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Zinc in PDB 1k9z: The Papase HAL2P Complexed with Zinc Ions

Enzymatic activity of The Papase HAL2P Complexed with Zinc Ions

All present enzymatic activity of The Papase HAL2P Complexed with Zinc Ions:
3.1.3.7;

Protein crystallography data

The structure of The Papase HAL2P Complexed with Zinc Ions, PDB code: 1k9z was solved by S.Patel, A.Albert, T.L.Blundell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.94 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.682, 45.359, 71.280, 90.00, 111.40, 90.00
R / Rfree (%) 16 / 19

Zinc Binding Sites:

The binding sites of Zinc atom in the The Papase HAL2P Complexed with Zinc Ions (pdb code 1k9z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the The Papase HAL2P Complexed with Zinc Ions, PDB code: 1k9z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 1k9z

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Zinc binding site 1 out of 9 in the The Papase HAL2P Complexed with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Papase HAL2P Complexed with Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:11.9
occ:1.00
 OE2 A:GLU72 2.0 10.8 1.0
O A:HOH518 2.0 10.4 1.0
O A:HOH503 2.1 18.5 1.0
O A:HOH517 2.1 14.0 1.0
O A:HOH793 2.1 12.8 1.0
O A:HOH502 2.2 13.8 1.0
CD A:GLU72 3.0 12.8 1.0
OE1 A:GLU72 3.4 9.6 1.0
ZN A:ZN402 3.5 10.2 1.0
O A:HOH504 3.7 19.5 1.0
O A:HOH505 3.9 23.6 1.0
NZ A:LYS39 4.0 13.3 1.0
O A:PRO44 4.0 12.8 1.0
OE2 A:GLU73 4.0 10.8 1.0
OG1 A:THR147 4.1 11.7 1.0
O A:HOH632 4.2 31.2 1.0
O A:HOH509 4.2 22.9 1.0
OG A:SER43 4.3 16.2 1.0
CG A:GLU72 4.3 10.0 1.0
O A:HOH794 4.4 12.8 1.0
CE A:LYS39 4.4 18.4 1.0
O A:HOH715 4.6 36.0 1.0
CB A:THR147 4.8 10.2 1.0
CB A:SER43 4.9 11.5 1.0
O A:ILE144 5.0 8.0 1.0

Zinc binding site 2 out of 9 in 1k9z

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Zinc binding site 2 out of 9 in the The Papase HAL2P Complexed with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Papase HAL2P Complexed with Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:10.2
occ:1.00
 O A:HOH518 2.0 10.4 1.0
OE1 A:GLU72 2.1 9.6 1.0
OD1 A:ASP142 2.1 8.1 1.0
O A:HOH794 2.1 12.8 1.0
O A:ILE144 2.2 8.0 1.0
CG A:ASP142 2.9 8.2 1.0
OD2 A:ASP142 3.1 11.3 1.0
CD A:GLU72 3.1 12.8 1.0
C A:ILE144 3.2 9.1 1.0
OE2 A:GLU72 3.5 10.8 1.0
ZN A:ZN401 3.5 11.9 1.0
O A:HOH504 3.8 19.5 1.0
OG1 A:THR147 3.9 11.7 1.0
N A:ASP145 3.9 9.8 1.0
N A:ILE144 3.9 8.8 1.0
O A:HOH505 4.0 23.6 1.0
OE2 A:GLU73 4.0 10.8 1.0
OD2 A:ASP49 4.0 10.7 1.0
ZN A:ZN403 4.0 13.2 0.4
CA A:ASP145 4.0 8.7 1.0
CA A:ILE144 4.1 8.9 1.0
O A:HOH503 4.2 18.5 1.0
O A:HOH502 4.3 13.8 1.0
CD A:PRO143 4.3 9.5 1.0
CB A:ASP142 4.3 9.2 1.0
CG A:GLU72 4.4 10.0 1.0
N A:PRO143 4.5 7.7 1.0
CA A:ASP142 4.6 9.6 1.0
C A:ASP142 4.6 8.2 1.0
CB A:GLU72 4.6 9.7 1.0
CB A:ILE144 4.7 9.2 1.0
CG A:PRO143 4.8 8.9 1.0
N A:GLY146 4.9 10.6 1.0
C A:ASP145 4.9 9.5 1.0

