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Magnesium in PDB 1ktg: Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex

Enzymatic activity of Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex

All present enzymatic activity of Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex:
3.6.1.17;

Protein crystallography data

The structure of Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex, PDB code: 1ktg was solved by S.Bailey, S.E.Sedelnikova, G.M.Blackburn, H.M.Abdelghany, P.J.Baker, A.G.Mclennan, J.B.Rafferty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.563, 36.758, 68.941, 90.00, 114.16, 90.00
R / Rfree (%) 18.8 / 22.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex (pdb code 1ktg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex, PDB code: 1ktg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 1ktg

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Magnesium binding site 1 out of 9 in the Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:11.1
occ:1.00
 OE2 A:GLU111 2.1 6.8 1.0
O A:HOH737 2.2 7.5 1.0
O A:HOH729 2.2 10.4 1.0
CD A:GLU111 3.2 7.0 1.0
OE2 A:GLU19 3.7 6.2 1.0
CG A:GLU111 3.7 6.0 1.0
O A:HOH723 3.9 14.3 1.0
OE1 A:GLU111 4.2 7.0 1.0
O A:HOH707 4.4 9.0 1.0
O A:HOH724 4.4 11.6 1.0
CD A:GLU19 4.8 6.7 1.0
NZ A:LYS17 4.8 10.7 1.0
CG A:LYS17 5.0 8.0 1.0

Magnesium binding site 2 out of 9 in 1ktg

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Magnesium binding site 2 out of 9 in the Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:9.0
occ:1.00
 O A:LYS36 2.0 6.5 1.0
OE2 A:GLU56 2.1 5.8 1.0
O1 A:PO4402 2.1 10.6 1.0
O A:HOH722 2.1 9.7 1.0
O A:HOH734 2.1 6.1 1.0
O A:HOH732 2.1 8.1 1.0
CD A:GLU56 3.0 5.9 1.0
MG A:MG505 3.1 8.4 1.0
OE1 A:GLU56 3.2 5.8 1.0
C A:LYS36 3.2 6.1 1.0
P A:PO4402 3.3 10.6 1.0
O4 A:PO4402 3.4 11.4 1.0
OE1 A:GLU103 3.8 6.7 1.0
CA A:GLY37 3.8 6.2 1.0
OE1 A:GLU52 3.9 6.7 1.0
N A:GLY37 4.0 6.1 1.0
O A:HOH741 4.0 17.8 1.0
O A:HOH843 4.1 16.4 1.0
O2 A:PO4402 4.2 11.9 1.0
NZ A:LYS36 4.2 9.7 1.0
N A:LYS36 4.2 6.4 1.0
CE1 A:HIS104 4.2 8.4 1.0
CA A:LYS36 4.3 6.2 1.0
O3 A:PO4402 4.4 10.7 1.0
CG A:GLU56 4.4 6.4 1.0
CD A:LYS36 4.4 7.2 1.0
CG A:LYS36 4.6 6.7 1.0
NE2 A:HIS104 4.6 5.7 1.0
CD A:GLU52 4.7 8.0 1.0
O A:HOH827 4.8 28.4 1.0
CD A:GLU103 4.9 6.6 1.0
CE A:LYS36 4.9 8.3 1.0
O A:OH506 4.9 9.1 1.0

