Magnesium in PDB 7vp9: Crystal Structure of Human Clpp in Complex with ZG111

Enzymatic activity of Crystal Structure of Human Clpp in Complex with ZG111

All present enzymatic activity of Crystal Structure of Human Clpp in Complex with ZG111:
3.4.21.92;

Protein crystallography data

The structure of Crystal Structure of Human Clpp in Complex with ZG111, PDB code: 7vp9 was solved by P.Y.Wang, J.H.Gan, C.-G.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.84 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.806, 97.408, 146.686, 90, 90.63, 90
R / Rfree (%) 20.2 / 23.2

Other elements in 7vp9:

The structure of Crystal Structure of Human Clpp in Complex with ZG111 also contains other interesting chemical elements:

Bromine (Br) 14 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Clpp in Complex with ZG111 (pdb code 7vp9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Crystal Structure of Human Clpp in Complex with ZG111, PDB code: 7vp9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 7vp9

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Magnesium binding site 1 out of 14 in the Crystal Structure of Human Clpp in Complex with ZG111


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 ZG111 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:66.0
occ:1.00
 O A:ASN141 3.1 76.0 1.0
O A:MET136 3.6 61.6 1.0
OG1 A:THR163 3.7 59.5 1.0
O A:ILE139 4.2 65.5 1.0
C A:ASN141 4.3 72.5 1.0
CD1 A:ILE143 4.5 67.1 1.0
CG1 A:ILE143 4.6 69.2 1.0
C A:MET136 4.7 56.1 1.0
N A:ILE143 4.7 74.5 1.0
CA A:PRO142 4.7 73.3 1.0
CB A:THR163 4.9 59.9 1.0
CB A:ILE143 5.0 69.9 1.0
N A:PRO142 5.0 70.3 1.0

Magnesium binding site 2 out of 14 in 7vp9

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Magnesium binding site 2 out of 14 in the Crystal Structure of Human Clpp in Complex with ZG111


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 ZG111 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:78.7
occ:1.00
 O B:ILE139 2.9 81.3 1.0
O B:MET136 3.2 74.1 1.0
O B:ASN141 3.5 86.8 1.0
O B:GLN137 3.6 77.5 1.0
CA B:GLN137 4.0 71.5 1.0
C B:GLN137 4.0 75.4 1.0
C B:ILE139 4.1 81.3 1.0
C B:MET136 4.2 72.0 1.0
C B:LEU140 4.4 77.3 1.0
CA B:LEU140 4.5 82.3 1.0
N B:GLN137 4.6 64.6 1.0
C B:ASN141 4.6 81.6 1.0
O B:LEU140 4.7 79.4 1.0
N B:ASN141 4.7 76.6 1.0
NE2 B:GLN137 4.7 76.9 1.0
N B:LEU140 4.8 79.9 1.0
CG2 B:THR163 4.9 76.6 1.0
CG1 B:ILE139 4.9 70.4 1.0
CD1 B:ILE143 5.0 61.1 1.0

Magnesium binding site 3 out of 14 in 7vp9

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Magnesium binding site 3 out of 14 in the Crystal Structure of Human Clpp in Complex with ZG111


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 ZG111 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:98.5
occ:1.00
 O C:ILE139 2.2 91.2 1.0
O C:GLN137 2.6 89.2 1.0
O C:MET136 3.1 90.3 1.0
C C:GLN137 3.2 89.1 1.0
C C:ILE139 3.4 92.6 1.0
CA C:GLN137 3.5 86.6 1.0
NE2 D:HIS247 3.8 99.8 1.0
O C:ASN141 4.1 87.1 1.0
C C:MET136 4.1 88.8 1.0
CD2 D:HIS247 4.1 100.1 1.0
N C:ILE139 4.3 92.9 1.0
N C:GLN137 4.3 86.9 1.0
N C:TYR138 4.3 85.3 1.0
N C:LEU140 4.3 98.2 1.0
CA C:LEU140 4.4 95.8 1.0
C C:TYR138 4.4 92.3 1.0
CA C:ILE139 4.5 93.9 1.0
C C:LEU140 4.5 89.1 1.0
N C:ASN141 4.6 88.7 1.0
CG1 C:ILE139 4.6 97.3 1.0
O C:TYR138 4.7 94.8 1.0
CB C:GLN137 4.7 81.8 1.0
CA C:TYR138 4.9 89.6 1.0
O C:LEU140 5.0 86.4 1.0

Magnesium binding site 4 out of 14 in 7vp9

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Magnesium binding site 4 out of 14 in the Crystal Structure of Human Clpp in Complex with ZG111


