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Magnesium in PDB 4quy: Ycp BETA5-A49S-Mutant

Enzymatic activity of Ycp BETA5-A49S-Mutant

All present enzymatic activity of Ycp BETA5-A49S-Mutant:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-A49S-Mutant, PDB code: 4quy was solved by E.M.Huber, W.Heinemeyer, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.500, 300.140, 144.190, 90.00, 112.83, 90.00
R / Rfree (%) 19.1 / 22.6

Other elements in 4quy:

The structure of Ycp BETA5-A49S-Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-A49S-Mutant (pdb code 4quy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Ycp BETA5-A49S-Mutant, PDB code: 4quy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4quy

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Magnesium binding site 1 out of 8 in the Ycp BETA5-A49S-Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ycp BETA5-A49S-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:43.9
occ:1.00
 O G:MET125 2.0 57.9 1.0
O G:HOH403 2.5 29.9 1.0
O G:TYR119 2.6 46.0 1.0
O G:ARG122 2.6 48.9 1.0
OG1 G:THR8 2.7 49.5 1.0
C G:MET125 3.1 56.4 1.0
CG2 G:THR8 3.3 51.6 1.0
O G:ALA123 3.5 53.4 1.0
CB G:THR8 3.6 50.8 1.0
C G:ARG122 3.8 50.8 1.0
C G:TYR119 3.8 44.7 1.0
C G:ALA123 3.8 54.5 1.0
CA G:ARG126 3.9 49.7 1.0
CA G:ALA123 3.9 52.5 1.0
N G:ARG126 3.9 50.8 1.0
N G:MET125 4.1 60.0 1.0
CA G:MET125 4.2 60.4 1.0
N G:ALA123 4.3 51.0 1.0
CD G:PRO127 4.3 46.5 1.0
N G:THR8 4.3 55.1 1.0
CA G:TYR119 4.5 43.9 1.0
C G:ARG126 4.5 50.7 1.0
CA G:THR8 4.6 52.1 1.0
N G:TYR124 4.7 57.3 1.0
N G:PRO127 4.7 48.1 1.0
CB G:MET125 4.8 63.9 1.0
N G:THR120 4.8 44.7 1.0
C G:TYR124 4.9 58.3 1.0
CB G:TYR119 4.9 42.6 1.0
CA G:THR120 5.0 44.8 1.0

Magnesium binding site 2 out of 8 in 4quy

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Magnesium binding site 2 out of 8 in the Ycp BETA5-A49S-Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ycp BETA5-A49S-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:55.6
occ:1.00
 O I:ASP177 2.2 52.1 1.0
O I:SER180 2.7 47.7 1.0
O I:HOH403 2.9 39.8 1.0
O I:ALA174 3.2 59.5 1.0
C I:ASP177 3.3 47.8 1.0
O I:ALA178 3.6 45.1 1.0
OXT I:ASP204 3.7 59.0 1.0
CA I:ALA178 3.7 46.2 1.0
C I:ALA178 3.8 49.4 1.0
C I:SER180 3.9 48.3 1.0
N I:ALA178 4.0 43.4 1.0
NH1 Y:ARG19 4.0 62.4 1.0
O I:ASP204 4.3 54.2 1.0
N I:SER180 4.3 47.2 1.0
C I:ALA174 4.4 51.5 1.0
C I:ASP204 4.4 54.7 1.0
CA I:ASP177 4.5 48.5 1.0
N I:ASP177 4.5 47.6 1.0
NH2 Y:ARG19 4.5 55.3 1.0
N I:LEU179 4.6 50.7 1.0
CZ Y:ARG19 4.6 59.2 1.0
CA I:SER180 4.7 47.8 1.0
CA I:ASP175 4.7 50.0 1.0
C I:ASP175 4.9 50.6 1.0
N I:GLY181 4.9 49.5 1.0
O I:ASP175 4.9 55.3 1.0
CA I:GLY181 5.0 50.6 1.0

Magnesium binding site 3 out of 8 in 4quy

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Magnesium binding site 3 out of 8 in the Ycp BETA5-A49S-Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ycp BETA5-A49S-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:45.0
occ:1.00
 O K:ALA165 2.3 48.4 1.0
O K:ASP168 2.4 44.4 1.0
O W:ASP204 2.4 56.7 1.0
O K:SER171 2.9 48.8 1.0
C W:ASP204 3.0 58.5 1.0
C K:ASP168 3.3 45.1 1.0
C K:ALA165 3.5 47.0 1.0
CA W:ASP204 3.5 57.8 1.0
O K:HIS166 3.6 54.9 1.0
CA K:ALA169 3.6 46.3 1.0
N K:ALA169 3.8 45.5 1.0
OXT W:ASP204 3.9 66.5 1.0
CB W:ASP204 3.9 56.2 1.0
O K:ALA169 3.9 50.6 1.0
NH1 K:ARG19 3.9 58.9 1.0
C K:ALA169 3.9 48.4 1.0
C K:HIS166 4.1 49.3 1.0
C K:SER171 4.1 49.5 1.0
N K:ASP168 4.4 46.2 1.0
CA K:ALA165 4.4 46.4 1.0
N K:HIS166 4.4 46.6 1.0
CA K:ASP168 4.4 45.1 1.0
CA K:HIS166 4.5 48.3 1.0
N K:SER171 4.5 46.8 1.0
C K:ARG167 4.6 46.6 1.0
CZ K:ARG19 4.6 56.9 1.0
O K:ALA164 4.7 43.8 1.0
O K:ARG167 4.7 45.9 1.0
N K:ARG167 4.7 47.7 1.0
N K:TYR170 4.8 48.7 1.0
CA K:SER171 4.9 46.1 1.0
N W:ASP204 4.9 56.8 1.0
NH2 K:ARG19 4.9 60.4 1.0
CG W:ASP204 5.0 56.0 1.0
CB K:ALA169 5.0 45.8 1.0

Magnesium binding site 4 out of 8 in 4quy

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Magnesium binding site 4 out of 8 in the Ycp BETA5-A49S-Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ycp BETA5-A49S-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:52.1
occ:1.00
 O K:ILE82 2.8 40.6 1.0
CA K:ILE82 3.6 41.4 1.0
C K:ILE82 3.6 41.2 1.0
CB K:ASN85 3.7 40.8 1.0
CG2 K:ILE82 3.8 41.0 1.0
N K:LEU86 3.9 40.1 1.0
CB K:ILE82 4.2 41.1 1.0
C K:ASN85 4.4 39.9 1.0
CB K:LEU86 4.4 38.9 1.0
CA K:LEU86 4.4 39.6 1.0
CH2 K:TRP58 4.4 39.3 1.0
O K:LYS81 4.5 39.7 1.0
CA K:ASN85 4.5 40.5 1.0
CG1 K:ILE82 4.6 42.0 1.0
OD1 K:ASN85 4.7 46.6 1.0
CG K:ASN85 4.7 41.3 1.0
N K:ILE82 4.8 41.1 1.0
N K:LEU83 4.9 40.8 1.0
N K:ASN85 5.0 39.7 1.0

Magnesium binding site 5 out of 8 in 4quy

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Magnesium binding site 5 out of 8 in the Ycp BETA5-A49S-Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ycp BETA5-A49S-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:44.8
occ:1.00
 O N:SER169 3.0 45.0 1.0
O N:ILE163 3.0 41.9 1.0
NH1 N:ARG19 3.4 42.4 1.0
O N:ASP166 3.5 49.0 1.0
CD1 a:LEU34 3.5 51.9 1.0
CZ N:ARG19 3.9 42.4 1.0
NH2 N:ARG19 4.0 44.3 1.0
CG2 N:ILE163 4.1 44.7 1.0
C N:ILE163 4.1 44.0 1.0
C N:SER169 4.1 44.1 1.0
O a:HOH317 4.2 39.4 1.0
CA N:GLY167 4.4 44.2 1.0
CA N:GLY170 4.4 45.4 1.0
C N:ASP166 4.4 45.7 1.0
O N:GLY167 4.6 44.4 1.0
C N:GLY167 4.8 43.2 1.0
N N:GLY170 4.8 44.2 1.0
CA N:ILE163 4.8 45.1 1.0
N N:GLY167 4.8 44.3 1.0
CG a:LEU34 4.9 51.5 1.0
NE N:ARG19 4.9 43.5 1.0

Magnesium binding site 6 out of 8 in 4quy

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Magnesium binding site 6 out of 8 in the Ycp BETA5-A49S-Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ycp BETA5-A49S-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:51.7
occ:1.00
 OD1 N:ASP51 2.8 38.9 1.0
NE2 H:GLN91 3.2 70.4 1.0
OD2 N:ASP51 3.4 46.8 1.0
CG N:ASP51 3.5 34.1 1.0
O N:ASN92 3.6 52.6 1.0
CD H:GLN91 4.2 69.5 1.0
OE1 H:GLN91 4.6 80.9 1.0
C N:ASN92 4.7 51.0 1.0
CE1 H:PHE88 4.9 37.6 1.0
OG N:SER48 4.9 44.5 1.0

Magnesium binding site 7 out of 8 in 4quy

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Magnesium binding site 7 out of 8 in the Ycp BETA5-A49S-Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ycp BETA5-A49S-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:47.6
occ:1.00
 O I:ASP204 2.4 54.2 1.0
O Y:ASP168 2.4 46.4 1.0
O Y:ALA165 2.5 44.0 1.0
C I:ASP204 3.0 54.7 1.0
O Y:SER171 3.1 49.1 1.0
C Y:ASP168 3.3 45.0 1.0
CA I:ASP204 3.6 56.0 1.0
CA Y:ALA169 3.6 46.5 1.0
O Y:HIS166 3.6 41.4 1.0
C Y:ALA165 3.7 45.7 1.0
N Y:ALA169 3.8 46.4 1.0
O Y:ALA169 3.8 48.1 1.0
OXT I:ASP204 3.8 59.0 1.0
C Y:ALA169 3.9 47.1 1.0
NH1 Y:ARG19 3.9 62.4 1.0
CB I:ASP204 4.0 57.7 1.0
C Y:HIS166 4.1 45.0 1.0
C Y:SER171 4.3 47.1 1.0
N Y:ASP168 4.4 44.7 1.0
CA Y:ASP168 4.5 44.2 1.0
N Y:HIS166 4.5 48.3 1.0
CA Y:HIS166 4.6 45.4 1.0
C Y:ARG167 4.6 42.9 1.0
CA Y:ALA165 4.6 44.6 1.0
N Y:SER171 4.6 43.2 1.0
CZ Y:ARG19 4.7 59.2 1.0
O Y:ARG167 4.7 42.0 1.0
N Y:TYR170 4.8 46.1 1.0
N Y:ARG167 4.8 42.9 1.0
O Y:ALA164 4.8 46.0 1.0
CB Y:ALA169 4.9 45.1 1.0
N I:ASP204 4.9 56.8 1.0
NH2 Y:ARG19 4.9 55.3 1.0

Magnesium binding site 8 out of 8 in 4quy

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Magnesium binding site 8 out of 8 in the Ycp BETA5-A49S-Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ycp BETA5-A49S-Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:56.5
occ:1.00
 O Z:VAL198 2.5 58.9 1.0
O Z:HIS195 2.7 46.4 1.0
O Z:THR192 3.0 61.5 1.0
O Z:ILE196 3.4 61.3 1.0
NH2 Z:ARG28 3.5 66.3 1.0
O Z:ASP222 3.6 73.4 1.0
CA Z:ILE196 3.6 54.6 1.0
C Z:ILE196 3.6 57.0 1.0
C Z:VAL198 3.7 57.1 1.0
C Z:HIS195 3.7 51.8 1.0
C Z:THR192 4.0 63.2 1.0
CG2 Z:THR192 4.1 65.2 1.0
N Z:ILE196 4.1 52.6 1.0
N Z:VAL198 4.2 51.8 1.0
NH2 H:ARG19 4.3 68.5 1.0
CA Z:THR192 4.3 63.3 1.0
CA Z:VAL198 4.5 53.4 1.0
CZ Z:ARG28 4.6 62.1 1.0
N Z:GLN197 4.6 55.8 1.0
C Z:ASP222 4.6 78.8 1.0
N Z:GLY199 4.6 57.5 1.0
OD1 Z:ASP222 4.7 65.8 1.0
NH1 H:ARG19 4.8 70.2 1.0
CA Z:GLY199 4.8 58.5 1.0
NH1 Z:ARG28 4.8 61.0 1.0
CB Z:THR192 4.8 63.7 1.0
CZ H:ARG19 4.9 67.5 1.0
CB Z:ILE196 4.9 54.1 1.0
CB Z:VAL198 5.0 53.4 1.0
OXT Z:ASP222 5.0 80.1 1.0
CA Z:HIS195 5.0 53.6 1.0

Reference:

E.M.Huber, W.Heinemeyer, M.Groll. Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and Onx 0914. Structure 2015.
ISSN: ISSN 0969-2126
PubMed: 25599643
DOI: 10.1016/J.STR.2014.11.019
Page generated: Tue Aug 20 02:11:52 2024

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