Atomistry » Zinc » PDB 5y6d-5yjp » 5yi3
Atomistry »
  Zinc »
    PDB 5y6d-5yjp »
      5yi3 »

Zinc in PDB 5yi3: Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna

Protein crystallography data

The structure of Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna, PDB code: 5yi3 was solved by Y.Song, H.Liu, R.Zhu, C.Yi, P.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.49 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.522, 103.058, 104.855, 90.00, 94.20, 90.00
R / Rfree (%) 20.5 / 26.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna (pdb code 5yi3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna, PDB code: 5yi3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5yi3

Go back to Zinc Binding Sites List in 5yi3
Zinc binding site 1 out of 8 in the Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:88.5
occ:1.00
ND1 A:HIS42 2.0 93.7 1.0
NE2 A:HIS108 2.1 91.4 1.0
OE2 A:GLU24 2.2 87.6 1.0
NE2 A:HIS112 2.3 0.7 1.0
OE1 A:GLU24 2.4 94.3 1.0
CD A:GLU24 2.6 93.3 1.0
CE1 A:HIS108 3.0 92.3 1.0
CE1 A:HIS42 3.0 96.3 1.0
CG A:HIS42 3.0 90.4 1.0
CD2 A:HIS112 3.1 0.2 1.0
CD2 A:HIS108 3.2 97.6 1.0
CB A:HIS42 3.4 85.7 1.0
CE1 A:HIS112 3.5 0.5 1.0
CA A:HIS42 4.0 86.4 1.0
CG A:GLU24 4.1 95.9 1.0
NE2 A:HIS42 4.1 89.9 1.0
ND1 A:HIS108 4.1 97.9 1.0
CD2 A:HIS42 4.2 89.1 1.0
CG A:HIS108 4.3 97.8 1.0
CG A:HIS112 4.3 0.0 1.0
ND1 A:HIS112 4.5 0.2 1.0
N A:HIS42 4.5 89.7 1.0
CD1 A:LEU26 4.6 0.9 1.0

Zinc binding site 2 out of 8 in 5yi3

Go back to Zinc Binding Sites List in 5yi3
Zinc binding site 2 out of 8 in the Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:80.0
occ:1.00
NE2 B:HIS108 2.0 76.9 1.0
OE1 B:GLU24 2.1 85.6 1.0
ND1 B:HIS42 2.1 83.6 1.0
OE2 B:GLU24 2.5 82.7 1.0
CD B:GLU24 2.6 88.0 1.0
NE2 B:HIS112 2.6 91.0 1.0
CE1 B:HIS108 2.6 78.3 1.0
CD2 B:HIS112 3.1 89.7 1.0
CE1 B:HIS42 3.1 87.8 1.0
CG B:HIS42 3.1 78.9 1.0
CD2 B:HIS108 3.2 77.8 1.0
CB B:HIS42 3.4 76.2 1.0
ND1 B:HIS108 3.8 79.8 1.0
CE1 B:HIS112 3.8 95.3 1.0
CA B:HIS42 4.1 77.6 1.0
CG B:HIS108 4.1 79.0 1.0
CG B:GLU24 4.1 84.2 1.0
CD1 B:LEU26 4.2 93.5 1.0
NE2 B:HIS42 4.2 90.0 1.0
CD2 B:HIS42 4.2 82.2 1.0
CG B:HIS112 4.4 94.5 1.0
N B:HIS42 4.7 75.3 1.0
ND1 B:HIS112 4.7 97.7 1.0
CE B:MET45 4.9 84.2 1.0
SD B:MET45 4.9 90.5 1.0
O B:HIS108 5.0 84.0 1.0
CB B:GLU24 5.0 90.0 1.0

Zinc binding site 3 out of 8 in 5yi3

Go back to Zinc Binding Sites List in 5yi3
Zinc binding site 3 out of 8 in the Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:77.1
occ:1.00
OE2 E:GLU24 2.1 83.1 1.0
ND1 E:HIS42 2.1 77.3 1.0
NE2 E:HIS108 2.2 81.4 1.0
NE2 E:HIS112 2.2 85.0 1.0
OE1 E:GLU24 2.4 82.8 1.0
CD E:GLU24 2.5 86.7 1.0
CE1 E:HIS42 2.8 73.0 1.0
CD2 E:HIS112 2.9 85.2 1.0
CE1 E:HIS108 2.9 81.2 1.0
CD2 E:HIS108 3.3 82.2 1.0
CG E:HIS42 3.3 75.4 1.0
CE1 E:HIS112 3.4 90.4 1.0
CB E:HIS42 3.9 65.7 1.0
CG E:GLU24 3.9 85.6 1.0
NE2 E:HIS42 4.0 68.6 1.0
ND1 E:HIS108 4.1 84.5 1.0
CG E:HIS112 4.1 86.0 1.0
CD2 E:HIS42 4.3 73.5 1.0
CA E:HIS42 4.3 68.7 1.0
CG E:HIS108 4.3 83.4 1.0
ND1 E:HIS112 4.4 88.7 1.0
CD1 E:LEU26 4.5 84.5 1.0
N E:HIS42 4.7 77.2 1.0
CD2 E:LEU26 4.9 89.6 1.0
CB E:GLU24 4.9 84.3 1.0

