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Zinc in PDB 1z83: Crystal Structure of Human AK1A in Complex with AP5A

Enzymatic activity of Crystal Structure of Human AK1A in Complex with AP5A

All present enzymatic activity of Crystal Structure of Human AK1A in Complex with AP5A:
2.7.4.3;

Protein crystallography data

The structure of Crystal Structure of Human AK1A in Complex with AP5A, PDB code: 1z83 was solved by P.Filippakopoulos, G.Bunkoczi, A.Jansson, A.Schreurs, S.Knapp, A.Edwards, F.Von Delft, M.Sundstrom, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.194, 46.259, 119.576, 90.00, 116.01, 90.00
R / Rfree (%) 16.9 / 21.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human AK1A in Complex with AP5A (pdb code 1z83). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Human AK1A in Complex with AP5A, PDB code: 1z83:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1z83

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Zinc binding site 1 out of 8 in the Crystal Structure of Human AK1A in Complex with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human AK1A in Complex with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:9.8
occ:1.00
 O A:HOH845 2.0 9.2 1.0
O2D A:AP5631 2.0 8.7 1.0
O1G A:AP5631 2.1 13.1 1.0
O A:HOH838 2.1 7.2 1.0
O A:HOH703 2.1 9.9 1.0
O A:HOH704 2.2 6.5 1.0
PG A:AP5631 3.3 11.0 1.0
PD A:AP5631 3.3 10.1 1.0
O3G A:AP5631 3.6 13.7 1.0
O1E A:AP5631 4.1 10.3 1.0
O2A A:AP5631 4.1 10.8 1.0
O A:HOH730 4.2 13.5 1.0
OD2 A:ASP93 4.2 16.7 1.0
N A:GLY22 4.2 18.8 1.0
O2B A:AP5631 4.2 18.6 1.0
OD1 A:ASP93 4.3 17.1 1.0
O3B A:AP5631 4.4 17.0 1.0
O2G A:AP5631 4.4 11.2 1.0
O3D A:AP5631 4.4 10.4 1.0
NH1 A:ARG138 4.4 17.8 1.0
O1D A:AP5631 4.4 7.5 1.0
CA A:GLY22 4.5 19.1 1.0
OG A:SER38 4.6 20.5 1.0
PA A:AP5631 4.6 8.9 1.0
O3A A:AP5631 4.6 6.4 1.0
O1A A:AP5631 4.6 12.7 1.0
PB A:AP5631 4.7 11.0 1.0
CG A:ASP93 4.7 21.0 1.0
PE A:AP5631 4.7 11.3 1.0
O A:HOH723 4.8 11.2 1.0
O A:HOH802 4.9 22.8 1.0
O A:HOH810 4.9 27.5 1.0

Zinc binding site 2 out of 8 in 1z83

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Zinc binding site 2 out of 8 in the Crystal Structure of Human AK1A in Complex with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human AK1A in Complex with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn641

b:15.3
occ:1.00
 OE2 A:GLU26 2.0 15.3 1.0
O A:HOH840 2.0 15.0 1.0
O A:HOH846 2.1 11.4 1.0
ND1 A:HIS36 2.3 17.6 1.0
CD A:GLU26 3.0 23.7 1.0
CG A:HIS36 3.3 15.5 1.0
CE1 A:HIS36 3.3 29.6 1.0
OE1 A:GLU26 3.3 22.6 1.0
CB A:HIS36 3.5 17.0 1.0
O A:HOH773 4.0 22.3 1.0
O A:HIS36 4.3 15.4 1.0
CG A:GLU26 4.3 20.0 1.0
NE2 A:HIS36 4.4 20.2 1.0
CD2 A:HIS36 4.4 18.8 1.0
C A:HIS36 4.7 16.8 1.0
CA A:HIS36 4.7 17.1 1.0
O A:HOH777 4.8 21.7 1.0
O A:HOH730 5.0 13.5 1.0

Zinc binding site 3 out of 8 in 1z83

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Zinc binding site 3 out of 8 in the Crystal Structure of Human AK1A in Complex with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human AK1A in Complex with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn611

b:13.9
occ:1.00
 O B:HOH805 1.9 11.8 1.0
O1G B:AP5632 2.0 10.9 1.0
O B:HOH776 2.0 14.5 1.0
O B:HOH811 2.2 17.1 1.0
O2D B:AP5632 2.2 12.3 1.0
O B:HOH704 2.3 9.2 1.0
PG B:AP5632 3.3 14.4 1.0
PD B:AP5632 3.4 17.1 1.0
O3G B:AP5632 3.7 13.6 1.0
O1E B:AP5632 4.0 16.6 1.0
O B:HOH741 4.0 19.5 1.0
O2A B:AP5632 4.1 14.4 1.0
O2B B:AP5632 4.1 24.4 1.0
N B:GLY22 4.2 19.5 1.0
OD2 B:ASP93 4.2 22.4 1.0
OD1 B:ASP93 4.3 22.5 1.0
O3B B:AP5632 4.3 14.2 1.0
CA B:GLY22 4.4 18.3 1.0
O3D B:AP5632 4.4 19.7 1.0
O2G B:AP5632 4.4 18.1 1.0
O1A B:AP5632 4.5 18.3 1.0
O1D B:AP5632 4.5 19.5 1.0
NH1 B:ARG138 4.5 20.4 1.0
OG B:SER38 4.6 20.8 1.0
PA B:AP5632 4.6 17.1 1.0
O3A B:AP5632 4.6 12.6 1.0
PB B:AP5632 4.6 16.5 1.0
PE B:AP5632 4.6 18.2 1.0
CG B:ASP93 4.7 18.7 1.0
O B:HOH726 4.7 15.9 1.0
O B:HOH757 4.8 35.9 1.0
O2E B:AP5632 5.0 23.0 1.0

Zinc binding site 4 out of 8 in 1z83

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Zinc binding site 4 out of 8 in the Crystal Structure of Human AK1A in Complex with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human AK1A in Complex with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn642

b:18.4
occ:1.00
 OE1 B:GLU104 2.0 18.7 1.0
OD2 A:ASP74 2.1 22.0 1.0
OE1 B:GLU70 2.1 21.0 1.0
OE2 A:GLU70 2.1 13.9 1.0
CD B:GLU70 2.9 22.7 1.0
CD B:GLU104 3.0 26.8 1.0
CG A:ASP74 3.0 23.1 1.0
OE2 B:GLU70 3.0 21.8 1.0
CD A:GLU70 3.0 25.5 1.0
CG A:GLU70 3.2 24.2 1.0
OE2 B:GLU104 3.2 22.3 1.0
OD1 A:ASP74 3.2 18.7 1.0
NH2 B:ARG108 3.5 18.3 1.0
O B:HOH709 3.9 13.9 1.0
OE1 A:GLU70 4.2 33.8 1.0
O A:HOH884 4.2 35.2 1.0
NH1 B:ARG107 4.3 46.1 1.0
CG B:GLU70 4.3 28.1 1.0
CG B:GLU104 4.3 19.1 1.0
CB A:ASP74 4.4 14.0 1.0
CZ B:ARG108 4.5 15.1 1.0
CB A:GLU70 4.7 22.7 1.0
O A:GLU70 4.8 18.1 1.0
O A:HOH775 4.9 21.2 1.0
CD2 B:LEU69 5.0 29.5 1.0

Zinc binding site 5 out of 8 in 1z83

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Zinc binding site 5 out of 8 in the Crystal Structure of Human AK1A in Complex with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human AK1A in Complex with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn643

b:20.5
occ:1.00
 O B:HOH806 1.8 20.7 1.0
O B:HOH812 2.0 18.0 1.0
OE2 B:GLU26 2.0 23.7 1.0
ND1 B:HIS36 2.2 19.6 1.0
CD B:GLU26 3.0 24.5 1.0
CE1 B:HIS36 3.0 14.7 1.0
CG B:HIS36 3.2 19.2 1.0
OE1 B:GLU26 3.2 28.1 1.0
CB B:HIS36 3.6 15.8 1.0
O B:HOH748 4.0 26.4 1.0
NE2 B:HIS36 4.2 20.1 1.0
CD2 B:HIS36 4.3 21.1 1.0
CG B:GLU26 4.3 26.4 1.0
O B:HIS36 4.4 15.7 1.0
CA B:HIS36 4.8 14.8 1.0
C B:HIS36 4.9 17.0 1.0
O B:HOH741 4.9 19.5 1.0