Magnesium binding site 3 out of 9 in 1ktg

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Magnesium binding site 3 out of 9 in the Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:10.5
occ:1.00
 O3 A:PO4402 1.9 10.7 1.0
O A:HOH715 2.0 11.1 1.0
OE2 A:GLU52 2.0 6.1 1.0
O A:OH506 2.1 9.1 1.0
O A:HOH756 2.2 9.1 1.0
O A:HOH752 2.3 15.3 1.0
P A:PO4402 3.0 10.6 1.0
CD A:GLU52 3.0 8.0 1.0
MG A:MG504 3.1 12.5 1.0
O2 A:PO4402 3.4 11.9 1.0
OE1 A:GLU52 3.4 6.7 1.0
O1 A:PO4402 3.5 10.6 1.0
MG A:MG505 3.5 8.4 1.0
N A:HIS38 3.9 5.9 1.0
O A:HOH768 4.0 21.1 1.0
O A:HOH742 4.1 13.8 1.0
NH1 A:ARG51 4.2 7.1 1.0
O A:HOH811 4.2 16.2 1.0
O A:HOH770 4.3 20.0 1.0
O A:HIS38 4.3 6.3 1.0
CA A:GLY37 4.3 6.2 1.0
CG A:GLU52 4.4 6.6 1.0
O4 A:PO4402 4.4 11.4 1.0
C A:GLY37 4.5 6.0 1.0
OD1 A:ASP40 4.5 8.3 1.0
O A:HOH708 4.5 7.6 1.0
OD2 A:ASP40 4.6 8.5 1.0
OE1 A:GLU55 4.6 6.2 1.0
NH2 A:ARG51 4.7 8.5 1.0
CB A:HIS38 4.7 6.7 1.0
CA A:HIS38 4.7 6.4 1.0
OE2 A:GLU103 4.8 7.4 1.0
O A:HOH749 4.9 13.2 1.0
CZ A:ARG51 4.9 7.7 1.0
CG A:ASP40 5.0 8.7 1.0
C A:HIS38 5.0 6.2 1.0
OE1 A:GLU103 5.0 6.7 1.0

Magnesium binding site 4 out of 9 in 1ktg

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Magnesium binding site 4 out of 9 in the Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:12.5
occ:1.00
 O A:OH506 2.0 9.1 1.0
O2 A:PO4402 2.0 11.9 1.0
OE2 A:GLU103 2.1 7.4 1.0
O A:HOH749 2.2 13.2 1.0
O A:HOH756 2.3 9.1 1.0
O A:HOH742 2.3 13.8 1.0
CD A:GLU103 3.1 6.6 1.0
MG A:MG503 3.1 10.5 1.0
P A:PO4402 3.1 10.6 1.0
O3 A:PO4402 3.4 10.7 1.0
OE1 A:GLU103 3.4 6.7 1.0
MG A:MG505 3.6 8.4 1.0
O1 A:PO4402 3.7 10.6 1.0
O A:HOH768 3.8 21.1 1.0
O A:HOH827 4.0 28.4 1.0
O A:HOH752 4.1 15.3 1.0
O A:HOH770 4.1 20.0 1.0
O A:HOH840 4.1 19.6 1.0
O A:HOH811 4.3 16.2 1.0
CG A:GLU103 4.4 6.8 1.0
O4 A:PO4402 4.4 11.4 1.0
O A:HOH708 4.4 7.6 1.0
O A:HOH715 4.7 11.1 1.0
OE2 A:GLU52 4.8 6.1 1.0
OE1 A:GLU52 5.0 6.7 1.0

Magnesium binding site 5 out of 9 in 1ktg

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Magnesium binding site 5 out of 9 in the Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:8.4
occ:1.00
 O1 A:PO4402 2.0 10.6 1.0
OE1 A:GLU52 2.1 6.7 1.0
OE2 A:GLU56 2.1 5.8 1.0
O A:OH506 2.2 9.1 1.0
OE1 A:GLU103 2.2 6.7 1.0
O A:HOH708 2.2 7.6 1.0
CD A:GLU56 3.1 5.9 1.0
CD A:GLU52 3.1 8.0 1.0
MG A:MG502 3.1 9.0 1.0
P A:PO4402 3.2 10.6 1.0
CD A:GLU103 3.2 6.6 1.0
CG A:GLU56 3.5 6.4 1.0
O2 A:PO4402 3.5 11.9 1.0
OE2 A:GLU52 3.5 6.1 1.0
MG A:MG503 3.5 10.5 1.0
MG A:MG504 3.6 12.5 1.0
O A:HOH732 3.6 8.1 1.0
OE2 A:GLU103 3.6 7.4 1.0
O3 A:PO4402 3.6 10.7 1.0
O A:LYS36 4.0 6.5 1.0
OE1 A:GLU56 4.2 5.8 1.0
OE1 A:GLU55 4.3 6.2 1.0
O A:HOH786 4.3 12.9 1.0
O4 A:PO4402 4.4 11.4 1.0
CG A:GLU52 4.5 6.6 1.0
CG A:GLU103 4.5 6.8 1.0
CA A:GLY37 4.6 6.2 1.0
O A:HOH752 4.8 15.3 1.0
CB A:GLU52 4.8 5.8 1.0
O A:HOH756 4.8 9.1 1.0
O A:HOH742 4.8 13.8 1.0
O A:HOH722 4.8 9.7 1.0
C A:LYS36 4.9 6.1 1.0
CB A:GLU103 4.9 6.1 1.0
O A:HOH734 4.9 6.1 1.0
CB A:GLU56 5.0 5.9 1.0

