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Magnesium in PDB 4qv1: Ycp BETA5-M45A Mutant

Enzymatic activity of Ycp BETA5-M45A Mutant

All present enzymatic activity of Ycp BETA5-M45A Mutant:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-M45A Mutant, PDB code: 4qv1 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 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.540, 300.510, 144.280, 90.00, 112.67, 90.00
R / Rfree (%) 19.4 / 21.6

Other elements in 4qv1:

The structure of Ycp BETA5-M45A Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-M45A Mutant (pdb code 4qv1). 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-M45A Mutant, PDB code: 4qv1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 4qv1

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Magnesium binding site 1 out of 10 in the Ycp BETA5-M45A 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-M45A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:49.8
occ:1.00
 O G:MET125 2.1 46.2 1.0
O G:ARG122 2.4 42.9 1.0
O G:TYR119 2.5 35.9 1.0
OG1 G:THR8 2.7 44.7 1.0
C G:MET125 3.3 46.9 1.0
CG2 G:THR8 3.3 42.1 1.0
O G:ALA123 3.4 47.0 1.0
C G:ARG122 3.5 42.5 1.0
CB G:THR8 3.6 42.8 1.0
C G:ALA123 3.7 46.0 1.0
CA G:ALA123 3.7 44.5 1.0
C G:TYR119 3.7 35.5 1.0
N G:ALA123 4.1 42.6 1.0
N G:MET125 4.1 49.7 1.0
N G:ARG126 4.1 42.9 1.0
CA G:ARG126 4.2 41.1 1.0
CA G:MET125 4.2 50.4 1.0
N G:THR8 4.4 45.5 1.0
CA G:TYR119 4.4 34.0 1.0
CD G:PRO127 4.5 38.2 1.0
N G:TYR124 4.6 47.5 1.0
CA G:THR8 4.6 44.0 1.0
CA G:ARG122 4.7 45.2 1.0
N G:THR120 4.7 35.7 1.0
C G:ARG126 4.7 39.7 1.0
CB G:MET125 4.8 55.6 1.0
N G:ARG122 4.8 41.8 1.0
C G:TYR124 4.9 47.9 1.0
CA G:THR120 4.9 35.9 1.0
CB G:TYR119 4.9 32.5 1.0
N G:PRO127 4.9 38.0 1.0
C G:THR120 5.0 36.6 1.0

Magnesium binding site 2 out of 10 in 4qv1

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Magnesium binding site 2 out of 10 in the Ycp BETA5-M45A 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-M45A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:58.2
occ:1.00
 O N:HOH338 2.3 37.8 1.0
OE1 H:GLN91 2.9 56.7 1.0
OD1 N:ASP51 3.2 29.0 1.0
OD2 N:ASP51 3.7 37.0 1.0
CD H:GLN91 3.8 53.5 1.0
O N:ASN92 3.9 44.2 1.0
CG N:ASP51 3.9 26.5 1.0
O H:HOH401 3.9 38.1 1.0
NE2 H:GLN91 4.1 55.2 1.0
O N:HOH316 4.8 33.0 1.0
CD2 H:HIS116 4.9 34.8 1.0
OG N:SER48 4.9 34.6 1.0
C N:ASN92 5.0 42.8 1.0

Magnesium binding site 3 out of 10 in 4qv1

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Magnesium binding site 3 out of 10 in the Ycp BETA5-M45A 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-M45A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:61.8
occ:1.00
 O I:ASP177 2.6 39.1 1.0
O I:SER180 2.8 39.5 1.0
OXT I:ASP204 3.4 51.9 1.0
O I:ALA174 3.5 43.2 1.0
C I:ASP177 3.6 38.2 1.0
O I:ALA178 3.7 40.8 1.0
NH1 Y:ARG19 3.8 50.9 1.0
CA I:ALA178 3.9 38.6 1.0
C I:ALA178 3.9 40.3 1.0
C I:SER180 4.0 40.8 1.0
O I:ASP204 4.0 48.1 1.0
C I:ASP204 4.2 49.3 1.0
N I:ALA178 4.2 36.5 1.0
NH2 Y:ARG19 4.3 51.0 1.0
CZ Y:ARG19 4.5 50.0 1.0
N I:SER180 4.5 39.9 1.0
C I:ALA174 4.6 41.8 1.0
CA I:ASP175 4.8 41.4 1.0
N I:LEU179 4.8 40.5 1.0
N I:ASP177 4.8 39.8 1.0
CA I:ASP177 4.8 39.4 1.0
CA I:SER180 4.9 40.1 1.0
N I:GLY181 4.9 40.7 1.0
CA I:GLY181 5.0 41.7 1.0

