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Zinc in PDB 4ols: The Amidase-2 Domain of LYSGH15

Protein crystallography data

The structure of The Amidase-2 Domain of LYSGH15, PDB code: 4ols was solved by J.Gu, S.Ouyang, Z.J.Liu, W.Han, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.57 / 2.27
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 135.400, 135.400, 107.077, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 16.1

Other elements in 4ols:

The structure of The Amidase-2 Domain of LYSGH15 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Iron (Fe) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Zinc atom in the The Amidase-2 Domain of LYSGH15 (pdb code 4ols). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 17 binding sites of Zinc where determined in the The Amidase-2 Domain of LYSGH15, PDB code: 4ols:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 17 in 4ols

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Zinc binding site 1 out of 17 in the The Amidase-2 Domain of LYSGH15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Amidase-2 Domain of LYSGH15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:35.9
occ:0.49
CD2 A:HIS324 2.1 29.6 1.0
ND1 A:HIS214 2.2 25.8 1.0
O A:HOH692 2.3 29.4 1.0
SG A:CYS332 2.6 17.6 1.0
CG A:HIS324 2.9 29.5 1.0
CE1 A:HIS214 3.1 24.6 1.0
CG A:HIS214 3.2 24.9 1.0
CB A:HIS324 3.2 24.1 1.0
NE2 A:HIS324 3.3 31.1 1.0
O A:HOH752 3.3 53.6 1.0
CB A:HIS214 3.4 19.9 1.0
CB A:CYS332 3.5 27.7 1.0
ND1 A:HIS324 4.1 35.0 1.0
CA A:HIS214 4.2 19.3 1.0
CE1 A:HIS324 4.3 30.3 1.0
NE2 A:HIS214 4.3 26.2 1.0
CD2 A:HIS214 4.3 25.0 1.0
O A:HIS264 4.3 29.6 1.0
O A:HOH601 4.4 22.3 1.0
O A:HOH650 4.4 40.3 1.0
O A:ASN215 4.4 24.0 1.0
O A:HOH649 4.6 34.3 1.0
CA A:HIS324 4.7 20.5 1.0
N A:ASN215 4.7 19.3 1.0
CA A:CYS332 4.9 27.9 1.0

Zinc binding site 2 out of 17 in 4ols

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Zinc binding site 2 out of 17 in the The Amidase-2 Domain of LYSGH15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Amidase-2 Domain of LYSGH15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:78.5
occ:1.00
NE A:ARG219 3.5 31.3 1.0
NH2 A:ARG219 3.5 31.2 1.0
O A:HOH665 3.6 48.5 1.0
CZ A:ARG219 4.0 32.4 1.0
CD A:ARG219 4.7 30.4 1.0
CB A:ARG219 5.0 28.4 1.0

Zinc binding site 3 out of 17 in 4ols

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Zinc binding site 3 out of 17 in the The Amidase-2 Domain of LYSGH15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Amidase-2 Domain of LYSGH15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:74.2
occ:1.00
O A:HOH602 3.7 26.9 1.0
CB A:SER290 3.9 28.0 1.0
O A:HOH738 3.9 67.7 1.0
CA A:SER290 4.1 29.6 1.0
O A:HOH682 4.1 46.9 1.0
N A:SER290 4.8 28.3 1.0

Zinc binding site 4 out of 17 in 4ols

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Zinc binding site 4 out of 17 in the The Amidase-2 Domain of LYSGH15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Amidase-2 Domain of LYSGH15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:82.4
occ:1.00
NH2 C:ARG350 3.6 60.6 1.0
CG A:LYS207 3.7 44.0 1.0
N A:LYS207 3.7 38.4 1.0
NH1 C:ARG350 3.9 59.7 1.0
CB A:LYS207 4.2 35.1 1.0
CZ C:ARG350 4.2 63.0 1.0
CA A:LYS206 4.3 45.4 1.0
CB A:LYS206 4.3 43.6 1.0
C A:LYS206 4.5 41.7 1.0
CA A:LYS207 4.6 36.5 1.0
CD A:LYS207 4.9 52.5 1.0
NZ A:LYS207 4.9 64.2 1.0
CE A:LYS207 4.9 58.1 1.0

Zinc binding site 5 out of 17 in 4ols

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Zinc binding site 5 out of 17 in the The Amidase-2 Domain of LYSGH15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Amidase-2 Domain of LYSGH15 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:42.6
occ:0.48
ND1 B:HIS324 2.0 33.2 1.0
ND1 B:HIS214 2.0 32.2 1.0
O B:HOH665 2.5 31.7 1.0
SG B:CYS332 2.7 35.7 1.0
CG B:HIS324 2.9 34.4 1.0
CE1 B:HIS214 2.9 33.5 1.0
CE1 B:HIS324 3.0 33.4 1.0
CG B:HIS214 3.1 30.1 1.0
CB B:HIS324 3.1 33.1 1.0
CB B:CYS332 3.5 34.0 1.0
CB B:HIS214 3.5 26.6 1.0
CD2 B:HIS324 4.0 34.7 1.0
NE2 B:HIS214 4.0 32.5 1.0
NE2 B:HIS324 4.0 30.7 1.0
CD2 B:HIS214 4.1 31.0 1.0
CA B:HIS214 4.2 26.4 1.0
O B:HOH605 4.3 28.7 1.0
O B:HOH687 4.3 47.6 1.0
O B:HIS264 4.4 36.8 1.0
O B:HOH620 4.5 35.4 1.0
O B:ASN215 4.5 29.7 1.0
CA B:HIS324 4.6 35.3 1.0
N B:ASN215 4.8 26.1 1.0
CA B:CYS332 4.8 34.0 1.0

