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Magnesium in PDB 4qv9: Ycp BETA5-C63F Mutant

Enzymatic activity of Ycp BETA5-C63F Mutant

All present enzymatic activity of Ycp BETA5-C63F Mutant:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-C63F Mutant, PDB code: 4qv9 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 (°) 134.200, 300.450, 143.410, 90.00, 113.07, 90.00
R / Rfree (%) 19.6 / 21.8

Other elements in 4qv9:

The structure of Ycp BETA5-C63F Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-C63F Mutant (pdb code 4qv9). 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-C63F Mutant, PDB code: 4qv9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 4qv9

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Magnesium binding site 1 out of 10 in the Ycp BETA5-C63F 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-C63F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:45.4
occ:1.00
 O G:MET125 2.1 44.3 1.0
O G:ARG122 2.3 39.6 1.0
O G:TYR119 2.5 33.4 1.0
OG1 G:THR8 2.7 40.5 1.0
O G:HOH409 2.9 49.5 1.0
C G:MET125 3.3 43.7 1.0
CG2 G:THR8 3.3 40.6 1.0
C G:ARG122 3.4 40.7 1.0
O G:ALA123 3.4 44.8 1.0
CB G:THR8 3.6 40.5 1.0
CA G:ALA123 3.6 42.2 1.0
C G:ALA123 3.6 43.9 1.0
C G:TYR119 3.7 33.1 1.0
N G:ALA123 4.0 40.9 1.0
N G:MET125 4.1 46.4 1.0
N G:ARG126 4.1 39.7 1.0
CA G:ARG126 4.2 38.3 1.0
CA G:MET125 4.2 47.4 1.0
N G:THR8 4.4 43.4 1.0
CA G:TYR119 4.4 31.9 1.0
N G:TYR124 4.5 45.8 1.0
CD G:PRO127 4.6 35.6 1.0
CA G:THR8 4.6 41.5 1.0
CA G:ARG122 4.7 42.9 1.0
N G:THR120 4.7 33.3 1.0
N G:ARG122 4.7 39.4 1.0
CB G:MET125 4.7 52.3 1.0
C G:ARG126 4.8 36.7 1.0
C G:TYR124 4.9 45.5 1.0
CA G:THR120 4.9 34.0 1.0
CB G:TYR119 4.9 30.5 1.0
N G:PRO127 5.0 35.8 1.0
CB G:ALA123 5.0 42.1 1.0
C G:THR120 5.0 35.0 1.0

Magnesium binding site 2 out of 10 in 4qv9

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Magnesium binding site 2 out of 10 in the Ycp BETA5-C63F 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-C63F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:57.0
occ:1.00
 O N:HOH319 2.3 33.8 1.0
O N:HOH332 2.5 30.5 1.0
NE2 H:GLN91 3.4 60.6 1.0
OD1 N:ASP51 3.4 27.3 1.0
O N:ASN92 3.5 43.2 1.0
OD2 N:ASP51 3.7 33.8 1.0
CG N:ASP51 4.0 24.6 1.0
O H:HOH404 4.1 31.3 1.0
O N:HOH308 4.2 35.3 1.0
CD H:GLN91 4.6 57.2 1.0
C N:ASN92 4.6 41.8 1.0

Magnesium binding site 3 out of 10 in 4qv9

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Magnesium binding site 3 out of 10 in the Ycp BETA5-C63F 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-C63F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:57.4
occ:1.00
 O I:ASP177 2.5 35.8 1.0
O I:SER180 2.7 42.5 1.0
O I:ALA174 3.2 40.5 1.0
OXT I:ASP204 3.5 52.8 1.0
C I:ASP177 3.6 35.3 1.0
O I:ALA178 3.8 36.9 1.0
C I:SER180 3.9 39.6 1.0
NH1 Y:ARG19 4.0 47.1 1.0
CA I:ALA178 4.0 35.3 1.0
C I:ALA178 4.0 36.6 1.0
O I:HOH401 4.1 34.1 1.0
N I:ALA178 4.2 33.5 1.0
O I:ASP204 4.2 47.3 1.0
C I:ASP204 4.3 47.5 1.0
C I:ALA174 4.3 38.9 1.0
NH2 Y:ARG19 4.4 46.5 1.0
N I:SER180 4.5 38.3 1.0
CZ Y:ARG19 4.6 46.0 1.0
CA I:ASP175 4.6 39.0 1.0
N I:ASP177 4.6 35.9 1.0
CA I:ASP177 4.7 35.9 1.0
CA I:SER180 4.8 38.8 1.0
N I:LEU179 4.8 36.7 1.0
N I:GLY181 4.8 39.8 1.0
C I:ASP175 4.8 39.7 1.0
CA I:GLY181 4.9 40.5 1.0
O I:ASP175 4.9 42.4 1.0
N I:ASP175 4.9 39.1 1.0

Magnesium binding site 4 out of 10 in 4qv9

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Magnesium binding site 4 out of 10 in the Ycp BETA5-C63F 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-C63F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:52.2
occ:1.00
 OE1 J:GLN118 2.8 31.5 1.0
O J:THR124 3.3 33.6 1.0
CD J:GLN118 3.6 31.2 1.0
CG J:GLN118 3.6 30.6 1.0
N J:ASP120 3.7 30.5 1.0
CB J:ASP120 3.8 33.3 1.0
CE1 J:HIS133 3.9 32.4 1.0
O J:GLN118 4.0 29.9 1.0
OD2 J:ASP120 4.1 36.7 1.0
CG J:ASP120 4.1 34.1 1.0
C J:GLN118 4.2 29.9 1.0
C J:ILE119 4.3 30.1 1.0
CB J:THR124 4.3 31.9 1.0
CA J:ASP120 4.4 31.9 1.0
CA J:ILE119 4.4 28.9 1.0
C J:THR124 4.4 32.9 1.0
N J:ILE119 4.4 29.2 1.0
CB J:GLN118 4.5 30.2 1.0
CG2 J:THR124 4.6 31.8 1.0
ND1 J:HIS133 4.6 32.7 1.0
CG1 I:VAL35 4.6 39.0 1.0
NE2 J:HIS133 4.8 32.1 1.0
OD1 J:ASP120 4.9 35.2 1.0
NE2 J:GLN118 4.9 31.8 1.0

Magnesium binding site 5 out of 10 in 4qv9

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Magnesium binding site 5 out of 10 in the Ycp BETA5-C63F 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-C63F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:38.9
occ:1.00
 O K:ALA165 2.3 37.4 1.0
O W:ASP204 2.3 45.7 1.0
O K:ASP168 2.3 34.8 1.0
O K:SER171 2.6 38.4 1.0
C W:ASP204 3.1 46.8 1.0
C K:ASP168 3.4 35.5 1.0
C K:ALA165 3.5 36.4 1.0
CA W:ASP204 3.5 46.6 1.0
CA K:ALA169 3.7 36.2 1.0
NH1 K:ARG19 3.7 47.5 1.0
C K:SER171 3.9 38.5 1.0
CB W:ASP204 3.9 45.8 1.0
O K:HIS166 3.9 41.0 1.0
O K:ALA169 3.9 41.5 1.0
C K:ALA169 3.9 38.3 1.0
N K:ALA169 3.9 35.3 1.0
OXT W:ASP204 4.0 49.3 1.0
C K:HIS166 4.3 38.3 1.0
CA K:ALA165 4.3 37.4 1.0
N K:SER171 4.4 36.5 1.0
CZ K:ARG19 4.4 46.6 1.0
N K:HIS166 4.4 36.3 1.0
N K:ASP168 4.5 37.3 1.0
CA K:ASP168 4.5 35.5 1.0
CA K:HIS166 4.6 38.2 1.0
CA K:SER171 4.6 36.5 1.0
O K:ALA164 4.7 34.6 1.0
NH2 K:ARG19 4.7 48.8 1.0
N K:TYR170 4.7 37.9 1.0
C K:ARG167 4.8 37.6 1.0
N K:GLY172 4.8 40.0 1.0
CG W:ASP204 4.9 45.1 1.0
N W:ASP204 4.9 46.1 1.0
N K:ARG167 4.9 37.8 1.0
CA K:GLY172 4.9 41.2 1.0

