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Magnesium in PDB 2i6k: Crystal Structure of Human Type I Ipp Isomerase Complexed with A Substrate Analog

Enzymatic activity of Crystal Structure of Human Type I Ipp Isomerase Complexed with A Substrate Analog

All present enzymatic activity of Crystal Structure of Human Type I Ipp Isomerase Complexed with A Substrate Analog:
5.3.3.2;

Protein crystallography data

The structure of Crystal Structure of Human Type I Ipp Isomerase Complexed with A Substrate Analog, PDB code: 2i6k was solved by C.Zhang, Z.Wei, W.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.40 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.363, 43.074, 70.466, 80.26, 89.98, 67.95
R / Rfree (%) 22 / 26.2

Other elements in 2i6k:

The structure of Crystal Structure of Human Type I Ipp Isomerase Complexed with A Substrate Analog also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Type I Ipp Isomerase Complexed with A Substrate Analog (pdb code 2i6k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Type I Ipp Isomerase Complexed with A Substrate Analog, PDB code: 2i6k:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2i6k

Go back to Magnesium Binding Sites List in 2i6k
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Type I Ipp Isomerase Complexed with A Substrate Analog


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 Human Type I Ipp Isomerase Complexed with A Substrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:27.1
occ:1.00
 O A:HOH541 1.8 26.5 1.0
O5P A:EA2401 1.9 32.5 1.0
O2P A:EA2401 1.9 37.4 1.0
OE2 A:GLU115 2.1 31.6 1.0
O A:CYS86 2.2 31.9 1.0
O A:HOH515 2.3 27.6 1.0
CD A:GLU115 3.1 33.0 1.0
P2 A:EA2401 3.2 37.5 1.0
P1 A:EA2401 3.2 35.4 1.0
C A:CYS86 3.4 33.5 1.0
OE1 A:GLU115 3.4 32.6 1.0
O4P A:EA2401 3.4 36.8 1.0
OG A:SER87 3.5 30.4 0.5
O7P A:EA2401 3.8 37.8 1.0
O3P A:EA2401 3.9 35.4 1.0
N A:CYS86 4.0 34.5 1.0
NH2 A:ARG111 4.1 38.3 1.0
O A:HOH516 4.1 32.0 1.0
CA A:CYS86 4.1 34.5 1.0
NH1 A:ARG70 4.2 34.8 1.0
O1P A:EA2401 4.3 32.3 1.0
O A:HOH508 4.3 36.0 1.0
O6P A:EA2401 4.4 33.6 1.0
N A:SER87 4.4 32.1 1.0
CG A:GLU115 4.4 33.1 1.0
CB A:SER87 4.4 31.4 0.5
CB A:CYS86 4.5 34.8 1.0
NE A:ARG111 4.5 38.4 1.0
CB A:SER87 4.6 32.3 0.5
CA A:SER87 4.6 31.1 0.5
CA A:SER87 4.6 31.7 0.5
NZ A:LYS74 4.6 26.8 1.0
OE1 A:GLU167 4.6 42.0 1.0
CZ A:ARG111 4.8 38.8 1.0
CE A:LYS74 4.9 28.9 1.0

Magnesium binding site 2 out of 4 in 2i6k

Go back to Magnesium Binding Sites List in 2i6k
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Type I Ipp Isomerase Complexed with A Substrate Analog


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 Human Type I Ipp Isomerase Complexed with A Substrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:29.1
occ:0.50
 O A:HOH556 1.9 40.4 1.0
O B:HOH552 1.9 44.2 1.0
OE2 A:GLU97 2.1 41.1 1.0
O A:HOH557 2.1 51.7 1.0
O A:HOH521 2.2 41.1 1.0
OG A:SER99 2.3 45.9 1.0
CD A:GLU97 2.9 40.7 1.0
OE1 A:GLU97 3.1 40.5 1.0
CB A:SER99 3.4 43.8 1.0
NZ B:LYS47 3.7 42.5 1.0
CG A:GLU97 4.3 37.5 1.0
OD1 B:ASN44 4.3 38.2 1.0
O B:HOH520 4.3 38.8 1.0
O A:HOH530 4.3 37.7 1.0
N A:SER99 4.4 43.3 1.0
CA A:SER99 4.5 43.7 1.0
CE B:LYS47 4.8 40.7 1.0