Magnesium binding site 4 out of 10 in 4qv1

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Magnesium binding site 4 out of 10 in the Ycp BETA5-M45A 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-M45A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:59.7
occ:1.00
 OE1 J:GLN118 2.9 35.6 1.0
O J:THR124 3.3 37.2 1.0
CD J:GLN118 3.6 33.1 1.0
CG J:GLN118 3.7 32.6 1.0
N J:ASP120 3.8 32.9 1.0
CB J:ASP120 3.9 34.6 1.0
O J:GLN118 4.0 31.2 1.0
CE1 J:HIS133 4.0 32.9 1.0
OD2 J:ASP120 4.2 39.3 1.0
CG J:ASP120 4.2 35.8 1.0
C J:GLN118 4.3 31.5 1.0
CB J:THR124 4.3 33.0 1.0
C J:ILE119 4.4 32.2 1.0
C J:THR124 4.4 34.5 1.0
CA J:ILE119 4.5 30.3 1.0
CA J:ASP120 4.5 33.3 1.0
CB J:GLN118 4.5 32.2 1.0
N J:ILE119 4.5 30.7 1.0
CG2 J:THR124 4.5 32.4 1.0
CG1 I:VAL35 4.7 40.9 1.0
ND1 J:HIS133 4.8 32.6 1.0
NE2 J:HIS133 4.9 32.7 1.0
OD1 J:ASP120 4.9 36.5 1.0
NE2 J:GLN118 4.9 32.7 1.0

Magnesium binding site 5 out of 10 in 4qv1

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Magnesium binding site 5 out of 10 in the Ycp BETA5-M45A 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-M45A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:39.2
occ:1.00
 O K:ALA165 2.2 40.7 1.0
O W:ASP204 2.3 45.4 1.0
O K:ASP168 2.3 41.7 1.0
O K:SER171 2.4 41.5 1.0
O K:HOH434 2.6 51.8 1.0
C W:ASP204 3.1 49.6 1.0
C K:ASP168 3.4 38.8 1.0
C K:ALA165 3.4 40.2 1.0
CA W:ASP204 3.6 49.9 1.0
C K:SER171 3.6 41.2 1.0
NH1 K:ARG19 3.7 49.8 1.0
CA K:ALA169 3.8 38.9 1.0
CB W:ASP204 3.8 50.2 1.0
O K:ALA169 3.9 39.7 1.0
C K:ALA169 3.9 40.0 1.0
N K:ALA169 4.0 38.0 1.0
OXT W:ASP204 4.1 52.6 1.0
O K:HIS166 4.1 42.3 1.0
CA K:ALA165 4.2 41.3 1.0
N K:SER171 4.2 39.4 1.0
CZ K:ARG19 4.3 48.2 1.0
C K:HIS166 4.4 41.8 1.0
N K:HIS166 4.4 39.6 1.0
CA K:SER171 4.5 39.0 1.0
N K:ASP168 4.5 39.5 1.0
CA K:ASP168 4.5 38.7 1.0
NH2 K:ARG19 4.6 49.8 1.0
N K:GLY172 4.6 42.8 1.0
O K:ALA164 4.6 38.0 1.0
CA K:HIS166 4.7 41.5 1.0
CA K:GLY172 4.7 44.2 1.0
N K:TYR170 4.7 41.0 1.0
CG W:ASP204 4.8 49.2 1.0
CB K:SER171 4.9 38.7 1.0
C K:ARG167 4.9 39.4 1.0

