Zinc in PDB 6ghc: Modification Dependent Ecokmcra Restriction Endonuclease

Protein crystallography data

The structure of Modification Dependent Ecokmcra Restriction Endonuclease, PDB code: 6ghc was solved by H.Czapinska, M.Kowalska, E.Zagorskaite, E.Manakova, S.Xu, V.Siksnys, G.Sasnauskas, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.19 / 2.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.045, 90.383, 95.406, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 28.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Modification Dependent Ecokmcra Restriction Endonuclease (pdb code 6ghc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Modification Dependent Ecokmcra Restriction Endonuclease, PDB code: 6ghc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6ghc

Go back to Zinc Binding Sites List in 6ghc
Zinc binding site 1 out of 4 in the Modification Dependent Ecokmcra Restriction Endonuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Modification Dependent Ecokmcra Restriction Endonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:0.1
occ:1.00
SG A:CYS251 2.3 1.0 1.0
SG A:CYS248 2.4 0.8 1.0
SG A:CYS210 2.5 0.4 1.0
SG A:CYS207 2.9 0.1 1.0
CB A:CYS251 3.1 0.7 1.0
CB A:CYS207 3.2 0.8 1.0
CB A:CYS248 3.5 0.5 1.0
CB A:CYS210 3.5 1.0 1.0
N A:CYS248 3.8 0.3 1.0
ND2 A:ASN209 4.1 0.8 1.0
CA A:CYS248 4.2 0.8 1.0
N A:CYS251 4.2 0.5 1.0
N A:CYS210 4.3 0.9 1.0
CA A:CYS251 4.3 0.1 1.0
CA A:CYS210 4.4 0.3 1.0
O A:CYS210 4.5 0.1 1.0
O A:CYS248 4.6 0.4 1.0
C A:CYS210 4.7 0.2 1.0
CA A:CYS207 4.7 0.1 1.0
C A:CYS248 4.8 0.7 1.0
C A:LEU247 5.0 0.4 1.0

Zinc binding site 2 out of 4 in 6ghc

Go back to Zinc Binding Sites List in 6ghc
Zinc binding site 2 out of 4 in the Modification Dependent Ecokmcra Restriction Endonuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Modification Dependent Ecokmcra Restriction Endonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:99.8
occ:0.53
ND1 A:HIS228 2.3 0.6 1.0
NE2 A:HIS252 2.3 0.8 1.0
NE2 A:HIS256 2.5 0.4 1.0
O A:HOH428 2.6 89.5 1.0
CE1 A:HIS256 3.2 0.2 1.0
CG A:HIS228 3.3 1.0 1.0
CD2 A:HIS252 3.3 0.0 1.0
CE1 A:HIS228 3.3 0.4 1.0
CE1 A:HIS252 3.3 0.5 1.0
O A:HOH417 3.4 0.8 1.0
CB A:HIS228 3.5 0.6 1.0
O A:HOH413 3.5 93.9 1.0
CD2 A:HIS256 3.6 0.3 1.0
CA A:HIS228 3.9 0.0 1.0
NE2 A:HIS228 4.4 0.1 1.0
ND1 A:HIS256 4.4 0.1 1.0
CD2 A:HIS228 4.4 0.2 1.0
ND1 A:HIS252 4.4 0.2 1.0
CG A:HIS252 4.5 0.9 1.0
N A:HIS229 4.5 0.4 1.0
CG A:HIS256 4.6 0.3 1.0
O A:VAL227 4.7 0.2 1.0
C A:HIS228 4.7 0.5 1.0

Zinc binding site 3 out of 4 in 6ghc

Go back to Zinc Binding Sites List in 6ghc
Zinc binding site 3 out of 4 in the Modification Dependent Ecokmcra Restriction Endonuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Modification Dependent Ecokmcra Restriction Endonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:0.6
occ:1.00
SG B:CYS248 2.1 0.3 1.0
SG B:CYS210 2.3 0.8 1.0
SG B:CYS207 2.4 0.7 1.0
SG B:CYS251 2.8 0.0 1.0
CB B:CYS207 3.0 0.1 1.0
CB B:CYS248 3.3 0.5 1.0
CB B:CYS251 3.4 0.3 1.0
CB B:CYS210 3.6 0.9 1.0
N B:CYS248 3.8 0.0 1.0
CA B:CYS248 4.1 0.9 1.0
N B:CYS210 4.2 0.4 1.0
N B:CYS251 4.4 0.6 1.0
CA B:CYS210 4.4 0.8 1.0
O B:CYS210 4.5 0.9 1.0
CA B:CYS207 4.5 0.5 1.0
CA B:CYS251 4.5 0.5 1.0
O B:CYS248 4.6 0.1 1.0
C B:CYS248 4.7 0.7 1.0
C B:CYS210 4.8 0.5 1.0
C B:LEU247 5.0 0.5 1.0

Zinc binding site 4 out of 4 in 6ghc

Go back to Zinc Binding Sites List in 6ghc
Zinc binding site 4 out of 4 in the Modification Dependent Ecokmcra Restriction Endonuclease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Modification Dependent Ecokmcra Restriction Endonuclease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:0.8
occ:0.55
ND1 B:HIS228 2.2 0.3 1.0
NE2 B:HIS252 2.5 0.6 1.0
O B:HOH422 2.6 84.6 1.0
O B:HOH421 2.7 95.8 1.0
O B:HOH420 3.0 0.7 1.0
CE1 B:HIS228 3.0 0.6 1.0
NE2 B:HIS256 3.2 0.8 1.0
CG B:HIS228 3.3 0.3 1.0
CE1 B:HIS252 3.4 0.9 1.0
CD2 B:HIS252 3.6 0.8 1.0
CE1 B:HIS256 3.6 0.8 1.0
CA B:HIS228 3.7 1.0 1.0
CB B:HIS228 3.8 0.4 1.0
N B:HIS229 4.0 0.4 1.0
NE2 B:HIS228 4.2 0.5 1.0
CD2 B:HIS228 4.3 0.5 1.0
C B:HIS228 4.4 0.3 1.0
CD2 B:HIS256 4.4 0.8 1.0
ND1 B:HIS252 4.6 0.2 1.0
O B:VAL227 4.6 0.9 1.0
CG B:HIS252 4.7 0.6 1.0
O B:HIS229 4.7 0.7 1.0
ND1 B:HIS256 4.9 0.2 1.0
N B:HIS228 4.9 0.6 1.0

Reference:

H.Czapinska, M.Kowalska, E.Zagorskaite, E.Manakova, A.Slyvka, S.Y.Xu, V.Siksnys, G.Sasnauskas, M.Bochtler. Activity and Structure of Ecokmcra. Nucleic Acids Res. V. 46 9829 2018.
ISSN: ESSN 1362-4962
PubMed: 30107581
DOI: 10.1093/NAR/GKY731
Page generated: Wed Dec 16 11:52:26 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy