Atomistry » Magnesium » PDB 6hns-6hvv » 6huq
Atomistry »
  Magnesium »
    PDB 6hns-6hvv »
      6huq »

Magnesium in PDB 6huq: Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20

Enzymatic activity of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20

All present enzymatic activity of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20, PDB code: 6huq was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 133.990, 299.300, 143.470, 90.00, 112.24, 90.00
R / Rfree (%) 17.8 / 20.7

Other elements in 6huq:

The structure of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20 (pdb code 6huq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20, PDB code: 6huq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6huq

Go back to Magnesium Binding Sites List in 6huq
Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:69.3
occ:1.00
 O G:MET125 2.1 62.5 1.0
OG1 G:THR8 2.7 64.6 1.0
O G:TYR119 2.7 55.5 1.0
O G:ARG122 2.8 63.4 1.0
CG2 G:THR8 3.2 60.8 1.0
C G:MET125 3.3 62.3 1.0
CB G:THR8 3.5 61.3 1.0
O G:ALA123 3.5 65.7 1.0
C G:ALA123 3.8 65.0 1.0
CA G:ALA123 3.9 64.0 1.0
C G:ARG122 3.9 63.9 1.0
C G:TYR119 3.9 56.4 1.0
CA G:ARG126 4.0 57.3 1.0
N G:ARG126 4.1 58.3 1.0
N G:THR8 4.1 65.0 1.0
CD G:PRO127 4.2 56.0 1.0
N G:MET125 4.3 66.0 1.0
CA G:MET125 4.4 67.0 1.0
N G:ALA123 4.4 64.1 1.0
CA G:THR8 4.4 62.8 1.0
C G:ARG126 4.6 57.6 1.0
CA G:TYR119 4.7 54.5 1.0
N G:TYR124 4.7 67.3 1.0
N G:PRO127 4.8 56.1 1.0
N G:THR120 4.9 57.1 1.0
CB G:MET125 4.9 72.3 1.0
C G:TYR124 5.0 64.9 1.0

Magnesium binding site 2 out of 8 in 6huq

Go back to Magnesium Binding Sites List in 6huq
Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:84.2
occ:1.00
 O I:ALA174 2.7 65.6 1.0
O I:SER180 2.9 68.6 1.0
O I:ASP177 2.9 58.5 1.0
OXT I:ASP204 3.5 88.7 1.0
C I:ALA174 3.6 65.2 1.0
CA I:ASP175 3.7 67.0 1.0
C I:SER180 4.0 66.5 1.0
C I:ASP177 4.1 60.6 1.0
N I:ASP175 4.1 65.5 1.0
OD1 I:ASP175 4.2 74.2 1.0
C I:ASP175 4.2 65.3 1.0
O I:ASP175 4.3 65.2 1.0
C I:ASP204 4.4 82.4 1.0
NH2 Y:ARG19 4.6 81.3 1.0
O I:ASP204 4.6 83.1 1.0
CA I:GLY181 4.6 68.6 1.0
N I:ASP177 4.6 62.5 1.0
N I:GLY181 4.8 67.2 1.0
O I:ALA178 4.8 61.6 1.0
CA I:ALA174 4.9 63.1 1.0
CB I:ASP175 4.9 68.8 1.0
N I:ALA178 4.9 60.2 1.0
CA I:ALA178 4.9 61.7 1.0
CA I:ASP177 4.9 62.4 1.0
N I:SER180 5.0 61.1 1.0
NH1 Y:ARG19 5.0 82.6 1.0
C I:ALA178 5.0 61.4 1.0

Magnesium binding site 3 out of 8 in 6huq

Go back to Magnesium Binding Sites List in 6huq
Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:92.0
occ:1.00
 O K:HIS166 2.6 56.9 1.0
O K:ASP168 2.7 54.4 1.0
O W:ASP204 2.8 81.9 1.0
O K:ALA165 3.1 59.1 1.0
C K:ASP168 3.3 59.1 1.0
C W:ASP204 3.3 79.7 1.0
C K:HIS166 3.4 59.8 1.0
CA K:ALA169 3.6 63.5 1.0
N K:ALA169 3.7 62.5 1.0
CA W:ASP204 3.8 74.2 1.0
O K:ARG167 3.8 58.6 1.0
C K:ARG167 3.8 60.9 1.0
OXT W:ASP204 3.9 87.3 1.0
N K:ASP168 4.1 59.2 1.0
C K:ALA165 4.2 60.1 1.0
N K:ARG167 4.2 59.0 1.0
NE1 W:TRP182 4.2 64.2 1.0
CA K:HIS166 4.3 61.0 1.0
CA K:ASP168 4.3 59.0 1.0
C K:ALA169 4.4 61.9 1.0
CA K:ARG167 4.4 60.5 1.0
O K:SER171 4.4 59.8 1.0
O K:ALA169 4.5 59.6 1.0
CB W:ASP204 4.6 73.3 1.0
CB K:ALA169 4.7 64.5 1.0
N K:HIS166 4.7 58.9 1.0
CD1 W:TRP182 4.9 62.7 1.0
CE2 W:TRP182 4.9 63.5 1.0
NH1 K:ARG19 4.9 77.2 1.0
N W:ASP204 5.0 70.4 1.0

