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Zinc in PDB 5x1h: Structure of Legionella Pneumophila Dotn

Protein crystallography data

The structure of Structure of Legionella Pneumophila Dotn, PDB code: 5x1h was solved by M.J.Kwak, B.H.Oh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.93 / 3.01
Space group P 65 2 2 1
Cell size a, b, c (Å), α, β, γ (°) 155.357, 155.357, 527.711, 90.00, 90.00, 120.00
R / Rfree (%) 25.6 / 29.7

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of Legionella Pneumophila Dotn (pdb code 5x1h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of Legionella Pneumophila Dotn, PDB code: 5x1h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 5x1h

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Zinc binding site 1 out of 12 in the Structure of Legionella Pneumophila Dotn


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Legionella Pneumophila Dotn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:42.2
occ:1.00
 SG A:CYS52 2.4 42.9 1.0
SG A:CYS55 2.4 43.5 1.0
SG A:CYS87 2.4 44.6 1.0
SG A:CYS84 2.4 42.2 1.0
CB A:CYS52 3.2 42.5 1.0
CB A:CYS84 3.4 42.5 1.0
CB A:CYS55 3.5 43.5 1.0
CB A:CYS87 3.5 43.3 1.0
N A:CYS55 3.7 43.5 1.0
N A:CYS84 3.7 42.1 1.0
CA A:CYS84 4.1 42.0 1.0
CA A:CYS55 4.1 43.7 1.0
N A:CYS87 4.2 41.8 1.0
O A:CYS84 4.3 43.8 1.0
CA A:CYS87 4.5 43.0 1.0
CB A:PHE54 4.6 43.7 1.0
C A:CYS84 4.6 42.3 1.0
C A:PHE54 4.7 43.5 1.0
CA A:CYS52 4.7 42.3 1.0
C A:CYS55 4.7 44.1 1.0
CB A:PHE57 4.8 45.0 1.0
C A:ALA83 4.8 42.6 1.0
NE2 A:HIS122 5.0 43.3 1.0
CA A:PHE54 5.0 43.4 1.0
N A:PHE54 5.0 43.0 1.0
CB A:ASN118 5.0 42.9 1.0
N A:GLY56 5.0 43.7 1.0

Zinc binding site 2 out of 12 in 5x1h

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Zinc binding site 2 out of 12 in the Structure of Legionella Pneumophila Dotn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Legionella Pneumophila Dotn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:46.0
occ:1.00
 SG C:CYS55 2.4 47.5 1.0
SG C:CYS84 2.5 46.2 1.0
SG C:CYS87 2.5 53.8 1.0
SG C:CYS52 2.6 47.9 1.0
CB C:CYS55 3.4 47.3 1.0
CB C:CYS87 3.5 45.9 1.0
CB C:CYS52 3.6 48.0 1.0
N C:CYS55 3.8 47.9 1.0
CB C:CYS84 3.9 46.1 1.0
N C:CYS84 4.2 46.5 1.0
CA C:CYS55 4.2 47.5 1.0
N C:CYS87 4.3 44.3 1.0
CB C:PHE54 4.5 48.9 1.0
CA C:CYS87 4.5 44.5 1.0
CA C:CYS84 4.6 46.1 1.0
CE1 C:HIS122 4.6 46.7 1.0
CB C:PHE57 4.6 47.1 1.0
CB C:ASN118 4.7 45.9 1.0
C C:PHE54 4.8 48.8 1.0
N C:GLY56 4.9 47.5 1.0
C C:CYS55 4.9 47.5 1.0
ND2 C:ASN118 4.9 44.8 1.0
N C:PHE57 4.9 47.2 1.0