Zinc binding site 4 out of 8 in 5yi3

Go back to Zinc Binding Sites List in 5yi3
Zinc binding site 4 out of 8 in the Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:76.3
occ:1.00
NE2 F:HIS108 2.0 75.3 1.0
NE2 F:HIS112 2.2 76.8 1.0
ND1 F:HIS42 2.2 75.1 1.0
OE1 F:GLU24 2.3 81.2 1.0
OE2 F:GLU24 2.6 82.5 1.0
CD F:GLU24 2.7 85.6 1.0
CD2 F:HIS112 2.9 77.6 1.0
CD2 F:HIS108 2.9 77.6 1.0
CE1 F:HIS42 3.0 77.6 1.0
CE1 F:HIS108 3.0 71.7 1.0
CG F:HIS42 3.3 66.8 1.0
CE1 F:HIS112 3.3 81.4 1.0
CB F:HIS42 3.7 66.8 1.0
CG F:HIS108 4.1 80.0 1.0
ND1 F:HIS108 4.1 75.9 1.0
CG F:HIS112 4.1 79.8 1.0
NE2 F:HIS42 4.2 73.1 1.0
CG F:GLU24 4.2 85.4 1.0
CA F:HIS42 4.3 65.1 1.0
ND1 F:HIS112 4.3 80.5 1.0
CD2 F:HIS42 4.3 67.6 1.0
CD1 F:LEU26 4.4 85.1 1.0
CD2 F:LEU26 4.7 89.9 1.0
OG F:SER38 4.8 84.7 1.0
CE F:MET45 4.9 73.2 1.0
N F:HIS42 4.9 68.6 1.0
O F:HIS108 4.9 83.2 1.0
CG F:LEU26 4.9 89.3 1.0
SD F:MET45 5.0 75.6 1.0

Zinc binding site 5 out of 8 in 5yi3

Go back to Zinc Binding Sites List in 5yi3
Zinc binding site 5 out of 8 in the Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:70.6
occ:1.00
ND1 I:HIS42 2.0 68.3 1.0
NE2 I:HIS112 2.1 68.2 1.0
OE1 I:GLU24 2.2 73.4 1.0
OE2 I:GLU24 2.2 75.6 1.0
NE2 I:HIS108 2.2 72.6 1.0
CD I:GLU24 2.5 75.7 1.0
CE1 I:HIS42 2.8 62.4 1.0
CE1 I:HIS108 2.9 73.6 1.0
CD2 I:HIS112 3.0 68.9 1.0
CE1 I:HIS112 3.1 69.8 1.0
CG I:HIS42 3.2 66.4 1.0
CD2 I:HIS108 3.4 74.2 1.0
CB I:HIS42 3.7 64.3 1.0
NE2 I:HIS42 4.0 63.1 1.0
CG I:GLU24 4.0 73.3 1.0
ND1 I:HIS108 4.1 74.9 1.0
CG I:HIS112 4.2 66.4 1.0
ND1 I:HIS112 4.2 64.8 1.0
CD2 I:HIS42 4.2 65.0 1.0
CA I:HIS42 4.2 65.5 1.0
CG I:HIS108 4.4 75.2 1.0
CD2 I:LEU26 4.7 73.5 1.0
CE I:MET45 4.7 66.9 1.0
N I:HIS42 4.7 68.7 1.0
CB I:GLU24 4.9 75.1 1.0
CD1 I:LEU26 4.9 70.8 1.0
O I:SER38 4.9 67.8 1.0