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 ZG111 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:79.2
occ:1.00
 O D:MET136 3.3 94.2 1.0
O D:ASN141 3.3 98.8 1.0
CG2 D:THR163 3.7 89.0 1.0
O D:ILE139 4.0 104.1 1.0
CD1 D:ILE143 4.3 85.7 1.0
C D:MET136 4.4 90.9 1.0
C D:ASN141 4.5 95.2 1.0
CG1 D:ILE143 4.6 87.7 1.0
O D:GLN137 4.7 88.5 1.0
CA D:GLN137 4.8 89.6 1.0
N D:ILE143 4.9 94.5 1.0
CB D:ILE143 5.0 90.4 1.0
CG1 D:ILE139 5.0 82.9 1.0
N D:GLN137 5.0 88.4 1.0

Magnesium binding site 5 out of 14 in 7vp9

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Magnesium binding site 5 out of 14 in the Crystal Structure of Human Clpp in Complex with ZG111


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 ZG111 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:67.7
occ:1.00
 O E:MET136 3.1 69.4 1.0
O E:ILE139 3.3 69.7 1.0
O E:ASN141 3.3 92.4 1.0
O E:GLN137 4.0 73.3 1.0
C E:MET136 4.2 71.5 1.0
CA E:GLN137 4.2 75.7 1.0
C E:GLN137 4.3 75.2 1.0
CG2 E:THR163 4.4 80.1 1.0
C E:ILE139 4.4 75.5 1.0
C E:ASN141 4.5 89.8 1.0
CD1 E:ILE143 4.6 57.7 1.0
N E:GLN137 4.7 73.9 1.0
N E:ASN141 4.8 80.0 1.0
C E:LEU140 4.8 78.9 1.0
CG1 E:ILE139 4.9 74.8 1.0
CG1 E:ILE143 5.0 67.2 1.0

Magnesium binding site 6 out of 14 in 7vp9

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Magnesium binding site 6 out of 14 in the Crystal Structure of Human Clpp in Complex with ZG111


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human Clpp in Complex with ZG111 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:74.7
occ:1.00
 O F:MET136 2.8 48.6 1.0
O F:ILE139 3.1 69.0 1.0
O F:ASN141 3.3 79.6 1.0
O F:GLN137 3.8 66.5 1.0
C F:MET136 3.9 51.3 1.0
CA F:GLN137 4.1 55.4 1.0
C F:GLN137 4.2 58.3 1.0
C F:ILE139 4.2 72.0 1.0
CD1 F:ILE143 4.4 71.1 1.0
N F:GLN137 4.5 52.2 1.0
C F:ASN141 4.5 80.7 1.0
CG1 F:ILE139 4.5 63.5 1.0
N F:ASN141 4.7 85.2 1.0
C F:LEU140 4.9 83.1 1.0
CG1 F:ILE143 4.9 72.6 1.0

Magnesium binding site 7 out of 14 in 7vp9

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Magnesium binding site 7 out of 14 in the Crystal Structure of Human Clpp in Complex with ZG111


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Human Clpp in Complex with ZG111 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg302

b:60.2
occ:1.00
 O G:ILE139 2.5 65.3 1.0
O G:HOH404 2.7 47.2 1.0
O G:MET136 3.0 61.1 1.0
O G:GLN137 3.2 54.7 1.0
C G:ILE139 3.7 64.3 1.0
C G:GLN137 3.8 57.7 1.0
O G:ASN141 3.8 72.2 1.0
CA G:GLN137 3.9 59.0 1.0
C G:MET136 4.1 59.4 1.0
N G:GLN137 4.5 56.0 1.0
CG1 G:ILE139 4.5 62.4 1.0
N G:ILE139 4.6 63.1 1.0
CA G:LEU140 4.6 67.4 1.0
N G:LEU140 4.6 67.7 1.0
C G:LEU140 4.6 65.7 1.0
CA G:ILE139 4.7 59.5 1.0
N G:ASN141 4.8 65.3 1.0
N G:TYR138 4.8 60.5 1.0
C G:TYR138 4.9 59.0 1.0
C G:ASN141 4.9 67.1 1.0
O G:LEU140 5.0 60.9 1.0

Magnesium binding site 8 out of 14 in 7vp9

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Magnesium binding site 8 out of 14 in the Crystal Structure of Human Clpp in Complex with ZG111