Magnesium binding site 6 out of 10 in 4qv9

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Magnesium binding site 6 out of 10 in the Ycp BETA5-C63F 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-C63F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:52.9
occ:1.00
 O K:ILE82 2.8 35.2 1.0
C K:ILE82 3.6 33.0 1.0
CA K:ILE82 3.6 32.5 1.0
CB K:ASN85 3.7 31.9 1.0
CG2 K:ILE82 3.8 32.6 1.0
N K:LEU86 3.8 30.7 1.0
CB K:ILE82 4.2 32.5 1.0
C K:ASN85 4.3 30.4 1.0
CB K:LEU86 4.3 30.7 1.0
CA K:LEU86 4.3 30.9 1.0
CA K:ASN85 4.5 31.4 1.0
CH2 K:TRP58 4.5 31.3 1.0
O K:LYS81 4.6 32.0 1.0
CG1 K:ILE82 4.6 32.9 1.0
CG K:ASN85 4.7 32.8 1.0
OD1 K:ASN85 4.7 36.1 1.0
N K:ILE82 4.9 32.3 1.0
N K:LEU83 4.9 32.5 1.0
O K:ASN85 4.9 29.3 1.0
N K:ASN85 5.0 31.0 1.0

Magnesium binding site 7 out of 10 in 4qv9

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Magnesium binding site 7 out of 10 in the Ycp BETA5-C63F 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-C63F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:48.2
occ:1.00
 O N:SER169 2.8 33.6 1.0
O N:ILE163 2.9 36.9 1.0
O N:ASP166 3.3 40.4 1.0
NH1 N:ARG19 3.4 36.6 1.0
CD1 a:LEU34 3.5 41.5 1.0
CZ N:ARG19 4.0 36.2 1.0
C N:ILE163 4.0 37.1 1.0
C N:SER169 4.0 33.9 1.0
CG2 N:ILE163 4.0 35.8 1.0
NH2 N:ARG19 4.1 37.7 1.0
C N:ASP166 4.2 37.5 1.0
CA N:GLY167 4.3 35.9 1.0
O N:GLY167 4.4 34.0 1.0
CA N:GLY170 4.4 36.0 1.0
C N:GLY167 4.6 34.9 1.0
N N:GLY167 4.7 36.2 1.0
CA N:ILE163 4.7 35.9 1.0
N N:GLY170 4.7 34.9 1.0
CG a:LEU34 4.8 41.3 1.0
NE N:ARG19 4.9 36.2 1.0
CB N:ILE163 5.0 35.3 1.0

Magnesium binding site 8 out of 10 in 4qv9

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Magnesium binding site 8 out of 10 in the Ycp BETA5-C63F 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-C63F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:44.9
occ:1.00
 O V:ILE163 2.0 43.9 1.0
OXT L:ASP222 2.1 56.5 1.0
O V:ASP166 2.2 38.1 1.0
O V:SER169 2.3 39.3 1.0
O L:HOH301 2.6 38.5 1.0
C L:ASP222 3.1 58.4 1.0
C V:ILE163 3.1 43.4 1.0
C V:ASP166 3.3 37.7 1.0
C V:SER169 3.5 38.5 1.0
CA L:ASP222 3.6 58.2 1.0
O V:GLY162 3.8 40.5 1.0
NH1 V:ARG19 3.9 49.5 1.0
CA V:LEU167 4.0 37.8 1.0
CA V:ILE163 4.0 42.3 1.0
N V:LEU167 4.0 38.5 1.0
O L:ASP222 4.0 59.3 1.0
N V:TRP164 4.1 43.6 1.0
C V:TRP164 4.1 43.4 1.0
O V:TRP164 4.1 45.3 1.0
CB L:ASP222 4.1 58.6 1.0
N V:ASP166 4.2 37.6 1.0
CA V:GLY170 4.3 42.4 1.0
CA V:TRP164 4.3 43.3 1.0
N V:GLY170 4.3 40.1 1.0
CA V:ASP166 4.3 37.3 1.0
C V:LEU167 4.3 37.7 1.0
N V:SER169 4.3 37.9 1.0
CA V:SER169 4.4 37.8 1.0
O V:LEU167 4.5 36.7 1.0
CZ V:ARG19 4.5 48.1 1.0
N V:ASN165 4.6 42.8 1.0
NH2 V:ARG19 4.7 49.2 1.0
C V:GLY162 4.7 41.1 1.0
CB V:SER169 4.8 38.2 1.0
N V:ILE163 4.9 41.4 1.0
C V:ASN165 4.9 39.5 1.0
O L:ARG221 4.9 54.5 1.0
N L:ASP222 5.0 55.7 1.0
CG2 V:ILE163 5.0 43.8 1.0