Zinc binding site 3 out of 12 in 5x1h

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Zinc binding site 3 out of 12 in the Structure of Legionella Pneumophila Dotn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Legionella Pneumophila Dotn within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:46.4
occ:1.00
 SG E:CYS87 2.4 46.6 1.0
SG E:CYS84 2.4 45.7 1.0
SG E:CYS52 2.5 46.7 1.0
SG E:CYS55 2.6 49.4 1.0
CB E:CYS52 3.3 45.5 1.0
CB E:CYS87 3.5 45.9 1.0
CB E:CYS55 3.7 50.1 1.0
CB E:CYS84 3.7 45.4 1.0
N E:CYS84 3.9 44.6 1.0
N E:CYS55 4.1 48.3 1.0
N E:CYS87 4.3 45.4 1.0
CA E:CYS84 4.4 45.7 1.0
CA E:CYS55 4.5 48.9 1.0
CA E:CYS87 4.6 45.3 1.0
O E:CYS84 4.7 46.1 1.0
CB E:PHE54 4.7 48.1 1.0
CB E:PHE57 4.8 46.9 1.0
NE2 E:HIS122 4.8 48.7 1.0
CA E:CYS52 4.8 45.8 1.0
C E:CYS84 4.8 44.3 1.0

Zinc binding site 4 out of 12 in 5x1h

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Zinc binding site 4 out of 12 in the Structure of Legionella Pneumophila Dotn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Legionella Pneumophila Dotn within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:54.8
occ:1.00
 SG G:CYS87 2.4 52.5 1.0
SG G:CYS52 2.5 57.0 1.0
SG G:CYS55 2.5 53.2 1.0
SG G:CYS84 2.7 53.5 1.0
CB G:CYS55 3.4 53.0 1.0
CB G:CYS87 3.6 53.2 1.0
CB G:CYS52 3.6 57.2 1.0
N G:CYS55 3.7 54.6 1.0
CA G:CYS55 4.1 53.9 1.0
CB G:CYS84 4.3 55.0 1.0
CB G:PHE54 4.3 56.5 1.0
N G:CYS84 4.4 57.4 1.0
N G:CYS87 4.5 52.6 1.0
C G:PHE54 4.6 55.0 1.0
CA G:CYS87 4.7 53.0 1.0
CB G:ASN118 4.7 49.3 1.0
CA G:PHE54 4.8 56.9 1.0
N G:PHE54 4.8 57.5 1.0
CA G:CYS84 4.9 56.1 1.0
ND2 G:ASN118 4.9 50.0 1.0
N G:GLY56 4.9 56.2 1.0
C G:CYS55 4.9 54.5 1.0
CD2 G:PHE54 5.0 57.7 1.0
NE2 G:HIS122 5.0 52.2 1.0
CB G:PHE57 5.0 56.3 1.0

Zinc binding site 5 out of 12 in 5x1h

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Zinc binding site 5 out of 12 in the Structure of Legionella Pneumophila Dotn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Legionella Pneumophila Dotn within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn301

b:0.3
occ:1.00
 SG I:CYS52 2.4 64.8 1.0
SG I:CYS84 2.4 62.7 1.0
SG I:CYS55 2.4 64.6 1.0
SG I:CYS87 2.5 62.7 1.0
CB I:CYS52 3.2 64.6 1.0
CB I:CYS87 3.5 60.1 1.0
CB I:CYS84 3.6 63.4 1.0
N I:CYS84 3.7 62.3 1.0
CB I:CYS55 3.7 62.7 1.0
N I:CYS55 4.0 63.8 1.0
CA I:CYS84 4.2 61.9 1.0
N I:CYS87 4.4 58.9 1.0
CA I:CYS55 4.4 63.3 1.0
N I:GLY56 4.5 64.3 1.0
CA I:CYS87 4.6 58.8 1.0
CA I:CYS52 4.6 63.7 1.0
CB I:PHE54 4.7 63.4 1.0
CB I:PHE57 4.7 61.8 1.0
O I:CYS84 4.7 60.0 1.0
N I:PHE57 4.7 63.5 1.0
C I:ALA83 4.8 61.6 1.0
C I:CYS84 4.8 60.4 1.0
CA I:ALA83 4.9 61.0 1.0