Magnesium binding site 6 out of 9 in 1ktg

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Magnesium binding site 6 out of 9 in the Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:11.5
occ:1.00
 O B:OH605 2.0 8.0 1.0
O4 B:PO4401 2.0 8.9 1.0
O B:HOH611 2.1 10.0 1.0
OE2 B:GLU103 2.1 7.9 1.0
O B:HOH672 2.1 11.8 1.0
O B:HOH654 2.2 6.4 1.0
P B:PO4401 3.1 10.5 1.0
MG B:MG604 3.1 8.3 1.0
CD B:GLU103 3.1 8.1 1.0
O1 B:PO4401 3.3 8.2 1.0
OE1 B:GLU103 3.4 7.4 1.0
MG B:MG603 3.5 10.3 1.0
O3 B:PO4401 3.6 8.4 1.0
O B:HOH703 3.8 19.4 1.0
O B:HOH633 3.9 10.4 1.0
O B:HOH708 4.0 21.1 1.0
O B:HOH700 4.1 25.8 1.0
O B:HOH686 4.1 20.4 1.0
O B:HOH680 4.3 20.7 1.0
O2 B:PO4401 4.4 10.0 1.0
CG B:GLU103 4.4 7.5 1.0
O B:HOH650 4.4 7.0 1.0
O B:HOH705 4.5 20.7 1.0
O B:HOH635 4.7 7.3 1.0
OE2 B:GLU52 4.8 6.0 1.0
O B:HOH669 4.9 10.6 1.0
OE1 B:GLU52 5.0 6.3 1.0

Magnesium binding site 7 out of 9 in 1ktg

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Magnesium binding site 7 out of 9 in the Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:8.2
occ:1.00
 O B:LYS36 2.0 6.1 1.0
O3 B:PO4401 2.0 8.4 1.0
O B:HOH615 2.1 8.5 1.0
O B:HOH607 2.1 7.0 1.0
OE2 B:GLU56 2.1 6.2 1.0
O B:HOH669 2.2 10.6 1.0
CD B:GLU56 3.1 6.4 1.0
MG B:MG603 3.2 10.3 1.0
C B:LYS36 3.2 6.5 1.0
P B:PO4401 3.3 10.5 1.0
OE1 B:GLU56 3.3 4.8 1.0
O2 B:PO4401 3.4 10.0 1.0
CA B:GLY37 3.7 6.1 1.0
OE1 B:GLU103 3.8 7.4 1.0
OE1 B:GLU52 3.9 6.3 1.0
N B:GLY37 3.9 5.9 1.0
NZ B:LYS36 4.2 11.6 1.0
O B:HOH652 4.2 14.2 1.0
O4 B:PO4401 4.2 8.9 1.0
O1 B:PO4401 4.3 8.2 1.0
CD B:LYS36 4.3 8.9 1.0
N B:LYS36 4.3 6.7 1.0
CA B:LYS36 4.3 6.4 1.0
NE2 B:HIS104 4.4 6.9 1.0
CG B:GLU56 4.5 6.5 1.0
CG B:LYS36 4.5 7.7 1.0
O B:HOH703 4.5 19.4 1.0
OH B:TYR27 4.6 14.7 1.0
CE B:LYS36 4.7 11.9 1.0
O B:OH605 4.7 8.0 1.0
CD B:GLU52 4.7 6.3 1.0
CD B:GLU103 4.9 8.1 1.0
CE1 B:HIS104 4.9 4.5 1.0
O B:HOH650 5.0 7.0 1.0
CB B:LYS36 5.0 6.7 1.0

