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Magnesium in PDB 8hgk: Crystal Structure of Human Clpp in Complex with ZK53

Enzymatic activity of Crystal Structure of Human Clpp in Complex with ZK53

All present enzymatic activity of Crystal Structure of Human Clpp in Complex with ZK53:
3.4.21.92;

Protein crystallography data

The structure of Crystal Structure of Human Clpp in Complex with ZK53, PDB code: 8hgk was solved by C.-G.Yang, J.H.Gan, L.-L.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.53 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 120.31, 97, 123.84, 90, 93.98, 90
R / Rfree (%) 18.6 / 22.1

Other elements in 8hgk:

The structure of Crystal Structure of Human Clpp in Complex with ZK53 also contains other interesting chemical elements:

Bromine (Br) 14 atoms
Fluorine (F) 28 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Clpp in Complex with ZK53 (pdb code 8hgk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Human Clpp in Complex with ZK53, PDB code: 8hgk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8hgk

Go back to Magnesium Binding Sites List in 8hgk
Magnesium binding site 1 out of 5 in the Crystal Structure of Human Clpp in Complex with ZK53


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 Clpp in Complex with ZK53 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:60.5
occ:1.00
 O I:HOH401 2.3 55.3 1.0
O A:HOH407 2.4 59.9 1.0
OD2 I:ASP227 2.8 33.8 1.0
NE2 A:HIS178 2.8 26.4 1.0
OD2 A:ASP227 3.1 33.7 1.0
O H:HOH417 3.3 75.3 1.0
CG A:ASP227 3.7 29.8 1.0
CA A:PRO180 3.7 41.5 1.0
CD2 A:HIS178 3.7 26.7 1.0
CE1 A:HIS178 3.7 27.1 1.0
OG I:SER181 3.8 65.0 1.0
CG I:ASP227 3.9 31.7 1.0
NE2 H:GLN194 3.9 28.0 1.0
C A:PRO180 4.0 45.7 1.0
OD1 A:ASP227 4.2 29.6 1.0
CB A:PRO180 4.4 38.7 1.0
CB A:ASP227 4.4 31.4 1.0
CB I:ASP227 4.5 31.6 1.0
NE2 I:HIS178 4.6 29.8 1.0
O A:GLN179 4.6 41.6 1.0
N A:PRO180 4.8 39.5 1.0
OD1 I:ASP227 4.8 34.9 1.0
ND1 A:HIS178 4.9 26.6 1.0
CG A:HIS178 4.9 27.2 1.0

Magnesium binding site 2 out of 5 in 8hgk

Go back to Magnesium Binding Sites List in 8hgk
Magnesium binding site 2 out of 5 in the Crystal Structure of Human Clpp in Complex with ZK53


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 Clpp in Complex with ZK53 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:49.6
occ:1.00
 O L:HOH411 2.1 37.8 1.0
O E:HOH454 2.1 39.6 1.0
O L:HOH403 2.2 41.4 1.0
OD2 E:ASP227 2.3 23.2 1.0
O E:HOH449 2.3 49.3 1.0
O E:HOH419 2.3 52.1 1.0
CG E:ASP227 3.2 20.9 1.0
OD1 E:ASP227 3.7 20.6 1.0
OD2 L:ASP227 4.0 23.8 1.0
NE2 E:HIS178 4.0 22.9 1.0
NE2 L:HIS178 4.3 22.3 1.0
NE2 D:GLN194 4.3 25.9 1.0
OG E:SER181 4.3 35.8 1.0
CB E:ASP227 4.3 18.8 1.0
N E:SER181 4.5 35.0 1.0
CA E:PRO180 4.7 29.9 1.0
CD2 E:HIS178 4.7 20.2 1.0
CE1 L:HIS178 4.8 21.9 1.0
CB E:PRO180 4.8 28.1 1.0
CG L:ASP227 4.9 22.3 1.0
C L:PRO180 4.9 40.2 1.0
O E:SER181 4.9 45.0 1.0

Magnesium binding site 3 out of 5 in 8hgk

Go back to Magnesium Binding Sites List in 8hgk
Magnesium binding site 3 out of 5 in the Crystal Structure of Human Clpp in Complex with ZK53