Magnesium binding site 6 out of 10 in 4qv1

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Magnesium binding site 6 out of 10 in the Ycp BETA5-M45A 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-M45A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:52.0
occ:1.00
 O K:HOH427 2.3 47.3 1.0
O K:ILE82 2.8 36.1 1.0
CB K:ASN85 3.6 33.9 1.0
C K:ILE82 3.6 34.3 1.0
CA K:ILE82 3.7 34.3 1.0
N K:LEU86 3.7 32.4 1.0
CG2 K:ILE82 4.0 34.4 1.0
C K:ASN85 4.1 32.5 1.0
CA K:LEU86 4.2 32.2 1.0
CB K:LEU86 4.2 31.9 1.0
CB K:ILE82 4.4 34.4 1.0
CA K:ASN85 4.4 33.0 1.0
CH2 K:TRP58 4.5 32.4 1.0
O K:LYS81 4.6 36.8 1.0
CG K:ASN85 4.7 35.2 1.0
OD1 K:ASN85 4.7 38.4 1.0
CG1 K:ILE82 4.8 34.9 1.0
O K:ASN85 4.8 32.9 1.0
N K:ASN85 4.9 33.1 1.0
N K:ILE82 4.9 34.8 1.0
N K:LEU83 4.9 34.0 1.0

Magnesium binding site 7 out of 10 in 4qv1

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Magnesium binding site 7 out of 10 in the Ycp BETA5-M45A 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-M45A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:50.4
occ:1.00
 O N:SER169 2.8 36.6 1.0
O N:ILE163 2.8 35.9 1.0
O N:ASP166 3.1 38.7 1.0
CD1 a:LEU34 3.5 43.6 1.0
NH1 N:ARG19 3.5 37.8 1.0
C N:ILE163 3.9 38.0 1.0
C N:SER169 3.9 36.2 1.0
C N:ASP166 4.1 37.3 1.0
CG2 N:ILE163 4.1 37.4 1.0
CZ N:ARG19 4.1 37.0 1.0
CA N:GLY167 4.1 36.3 1.0
NH2 N:ARG19 4.3 36.9 1.0
O N:GLY167 4.4 36.6 1.0
CA N:GLY170 4.5 38.0 1.0
N N:GLY167 4.5 36.1 1.0
C N:GLY167 4.5 36.1 1.0
CA N:ILE163 4.6 37.1 1.0
N N:GLY170 4.7 37.4 1.0
CG a:LEU34 4.7 43.3 1.0
N N:LYS164 5.0 39.9 1.0
N N:SER169 5.0 34.2 1.0
NE N:ARG19 5.0 37.0 1.0
CB N:ILE163 5.0 36.8 1.0
CA N:SER169 5.0 33.9 1.0
O N:LYS164 5.0 42.2 1.0

Magnesium binding site 8 out of 10 in 4qv1

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Magnesium binding site 8 out of 10 in the Ycp BETA5-M45A 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-M45A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:48.1
occ:1.00
 O V:ILE163 1.9 47.6 1.0
OXT L:ASP222 2.1 59.6 1.0
O V:ASP166 2.3 38.8 1.0
O V:SER169 2.4 44.0 1.0
C V:ILE163 3.0 47.1 1.0
C L:ASP222 3.1 61.5 1.0
C V:ASP166 3.3 40.5 1.0
C V:SER169 3.6 41.7 1.0
CA L:ASP222 3.6 61.2 1.0
O V:GLY162 3.7 44.5 1.0
CA V:ILE163 3.9 46.1 1.0
O V:TRP164 3.9 51.5 1.0
C V:TRP164 4.0 47.4 1.0
N V:TRP164 4.0 46.8 1.0
O L:ASP222 4.0 59.7 1.0
NH1 V:ARG19 4.1 50.2 1.0
N V:LEU167 4.1 41.8 1.0
CA V:LEU167 4.1 41.0 1.0
N V:ASP166 4.1 40.3 1.0
CB L:ASP222 4.2 62.7 1.0
CA V:TRP164 4.2 47.1 1.0
CA V:ASP166 4.3 40.2 1.0
CA V:GLY170 4.4 45.5 1.0
N V:GLY170 4.4 43.2 1.0
N V:ASN165 4.5 45.6 1.0
N V:SER169 4.5 40.3 1.0
C V:LEU167 4.5 41.0 1.0
CA V:SER169 4.5 41.3 1.0
CZ V:ARG19 4.6 51.5 1.0
O V:LEU167 4.7 40.3 1.0
C V:GLY162 4.7 44.8 1.0
C V:ASN165 4.8 42.4 1.0
N V:ILE163 4.8 45.3 1.0
NH2 V:ARG19 4.8 53.5 1.0
CB V:SER169 4.9 41.8 1.0
O L:ARG221 4.9 58.4 1.0
CG2 V:ILE163 4.9 47.6 1.0
N L:ASP222 5.0 59.2 1.0