Zinc binding site 3 out of 9 in 1k9z

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Zinc binding site 3 out of 9 in the The Papase HAL2P Complexed with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Papase HAL2P Complexed with Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:13.2
occ:0.40
 OD2 A:ASP142 1.9 11.3 1.0
OD1 A:ASP294 2.1 16.1 1.0
OD1 A:ASP145 2.3 19.2 1.0
O A:HOH505 2.5 23.6 1.0
O A:HOH803 2.8 40.4 1.0
O A:HOH511 3.0 14.8 0.5
CG A:ASP145 3.2 13.4 1.0
CG A:ASP142 3.2 8.2 1.0
O A:HOH504 3.2 19.5 1.0
CG A:ASP294 3.2 17.4 1.0
CA A:ASP145 3.6 8.7 1.0
CB A:ASP145 3.6 10.8 1.0
OD2 A:ASP294 3.8 19.8 1.0
OD1 A:ASP142 3.9 8.1 1.0
O A:HOH503 3.9 18.5 1.0
ZN A:ZN402 4.0 10.2 1.0
O A:HOH511 4.1 24.2 0.5
OD2 A:ASP145 4.1 23.7 1.0
N A:GLY146 4.1 10.6 1.0
CD1 A:TRP293 4.2 9.1 1.0
O A:HOH518 4.2 10.4 1.0
CB A:ASP142 4.3 9.2 1.0
CB A:ASP294 4.3 10.3 1.0
C A:ASP145 4.4 9.5 1.0
CA A:ASP294 4.4 9.4 1.0
O A:HOH506 4.5 19.1 1.0
OE1 A:GLU72 4.6 9.6 1.0
O A:ILE144 4.6 8.0 1.0
NE1 A:TRP293 4.6 11.3 1.0
N A:ASP145 4.7 9.8 1.0
N A:ASP294 5.0 10.4 1.0

Zinc binding site 4 out of 9 in 1k9z

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Zinc binding site 4 out of 9 in the The Papase HAL2P Complexed with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Papase HAL2P Complexed with Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:23.8
occ:0.50
 OE2 A:GLU27 1.8 31.1 0.5
OE2 A:GLU89 1.9 27.0 1.0
O A:HOH653 2.1 30.5 1.0
CD A:GLU27 2.5 28.2 0.5
OE1 A:GLU27 2.6 33.4 0.5
CD A:GLU89 2.8 23.7 1.0
OE1 A:GLU89 3.0 19.7 1.0
O A:HOH566 3.1 21.9 1.0
O A:HOH660 3.5 41.4 1.0
O A:HOH738 3.5 43.0 1.0
CG A:GLU27 3.9 27.5 0.5
O A:HOH783 4.0 33.2 1.0
CG A:GLU89 4.2 17.9 1.0
CG1 A:ILE24 4.9 23.6 1.0
CB A:GLU27 4.9 23.0 0.5
CB A:GLU27 4.9 22.9 0.5

Zinc binding site 5 out of 9 in 1k9z

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Zinc binding site 5 out of 9 in the The Papase HAL2P Complexed with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Papase HAL2P Complexed with Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:18.7
occ:0.75
 NE2 A:HIS221 2.1 16.8 1.0
O A:HOH668 2.1 31.2 1.0
NE2 A:HIS224 2.1 22.0 1.0
O A:HOH560 2.1 23.6 1.0
O A:HOH665 2.5 35.4 1.0
CE1 A:HIS221 3.0 13.6 1.0
CD2 A:HIS221 3.1 16.1 1.0
CE1 A:HIS224 3.1 23.3 1.0
CD2 A:HIS224 3.1 24.3 1.0
O A:HOH771 3.3 41.8 1.0
O A:HOH791 3.8 40.5 1.0
ND1 A:HIS221 4.1 16.1 1.0
ND1 A:HIS224 4.2 24.6 1.0
CG A:HIS221 4.2 13.0 1.0
CG A:HIS224 4.2 24.0 1.0
CG2 A:VAL222 4.3 12.8 1.0
O A:GLY306 4.5 13.6 1.0
O A:VAL222 4.8 13.9 1.0
CA A:GLY306 4.8 11.3 1.0