Magnesium binding site 8 out of 9 in 1ktg

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Magnesium binding site 8 out of 9 in the Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:10.3
occ:1.00
 O3 B:PO4401 2.0 8.4 1.0
O B:OH605 2.0 8.0 1.0
O B:HOH650 2.1 7.0 1.0
OE1 B:GLU52 2.1 6.3 1.0
OE2 B:GLU56 2.2 6.2 1.0
OE1 B:GLU103 2.2 7.4 1.0
P B:PO4401 3.1 10.5 1.0
CD B:GLU52 3.1 6.3 1.0
CD B:GLU56 3.2 6.4 1.0
MG B:MG602 3.2 8.2 1.0
CD B:GLU103 3.2 8.1 1.0
MG B:MG604 3.5 8.3 1.0
O B:HOH669 3.5 10.6 1.0
O1 B:PO4401 3.5 8.2 1.0
OE2 B:GLU52 3.5 6.0 1.0
MG B:MG601 3.5 11.5 1.0
CG B:GLU56 3.5 6.5 1.0
OE2 B:GLU103 3.5 7.9 1.0
O4 B:PO4401 3.5 8.9 1.0
O B:LYS36 4.0 6.1 1.0
OE1 B:GLU55 4.2 6.8 1.0
OE1 B:GLU56 4.3 4.8 1.0
O B:HOH665 4.3 12.3 1.0
O2 B:PO4401 4.4 10.0 1.0
O B:HOH633 4.4 10.4 1.0
CG B:GLU52 4.5 5.6 1.0
CA B:GLY37 4.6 6.1 1.0
CG B:GLU103 4.6 7.5 1.0
O B:HOH611 4.6 10.0 1.0
O B:HOH654 4.7 6.4 1.0
C B:LYS36 4.8 6.5 1.0
O B:HOH703 4.8 19.4 1.0
CB B:GLU52 4.8 4.9 1.0
O B:HOH615 4.8 8.5 1.0
O B:HOH607 4.9 7.0 1.0
CB B:GLU103 4.9 7.4 1.0

Magnesium binding site 9 out of 9 in 1ktg

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Magnesium binding site 9 out of 9 in the Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of A C. Elegans AP4A Hydrolase Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:8.3
occ:1.00
 O1 B:PO4401 2.0 8.2 1.0
O B:OH605 2.0 8.0 1.0
O B:HOH635 2.0 7.3 1.0
OE2 B:GLU52 2.1 6.0 1.0
O B:HOH654 2.2 6.4 1.0
O B:HOH633 2.2 10.4 1.0
CD B:GLU52 3.1 6.3 1.0
MG B:MG601 3.1 11.5 1.0
P B:PO4401 3.1 10.5 1.0
OE1 B:GLU52 3.4 6.3 1.0
MG B:MG603 3.5 10.3 1.0
O4 B:PO4401 3.5 8.9 1.0
O3 B:PO4401 3.6 8.4 1.0
O B:HOH611 3.9 10.0 1.0
NH1 B:ARG51 4.0 5.3 1.0
N B:HIS38 4.0 5.9 1.0
O B:HOH708 4.0 21.1 1.0
O B:HOH686 4.2 20.4 1.0
OE1 B:GLU55 4.2 6.8 1.0
O B:HOH723 4.2 13.5 1.0
O B:HIS38 4.3 6.6 1.0
O2 B:PO4401 4.4 10.0 1.0
O B:HOH650 4.4 7.0 1.0
CG B:GLU52 4.4 5.6 1.0
CA B:GLY37 4.4 6.1 1.0
C B:GLY37 4.6 6.0 1.0
CB B:HIS38 4.7 6.4 1.0
NH2 B:ARG51 4.7 6.8 1.0
CA B:HIS38 4.8 6.4 1.0
OE2 B:GLU103 4.8 7.9 1.0
CZ B:ARG51 4.8 6.0 1.0
O B:HOH672 4.8 11.8 1.0
OD1 B:ASP40 4.9 9.6 1.0
OE1 B:GLU103 5.0 7.4 1.0

Reference:

S.Bailey, S.E.Sedelnikova, G.M.Blackburn, H.M.Abdelghany, P.J.Baker, A.G.Mclennan, J.B.Rafferty. The Crystal Structure of Diadenosine Tetraphosphate Hydrolase From Caenorhabditis Elegans in Free and Binary Complex Forms Structure V. 10 589 2002.
ISSN: ISSN 0969-2126
PubMed: 11937063
DOI: 10.1016/S0969-2126(02)00746-3
Page generated: Tue Aug 13 08:09:02 2024

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