8 1.0
O A:HIS40 4.7 12.4 1.0
C A:HIS40 4.8 13.0 1.0
C A:CYS41 4.9 13.5 1.0
ND2 A:ASN102 4.9 11.9 1.0
N A:TYR42 4.9 11.6 1.0

Zinc binding site 3 out of 4 in 1a74

Go back to Zinc Binding Sites List in 1a74
Zinc binding site 3 out of 4 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:21.2
occ:1.00
ND1 B:HIS134 2.2 15.2 1.0
SG B:CYS125 2.4 16.2 1.0
SG B:CYS138 2.4 8.2 1.0
SG B:CYS132 2.5 17.9 1.0
CE1 B:HIS134 3.1 10.1 1.0
CG B:HIS134 3.2 13.4 1.0
CB B:CYS132 3.3 18.9 1.0
CB B:CYS138 3.3 13.7 1.0
CB B:CYS125 3.4 12.5 1.0
CB B:HIS134 3.6 12.3 1.0
CA B:CYS132 4.0 17.2 1.0
N B:CYS138 4.0 15.7 1.0
NE2 B:HIS134 4.2 9.6 1.0
CA B:CYS138 4.2 13.7 1.0
N B:HIS134 4.2 12.3 1.0
CD2 B:HIS134 4.3 12.1 1.0
N B:VAL133 4.5 14.0 1.0
NH2 B:ARG122 4.5 19.8 1.0
CA B:HIS134 4.6 13.9 1.0
C B:CYS132 4.6 17.0 1.0
CA B:CYS125 4.8 12.8 1.0
NE B:ARG122 4.9 23.5 1.0
O B:HOH613 4.9 10.8 1.0

Zinc binding site 4 out of 4 in 1a74

Go back to Zinc Binding Sites List in 1a74
Zinc binding site 4 out of 4 in the I-Ppol Homing Endonuclease/Dna Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of I-Ppol Homing Endonuclease/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:17.6
occ:1.00
ND1 B:HIS110 2.2 15.9 1.0
SG B:CYS100 2.4 12.0 1.0
SG B:CYS105 2.4 15.5 1.0
SG B:CYS41 2.5 16.0 1.0
CB B:CYS100 3.1 13.9 1.0
CB B:CYS105 3.1 12.3 1.0
CE1 B:HIS110 3.1 14.0 1.0
CG B:HIS110 3.2 15.6 1.0
CB B:CYS41 3.2 16.1 1.0
CB B:HIS110 3.5 15.0 1.0
CA B:CYS41 3.7 15.3 1.0
NE2 B:HIS110 4.3 17.1 1.0
CD2 B:HIS110 4.3 19.1 1.0
CB B:ASN102 4.4 12.2 1.0
N B:CYS41 4.4 16.7 1.0
CA B:CYS100 4.5 13.5 1.0
ND2 B:ASN102 4.5 10.3 1.0
CA B:CYS105 4.6 14.1 1.0
CB B:ASN107 4.7 12.0 1.0
O B:HIS40 4.7 16.0 1.0
C B:HIS40 4.8 17.2 1.0
C B:CYS41 4.8 15.7 1.0
CG B:ASN102 4.9 9.6 1.0
N B:TYR42 5.0 16.3 1.0

Reference:

K.E.Flick, M.S.Jurica, R.J.Monnat Jr., B.L.Stoddard. Dna Binding and Cleavage By the Nuclear Intron-Encoded Homing Endonuclease I-Ppoi. Nature V. 394 96 1998.
ISSN: ISSN 0028-0836
PubMed: 9665136
DOI: 10.1038/27952
Page generated: Wed Dec 16 02:44:28 2020

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