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Zinc in PDB 5zjk: Structure of Myroilysin

Protein crystallography data

The structure of Structure of Myroilysin, PDB code: 5zjk was solved by W.D.Li, T.T.Ran, D.Q.Xu, W.W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 125.176, 115.902, 163.354, 90.00, 93.71, 90.00
R / Rfree (%) 18.7 / 25.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Structure of Myroilysin (pdb code 5zjk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Structure of Myroilysin, PDB code: 5zjk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in 5zjk

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Zinc binding site 1 out of 18 in the Structure of Myroilysin


Mono view


Stereo pair view

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

b:29.8
occ:1.00
NE2 A:HIS150 2.2 20.2 1.0
NE2 A:HIS144 2.2 16.9 1.0
NE2 A:HIS140 2.2 17.4 1.0
CD2 A:HIS144 3.0 15.2 1.0
CD2 A:HIS150 3.0 18.6 1.0
CD2 A:HIS140 3.1 15.3 1.0
O A:HOH453 3.1 19.8 1.0
CE1 A:HIS140 3.3 15.9 1.0
CE1 A:HIS150 3.3 20.6 1.0
CE1 A:HIS144 3.3 15.3 1.0
O A:HOH458 3.7 14.6 1.0
OH A:TYR208 4.0 52.7 1.0
OE2 A:GLU141 4.0 30.0 1.0
CG A:HIS144 4.2 14.2 1.0
CG A:HIS150 4.2 18.8 1.0
CE1 A:TYR208 4.2 23.4 1.0
CG A:HIS140 4.3 14.0 1.0
ND1 A:HIS144 4.3 14.5 1.0
ND1 A:HIS150 4.3 19.6 1.0
ND1 A:HIS140 4.3 15.6 1.0
CZ A:TYR208 4.5 34.8 1.0
CE A:MET206 4.6 16.1 1.0
CD A:GLU141 4.7 30.0 1.0
OE1 A:GLU141 4.7 30.0 1.0

Zinc binding site 2 out of 18 in 5zjk

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Zinc binding site 2 out of 18 in the Structure of Myroilysin


Mono view


Stereo pair view

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

b:28.8
occ:1.00
O B:HOH440 2.2 17.6 1.0
NE2 B:HIS150 2.2 18.5 1.0
NE2 B:HIS140 2.2 17.9 1.0
NE2 B:HIS144 2.3 20.6 1.0
CD2 B:HIS150 2.8 17.4 1.0
OH B:TYR208 3.0 22.9 1.0
CE1 B:HIS140 3.2 16.6 1.0
CD2 B:HIS144 3.2 16.2 1.0
CD2 B:HIS140 3.2 16.3 1.0
CE1 B:HIS144 3.2 16.2 1.0
CE1 B:HIS150 3.4 17.0 1.0
CZ B:TYR208 3.7 17.4 1.0
O B:HOH450 3.7 18.5 1.0
CE2 B:TYR208 3.9 17.8 1.0
CG B:HIS150 4.1 17.0 1.0
OE2 B:GLU141 4.2 30.0 1.0
ND1 B:HIS140 4.3 16.4 1.0
ND1 B:HIS150 4.3 17.3 1.0
ND1 B:HIS144 4.3 16.1 1.0
CG B:HIS140 4.3 16.9 1.0
CG B:HIS144 4.3 15.3 1.0
OE1 B:GLU141 4.6 30.0 1.0
CE1 B:TYR208 4.7 17.5 1.0
CE B:MET206 4.8 16.3 1.0
CD B:GLU141 4.8 30.0 1.0

Zinc binding site 3 out of 18 in 5zjk

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Zinc binding site 3 out of 18 in the Structure of Myroilysin


