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Manganese in PDB 2q7d: Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Amppnp and MN2+

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

All present enzymatic activity of Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-Kinase (ITPK1) in Complex with Amppnp 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 Amppnp and MN2+, PDB code: 2q7d 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 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.157, 94.607, 130.583, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.6

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 Amppnp and MN2+ (pdb code 2q7d). 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 Amppnp and MN2+, PDB code: 2q7d:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2q7d

Go back to Manganese Binding Sites List in 2q7d
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 Amppnp 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 Amppnp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn901

b:8.4
occ:1.00
 O2B A:ANP917 2.1 6.1 1.0
O3G A:ANP917 2.1 7.2 1.0
ND2 A:ASN297 2.1 8.2 1.0
O A:HOH1007 2.3 9.0 1.0
O A:HOH1026 2.4 9.2 1.0
OD1 A:ASP295 2.4 10.9 1.0
OD2 A:ASP295 2.6 9.1 1.0
CG A:ASP295 2.8 7.5 1.0
CG A:ASN297 3.1 12.1 1.0
PB A:ANP917 3.3 8.4 1.0
PG A:ANP917 3.3 9.5 1.0
OD1 A:ASN297 3.4 13.8 1.0
N3B A:ANP917 3.6 7.3 1.0
O A:HOH978 3.9 13.3 1.0
O1G A:ANP917 4.1 10.4 1.0
O A:ALA161 4.1 13.1 1.0
O A:HOH992 4.1 15.0 1.0
O1B A:ANP917 4.2 9.6 1.0
O A:HOH1053 4.2 16.9 1.0
MN A:MN902 4.3 7.9 1.0
NH2 A:ARG106 4.3 12.5 1.0
O A:HOH924 4.3 9.5 1.0
O A:HOH1058 4.3 12.3 1.0
CB A:ASP295 4.3 8.6 1.0
O3A A:ANP917 4.4 7.9 1.0
CB A:ASN297 4.5 8.1 1.0
O2G A:ANP917 4.5 10.5 1.0
O A:ILE296 4.6 11.1 1.0
O A:HOH1235 4.7 29.1 1.0
O2A A:ANP917 4.7 5.8 1.0
PA A:ANP917 4.9 7.6 1.0
C A:ILE296 5.0 8.6 1.0
O1A A:ANP917 5.0 6.9 1.0

Manganese binding site 2 out of 4 in 2q7d

Go back to Manganese Binding Sites List in 2q7d
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 Amppnp 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 Amppnp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn902

b:7.9
occ:1.00
 O2A A:ANP917 2.0 5.8 1.0
OD2 A:ASP281 2.0 11.9 1.0
O A:HOH988 2.2 9.7 1.0
OD2 A:ASP295 2.2 9.1 1.0
O1G A:ANP917 2.2 10.4 1.0
N3B A:ANP917 2.7 7.3 1.0
PG A:ANP917 3.0 9.5 1.0
CG A:ASP295 3.1 7.5 1.0
CG A:ASP281 3.2 11.3 1.0
PA A:ANP917 3.3 7.6 1.0
CB A:ASP295 3.5 8.6 1.0
PB A:ANP917 3.7 8.4 1.0
O3G A:ANP917 3.7 7.2 1.0
O3A A:ANP917 3.8 7.9 1.0
NZ A:LYS199 3.8 11.3 1.0
OD1 A:ASP281 3.9 10.3 1.0
O2B A:ANP917 4.0 6.1 1.0
O A:HOH995 4.1 15.0 1.0
O A:HOH952 4.2 11.7 1.0
CB A:ASP281 4.2 8.7 1.0
O3' A:ANP917 4.2 8.0 1.0
MN A:MN901 4.3 8.4 1.0
O2G A:ANP917 4.3 10.5 1.0
OD1 A:ASP295 4.3 10.9 1.0
OD1 A:ASN297 4.3 13.8 1.0
O1A A:ANP917 4.3 6.9 1.0
O5' A:ANP917 4.4 4.7 1.0
C5' A:ANP917 4.6 6.8 1.0
C3' A:ANP917 4.6 7.2 1.0
CD2 A:LEU197 4.8 9.1 1.0
CA A:ASP295 5.0 8.2 1.0