Zinc binding site 6 out of 17 in 4ols

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Zinc binding site 6 out of 17 in the The Amidase-2 Domain of LYSGH15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Amidase-2 Domain of LYSGH15 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:0.7
occ:1.00
O B:HOH675 2.9 56.1 1.0
O B:HOH626 3.7 34.3 1.0
O B:HIS264 3.9 36.8 1.0
O B:HOH665 4.2 31.7 1.0
CE1 B:HIS324 4.5 33.4 1.0
C B:HIS264 4.5 35.3 1.0
O B:ASN239 4.6 41.2 1.0
O B:TRP263 4.8 35.0 1.0
CA B:HIS264 4.9 36.6 1.0
N B:GLY266 4.9 41.9 1.0
O B:HOH709 5.0 19.1 1.0

Zinc binding site 7 out of 17 in 4ols

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Zinc binding site 7 out of 17 in the The Amidase-2 Domain of LYSGH15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Amidase-2 Domain of LYSGH15 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:0.6
occ:1.00
O B:PRO329 4.7 40.9 1.0

Zinc binding site 8 out of 17 in 4ols

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Zinc binding site 8 out of 17 in the The Amidase-2 Domain of LYSGH15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Amidase-2 Domain of LYSGH15 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:0.8
occ:1.00
O B:HOH648 3.1 36.4 1.0
O B:HOH631 3.3 49.7 1.0
O B:GLY240 4.0 34.8 1.0
O B:HOH625 4.5 35.9 1.0
OH B:TYR245 4.6 42.2 1.0
CD2 B:LEU229 4.7 35.8 1.0
O B:HOH675 4.8 56.1 1.0
C B:GLY240 5.0 35.7 1.0

Zinc binding site 9 out of 17 in 4ols

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Zinc binding site 9 out of 17 in the The Amidase-2 Domain of LYSGH15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Amidase-2 Domain of LYSGH15 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn505

b:0.9
occ:1.00
CD2 B:TRP263 4.1 41.9 1.0
CE2 B:TRP263 4.2 43.8 1.0
CE3 B:TRP263 4.3 41.9 1.0
CG B:TRP263 4.4 42.3 1.0
CZ2 B:TRP263 4.5 44.3 1.0
CZ3 B:TRP263 4.5 44.1 1.0
NE1 B:TRP263 4.6 43.3 1.0
CH2 B:TRP263 4.6 44.8 1.0
CD1 B:TRP263 4.7 43.3 1.0
O B:HOH649 4.8 46.7 1.0
O B:ALA238 4.8 41.3 1.0
O B:HOH612 4.9 38.5 1.0

Zinc binding site 10 out of 17 in 4ols

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Zinc binding site 10 out of 17 in the The Amidase-2 Domain of LYSGH15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Amidase-2 Domain of LYSGH15 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:32.7
occ:0.49
ND1 C:HIS214 2.0 22.5 1.0
CD2 C:HIS324 2.1 22.8 1.0
O C:HOH678 2.3 25.7 1.0
SG C:CYS332 2.7 22.9 1.0
CG C:HIS324 2.8 28.4 1.0
CE1 C:HIS214 2.9 24.0 1.0
CB C:HIS324 3.0 24.4 1.0
CG C:HIS214 3.2 26.2 1.0
NE2 C:HIS324 3.3 27.6 1.0
CB C:CYS332 3.5 31.1 1.0
CB C:HIS214 3.7 21.0 1.0
ND1 C:HIS324 4.0 33.4 1.0
NE2 C:HIS214 4.0 27.7 1.0
CE1 C:HIS324 4.2 29.5 1.0
CD2 C:HIS214 4.2 25.5 1.0
O C:HOH648 4.3 41.1 1.0
O C:HOH606 4.3 26.6 1.0
CA C:HIS214 4.3 24.0 1.0
O C:HIS264 4.3 25.5 1.0
O C:HOH614 4.4 32.9 1.0
CA C:HIS324 4.5 23.8 1.0
O C:ASN215 4.6 25.2 1.0
N C:ASN215 4.9 27.2 1.0
CA C:CYS332 4.9 29.5 1.0

Reference:

J.Gu, F.Feng, X.Feng, C.Sun, L.Lei, W.Ding, F.Niu, L.Jiao, M.Yang, Y.Li, X.Liu, J.Song, Z.Cui, D.Han, C.Du, Y.Yang, S.Ouyang, Z.Liu, W.Han. Structural and Biochemical Characterization Reveals LYSGH15 As An Unprecedented "Ef-Hand-Like" Calcium-Binding Phage Lysin Plos Pathog. V. 10 04109 2014.
ISSN: ISSN 1553-7366
DOI: 10.1371/JOURNAL.PPAT.1004109
Page generated: Wed Dec 16 05:39:14 2020

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