Mono view


Stereo pair view

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

b:43.8
occ:1.00
O C:HOH456 2.2 21.4 1.0
NE2 C:HIS150 2.2 20.3 1.0
NE2 C:HIS144 2.2 17.3 1.0
NE2 C:HIS140 2.2 17.8 1.0
CD2 C:HIS150 3.0 19.5 1.0
CD2 C:HIS140 3.1 15.4 1.0
OH C:TYR208 3.1 18.7 1.0
CD2 C:HIS144 3.1 15.6 1.0
CE1 C:HIS150 3.2 19.7 1.0
CE1 C:HIS144 3.3 17.2 1.0
CE1 C:HIS140 3.3 17.2 1.0
O C:HOH464 3.8 15.1 1.0
CZ C:TYR208 3.9 18.9 1.0
O C:HOH444 4.1 16.2 1.0
CG C:HIS150 4.2 19.8 1.0
ND1 C:HIS150 4.3 20.2 1.0
CG C:HIS140 4.3 17.6 1.0
CE2 C:TYR208 4.3 19.2 1.0
CG C:HIS144 4.3 14.1 1.0
ND1 C:HIS140 4.3 15.0 1.0
ND1 C:HIS144 4.3 15.2 1.0
OE2 C:GLU141 4.4 30.0 1.0
OE1 C:GLU141 4.5 30.0 1.0
CE C:MET206 4.7 16.0 1.0
CE1 C:TYR208 4.8 18.5 1.0
CD C:GLU141 4.8 30.0 1.0
O C:HIS140 5.0 15.9 1.0

Zinc binding site 4 out of 18 in 5zjk

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Zinc binding site 4 out of 18 in the Structure of Myroilysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Myroilysin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:30.3
occ:1.00
O D:HOH426 2.2 19.0 1.0
NE2 D:HIS150 2.2 20.4 1.0
NE2 D:HIS140 2.2 18.8 1.0
NE2 D:HIS144 2.2 20.0 1.0
OH D:TYR208 2.9 22.4 1.0
CD2 D:HIS150 2.9 18.8 1.0
CE1 D:HIS144 3.2 17.8 1.0
CD2 D:HIS140 3.2 17.9 1.0
CE1 D:HIS140 3.2 18.0 1.0
CD2 D:HIS144 3.3 17.5 1.0
CE1 D:HIS150 3.3 19.6 1.0
CZ D:TYR208 3.8 19.6 1.0
O D:HOH461 3.9 17.9 1.0
O D:HOH473 4.1 31.3 1.0
OE2 D:GLU141 4.2 30.0 1.0
CG D:HIS150 4.2 19.0 1.0
CE2 D:TYR208 4.2 19.5 1.0
ND1 D:HIS144 4.3 17.4 1.0
ND1 D:HIS140 4.3 17.2 1.0
CG D:HIS140 4.3 17.4 1.0
ND1 D:HIS150 4.3 19.1 1.0
CG D:HIS144 4.4 17.1 1.0
CE1 D:TYR208 4.7 19.9 1.0
CE D:MET206 4.7 17.4 1.0
CD D:GLU141 4.9 30.0 1.0

Zinc binding site 5 out of 18 in 5zjk

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Zinc binding site 5 out of 18 in the Structure of Myroilysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Myroilysin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:31.8
occ:1.00
O E:HOH432 2.2 22.7 1.0
NE2 E:HIS150 2.2 24.1 1.0
NE2 E:HIS140 2.2 22.8 1.0
NE2 E:HIS144 2.2 22.3 1.0
CD2 E:HIS150 3.0 23.7 1.0
CD2 E:HIS140 3.1 23.1 1.0
CD2 E:HIS144 3.1 25.5 1.0
CE1 E:HIS150 3.3 22.6 1.0
CE1 E:HIS144 3.3 21.7 1.0
CE1 E:HIS140 3.3 22.7 1.0
OH E:TYR208 3.3 38.6 1.0
O E:HOH446 3.7 21.8 1.0
CZ E:TYR208 4.0 25.1 1.0
OE2 E:GLU141 4.1 30.0 1.0
CE2 E:TYR208 4.1 25.3 1.0
O E:HOH441 4.1 20.4 1.0
CG E:HIS150 4.2 23.5 1.0
CG E:HIS140 4.3 21.7 1.0
ND1 E:HIS150 4.3 22.6 1.0
CG E:HIS144 4.3 21.1 1.0
ND1 E:HIS140 4.3 21.9 1.0
ND1 E:HIS144 4.3 21.3 1.0
OE1 E:GLU141 4.7 30.0 1.0
CD E:GLU141 4.8 30.0 1.0
CE E:MET206 4.9 21.1 1.0