Zinc binding site 6 out of 9 in 1k9z

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Zinc binding site 6 out of 9 in the The Papase HAL2P Complexed with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Papase HAL2P Complexed with Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:12.7
occ:0.50
 NE2 A:HIS244 1.7 20.3 1.0
NE2 A:HIS261 2.0 16.9 1.0
OE2 A:GLU235 2.1 17.6 1.0
O A:HOH720 2.1 40.9 1.0
O A:HOH613 2.4 32.3 1.0
CE1 A:HIS244 2.4 27.9 1.0
CD2 A:HIS244 2.9 10.2 1.0
CE1 A:HIS261 3.0 17.6 1.0
CD A:GLU235 3.0 19.3 1.0
CD2 A:HIS261 3.0 19.0 1.0
OE1 A:GLU235 3.4 20.7 1.0
ND1 A:HIS244 3.6 28.3 1.0
CG A:HIS244 3.9 25.1 1.0
O A:HOH667 4.1 20.0 1.0
ND1 A:HIS261 4.1 16.8 1.0
CG A:HIS261 4.2 16.0 1.0
CG A:GLU235 4.3 13.7 1.0
OG1 A:THR248 4.5 20.7 1.0
CB A:GLU235 4.6 14.4 1.0
OG A:SER259 4.6 25.0 1.0
CB A:SER259 4.6 20.0 1.0
CE A:LYS251 4.8 22.4 1.0

Zinc binding site 7 out of 9 in 1k9z

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Zinc binding site 7 out of 9 in the The Papase HAL2P Complexed with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Papase HAL2P Complexed with Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:19.1
occ:0.65
 NE2 A:HIS191 2.1 15.8 1.0
O A:HOH620 2.1 17.2 1.0
O A:HOH729 2.5 39.0 1.0
O A:HOH646 2.8 15.4 0.5
CD2 A:HIS191 3.0 17.5 1.0
CE1 A:HIS191 3.1 19.8 1.0
CG A:GLU192 3.5 29.0 1.0
O A:HOH522 3.5 28.2 1.0
O A:HOH619 3.7 21.2 1.0
CG A:HIS191 4.2 16.9 1.0
ND1 A:HIS191 4.2 17.6 1.0
OE2 A:GLU192 4.2 29.0 1.0
CD A:GLU192 4.2 32.4 1.0
O A:HOH788 4.5 35.8 1.0
CB A:GLU192 4.7 20.1 1.0
O A:HOH770 4.7 25.4 1.0
O A:HOH768 4.9 37.1 1.0
CB A:ASP187 5.0 17.5 1.0

Zinc binding site 8 out of 9 in 1k9z

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Zinc binding site 8 out of 9 in the The Papase HAL2P Complexed with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Papase HAL2P Complexed with Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:16.7
occ:0.50
 OE1 A:GLU131 1.8 16.6 1.0
CD A:GLU131 2.6 26.3 1.0
OE2 A:GLU131 2.9 30.9 1.0
CD1 A:TYR130 3.8 12.3 1.0
CE1 A:TYR130 4.0 10.9 1.0
CG A:GLU131 4.1 20.8 1.0
N A:GLU131 4.3 12.7 1.0
CB A:GLU131 4.5 14.0 1.0
CA A:TYR130 4.8 12.6 1.0
O A:HOH605 4.9 34.4 1.0
CG A:TYR130 4.9 10.4 1.0

Zinc binding site 9 out of 9 in 1k9z

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Zinc binding site 9 out of 9 in the The Papase HAL2P Complexed with Zinc Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Papase HAL2P Complexed with Zinc Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:26.7
occ:0.50
 OD1 A:ASP342 1.8 17.6 1.0
O A:HOH748 2.0 27.8 1.0
OD2 A:ASP315 2.3 22.7 1.0
O A:HOH786 2.3 38.1 1.0
CG A:ASP342 2.8 19.4 1.0
CG A:ASP315 3.1 21.2 1.0
OD1 A:ASP315 3.1 19.6 1.0
OD2 A:ASP342 3.2 20.9 1.0
O A:HOH739 3.7 37.6 1.0
CB A:ASP342 4.1 13.1 1.0
CG A:ARG338 4.2 26.2 1.0
O A:ASP315 4.4 20.6 1.0
CB A:ASP315 4.5 18.0 1.0
CA A:ASP342 4.5 14.4 1.0
O A:ARG338 4.6 14.6 1.0
N A:ASP342 4.7 12.2 1.0
NE A:ARG338 4.8 47.2 1.0
CD A:ARG338 4.9 39.5 1.0
CD2 A:HIS341 4.9 13.2 1.0

Reference:

S.Patel, A.Albert, T.L.Blundell. HAL2P: Ion Selectivity and Implications on Inhibition Mechanism To Be Published.
Page generated: Sun Oct 13 04:09:47 2024

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