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 Clpp in Complex with ZK53 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:41.2
occ:1.00
 OD2 F:ASP227 2.1 19.2 1.0
O K:HOH409 2.1 35.7 1.0
O F:HOH439 2.2 41.9 1.0
O K:HOH447 2.2 45.4 1.0
O F:HOH451 2.3 51.7 1.0
O F:HOH403 2.5 49.6 1.0
CG F:ASP227 3.1 18.9 1.0
OD1 F:ASP227 3.5 18.7 1.0
NE2 F:HIS178 4.1 17.7 1.0
NE2 E:GLN194 4.1 26.1 1.0
OD2 K:ASP227 4.1 28.5 1.0
CB F:ASP227 4.2 19.2 1.0
NE2 K:HIS178 4.3 18.3 1.0
OG F:SER181 4.6 33.6 1.0
CD2 F:HIS178 4.7 19.6 1.0
N F:SER181 4.7 37.2 1.0
CA F:PRO180 4.7 28.3 1.0
CB F:PRO180 4.8 27.7 1.0
CE1 K:HIS178 4.8 21.0 1.0
C K:PRO180 4.9 47.0 1.0
CG K:ASP227 5.0 24.5 1.0

Magnesium binding site 4 out of 5 in 8hgk

Go back to Magnesium Binding Sites List in 8hgk
Magnesium binding site 4 out of 5 in the Crystal Structure of Human Clpp in Complex with ZK53


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 Clpp in Complex with ZK53 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg302

b:64.2
occ:1.00
 OD2 G:ASP227 2.1 28.2 1.0
O J:HOH408 2.1 44.5 1.0
O G:HOH405 2.1 50.3 1.0
O J:HOH403 2.2 46.0 1.0
CG G:ASP227 3.1 23.4 1.0
OD1 G:ASP227 3.6 23.3 1.0
NE2 G:HIS178 4.0 25.9 1.0
OD2 J:ASP227 4.0 30.7 1.0
CB G:ASP227 4.2 27.7 1.0
NE2 F:GLN194 4.3 24.6 1.0
NE2 J:HIS178 4.4 26.3 1.0
O J:HOH423 4.5 50.5 1.0
CD2 G:HIS178 4.6 25.7 1.0
CA G:PRO180 4.7 35.9 1.0
CB G:PRO180 4.8 36.4 1.0
C J:PRO180 4.9 42.1 1.0
CG J:ASP227 4.9 29.0 1.0

Magnesium binding site 5 out of 5 in 8hgk

Go back to Magnesium Binding Sites List in 8hgk
Magnesium binding site 5 out of 5 in the Crystal Structure of Human Clpp in Complex with ZK53


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 Human Clpp in Complex with ZK53 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg301

b:62.1
occ:1.00
 O M:HOH405 2.3 52.1 1.0
O D:HOH431 2.5 55.0 1.0
OD2 D:ASP227 2.7 35.6 1.0
OD2 M:ASP227 3.1 32.0 1.0
O M:HOH418 3.1 56.3 1.0
NE2 M:HIS178 3.2 27.1 1.0
CG M:ASP227 3.8 32.0 1.0
CG D:ASP227 3.8 29.7 1.0
CE1 M:HIS178 4.1 28.3 1.0
CD2 M:HIS178 4.2 25.3 1.0
CA M:PRO180 4.2 40.0 1.0
NE2 C:GLN194 4.2 30.6 1.0
OD1 M:ASP227 4.4 30.5 1.0
C M:PRO180 4.4 48.9 1.0
NE2 D:HIS178 4.4 27.9 1.0
CB D:ASP227 4.5 30.9 1.0
CB M:ASP227 4.5 30.0 1.0
OD1 D:ASP227 4.7 31.7 1.0
O M:GLN179 5.0 33.8 1.0
CB M:PRO180 5.0 38.4 1.0

Reference:

C.-G.Yang, J.H.Gan, L.-L.Zhou. Crystal Structure of Human Clpp in Complex with ZK53 To Be Published.
Page generated: Thu Dec 28 09:12:19 2023

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