Manganese binding site 3 out of 4 in 2q7d

Go back to Manganese Binding Sites List in 2q7d
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 Amppnp 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 Amppnp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn903

b:12.4
occ:1.00
 OD2 B:ASP281 2.0 14.4 1.0
O2A B:ANP918 2.0 11.9 1.0
O1G B:ANP918 2.1 12.8 1.0
OD2 B:ASP295 2.1 11.1 1.0
O B:HOH997 2.2 12.6 1.0
N3B B:ANP918 2.7 11.9 1.0
PG B:ANP918 3.0 12.3 1.0
CG B:ASP295 3.1 13.6 1.0
CG B:ASP281 3.2 13.1 1.0
PA B:ANP918 3.3 11.3 1.0
CB B:ASP295 3.5 15.2 1.0
PB B:ANP918 3.8 12.2 1.0
O3G B:ANP918 3.8 12.6 1.0
NZ B:LYS199 3.8 15.3 1.0
O3A B:ANP918 3.8 10.1 1.0
OD1 B:ASP281 3.9 14.6 1.0
O2B B:ANP918 4.0 11.2 1.0
O B:HOH1169 4.0 27.1 1.0
O B:HOH980 4.0 14.4 1.0
OD1 B:ASP295 4.2 15.2 1.0
CB B:ASP281 4.2 10.1 1.0
ND2 B:ASN297 4.2 13.9 1.0
O3' B:ANP918 4.3 13.2 1.0
MN B:MN904 4.3 11.5 1.0
O2G B:ANP918 4.3 13.5 1.0
O5' B:ANP918 4.4 9.6 1.0
O1A B:ANP918 4.4 10.7 1.0
C5' B:ANP918 4.6 10.8 1.0
C3' B:ANP918 4.6 10.7 1.0
CD2 B:LEU197 4.8 15.6 1.0

Manganese binding site 4 out of 4 in 2q7d

Go back to Manganese Binding Sites List in 2q7d
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 Amppnp 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 Amppnp and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn904

b:11.5
occ:1.00
 O2B B:ANP918 2.1 11.2 1.0
OD1 B:ASN297 2.2 14.5 1.0
O3G B:ANP918 2.2 12.6 1.0
O B:HOH1023 2.2 13.4 1.0
OD1 B:ASP295 2.3 15.2 1.0
O B:HOH1136 2.4 15.0 1.0
OD2 B:ASP295 2.7 11.1 1.0
CG B:ASP295 2.9 13.6 1.0
CG B:ASN297 3.1 14.8 1.0
PB B:ANP918 3.3 12.2 1.0
PG B:ANP918 3.3 12.3 1.0
ND2 B:ASN297 3.5 13.9 1.0
N3B B:ANP918 3.6 11.9 1.0
O1G B:ANP918 4.0 12.8 1.0
O B:ALA161 4.1 18.6 1.0
NH2 B:ARG106 4.2 13.4 1.0
O B:HOH1014 4.2 15.6 1.0
O B:HOH1042 4.2 18.6 1.0
O1B B:ANP918 4.3 13.6 1.0
MN B:MN903 4.3 12.4 1.0
O B:HOH938 4.3 11.2 1.0
O B:HOH1214 4.3 33.9 1.0
CB B:ASP295 4.4 15.2 1.0
O B:HOH1225 4.4 27.6 1.0
O3A B:ANP918 4.4 10.1 1.0
CB B:ASN297 4.4 10.5 1.0
O B:ILE296 4.5 12.8 1.0
O2G B:ANP918 4.6 13.5 1.0
O2A B:ANP918 4.8 11.9 1.0
PA B:ANP918 4.9 11.3 1.0
C B:ILE296 5.0 12.1 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 14:58:03 2024

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