Zinc binding site 6 out of 18 in 5zjk

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Zinc binding site 6 out of 18 in the Structure of Myroilysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Myroilysin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn302

b:32.2
occ:1.00
NE2 F:HIS144 2.2 25.6 1.0
NE2 F:HIS150 2.2 27.7 1.0
NE2 F:HIS140 2.2 25.8 1.0
CD2 F:HIS150 3.0 26.4 1.0
OH F:TYR208 3.1 34.7 1.0
CD2 F:HIS144 3.2 33.4 1.0
CE1 F:HIS144 3.2 29.1 1.0
CD2 F:HIS140 3.2 25.7 1.0
CE1 F:HIS140 3.2 26.0 1.0
CE1 F:HIS150 3.3 27.1 1.0
OE2 F:GLU141 3.8 30.0 1.0
O F:HOH418 3.8 23.6 1.0
CZ F:TYR208 3.8 26.6 1.0
O F:HOH442 3.9 23.6 1.0
CE2 F:TYR208 4.0 27.4 1.0
CG F:HIS150 4.2 25.4 1.0
ND1 F:HIS144 4.3 26.4 1.0
CG F:HIS144 4.3 24.9 1.0
ND1 F:HIS140 4.3 25.7 1.0
ND1 F:HIS150 4.3 26.2 1.0
CG F:HIS140 4.3 25.1 1.0
OE1 F:GLU141 4.4 30.0 1.0
CD F:GLU141 4.5 30.0 1.0
CE F:MET206 4.8 25.1 1.0
CE1 F:TYR208 4.9 26.3 1.0

Zinc binding site 7 out of 18 in 5zjk

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Zinc binding site 7 out of 18 in the Structure of Myroilysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Myroilysin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn302

b:28.3
occ:1.00
NE2 G:HIS150 2.2 27.7 1.0
NE2 G:HIS140 2.2 26.8 1.0
NE2 G:HIS144 2.2 28.8 1.0
CD2 G:HIS150 3.1 26.8 1.0
CD2 G:HIS144 3.1 26.3 1.0
OH G:TYR208 3.1 41.4 1.0
CD2 G:HIS140 3.1 27.6 1.0
CE1 G:HIS150 3.2 26.6 1.0
O G:HOH406 3.2 27.9 1.0
CE1 G:HIS140 3.2 27.3 1.0
CE1 G:HIS144 3.3 26.4 1.0
O G:HOH424 3.7 26.7 1.0
CZ G:TYR208 3.8 32.2 1.0
CE2 G:TYR208 4.0 28.5 1.0
OE2 G:GLU141 4.1 30.0 1.0
CG G:HIS150 4.2 25.9 1.0
ND1 G:HIS150 4.2 25.7 1.0
CG G:HIS140 4.3 26.8 1.0
ND1 G:HIS140 4.3 26.3 1.0
CG G:HIS144 4.3 25.6 1.0
ND1 G:HIS144 4.3 25.5 1.0
OE1 G:GLU141 4.4 30.0 1.0
CD G:GLU141 4.6 30.0 1.0
CE1 G:TYR208 4.7 29.3 1.0
CE G:MET206 4.7 25.9 1.0
O G:HIS140 4.9 26.2 1.0

Zinc binding site 8 out of 18 in 5zjk

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Zinc binding site 8 out of 18 in the Structure of Myroilysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Myroilysin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn302

b:24.5
occ:1.00
NE2 H:HIS150 2.2 24.6 1.0
NE2 H:HIS140 2.2 25.6 1.0
NE2 H:HIS144 2.2 23.7 1.0
CD2 H:HIS140 3.0 26.1 1.0
CD2 H:HIS144 3.1 23.9 1.0
CD2 H:HIS150 3.1 25.0 1.0
CE1 H:HIS150 3.2 24.8 1.0
OH H:TYR208 3.3 33.8 1.0
CE1 H:HIS144 3.3 23.5 1.0
CE1 H:HIS140 3.3 26.0 1.0
OE2 H:GLU141 3.5 30.0 1.0
O H:HOH419 3.8 27.8 1.0
O H:HOH424 3.9 26.2 1.0
CZ H:TYR208 3.9 26.7 1.0
CE2 H:TYR208 4.0 26.3 1.0
CG H:HIS140 4.2 26.1 1.0
OE1 H:GLU141 4.2 30.0 1.0
ND1 H:HIS150 4.2 23.8 1.0
CG H:HIS150 4.3 24.6 1.0
CD H:GLU141 4.3 30.0 1.0
CG H:HIS144 4.3 23.7 1.0
ND1 H:HIS140 4.3 25.6 1.0
ND1 H:HIS144 4.3 23.4 1.0
CE H:MET206 4.9 24.7 1.0
CE1 H:TYR208 5.0 27.4 1.0
O H:SER102 5.0 34.3 1.0