Magnesium binding site 9 out of 10 in 4qv9

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Magnesium binding site 9 out of 10 in the Ycp BETA5-C63F 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-C63F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:43.9
occ:1.00
 O Y:ASP168 2.2 36.9 1.0
O Y:ALA165 2.3 35.2 1.0
O I:ASP204 2.4 47.3 1.0
O Y:SER171 2.6 39.6 1.0
C I:ASP204 3.2 47.5 1.0
C Y:ASP168 3.2 34.9 1.0
C Y:ALA165 3.5 35.4 1.0
CA Y:ALA169 3.6 36.0 1.0
CA I:ASP204 3.7 47.7 1.0
NH1 Y:ARG19 3.7 47.1 1.0
O Y:ALA169 3.8 36.9 1.0
C Y:SER171 3.8 36.6 1.0
C Y:ALA169 3.8 36.8 1.0
N Y:ALA169 3.8 35.8 1.0
O Y:HIS166 3.9 36.0 1.0
CB I:ASP204 4.0 48.2 1.0
OXT I:ASP204 4.1 52.8 1.0
N Y:SER171 4.3 34.8 1.0
CA Y:ALA165 4.3 34.4 1.0
C Y:HIS166 4.3 35.3 1.0
CZ Y:ARG19 4.4 46.0 1.0
CA Y:ASP168 4.4 34.5 1.0
N Y:ASP168 4.4 34.9 1.0
N Y:HIS166 4.5 36.5 1.0
CA Y:SER171 4.6 34.7 1.0
O Y:ALA164 4.6 35.2 1.0
CA Y:HIS166 4.6 36.1 1.0
N Y:TYR170 4.6 36.4 1.0
NH2 Y:ARG19 4.8 46.5 1.0
C Y:ARG167 4.8 34.7 1.0
N Y:GLY172 4.8 37.6 1.0
N Y:ARG167 4.9 35.5 1.0
CA Y:GLY172 4.9 38.3 1.0
CG I:ASP204 5.0 47.6 1.0
CB Y:ALA169 5.0 35.3 1.0

Magnesium binding site 10 out of 10 in 4qv9

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Magnesium binding site 10 out of 10 in the Ycp BETA5-C63F 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-C63F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:64.8
occ:1.00
 O Z:VAL198 2.4 44.7 1.0
O Z:THR192 2.9 50.1 1.0
O Z:HIS195 3.2 38.4 1.0
O Z:ASP222 3.3 64.3 1.0
NH2 Z:ARG28 3.5 52.3 1.0
C Z:VAL198 3.6 45.4 1.0
CG2 Z:THR192 3.7 54.5 1.0
O Z:ILE196 3.8 47.4 1.0
C Z:THR192 3.9 52.1 1.0
C Z:ILE196 4.1 44.5 1.0
CA Z:THR192 4.2 52.6 1.0
CA Z:ILE196 4.2 45.0 1.0
OD1 Z:ASP222 4.2 61.6 1.0
C Z:HIS195 4.2 42.6 1.0
NH2 H:ARG19 4.2 55.2 1.0
CZ Z:ARG28 4.4 51.9 1.0
C Z:ASP222 4.4 66.4 1.0
CA Z:GLY199 4.4 47.7 1.0
N Z:GLY199 4.4 45.8 1.0
N Z:VAL198 4.5 42.0 1.0
NH1 Z:ARG28 4.5 51.9 1.0
CB Z:THR192 4.5 53.8 1.0
CA Z:VAL198 4.6 43.9 1.0
O Z:LYS220 4.6 56.3 1.0
N Z:ILE196 4.7 44.0 1.0
OXT Z:ASP222 4.9 65.6 1.0
NH1 H:ARG19 5.0 55.1 1.0
CZ H:ARG19 5.0 53.9 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 02:18:08 2024

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