Zinc binding site 6 out of 12 in 5x1h

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Zinc binding site 6 out of 12 in the Structure of Legionella Pneumophila Dotn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Legionella Pneumophila Dotn within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn301

b:72.6
occ:1.00
 SG K:CYS87 2.4 67.4 1.0
SG K:CYS84 2.4 69.9 1.0
SG K:CYS52 2.4 71.9 1.0
SG K:CYS55 2.7 74.4 1.0
CB K:CYS87 3.1 67.8 1.0
CB K:CYS52 3.5 72.8 1.0
N K:CYS84 3.7 68.8 1.0
CB K:CYS84 3.7 68.5 1.0
CB K:CYS55 3.9 72.8 1.0
N K:CYS55 4.1 73.8 1.0
CA K:CYS84 4.2 69.3 1.0
N K:CYS87 4.2 66.9 1.0
CA K:CYS87 4.3 66.5 1.0
O K:CYS84 4.5 69.0 1.0
CA K:CYS55 4.5 73.0 1.0
CB K:PHE54 4.6 72.4 1.0
C K:CYS84 4.7 70.0 1.0
CB K:PHE57 4.7 73.3 1.0
C K:ALA83 4.7 69.9 1.0
CB K:ALA83 4.8 70.8 1.0
CA K:ALA83 4.8 71.8 1.0
CE1 K:HIS122 4.8 71.3 1.0
CA K:CYS52 4.9 73.4 1.0
C K:PHE54 4.9 73.6 1.0

Zinc binding site 7 out of 12 in 5x1h

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Zinc binding site 7 out of 12 in the Structure of Legionella Pneumophila Dotn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Legionella Pneumophila Dotn within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn301

b:53.8
occ:1.00
 SG M:CYS55 2.4 58.3 1.0
SG M:CYS87 2.5 53.6 1.0
SG M:CYS84 2.5 53.8 1.0
SG M:CYS52 2.5 54.3 1.0
CB M:CYS84 3.4 52.6 1.0
N M:CYS84 3.5 51.2 1.0
CB M:CYS87 3.5 52.2 1.0
CB M:CYS52 3.5 54.0 1.0
CB M:CYS55 4.0 62.4 1.0
CA M:CYS84 4.0 51.6 1.0
N M:CYS55 4.1 59.3 1.0
N M:CYS87 4.3 51.5 1.0
O M:CYS84 4.5 51.1 1.0
CB M:PHE57 4.5 58.8 1.0
CA M:CYS87 4.5 51.4 1.0
C M:ALA83 4.5 50.6 1.0
C M:CYS84 4.6 51.2 1.0
CA M:CYS55 4.6 60.9 1.0
CA M:ALA83 4.7 50.4 1.0
CB M:PHE54 4.7 56.7 1.0
NE2 M:HIS122 4.8 57.7 1.0
CB M:ALA83 4.9 50.2 1.0
CA M:CYS52 5.0 53.4 1.0
ND2 M:ASN118 5.0 55.6 1.0

Zinc binding site 8 out of 12 in 5x1h

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Zinc binding site 8 out of 12 in the Structure of Legionella Pneumophila Dotn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Legionella Pneumophila Dotn within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn301

b:0.2
occ:1.00
 SG O:CYS52 2.7 99.3 1.0
SG O:CYS55 2.8 96.6 1.0
SG O:CYS87 2.9 97.5 1.0
SG O:CYS84 2.9 97.0 1.0
CB O:CYS52 3.3 99.3 1.0
CB O:CYS87 3.5 94.9 1.0
N O:CYS84 3.7 98.4 1.0
N O:CYS87 4.1 92.8 1.0
CB O:CYS84 4.2 97.7 1.0
CB O:CYS55 4.3 95.1 1.0
CA O:ALA83 4.4 0.2 1.0
CA O:CYS84 4.4 98.5 1.0
CB O:ALA83 4.4 99.3 1.0
CA O:CYS87 4.4 93.3 1.0
N O:CYS55 4.4 97.1 1.0
C O:ALA83 4.5 99.3 1.0
O O:CYS84 4.6 96.7 1.0
CB O:PHE57 4.6 95.3 1.0
NE2 O:HIS122 4.7 89.8 1.0
CA O:CYS52 4.7 99.9 1.0
CB O:PHE86 4.8 92.6 1.0
C O:CYS84 4.8 96.6 1.0
CA O:CYS55 4.9 97.2 1.0
CB O:PHE54 5.0 97.0 1.0
CD2 O:PHE54 5.0 99.8 1.0

