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Zinc in PDB 5mwl: Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5

Enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5

All present enzymatic activity of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5:
2.7.1.158;

Protein crystallography data

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5, PDB code: 5mwl was solved by E.Franco-Echevarria, J.Sanz-Aparicio, B.Gonzalez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.38 / 3.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.623, 140.758, 68.662, 90.00, 106.53, 90.00
R / Rfree (%) 22.5 / 24.5

Other elements in 5mwl:

The structure of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5 (pdb code 5mwl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5, PDB code: 5mwl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5mwl

Go back to Zinc Binding Sites List in 5mwl
Zinc binding site 1 out of 4 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:79.1
occ:1.00
 SG A:CYS181 2.0 69.1 1.0
SG A:CYS162 2.2 79.2 1.0
SG A:CYS159 2.6 79.8 1.0
SG A:CYS291 2.6 86.9 1.0
CB A:CYS181 3.1 68.8 1.0
CB A:CYS291 3.4 86.2 1.0
CB A:CYS162 3.5 78.6 1.0
CA A:CYS181 3.7 66.6 1.0
CB A:CYS159 3.8 84.7 1.0
CB A:ALA293 3.9 0.6 1.0
N A:CYS159 4.3 90.8 1.0
CD A:PRO182 4.3 61.9 1.0
C A:CYS181 4.6 64.8 1.0
N A:CYS162 4.6 78.4 1.0
CA A:CYS162 4.6 79.9 1.0
CA A:CYS159 4.6 86.0 1.0
N A:PRO182 4.7 62.2 1.0
OG A:SER294 4.8 0.4 1.0
CA A:CYS291 4.9 87.6 1.0
N A:CYS181 4.9 67.7 1.0
CD1 A:LEU183 4.9 72.8 1.0
O A:CYS159 5.0 83.9 1.0

Zinc binding site 2 out of 4 in 5mwl

Go back to Zinc Binding Sites List in 5mwl
Zinc binding site 2 out of 4 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:70.6
occ:1.00
 SG A:CYS410 2.0 66.8 1.0
O A:HOH601 2.2 36.9 1.0
NE2 A:HIS129 2.4 63.9 1.0
ND1 A:HIS125 2.6 77.9 1.0
CE1 A:HIS125 2.9 77.4 1.0
CG A:HIS125 3.2 77.4 1.0
CD2 A:HIS129 3.2 64.2 1.0
CB A:CYS410 3.3 68.6 1.0
CE1 A:HIS129 3.4 66.0 1.0
CA A:CYS410 3.6 71.2 1.0
NE2 A:HIS125 3.7 76.2 1.0
N A:LEU411 3.8 80.7 1.0
CD2 A:HIS125 3.8 76.7 1.0
CB A:HIS125 3.9 77.5 1.0
C A:CYS410 4.2 76.5 1.0
CG A:HIS129 4.4 66.0 1.0
CD B:PRO131 4.4 71.1 1.0
ND1 A:HIS129 4.5 67.2 1.0
CG B:PRO131 4.5 73.1 1.0
O A:PRO409 4.7 67.1 1.0
N A:GLN412 4.9 85.9 1.0
N A:CYS410 4.9 69.3 1.0
CA A:LEU411 5.0 82.1 1.0

Zinc binding site 3 out of 4 in 5mwl

Go back to Zinc Binding Sites List in 5mwl
Zinc binding site 3 out of 4 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:96.2
occ:1.00
 SG B:CYS162 2.3 91.2 1.0
SG B:CYS181 2.4 88.4 1.0
SG B:CYS159 2.5 82.6 1.0
SG B:CYS291 2.5 0.9 1.0
CB B:CYS162 3.1 93.9 1.0
CB B:CYS181 3.3 86.7 1.0
CB B:CYS291 3.3 99.1 1.0
CB B:CYS159 4.0 89.5 1.0
CB B:ALA293 4.0 0.2 1.0
CA B:CYS181 4.1 83.4 1.0
N B:CYS159 4.3 92.7 1.0
N B:SER294 4.3 0.6 1.0
CA B:CYS162 4.4 93.2 1.0
N B:CYS162 4.5 91.2 1.0
CA B:CYS159 4.7 91.2 1.0
C B:ALA293 4.7 0.2 1.0
CA B:ALA293 4.7 0.3 1.0
CG1 B:VAL158 4.8 94.7 1.0
N B:ALA293 4.8 0.3 1.0
CA B:CYS291 4.8 97.7 1.0
CB B:SER294 4.8 0.0 1.0
CD B:PRO182 4.8 72.5 1.0
C B:CYS181 4.9 78.0 1.0
CA B:SER294 5.0 0.9 1.0

Zinc binding site 4 out of 4 in 5mwl

Go back to Zinc Binding Sites List in 5mwl
Zinc binding site 4 out of 4 in the Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase From M. Musculus in Complex with Atp and IP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:72.0
occ:1.00
 SG B:CYS410 2.2 62.5 1.0
O B:HOH601 2.2 60.7 1.0
NE2 B:HIS129 2.4 72.9 1.0
ND1 B:HIS125 2.5 88.1 1.0
CE1 B:HIS125 2.8 91.0 1.0
CG B:HIS125 3.2 87.7 1.0
CE1 B:HIS129 3.2 73.1 1.0
CD2 B:HIS129 3.2 70.3 1.0
NE2 B:HIS125 3.5 90.0 1.0
CB B:CYS410 3.7 68.9 1.0
CD2 B:HIS125 3.7 90.8 1.0
CB B:HIS125 3.9 86.9 1.0
CA B:CYS410 4.1 74.7 1.0
ND1 B:HIS129 4.2 71.2 1.0
CG B:HIS129 4.2 69.0 1.0
N B:LEU411 4.3 79.6 1.0
CD A:PRO131 4.3 66.8 1.0
CG A:PRO131 4.6 65.9 1.0
C B:CYS410 4.7 76.6 1.0

Reference:

E.Franco-Echevarria, J.Sanz-Aparicio, C.A.Brearley, J.M.Gonzalez-Rubio, B.Gonzalez. The Crystal Structure of Mammalian Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase Reveals A New Zinc-Binding Site and Key Features For Protein Function. J. Biol. Chem. V. 292 10534 2017.
ISSN: ESSN 1083-351X
PubMed: 28450399
DOI: 10.1074/JBC.M117.780395
Page generated: Sun Oct 27 22:22:49 2024

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