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Zinc in PDB 5zmm: Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra

Protein crystallography data

The structure of Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra, PDB code: 5zmm was solved by G.Liu, W.Fu, Z.Zhang, Y.He, H.Yu, Y.Zhao, Z.Deng, G.Wu, X.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 140.50 / 3.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 130.183, 139.367, 281.005, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 28

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra (pdb code 5zmm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra, PDB code: 5zmm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5zmm

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Zinc binding site 1 out of 6 in the Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:59.7
occ:1.00
SG A:CYS484 1.8 60.8 1.0
SG A:CYS489 2.2 53.6 1.0
SG A:CYS530 2.3 54.4 1.0
SG A:CYS527 2.6 51.4 1.0
CB A:CYS484 3.1 55.5 1.0
CB A:CYS489 3.2 59.4 1.0
CB A:CYS530 3.3 54.2 1.0
CB A:CYS527 3.5 48.1 1.0
N A:CYS527 3.9 44.1 1.0
CA A:CYS489 4.0 59.2 1.0
CA A:CYS527 4.3 43.7 1.0
N A:CYS530 4.3 51.0 1.0
CA A:CYS530 4.4 52.6 1.0
CA A:CYS484 4.5 55.7 1.0
CB A:ASN486 4.5 72.3 1.0
CB A:HIS492 4.8 58.0 1.0
O A:CYS527 4.9 40.6 1.0
C A:CYS527 5.0 40.8 1.0
C A:CYS489 5.0 57.6 1.0
ND2 A:ASN486 5.0 69.0 1.0

Zinc binding site 2 out of 6 in 5zmm

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Zinc binding site 2 out of 6 in the Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:52.9
occ:1.00
SG B:CYS489 2.0 54.1 1.0
SG B:CYS484 2.2 50.1 1.0
SG B:CYS527 2.4 45.0 1.0
SG B:CYS530 2.5 47.9 1.0
CB B:CYS484 3.1 53.6 1.0
CB B:CYS489 3.1 51.3 1.0
CB B:CYS530 3.4 43.3 1.0
CB B:CYS527 3.5 49.8 1.0
N B:CYS527 4.0 40.9 1.0
CA B:CYS489 4.0 49.2 1.0
N B:CYS530 4.3 40.6 1.0
CA B:CYS527 4.3 45.7 1.0
CA B:CYS530 4.5 41.6 1.0
CA B:CYS484 4.5 58.7 1.0
CB B:HIS492 4.6 77.1 1.0
CB B:ASN486 4.7 52.5 1.0
CD2 B:HIS492 4.8 71.5 1.0
C B:CYS489 4.8 42.8 1.0
CG B:HIS492 4.9 77.4 1.0
O B:CYS527 4.9 48.4 1.0
O B:GLY491 4.9 73.0 1.0
N B:ALA490 5.0 46.0 1.0

Zinc binding site 3 out of 6 in 5zmm

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Zinc binding site 3 out of 6 in the Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:43.4
occ:1.00
SG C:CYS530 2.2 38.1 1.0
SG C:CYS484 2.2 34.4 1.0
SG C:CYS489 2.3 42.0 1.0
SG C:CYS527 2.3 31.1 1.0
CB C:CYS530 3.2 36.0 1.0
CB C:CYS484 3.2 36.6 1.0
CB C:CYS489 3.3 43.6 1.0
CB C:CYS527 3.5 30.8 1.0
N C:CYS527 3.9 33.8 1.0
CA C:CYS489 4.1 42.4 1.0
N C:CYS530 4.1 32.0 1.0
CA C:CYS530 4.3 34.9 1.0
CA C:CYS527 4.3 30.0 1.0
CA C:CYS484 4.6 38.0 1.0
CB C:ASN486 4.7 42.4 1.0
CB C:HIS492 4.8 47.1 1.0
O C:CYS527 4.8 27.6 1.0
C C:CYS527 4.9 29.4 1.0
C C:CYS489 5.0 41.7 1.0

