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Manganese in PDB 2qb5: Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+

Enzymatic activity of Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+

All present enzymatic activity of Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+:
2.7.1.134; 2.7.1.159;

Protein crystallography data

The structure of Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+, PDB code: 2qb5 was solved by P.P.Chamberlain, S.A.Lesley, G.Spraggon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.704, 94.315, 130.242, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+ (pdb code 2qb5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+, PDB code: 2qb5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2qb5

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Manganese binding site 1 out of 4 in the Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn553

b:18.4
occ:1.00
 ND2 A:ASN297 2.1 13.0 1.0
O2 A:SO4552 2.2 10.5 0.5
O3B A:ADP557 2.2 17.1 1.0
O A:HOH807 2.2 22.3 1.0
OD2 A:ASP295 2.4 15.4 1.0
OD1 A:ASP295 2.5 15.4 1.0
CG A:ASP295 2.8 16.9 1.0
CG A:ASN297 3.2 20.5 1.0
PB A:ADP557 3.2 18.7 1.0
S A:SO4552 3.4 16.6 0.5
O1B A:ADP557 3.5 19.4 1.0
OD1 A:ASN297 3.5 26.7 1.0
O4 A:SO4552 3.7 8.0 0.5
MN A:MN554 3.8 15.8 1.0
O1 A:SO4552 4.2 14.2 0.5
O A:HOH731 4.2 25.1 1.0
O3A A:ADP557 4.2 20.7 1.0
CB A:ASP295 4.3 16.7 1.0
O2B A:ADP557 4.3 20.3 1.0
CB A:ASN297 4.4 15.6 1.0
NH2 A:ARG106 4.4 17.5 1.0
O3 A:SO4552 4.5 13.9 0.5
O A:ALA161 4.5 21.5 1.0
O A:HOH584 4.6 15.6 1.0
CE1 A:HIS167 4.7 31.5 1.0
O1A A:ADP557 4.7 15.3 1.0
O A:ILE296 4.8 14.8 1.0
O A:HOH639 4.9 20.4 1.0
PA A:ADP557 5.0 15.9 1.0
CA A:ASN297 5.0 14.8 1.0

Manganese binding site 2 out of 4 in 2qb5

Go back to Manganese Binding Sites List in 2qb5
Manganese binding site 2 out of 4 in the Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn554

b:15.8
occ:1.00
 O A:HOH618 2.0 15.6 1.0
OD1 A:ASP281 2.1 15.6 1.0
O1A A:ADP557 2.1 15.3 1.0
OD2 A:ASP295 2.1 15.4 1.0
O1B A:ADP557 2.2 19.4 1.0
O4 A:SO4552 2.2 8.0 0.5
CG A:ASP295 3.1 16.9 1.0
CG A:ASP281 3.3 14.9 1.0
PB A:ADP557 3.3 18.7 1.0
S A:SO4552 3.3 16.6 0.5
PA A:ADP557 3.3 15.9 1.0
CB A:ASP295 3.6 16.7 1.0
O3A A:ADP557 3.6 20.7 1.0
O1 A:SO4552 3.7 14.2 0.5
O2 A:SO4552 3.7 10.5 0.5
O A:HOH771 3.8 41.7 1.0
MN A:MN553 3.8 18.4 1.0
O3B A:ADP557 3.9 17.1 1.0
NZ A:LYS199 4.0 22.8 1.0
OD2 A:ASP281 4.0 17.2 1.0
OD1 A:ASN297 4.1 26.7 1.0
OD1 A:ASP295 4.3 15.4 1.0
O A:HOH646 4.3 23.7 1.0
CB A:ASP281 4.3 13.9 1.0
O3' A:ADP557 4.4 12.2 1.0
O2A A:ADP557 4.4 16.3 1.0
O5' A:ADP557 4.4 16.0 1.0
C5' A:ADP557 4.5 14.7 1.0
O3 A:SO4552 4.6 13.9 0.5
O2B A:ADP557 4.6 20.3 1.0
C3' A:ADP557 4.8 13.0 1.0
ND2 A:ASN297 4.8 13.0 1.0
CG A:ASN297 4.9 20.5 1.0