Zinc binding site 6 out of 8 in 1z83

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Zinc binding site 6 out of 8 in the Crystal Structure of Human AK1A in Complex with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human AK1A in Complex with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn621

b:13.0
occ:1.00
 O C:HOH741 2.1 11.7 1.0
O1G C:AP5633 2.1 11.6 1.0
O C:HOH647 2.1 13.7 1.0
O2D C:AP5633 2.1 10.2 1.0
O C:HOH732 2.2 14.6 1.0
O C:HOH646 2.2 12.6 1.0
PD C:AP5633 3.3 17.6 1.0
PG C:AP5633 3.3 13.2 1.0
O3G C:AP5633 3.6 17.6 1.0
O1E C:AP5633 4.0 11.8 1.0
O C:HOH660 4.0 19.1 1.0
O2A C:AP5633 4.1 14.1 1.0
OD2 C:ASP93 4.1 18.7 1.0
N C:GLY22 4.2 18.6 1.0
OD1 C:ASP93 4.3 20.0 1.0
O3B C:AP5633 4.3 14.6 1.0
O C:HOH721 4.3 37.7 1.0
O2B C:AP5633 4.4 24.2 1.0
O1D C:AP5633 4.4 15.2 1.0
O3D C:AP5633 4.4 18.8 1.0
O1A C:AP5633 4.4 17.6 1.0
CA C:GLY22 4.5 17.1 1.0
O2G C:AP5633 4.5 17.4 1.0
NH1 C:ARG138 4.5 16.4 1.0
OG C:SER38 4.5 23.4 1.0
PA C:AP5633 4.5 15.2 1.0
O3A C:AP5633 4.6 16.7 1.0
CG C:ASP93 4.6 19.5 1.0
PE C:AP5633 4.7 16.0 1.0
O C:HOH672 4.7 16.6 1.0
PB C:AP5633 4.7 17.2 1.0
O2E C:AP5633 5.0 16.9 1.0

Zinc binding site 7 out of 8 in 1z83

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Zinc binding site 7 out of 8 in the Crystal Structure of Human AK1A in Complex with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human AK1A in Complex with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn644

b:19.2
occ:1.00
 O C:HOH742 1.9 18.8 1.0
O C:HOH733 2.0 15.9 1.0
OE2 C:GLU26 2.1 20.0 1.0
ND1 C:HIS36 2.1 19.8 1.0
CD C:GLU26 3.0 26.0 1.0
CE1 C:HIS36 3.1 24.9 1.0
CG C:HIS36 3.1 20.9 1.0
OE1 C:GLU26 3.2 27.5 1.0
CB C:HIS36 3.5 17.4 1.0
O C:HOH656 3.9 22.8 1.0
NE2 C:HIS36 4.2 17.9 1.0
CD2 C:HIS36 4.3 15.3 1.0
O C:HIS36 4.3 16.9 1.0
CG C:GLU26 4.4 24.1 1.0
CA C:HIS36 4.7 17.2 1.0
C C:HIS36 4.7 17.1 1.0
O C:HOH662 4.9 23.2 1.0
O C:HOH660 4.9 19.1 1.0

Zinc binding site 8 out of 8 in 1z83

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Zinc binding site 8 out of 8 in the Crystal Structure of Human AK1A in Complex with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Human AK1A in Complex with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn645

b:15.5
occ:0.50
 OD2 C:ASP74 1.9 18.6 1.0
OE2 C:GLU70 2.1 13.9 1.0
CG C:ASP74 2.7 18.4 1.0
OD1 C:ASP74 2.8 15.9 1.0
CD C:GLU70 3.0 26.2 1.0
CG C:GLU70 3.2 23.0 1.0
O C:HOH657 3.8 26.1 1.0
NH1 C:ARG108 3.9 28.8 1.0
CB C:ASP74 4.1 17.4 1.0
OE1 C:GLU70 4.2 18.7 1.0
O C:GLU70 4.5 16.3 1.0
O C:HOH737 4.6 30.9 0.5
CB C:GLU70 4.7 18.9 1.0
CZ C:ARG108 4.8 38.1 1.0
O C:HOH708 4.8 30.1 1.0
NH2 C:ARG108 5.0 22.3 1.0

Reference:

P.Filippakopoulos, G.Bunkoczi, A.Jansson, A.Schreurs, S.Knapp, A.Edwards, F.Von Delft, M.Sundstrom. Crystal Structure of Human AK1A in Complex with AP5A To Be Published.
Page generated: Wed Oct 16 21:07:46 2024

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