Magnesium binding site 4 out of 8 in 6huq

Go back to Magnesium Binding Sites List in 6huq
Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:53.8
occ:1.00
 O N:ILE163 2.7 54.5 1.0
O N:SER169 2.8 57.8 1.0
O N:ASP166 3.1 53.5 1.0
CD1 a:LEU34 3.4 69.7 1.0
NH1 N:ARG19 3.6 61.3 1.0
C N:ILE163 3.7 56.1 1.0
CG2 N:ILE163 3.9 57.1 1.0
C N:SER169 4.0 56.8 1.0
C N:ASP166 4.1 53.9 1.0
CZ N:ARG19 4.2 59.8 1.0
CA N:GLY167 4.3 54.4 1.0
CA N:GLY170 4.4 61.2 1.0
NH2 N:ARG19 4.4 62.8 1.0
CA N:ILE163 4.5 55.5 1.0
N N:GLY167 4.6 53.9 1.0
N N:GLY170 4.6 58.9 1.0
CG a:LEU34 4.7 68.4 1.0
O N:GLY167 4.7 52.7 1.0
N N:LYS164 4.7 58.9 1.0
O N:LYS164 4.7 62.1 1.0
C N:GLY167 4.7 53.8 1.0
CB N:ILE163 4.8 55.4 1.0
C N:LYS164 4.9 60.8 1.0
CA N:LYS164 4.9 61.1 1.0

Magnesium binding site 5 out of 8 in 6huq

Go back to Magnesium Binding Sites List in 6huq
Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:88.4
occ:1.00
 OXT L:ASP222 2.1 84.4 1.0
O V:ILE163 2.4 60.4 1.0
O V:ASP166 2.5 57.9 1.0
O V:PHE164 2.9 67.2 1.0
C L:ASP222 2.9 81.8 1.0
C V:ASP166 3.1 62.7 1.0
C V:PHE164 3.3 69.1 1.0
C V:ILE163 3.5 65.2 1.0
CA L:ASP222 3.5 78.6 1.0
N V:LEU167 3.6 63.0 1.0
O V:SER169 3.7 61.4 1.0
CA V:LEU167 3.7 62.9 1.0
O L:ASP222 3.7 81.2 1.0
CA V:PHE164 3.7 68.7 1.0
N V:ASP166 3.8 62.7 1.0
N V:ASN165 4.0 65.8 1.0
N V:PHE164 4.0 67.1 1.0
CA V:ASP166 4.0 62.6 1.0
C V:ASN165 4.1 64.7 1.0
CD2 V:LEU167 4.2 62.7 1.0
CB L:ASP222 4.3 78.6 1.0
O V:GLY162 4.3 66.7 1.0
O L:ARG221 4.4 73.6 1.0
CA V:ASN165 4.5 66.3 1.0
C V:LEU167 4.6 62.5 1.0
CD1 L:ILE35 4.7 62.9 1.0
CA V:ILE163 4.7 64.4 1.0
NH1 V:ARG19 4.7 68.7 1.0
O V:ASN165 4.7 64.9 1.0
N L:ASP222 4.8 77.1 1.0
O V:LEU167 4.8 63.0 1.0
CB V:LEU167 4.8 62.1 1.0
C V:SER169 4.8 62.4 1.0
CG V:LEU167 5.0 61.9 1.0

Magnesium binding site 6 out of 8 in 6huq

Go back to Magnesium Binding Sites List in 6huq
Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:90.7
occ:1.00
 O W:SER180 2.8 64.0 1.0
O W:ASP177 2.8 58.2 1.0
OXT W:ASP204 3.1 87.3 1.0
O W:ALA174 3.3 58.5 1.0
C W:ASP204 3.9 79.7 1.0
O W:ASP204 4.0 81.9 1.0
C W:ASP177 4.0 59.4 1.0
C W:SER180 4.0 64.1 1.0
O W:ALA178 4.2 61.0 1.0
NH2 K:ARG19 4.3 79.2 1.0
C W:ALA174 4.3 61.2 1.0
CA W:ASP175 4.3 66.3 1.0
NH1 K:ARG19 4.4 77.2 1.0
CA W:ALA178 4.5 59.8 1.0
C W:ALA178 4.6 60.3 1.0
O W:ASP175 4.7 67.0 1.0
C W:ASP175 4.7 65.4 1.0
N W:ALA178 4.7 58.4 1.0
N W:ASP175 4.8 64.0 1.0
OD1 W:ASP175 4.8 71.8 1.0
CZ K:ARG19 4.8 75.8 1.0
CA W:GLY181 4.8 64.5 1.0
N W:SER180 4.8 60.0 1.0
OD1 W:ASP204 4.9 71.2 1.0
N W:GLY181 4.9 64.2 1.0
N W:ASP177 4.9 61.0 1.0