Zinc binding site 6 out of 8 in 5yi3

Go back to Zinc Binding Sites List in 5yi3
Zinc binding site 6 out of 8 in the Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn201

b:75.0
occ:1.00
NE2 J:HIS108 2.0 72.3 1.0
NE2 J:HIS112 2.1 74.0 1.0
OE1 J:GLU24 2.2 75.5 1.0
ND1 J:HIS42 2.2 72.4 1.0
OE2 J:GLU24 2.6 75.0 1.0
CD2 J:HIS112 2.6 73.5 1.0
CD J:GLU24 2.7 78.8 1.0
CE1 J:HIS108 2.8 72.5 1.0
CD2 J:HIS108 3.1 74.4 1.0
CG J:HIS42 3.2 69.5 1.0
CE1 J:HIS42 3.2 74.9 1.0
CE1 J:HIS112 3.3 78.6 1.0
CB J:HIS42 3.5 67.3 1.0
CD1 J:LEU26 3.8 79.6 1.0
CG J:HIS112 3.9 73.5 1.0
ND1 J:HIS108 4.0 77.6 1.0
CG J:HIS108 4.1 76.7 1.0
CA J:HIS42 4.1 66.3 1.0
CG J:GLU24 4.2 80.0 1.0
ND1 J:HIS112 4.2 76.1 1.0
NE2 J:HIS42 4.3 74.6 1.0
CD2 J:HIS42 4.3 69.2 1.0
CG J:LEU26 4.7 81.8 1.0
N J:HIS42 4.8 69.7 1.0
O J:HIS108 4.8 76.8 1.0
OG J:SER38 4.9 84.5 1.0
CD2 J:LEU26 5.0 82.0 1.0
O J:SER38 5.0 75.0 1.0

Zinc binding site 7 out of 8 in 5yi3

Go back to Zinc Binding Sites List in 5yi3
Zinc binding site 7 out of 8 in the Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:91.5
occ:1.00
ND1 M:HIS42 2.1 90.9 1.0
OE2 M:GLU24 2.1 95.7 1.0
NE2 M:HIS108 2.2 96.7 1.0
NE2 M:HIS112 2.3 98.1 1.0
OE1 M:GLU24 2.4 93.4 1.0
CD M:GLU24 2.5 96.0 1.0
CE1 M:HIS42 2.9 91.3 1.0
CD2 M:HIS112 2.9 99.8 1.0
CD2 M:HIS108 3.1 99.2 1.0
CG M:HIS42 3.2 88.8 1.0
CE1 M:HIS108 3.2 96.8 1.0
CE1 M:HIS112 3.5 0.7 1.0
CB M:HIS42 3.6 87.2 1.0
CG M:GLU24 3.9 94.5 1.0
NE2 M:HIS42 4.1 88.6 1.0
CG M:HIS112 4.2 0.0 1.0
CD2 M:HIS42 4.2 86.1 1.0
CA M:HIS42 4.2 88.1 1.0
CG M:HIS108 4.3 0.8 1.0
ND1 M:HIS108 4.3 98.6 1.0
CD1 M:LEU26 4.4 0.9 1.0
ND1 M:HIS112 4.4 0.7 1.0
N M:HIS42 4.9 91.6 1.0
CB M:GLU24 4.9 95.7 1.0
O M:SER38 5.0 86.1 1.0

Zinc binding site 8 out of 8 in 5yi3

Go back to Zinc Binding Sites List in 5yi3
Zinc binding site 8 out of 8 in the Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Lactococcus Lactis Zitr, C30S Mutant in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn201

b:81.6
occ:1.00
NE2 N:HIS108 2.1 81.1 1.0
ND1 N:HIS42 2.2 86.7 1.0
OE1 N:GLU24 2.2 90.8 1.0
OE2 N:GLU24 2.4 88.7 1.0
NE2 N:HIS112 2.4 91.7 1.0
CD N:GLU24 2.6 92.7 1.0
CD2 N:HIS112 2.9 93.2 1.0
CE1 N:HIS108 2.9 85.6 1.0
CE1 N:HIS42 3.1 87.8 1.0
CD2 N:HIS108 3.2 81.9 1.0
CG N:HIS42 3.2 88.6 1.0
CB N:HIS42 3.6 84.6 1.0
CE1 N:HIS112 3.7 98.6 1.0
ND1 N:HIS108 4.0 86.9 1.0
CG N:GLU24 4.1 88.0 1.0
CA N:HIS42 4.1 85.1 1.0
CD1 N:LEU26 4.2 98.4 1.0
CG N:HIS112 4.2 95.5 1.0
CG N:HIS108 4.2 83.6 1.0
NE2 N:HIS42 4.3 86.8 1.0
CD2 N:HIS42 4.4 86.0 1.0
ND1 N:HIS112 4.5 97.7 1.0
N N:HIS42 4.7 83.6 1.0
CG N:LEU26 4.9 95.0 1.0
CD2 N:LEU26 4.9 91.2 1.0
O N:SER38 4.9 89.7 1.0
CB N:GLU24 5.0 87.7 1.0

Reference:

Y.Song, H.Liu, R.Zhu, C.Yi, P.Chen. Structure of Lactococcus Lactis Zitr Proc.Natl.Acad.Sci.Usa 2017.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1708563115
Page generated: Wed Dec 16 11:23:01 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy