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

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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

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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

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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

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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

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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

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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

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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

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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

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