Magnesium binding site 7 out of 8 in 6huq

Go back to Magnesium Binding Sites List in 6huq
Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:1.0
occ:1.00
 O I:ASP204 2.6 83.1 1.0
O Y:ASP168 2.8 57.0 1.0
O Y:HIS166 3.1 57.3 1.0
C I:ASP204 3.1 82.4 1.0
O Y:ALA165 3.3 59.9 1.0
CA Y:ALA169 3.4 66.0 1.0
C Y:ASP168 3.4 63.4 1.0
N Y:ALA169 3.6 65.6 1.0
CA I:ASP204 3.7 80.0 1.0
OXT I:ASP204 3.8 88.7 1.0
C Y:HIS166 4.0 62.3 1.0
C Y:ALA169 4.1 64.9 1.0
O Y:ALA169 4.1 65.6 1.0
O Y:SER171 4.2 66.2 1.0
NE1 I:TRP182 4.2 75.5 1.0
O Y:ARG167 4.2 62.7 1.0
C Y:ARG167 4.3 66.4 1.0
NH1 Y:ARG19 4.4 82.6 1.0
CB Y:ALA169 4.4 66.8 1.0
N Y:ASP168 4.5 66.8 1.0
C Y:ALA165 4.5 63.0 1.0
CB I:ASP204 4.5 80.6 1.0
CA Y:ASP168 4.5 64.3 1.0
CA Y:HIS166 4.7 65.1 1.0
N Y:ARG167 4.8 63.1 1.0
CD1 I:TRP182 4.8 73.8 1.0
N I:ASP204 4.9 77.2 1.0
O I:ALA178 4.9 61.6 1.0
CA Y:ARG167 5.0 65.5 1.0
CE2 I:TRP182 5.0 74.0 1.0

Magnesium binding site 8 out of 8 in 6huq

Go back to Magnesium Binding Sites List in 6huq
Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast 20S Proteasome with Human BETA2C (S171G) in Complex with 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:81.1
occ:1.00
 O Z:VAL198 2.7 63.7 1.0
O Z:ASP222 3.0 81.2 1.0
O Z:THR192 3.2 68.1 1.0
O Z:HIS195 3.3 56.4 1.0
NH2 Z:ARG28 3.5 68.5 1.0
O Z:ILE196 3.6 64.8 1.0
C Z:VAL198 3.9 64.2 1.0
CA Z:ILE196 3.9 59.0 1.0
C Z:ILE196 4.0 61.6 1.0
NH2 H:ARG19 4.0 80.9 1.0
C Z:ASP222 4.1 82.9 1.0
OD1 Z:ASP222 4.2 75.8 1.0
CG2 Z:THR192 4.2 71.5 1.0
C Z:HIS195 4.2 59.1 1.0
C Z:THR192 4.3 69.9 1.0
CZ Z:ARG28 4.4 66.2 1.0
NH1 H:ARG19 4.4 82.5 1.0
NH1 Z:ARG28 4.5 67.7 1.0
O Z:LYS220 4.6 75.0 1.0
N Z:ILE196 4.6 57.6 1.0
OXT Z:ASP222 4.6 79.1 1.0
CE Z:LYS220 4.6 81.3 1.0
N Z:VAL198 4.6 61.1 1.0
CZ H:ARG19 4.6 79.2 1.0
CA Z:THR192 4.7 69.7 1.0
CA Z:GLY199 4.7 68.4 1.0
N Z:GLY199 4.7 66.2 1.0
CA Z:VAL198 4.9 62.5 1.0
NZ Z:LYS220 5.0 82.0 1.0

Reference:

B.T.Xin, E.M.Huber, G.De Bruin, W.Heinemeyer, E.Maurits, C.Espinal, Y.Du, M.Janssens, E.S.Weyburne, A.F.Kisselev, B.I.Florea, C.Driessen, G.A.Van Der Marel, M.Groll, H.S.Overkleeft. Structure-Based Design of Inhibitors Selective For Human Proteasome Beta 2C or Beta 2I Subunits. J.Med.Chem. V. 62 1626 2019.
ISSN: ISSN 0022-2623
PubMed: 30657666
DOI: 10.1021/ACS.JMEDCHEM.8B01884
Page generated: Tue Oct 1 02:19:01 2024

Last articles

Mg in 5GON
Mg in 5GPA
Mg in 5GP9
Mg in 5GOF
Mg in 5GMY
Mg in 5GOD
Mg in 5GKP
Mg in 5GKI
Mg in 5GKH
Mg in 5GKG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy