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Magnesium in PDB 4qv7: Ycp BETA5-A50V Mutant

Enzymatic activity of Ycp BETA5-A50V Mutant

All present enzymatic activity of Ycp BETA5-A50V Mutant:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-A50V Mutant, PDB code: 4qv7 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 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.110, 301.030, 144.330, 90.00, 113.18, 90.00
R / Rfree (%) 18.8 / 21.4

Other elements in 4qv7:

The structure of Ycp BETA5-A50V Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-A50V Mutant (pdb code 4qv7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Ycp BETA5-A50V Mutant, PDB code: 4qv7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 4qv7

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Magnesium binding site 1 out of 10 in the Ycp BETA5-A50V 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-A50V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:47.5
occ:1.00
 O G:MET125 2.1 51.6 1.0
O G:HOH409 2.3 37.9 1.0
O G:ARG122 2.3 46.0 1.0
O G:TYR119 2.5 40.7 1.0
OG1 G:THR8 2.6 43.0 1.0
C G:MET125 3.3 49.7 1.0
CG2 G:THR8 3.4 45.7 1.0
C G:ARG122 3.4 45.9 1.0
O G:ALA123 3.5 49.7 1.0
CB G:THR8 3.6 45.3 1.0
CA G:ALA123 3.6 46.9 1.0
C G:ALA123 3.7 48.1 1.0
C G:TYR119 3.7 38.9 1.0
N G:ALA123 4.0 45.6 1.0
N G:MET125 4.1 51.0 1.0
N G:ARG126 4.2 44.9 1.0
CA G:ARG126 4.2 43.7 1.0
CA G:MET125 4.2 52.5 1.0
N G:THR8 4.4 48.8 1.0
CA G:TYR119 4.4 36.8 1.0
N G:TYR124 4.5 48.9 1.0
CA G:THR8 4.6 46.9 1.0
CD G:PRO127 4.6 40.4 1.0
CA G:ARG122 4.6 47.9 1.0
N G:ARG122 4.7 44.4 1.0
N G:THR120 4.7 39.1 1.0
CB G:MET125 4.7 57.2 1.0
C G:ARG126 4.8 43.2 1.0
CA G:THR120 4.9 39.3 1.0
C G:TYR124 4.9 49.8 1.0
C G:THR120 4.9 40.4 1.0
CB G:TYR119 5.0 35.3 1.0

Magnesium binding site 2 out of 10 in 4qv7

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Magnesium binding site 2 out of 10 in the Ycp BETA5-A50V Mutant


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ycp BETA5-A50V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:62.0
occ:1.00
 O I:ASP177 2.4 44.9 1.0
O I:SER180 2.9 48.2 1.0
C I:ASP177 3.4 44.0 1.0
O I:ALA178 3.4 45.9 1.0
O I:ALA174 3.5 47.3 1.0
OXT I:ASP204 3.5 58.5 1.0
CA I:ALA178 3.6 44.4 1.0
C I:ALA178 3.7 46.3 1.0
NH1 Y:ARG19 3.7 57.6 1.0
N I:ALA178 3.9 41.9 1.0
O I:ASP204 4.0 51.8 1.0
C I:SER180 4.1 47.0 1.0
C I:ASP204 4.3 53.2 1.0
NH2 Y:ARG19 4.4 54.5 1.0
N I:SER180 4.4 45.1 1.0
CZ Y:ARG19 4.4 54.6 1.0
N I:LEU179 4.6 46.3 1.0
CA I:ASP177 4.6 44.6 1.0
C I:ALA174 4.7 46.7 1.0
N I:ASP177 4.7 43.7 1.0
CA I:SER180 4.9 45.9 1.0
CA I:ASP175 5.0 46.9 1.0

Magnesium binding site 3 out of 10 in 4qv7

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Magnesium binding site 3 out of 10 in the Ycp BETA5-A50V 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-A50V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:55.7
occ:1.00
 OE1 J:GLN118 3.0 36.8 1.0
O J:THR124 3.3 38.4 1.0
N J:ASP120 3.6 34.0 1.0
CG J:GLN118 3.6 35.0 1.0
CD J:GLN118 3.7 36.2 1.0
CB J:ASP120 3.7 36.8 1.0
CE1 J:HIS133 3.8 38.8 1.0
O J:GLN118 4.0 34.9 1.0
CG J:ASP120 4.0 38.2 1.0
OD2 J:ASP120 4.1 41.7 1.0
C J:ILE119 4.2 34.1 1.0
C J:GLN118 4.2 33.6 1.0
CA J:ASP120 4.2 35.3 1.0
CA J:ILE119 4.3 32.6 1.0
N J:ILE119 4.4 32.5 1.0
CB J:THR124 4.4 35.8 1.0
C J:THR124 4.4 36.6 1.0
CB J:GLN118 4.5 33.9 1.0
ND1 J:HIS133 4.6 38.6 1.0
CG2 J:THR124 4.7 35.0 1.0
NE2 J:HIS133 4.7 37.8 1.0
OD1 J:ASP120 4.7 39.6 1.0
CG1 I:VAL35 4.8 43.5 1.0
NE2 J:GLN118 5.0 37.3 1.0

Magnesium binding site 4 out of 10 in 4qv7

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Magnesium binding site 4 out of 10 in the Ycp BETA5-A50V 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-A50V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:41.5
occ:1.00
 O K:ASP168 2.2 41.4 1.0
O K:ALA165 2.3 45.5 1.0
O W:ASP204 2.5 51.2 1.0
O K:SER171 2.5 45.1 1.0
O K:HOH416 2.9 60.1 1.0
C W:ASP204 3.2 54.8 1.0
C K:ASP168 3.3 41.5 1.0
C K:ALA165 3.4 44.0 1.0
CA W:ASP204 3.6 53.8 1.0
CA K:ALA169 3.7 42.1 1.0
C K:SER171 3.7 44.8 1.0
NH1 K:ARG19 3.8 57.4 1.0
O K:ALA169 3.9 46.5 1.0
CB W:ASP204 3.9 51.9 1.0
C K:ALA169 3.9 44.1 1.0
N K:ALA169 3.9 41.0 1.0
O K:HIS166 4.0 46.5 1.0
OXT W:ASP204 4.1 60.1 1.0
CA K:ALA165 4.2 44.0 1.0
N K:SER171 4.2 42.7 1.0
C K:HIS166 4.3 45.1 1.0
N K:ASP168 4.4 44.6 1.0
N K:HIS166 4.4 44.5 1.0
CA K:ASP168 4.4 42.0 1.0
CZ K:ARG19 4.5 54.0 1.0
CA K:SER171 4.5 42.1 1.0
O K:ALA164 4.5 41.4 1.0
CA K:HIS166 4.6 45.6 1.0
N K:TYR170 4.7 44.4 1.0
N K:GLY172 4.7 46.3 1.0
NH2 K:ARG19 4.8 56.7 1.0
C K:ARG167 4.8 44.7 1.0
CA K:GLY172 4.8 47.4 1.0
N K:ARG167 4.9 44.0 1.0
CG W:ASP204 4.9 50.2 1.0
CB K:SER171 5.0 41.1 1.0

Magnesium binding site 5 out of 10 in 4qv7

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Magnesium binding site 5 out of 10 in the Ycp BETA5-A50V 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-A50V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:54.5
occ:1.00
 O K:ILE82 2.8 39.8 1.0
CB K:ASN85 3.6 36.9 1.0
C K:ILE82 3.6 37.5 1.0
CA K:ILE82 3.7 37.0 1.0
N K:LEU86 3.7 35.1 1.0
CG2 K:ILE82 4.0 36.4 1.0
C K:ASN85 4.1 35.3 1.0
CA K:LEU86 4.2 35.5 1.0
CB K:LEU86 4.2 35.6 1.0
CB K:ILE82 4.3 36.8 1.0
CA K:ASN85 4.4 36.5 1.0
CH2 K:TRP58 4.5 35.1 1.0
O K:LYS81 4.6 36.1 1.0
CG K:ASN85 4.8 36.8 1.0
CG1 K:ILE82 4.8 37.5 1.0
O K:ASN85 4.8 35.2 1.0
OD1 K:ASN85 4.8 41.0 1.0
N K:ASN85 4.9 35.5 1.0
N K:ILE82 4.9 36.5 1.0
N K:LEU83 4.9 37.2 1.0

Magnesium binding site 6 out of 10 in 4qv7

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Magnesium binding site 6 out of 10 in the Ycp BETA5-A50V 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-A50V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:55.6
occ:1.00
 O N:SER169 2.8 37.7 1.0
O N:ILE163 2.8 42.4 1.0
O N:ASP166 3.2 45.6 1.0
NH1 N:ARG19 3.5 40.1 1.0
CD1 a:LEU34 3.5 47.6 1.0
C N:ILE163 3.9 40.9 1.0
C N:SER169 3.9 37.7 1.0
CG2 N:ILE163 4.0 39.1 1.0
CZ N:ARG19 4.0 39.5 1.0
C N:ASP166 4.1 41.4 1.0
NH2 N:ARG19 4.2 41.4 1.0
CA N:GLY167 4.2 39.9 1.0
CA N:GLY170 4.4 38.4 1.0
O N:GLY167 4.4 37.7 1.0
CA N:ILE163 4.6 39.7 1.0
C N:GLY167 4.6 38.3 1.0
N N:GLY167 4.6 39.9 1.0
N N:GLY170 4.6 37.4 1.0
CG a:LEU34 4.8 46.0 1.0
CB N:ILE163 4.9 39.1 1.0
NE N:ARG19 4.9 40.0 1.0
N N:LYS164 4.9 42.1 1.0

Magnesium binding site 7 out of 10 in 4qv7

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Magnesium binding site 7 out of 10 in the Ycp BETA5-A50V 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-A50V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:56.2
occ:1.00
 O N:HOH317 2.3 37.2 1.0
NE2 H:GLN91 3.1 67.7 1.0
OD1 N:ASP51 3.2 34.3 1.0
O N:ASN92 3.5 46.7 1.0
OD2 N:ASP51 3.7 38.9 1.0
CG N:ASP51 3.8 27.5 1.0
O H:HOH303 3.9 32.1 1.0
CD H:GLN91 4.1 64.5 1.0
OE1 H:GLN91 4.5 76.1 1.0
C N:ASN92 4.6 45.8 1.0
O N:HOH309 4.6 43.2 1.0

Magnesium binding site 8 out of 10 in 4qv7

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Magnesium binding site 8 out of 10 in the Ycp BETA5-A50V 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-A50V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:57.4
occ:1.00
 OXT L:ASP222 2.0 66.3 1.0
O V:ILE163 2.2 47.0 1.0
O V:SER169 2.2 45.2 1.0
O V:ASP166 2.2 41.6 1.0
C L:ASP222 3.1 65.9 1.0
C V:ASP166 3.2 43.5 1.0
C V:ILE163 3.3 48.2 1.0
C V:SER169 3.4 44.9 1.0
CA L:ASP222 3.8 66.2 1.0
NH1 V:ARG19 3.8 55.5 1.0
O V:GLY162 3.8 44.8 1.0
CA V:LEU167 3.9 44.1 1.0
N V:LEU167 3.9 44.7 1.0
O L:ASP222 4.0 60.7 1.0
CA V:ILE163 4.0 47.5 1.0
C V:LEU167 4.2 43.4 1.0
N V:ASP166 4.2 43.7 1.0
N V:SER169 4.2 43.9 1.0
N V:TRP164 4.3 47.8 1.0
N V:GLY170 4.3 46.7 1.0
CA V:GLY170 4.3 48.7 1.0
CB L:ASP222 4.3 67.5 1.0
O V:LEU167 4.3 42.4 1.0
O V:TRP164 4.3 53.4 1.0
C V:TRP164 4.3 49.7 1.0
CA V:SER169 4.3 44.2 1.0
CA V:ASP166 4.3 43.4 1.0
CZ V:ARG19 4.4 55.1 1.0
CA V:TRP164 4.5 49.6 1.0
NH2 V:ARG19 4.6 56.7 1.0
CB V:SER169 4.8 44.7 1.0
N V:ASN165 4.8 47.6 1.0
C V:GLY162 4.8 46.8 1.0
C V:ASN165 4.9 44.5 1.0
N V:ILE163 4.9 46.7 1.0
N V:GLY168 4.9 43.6 1.0

Magnesium binding site 9 out of 10 in 4qv7

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Magnesium binding site 9 out of 10 in the Ycp BETA5-A50V Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Ycp BETA5-A50V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:51.6
occ:1.00
 O Y:ASP168 2.3 42.9 1.0
O Y:ALA165 2.4 42.6 1.0
O I:ASP204 2.5 51.8 1.0
O Y:SER171 2.8 41.2 1.0
C I:ASP204 3.1 53.2 1.0
C Y:ASP168 3.3 41.2 1.0
C Y:ALA165 3.5 42.3 1.0
CA I:ASP204 3.6 54.2 1.0
CA Y:ALA169 3.6 42.6 1.0
O Y:HIS166 3.8 42.9 1.0
N Y:ALA169 3.8 42.5 1.0
NH1 Y:ARG19 3.9 57.6 1.0
O Y:ALA169 3.9 44.5 1.0
C Y:ALA169 3.9 43.7 1.0
CB I:ASP204 4.0 54.4 1.0
OXT I:ASP204 4.0 58.5 1.0
C Y:SER171 4.0 41.6 1.0
C Y:HIS166 4.2 41.9 1.0
CA Y:ALA165 4.4 40.1 1.0
N Y:ASP168 4.4 41.3 1.0
CA Y:ASP168 4.4 40.3 1.0
N Y:SER171 4.5 40.5 1.0
N Y:HIS166 4.5 43.6 1.0
CA Y:HIS166 4.6 42.1 1.0
CZ Y:ARG19 4.6 54.6 1.0
O Y:ALA164 4.6 40.9 1.0
C Y:ARG167 4.7 40.8 1.0
N Y:TYR170 4.8 42.8 1.0
CA Y:SER171 4.8 40.1 1.0
N Y:ARG167 4.8 40.6 1.0
NH2 Y:ARG19 4.9 54.5 1.0
O Y:ARG167 4.9 40.9 1.0
N I:ASP204 5.0 53.2 1.0
CB Y:ALA169 5.0 41.4 1.0

Magnesium binding site 10 out of 10 in 4qv7

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Magnesium binding site 10 out of 10 in the Ycp BETA5-A50V Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Ycp BETA5-A50V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:65.0
occ:1.00
 O Z:VAL198 2.4 49.2 1.0
O Z:THR192 2.9 62.5 1.0
O Z:HIS195 3.1 43.7 1.0
O Z:ASP222 3.4 74.5 1.0
NH2 Z:ARG28 3.6 59.7 1.0
C Z:VAL198 3.6 50.1 1.0
O Z:ILE196 3.7 54.3 1.0
CG2 Z:THR192 3.8 61.3 1.0
C Z:THR192 3.9 61.0 1.0
C Z:ILE196 4.0 49.8 1.0
CA Z:ILE196 4.1 50.4 1.0
C Z:HIS195 4.1 49.0 1.0
CA Z:THR192 4.1 60.0 1.0
NH2 H:ARG19 4.3 60.0 1.0
OD1 Z:ASP222 4.3 64.8 1.0
N Z:VAL198 4.4 48.2 1.0
CZ Z:ARG28 4.5 59.5 1.0
N Z:GLY199 4.5 51.4 1.0
C Z:ASP222 4.5 77.9 1.0
N Z:ILE196 4.5 49.1 1.0
CA Z:VAL198 4.5 49.7 1.0
CA Z:GLY199 4.5 52.9 1.0
CB Z:THR192 4.6 60.1 1.0
NH1 Z:ARG28 4.6 60.4 1.0
O Z:LYS220 4.8 67.7 1.0
NH1 H:ARG19 4.9 60.6 1.0
N Z:GLN197 5.0 47.4 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 02:16:51 2024

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