Zinc binding site 4 out of 6 in 5zmm

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Zinc binding site 4 out of 6 in the Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:45.4
occ:1.00
SG D:CYS484 1.9 53.2 1.0
SG D:CYS530 2.2 42.1 1.0
SG D:CYS489 2.3 31.0 1.0
SG D:CYS527 2.5 35.4 1.0
CB D:CYS484 3.1 48.8 1.0
CB D:CYS530 3.2 36.0 1.0
CB D:CYS489 3.2 33.5 1.0
CB D:CYS527 3.6 39.5 1.0
N D:CYS527 4.0 39.6 1.0
CA D:CYS489 4.0 38.7 1.0
N D:CYS530 4.2 29.7 1.0
CA D:CYS530 4.3 31.4 1.0
CA D:CYS527 4.4 36.4 1.0
CA D:CYS484 4.5 46.7 1.0
CB D:ASN486 4.5 42.4 1.0
O D:CYS527 4.8 35.2 1.0
ND2 D:ASN486 4.9 39.0 1.0
CB D:HIS492 4.9 45.4 1.0
C D:CYS527 5.0 37.0 1.0
C D:CYS489 5.0 37.8 1.0

Zinc binding site 5 out of 6 in 5zmm

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Zinc binding site 5 out of 6 in the Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn601

b:50.1
occ:1.00
SG E:CYS484 2.0 55.1 1.0
SG E:CYS489 2.2 45.3 1.0
SG E:CYS530 2.3 49.4 1.0
SG E:CYS527 2.3 38.9 1.0
CB E:CYS530 3.2 45.7 1.0
CB E:CYS484 3.3 51.4 1.0
CB E:CYS527 3.4 43.4 1.0
CB E:CYS489 3.5 44.9 1.0
N E:CYS527 3.9 37.5 1.0
CA E:CYS489 4.1 43.1 1.0
N E:CYS530 4.2 41.5 1.0
CA E:CYS527 4.2 39.4 1.0
CA E:CYS530 4.3 45.1 1.0
CA E:CYS484 4.6 49.9 1.0
CB E:ASN486 4.7 40.9 1.0
CB E:HIS492 4.7 59.2 1.0
O E:CYS527 4.8 44.4 1.0
C E:CYS527 4.9 39.7 1.0
C E:LEU526 5.0 38.6 1.0
CD2 E:HIS492 5.0 64.1 1.0
O E:GLY491 5.0 61.1 1.0
CG E:HIS492 5.0 57.8 1.0

Zinc binding site 6 out of 6 in 5zmm

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Zinc binding site 6 out of 6 in the Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Type IV Phosphorothioation-Dependent Restriction Endonuclease Scomcra within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn601

b:48.0
occ:1.00
SG F:CYS484 2.0 46.5 1.0
SG F:CYS530 2.2 48.3 1.0
SG F:CYS489 2.4 57.4 1.0
SG F:CYS527 2.5 40.7 1.0
CB F:CYS484 3.0 47.4 1.0
CB F:CYS530 3.2 53.7 1.0
CB F:CYS489 3.3 59.5 1.0
CB F:CYS527 3.5 40.3 1.0
N F:CYS527 3.8 40.9 1.0
CA F:CYS489 4.1 56.3 1.0
CA F:CYS527 4.2 40.8 1.0
N F:CYS530 4.3 47.4 1.0
CA F:CYS530 4.3 52.3 1.0
CA F:CYS484 4.4 50.4 1.0
CB F:ASN486 4.5 50.5 1.0
O F:CYS527 4.7 36.0 1.0
ND2 F:ASN486 4.8 55.8 1.0
C F:CYS527 4.9 37.9 1.0
CB F:HIS492 4.9 47.8 1.0
C F:LEU526 4.9 41.5 1.0

Reference:

G.Liu, W.Fu, Z.Zhang, Y.He, H.Yu, Y.Wang, X.Wang, Y.Zhao, Z.Deng, G.Wu, X.He. Structural Basis For the Recognition of Sulfur in Phosphorothioated Dna. Nat Commun V. 9 4689 2018.
ISSN: ESSN 2041-1723
PubMed: 30409991
DOI: 10.1038/S41467-018-07093-1
Page generated: Wed Dec 16 11:27:11 2020

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