Zinc binding site 9 out of 18 in 5zjk

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Zinc binding site 9 out of 18 in the Structure of Myroilysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Myroilysin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn302

b:25.5
occ:1.00
O I:HOH412 2.2 29.6 1.0
NE2 I:HIS150 2.2 29.1 1.0
NE2 I:HIS140 2.2 29.3 1.0
NE2 I:HIS144 2.2 29.6 1.0
CD2 I:HIS150 2.9 29.4 1.0
OH I:TYR208 2.9 29.2 1.0
CE1 I:HIS140 3.0 31.5 1.0
CD2 I:HIS144 3.1 33.6 1.0
CD2 I:HIS140 3.3 29.5 1.0
CE1 I:HIS144 3.3 29.8 1.0
CE1 I:HIS150 3.4 28.5 1.0
CZ I:TYR208 3.7 29.7 1.0
CE2 I:TYR208 3.9 29.0 1.0
OE1 I:GLU141 3.9 37.0 1.0
CG I:HIS150 4.1 28.4 1.0
OE2 I:GLU141 4.2 51.2 1.0
ND1 I:HIS140 4.2 29.7 1.0
CG I:HIS144 4.3 30.4 1.0
ND1 I:HIS150 4.3 28.0 1.0
ND1 I:HIS144 4.3 35.5 1.0
CG I:HIS140 4.4 29.1 1.0
CD I:GLU141 4.5 30.4 1.0
CE I:MET206 4.7 29.7 1.0
CE1 I:TYR208 4.8 30.2 1.0

Zinc binding site 10 out of 18 in 5zjk

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Zinc binding site 10 out of 18 in the Structure of Myroilysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Myroilysin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn302

b:30.3
occ:1.00
O J:HOH431 2.2 19.1 1.0
NE2 J:HIS150 2.2 19.7 1.0
NE2 J:HIS140 2.2 19.0 1.0
NE2 J:HIS144 2.2 19.0 1.0
OH J:TYR208 3.0 31.0 1.0
CD2 J:HIS150 3.1 18.8 1.0
CD2 J:HIS140 3.1 17.9 1.0
CD2 J:HIS144 3.2 17.4 1.0
CE1 J:HIS150 3.2 18.7 1.0
CE1 J:HIS140 3.2 18.2 1.0
CE1 J:HIS144 3.2 17.9 1.0
CZ J:TYR208 3.7 22.5 1.0
OE2 J:GLU141 3.8 17.6 1.0
O J:HOH465 3.8 26.7 1.0
O J:HOH451 4.0 19.6 1.0
CE2 J:TYR208 4.1 20.6 1.0
O J:HOH416 4.2 19.2 1.0
CG J:HIS150 4.2 18.1 1.0
ND1 J:HIS150 4.2 18.5 1.0
CG J:HIS140 4.3 17.4 1.0
ND1 J:HIS140 4.3 17.6 1.0
OE1 J:GLU141 4.3 29.8 1.0
ND1 J:HIS144 4.3 17.0 1.0
CG J:HIS144 4.3 17.4 1.0
CD J:GLU141 4.4 22.7 1.0
CE1 J:TYR208 4.7 20.9 1.0
CE J:MET206 4.8 16.8 1.0
O J:HIS140 4.9 16.6 1.0

Reference:

W.D.Li, T.T.Ran, D.Q.Xu, M.X.Xu, W.W.Wang. Structure of Myroilysin To Be Published.
Page generated: Mon Oct 28 16:57:21 2024

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