Zinc binding site 9 out of 12 in 5x1h

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Zinc binding site 9 out of 12 in the Structure of Legionella Pneumophila Dotn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Legionella Pneumophila Dotn within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn301

b:81.3
occ:1.00
 SG Q:CYS87 2.4 53.5 1.0
SG Q:CYS84 2.5 54.6 1.0
SG Q:CYS55 2.6 56.1 1.0
SG Q:CYS52 2.6 57.8 1.0
CB Q:CYS52 3.3 57.2 1.0
CB Q:CYS84 3.4 55.1 1.0
CB Q:CYS87 3.4 53.0 1.0
N Q:CYS84 3.7 54.6 1.0
CB Q:CYS55 3.8 55.0 1.0
N Q:CYS55 3.9 55.8 1.0
CA Q:CYS84 4.1 54.3 1.0
N Q:CYS87 4.3 52.4 1.0
CA Q:CYS55 4.3 55.4 1.0
O Q:CYS84 4.4 53.6 1.0
CA Q:CYS87 4.5 52.2 1.0
CB Q:PHE57 4.5 55.8 1.0
C Q:CYS84 4.6 53.7 1.0
CB Q:PHE54 4.6 55.0 1.0
N Q:PHE57 4.7 56.5 1.0
NE2 Q:HIS122 4.8 53.8 1.0
CA Q:CYS52 4.8 57.2 1.0
C Q:ALA83 4.8 55.0 1.0
N Q:GLY56 4.8 56.4 1.0
C Q:CYS55 4.8 56.5 1.0

Zinc binding site 10 out of 12 in 5x1h

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Zinc binding site 10 out of 12 in the Structure of Legionella Pneumophila Dotn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Legionella Pneumophila Dotn within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn301

b:76.7
occ:1.00
 SG S:CYS55 2.4 75.2 1.0
SG S:CYS87 2.5 73.9 1.0
SG S:CYS52 2.6 79.9 1.0
SG S:CYS84 2.6 74.9 1.0
CB S:CYS55 3.2 75.0 1.0
CB S:CYS52 3.5 80.4 1.0
N S:CYS55 3.7 78.1 1.0
CB S:CYS87 3.9 75.2 1.0
CA S:CYS55 4.0 76.5 1.0
CB S:CYS84 4.1 76.5 1.0
N S:CYS84 4.3 78.2 1.0
CE1 S:HIS122 4.4 72.7 1.0
N S:GLY56 4.4 77.3 1.0
N S:CYS87 4.7 72.6 1.0
CB S:PHE57 4.7 77.0 1.0
C S:CYS55 4.7 76.8 1.0
CA S:CYS84 4.8 76.2 1.0
N S:PHE57 4.8 77.9 1.0
CB S:PHE54 4.8 75.8 1.0
CB S:ASN118 4.9 68.6 1.0
C S:PHE54 4.9 77.8 1.0
CA S:CYS52 4.9 81.5 1.0
CA S:CYS87 5.0 72.7 1.0

Reference:

M.J.Kwak, J.D.Kim, H.Kim, C.Kim, J.W.Bowman, S.Kim, K.Joo, J.Lee, K.S.Jin, Y.G.Kim, N.K.Lee, J.U.Jung, B.H.Oh. Architecture of the Type IV Coupling Protein Complex of Legionella Pneumophila Nat Microbiol V. 2 17114 2017.
ISSN: ESSN 2058-5276
PubMed: 28714967
DOI: 10.1038/NMICROBIOL.2017.114
Page generated: Mon Oct 28 14:46:12 2024

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