Magnesium binding site 3 out of 4 in 2i6k

Go back to Magnesium Binding Sites List in 2i6k
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Type I Ipp Isomerase Complexed with A Substrate Analog


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 Human Type I Ipp Isomerase Complexed with A Substrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:30.6
occ:1.00
 O2P B:EA2402 1.5 38.8 1.0
O5P B:EA2402 1.7 34.8 1.0
O B:HOH508 2.0 38.0 1.0
O B:CYS86 2.1 31.6 1.0
OE2 B:GLU115 2.1 31.4 1.0
O B:HOH549 2.5 40.9 1.0
P1 B:EA2402 2.9 40.0 1.0
P2 B:EA2402 3.0 38.3 1.0
CD B:GLU115 3.1 32.8 1.0
C B:CYS86 3.3 33.5 1.0
O4P B:EA2402 3.3 38.4 1.0
OG B:SER87 3.4 30.4 0.5
OE1 B:GLU115 3.4 32.6 1.0
O7P B:EA2402 3.7 31.5 1.0
O3P B:EA2402 3.8 41.1 1.0
O1P B:EA2402 3.9 37.3 1.0
N B:CYS86 4.0 34.4 1.0
NH2 B:ARG111 4.0 38.2 1.0
CA B:CYS86 4.1 34.6 1.0
O6P B:EA2402 4.2 33.1 1.0
NH1 B:ARG70 4.2 35.0 1.0
N B:SER87 4.3 32.2 1.0
O B:HOH511 4.3 27.6 1.0
CB B:SER87 4.3 31.5 0.5
NE B:ARG111 4.4 38.4 1.0
CG B:GLU115 4.4 33.1 1.0
CB B:SER87 4.4 32.4 0.5
CB B:CYS86 4.4 34.8 1.0
CA B:SER87 4.5 31.0 0.5
O B:HOH525 4.5 33.1 1.0
CA B:SER87 4.5 31.7 0.5
NZ B:LYS74 4.7 27.0 1.0
OE1 B:GLU167 4.7 42.2 1.0
CZ B:ARG111 4.7 39.0 1.0
C1 B:EA2402 4.9 31.5 1.0
CE B:LYS74 5.0 29.1 1.0

Magnesium binding site 4 out of 4 in 2i6k

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Type I Ipp Isomerase Complexed with A Substrate Analog


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 Human Type I Ipp Isomerase Complexed with A Substrate Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:36.6
occ:0.50
 O B:HOH558 1.9 51.1 1.0
OG B:SER99 2.0 45.9 1.0
O B:HOH559 2.0 49.8 1.0
OE2 B:GLU97 2.3 41.1 1.0
CD B:GLU97 3.2 40.8 1.0
CB B:SER99 3.2 43.9 1.0
OE1 B:GLU97 3.6 40.7 1.0
N B:SER99 4.3 43.3 1.0
CA B:SER99 4.3 43.7 1.0
CG B:GLU97 4.5 37.7 1.0
O B:HOH516 4.6 36.8 1.0

Reference:

C.Zhang, L.Liu, H.Xu, Z.Wei, Y.Wang, Y.Lin, W.Gong. Crystal Structures of Human Ipp Isomerase: New Insights Into the Catalytic Mechanism J.Mol.Biol. V. 366 1437 2007.
ISSN: ISSN 0022-2836
PubMed: 17137593
DOI: 10.1016/J.JMB.2006.10.092
Page generated: Wed Aug 14 00:05:31 2024

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