Manganese binding site 3 out of 4 in 2qb5

Go back to Manganese Binding Sites List in 2qb5
Manganese binding site 3 out of 4 in the Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn555

b:19.8
occ:1.00
 O1A B:ADP558 2.0 18.0 1.0
OD1 B:ASP281 2.0 20.2 1.0
O1B B:ADP558 2.0 19.7 1.0
O B:HOH629 2.1 18.0 1.0
OD1 B:ASP295 2.1 20.0 1.0
O1 B:SO4548 2.2 12.6 0.5
CG B:ASP295 3.2 16.9 1.0
CG B:ASP281 3.2 21.3 1.0
PB B:ADP558 3.2 24.5 1.0
PA B:ADP558 3.3 18.0 1.0
S B:SO4548 3.4 24.6 0.5
O3A B:ADP558 3.6 21.8 1.0
CB B:ASP295 3.6 14.9 1.0
O4 B:SO4548 3.7 23.6 0.5
O3 B:SO4548 3.8 15.8 0.5
NZ B:LYS199 3.8 21.6 1.0
MN B:MN556 3.8 20.8 1.0
O3B B:ADP558 3.8 20.8 1.0
OD2 B:ASP281 3.9 19.3 1.0
OD1 B:ASN297 4.1 26.3 1.0
O B:HOH696 4.2 25.8 1.0
OD2 B:ASP295 4.3 23.1 1.0
CB B:ASP281 4.3 17.0 1.0
O3' B:ADP558 4.3 17.2 1.0
O5' B:ADP558 4.4 17.5 1.0
O2A B:ADP558 4.4 16.8 1.0
C5' B:ADP558 4.5 14.0 1.0
O2B B:ADP558 4.6 25.1 1.0
O2 B:SO4548 4.6 22.3 0.5
C3' B:ADP558 4.8 15.3 1.0
ND2 B:ASN297 5.0 19.5 1.0
CG B:ASN297 5.0 24.6 1.0

Manganese binding site 4 out of 4 in 2qb5

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Manganese binding site 4 out of 4 in the Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Adp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn556

b:20.8
occ:1.00
 O B:HOH772 2.0 22.1 1.0
O3B B:ADP558 2.0 20.8 1.0
OD1 B:ASP295 2.2 20.0 1.0
O3 B:SO4548 2.2 15.8 0.5
ND2 B:ASN297 2.3 19.5 1.0
OD2 B:ASP295 2.4 23.1 1.0
CG B:ASP295 2.6 16.9 1.0
PB B:ADP558 3.1 24.5 1.0
CG B:ASN297 3.2 24.6 1.0
S B:SO4548 3.4 24.6 0.5
O1B B:ADP558 3.4 19.7 1.0
OD1 B:ASN297 3.5 26.3 1.0
O1 B:SO4548 3.8 12.6 0.5
MN B:MN555 3.8 19.8 1.0
O3A B:ADP558 4.1 21.8 1.0
O4 B:SO4548 4.1 23.6 0.5
CB B:ASP295 4.2 14.9 1.0
O2B B:ADP558 4.3 25.1 1.0
NH2 B:ARG106 4.3 16.6 1.0
O B:HOH618 4.4 25.3 1.0
O2 B:SO4548 4.5 22.3 0.5
O B:ALA161 4.5 24.6 1.0
CB B:ASN297 4.5 17.4 1.0
O B:HOH566 4.6 17.3 1.0
O1A B:ADP558 4.6 18.0 1.0
CE1 B:HIS167 4.6 27.0 1.0
O B:ILE296 4.8 16.4 1.0
O B:HOH613 4.8 23.1 1.0
PA B:ADP558 4.9 18.0 1.0
ND1 B:HIS167 5.0 27.4 1.0

Reference:

P.P.Chamberlain, X.Qian, A.R.Stiles, J.Cho, D.H.Jones, S.A.Lesley, E.A.Grabau, S.B.Shears, G.Spraggon. Integration of Inositol Phosphate Signaling Pathways Via Human ITPK1. J.Biol.Chem. V. 282 28117 2007.
ISSN: ISSN 0021-9258
PubMed: 17616525
DOI: 10.1074/JBC.M703121200
Page generated: Sat Oct 5 14:59:35 2024

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