Magnesium binding site 9 out of 10 in 4qv1

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Magnesium binding site 9 out of 10 in the Ycp BETA5-M45A 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-M45A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:48.5
occ:1.00
 O Y:ASP168 2.3 37.5 1.0
O I:ASP204 2.4 48.1 1.0
O Y:ALA165 2.4 37.2 1.0
O Y:SER171 2.7 41.6 1.0
C I:ASP204 3.2 49.3 1.0
C Y:ASP168 3.2 37.9 1.0
CA Y:ALA169 3.6 38.7 1.0
C Y:ALA165 3.6 38.6 1.0
NH1 Y:ARG19 3.7 50.9 1.0
CA I:ASP204 3.7 50.4 1.0
O Y:ALA169 3.8 38.9 1.0
N Y:ALA169 3.8 38.3 1.0
C Y:ALA169 3.8 39.1 1.0
C Y:SER171 3.9 40.2 1.0
O Y:HIS166 4.0 37.0 1.0
CB I:ASP204 4.0 52.0 1.0
OXT I:ASP204 4.0 51.9 1.0
N Y:SER171 4.3 38.9 1.0
C Y:HIS166 4.4 38.5 1.0
CZ Y:ARG19 4.4 50.0 1.0
CA Y:ALA165 4.4 38.0 1.0
CA Y:ASP168 4.4 37.1 1.0
N Y:ASP168 4.4 37.1 1.0
N Y:HIS166 4.6 39.8 1.0
N Y:TYR170 4.6 39.3 1.0
CA Y:SER171 4.6 38.3 1.0
NH2 Y:ARG19 4.7 51.0 1.0
CA Y:HIS166 4.7 39.2 1.0
O Y:ALA164 4.7 39.2 1.0
C Y:ARG167 4.8 36.6 1.0
N Y:GLY172 4.9 41.3 1.0
CB Y:ALA169 4.9 38.5 1.0
CA Y:GLY172 5.0 42.0 1.0
N Y:ARG167 5.0 37.9 1.0

Magnesium binding site 10 out of 10 in 4qv1

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Magnesium binding site 10 out of 10 in the Ycp BETA5-M45A 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-M45A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:63.6
occ:1.00
 O Z:VAL198 2.7 47.4 1.0
O Z:THR192 3.0 50.9 1.0
O Z:HIS195 3.1 39.6 1.0
O Z:ASP222 3.3 66.5 1.0
O Z:ILE196 3.5 49.0 1.0
NH2 Z:ARG28 3.6 57.4 1.0
CA Z:ILE196 3.8 46.4 1.0
C Z:ILE196 3.9 45.8 1.0
C Z:VAL198 3.9 47.0 1.0
NH2 H:ARG19 4.0 59.6 1.0
C Z:HIS195 4.0 44.2 1.0
C Z:THR192 4.1 55.1 1.0
CG2 Z:THR192 4.1 58.1 1.0
OD1 Z:ASP222 4.3 59.5 1.0
C Z:ASP222 4.3 68.9 1.0
N Z:ILE196 4.3 45.2 1.0
CA Z:THR192 4.4 57.1 1.0
N Z:VAL198 4.5 44.0 1.0
CZ Z:ARG28 4.5 55.9 1.0
NH1 H:ARG19 4.6 60.4 1.0
CZ H:ARG19 4.7 59.2 1.0
NH1 Z:ARG28 4.7 55.5 1.0
OXT Z:ASP222 4.7 66.9 1.0
CA Z:VAL198 4.8 45.3 1.0
N Z:GLY199 4.8 47.8 1.0
CA Z:GLY199 4.9 49.4 1.0
N Z:GLN197 4.9 43.4 1.0
CB Z:THR192 4.9 57.8 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 02:14:00 2024

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