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Human Clpp in Complex with ZG111 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:42.8
occ:1.00
 O H:HOH407 2.6 42.5 1.0
O H:MET136 2.7 33.4 1.0
O H:ILE139 2.9 58.1 1.0
O H:ASN141 3.3 50.4 1.0
O H:GLN137 3.7 40.7 1.0
C H:MET136 3.9 36.3 1.0
C H:ILE139 4.0 51.1 1.0
CA H:GLN137 4.0 29.8 1.0
C H:GLN137 4.1 28.6 1.0
C H:ASN141 4.4 46.6 1.0
CG1 H:ILE139 4.4 36.9 1.0
N H:GLN137 4.4 34.3 1.0
CD1 H:ILE143 4.5 35.4 1.0
N H:ASN141 4.5 42.9 1.0
C H:LEU140 4.6 48.2 1.0
CA H:LEU140 4.8 52.5 1.0
N H:LEU140 4.8 52.3 1.0
N H:ILE139 4.8 37.1 1.0
O H:HOH402 4.9 43.9 1.0
CG1 H:ILE143 4.9 38.2 1.0
O H:LEU140 4.9 54.0 1.0
CA H:ILE139 4.9 44.8 1.0

Magnesium binding site 9 out of 14 in 7vp9

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Magnesium binding site 9 out of 14 in the Crystal Structure of Human Clpp in Complex with ZG111


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Human Clpp in Complex with ZG111 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg303

b:53.0
occ:1.00
 O I:HOH413 2.5 37.1 1.0
O I:ILE139 2.9 46.6 1.0
O I:MET136 2.9 40.3 1.0
O I:ASN141 3.1 42.9 1.0
O I:GLN137 4.0 44.7 1.0
C I:ILE139 4.0 39.2 1.0
C I:MET136 4.1 36.5 1.0
C I:ASN141 4.2 37.3 1.0
CD1 I:ILE143 4.3 40.5 1.0
CA I:GLN137 4.3 37.3 1.0
C I:GLN137 4.3 40.1 1.0
CG1 I:ILE139 4.4 42.8 1.0
N I:ASN141 4.4 41.0 1.0
C I:LEU140 4.4 41.0 1.0
O I:HOH403 4.5 43.1 1.0
CA I:LEU140 4.7 44.8 1.0
O I:LEU140 4.7 42.8 1.0
CG1 I:ILE143 4.7 38.2 1.0
N I:GLN137 4.7 29.9 1.0
N I:LEU140 4.8 40.3 1.0
OG1 I:THR163 4.9 37.1 1.0
CA I:ASN141 4.9 38.6 1.0
N I:ILE139 5.0 34.2 1.0

Magnesium binding site 10 out of 14 in 7vp9

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Magnesium binding site 10 out of 14 in the Crystal Structure of Human Clpp in Complex with ZG111


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Human Clpp in Complex with ZG111 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg301

b:55.5
occ:1.00
 O J:HOH409 2.6 53.4 1.0
O J:ILE139 2.7 41.8 1.0
O J:MET136 2.8 39.8 1.0
O J:ASN141 3.4 43.5 1.0
O J:GLN137 3.6 39.8 1.0
C J:ILE139 3.8 43.5 1.0
C J:MET136 3.9 33.3 1.0
C J:GLN137 4.0 37.8 1.0
CA J:GLN137 4.1 36.9 1.0
C J:LEU140 4.4 48.7 1.0
CA J:LEU140 4.4 50.7 1.0
CG1 J:ILE139 4.5 45.5 1.0
N J:ASN141 4.5 48.8 1.0
C J:ASN141 4.5 39.3 1.0
N J:GLN137 4.5 33.8 1.0
CD1 J:ILE143 4.5 36.6 1.0
N J:LEU140 4.6 45.3 1.0
O J:LEU140 4.7 53.3 1.0
N J:ILE139 4.9 34.1 1.0
CA J:ILE139 4.9 41.8 1.0
CG1 J:ILE143 5.0 41.3 1.0
N J:TYR138 5.0 36.1 1.0

Reference:

P.Wang, T.Zhang, X.Wang, H.Xiao, H.Li, L.L.Zhou, T.Yang, B.Wei, Z.Zhu, L.Zhou, S.Yang, X.Lu, Y.Zhang, Y.Huang, J.Gan, C.G.Yang. Aberrant Human Clpp Activation Disturbs Mitochondrial Proteome Homeostasis to Suppress Pancreatic Ductal Adenocarcinoma. Cell Chem Biol V. 29 1396 2022.
ISSN: ESSN 2451-9456
PubMed: 35905743
DOI: 10.1016/J.CHEMBIOL.2022.07.002
Page generated: Fri Apr 7 00:44:48 2023

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