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Magnesium in PDB 4qv6: Ycp BETA5-A49V Mutant

Enzymatic activity of Ycp BETA5-A49V Mutant

All present enzymatic activity of Ycp BETA5-A49V Mutant:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-A49V Mutant, PDB code: 4qv6 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 (°) 134.580, 299.750, 144.660, 90.00, 112.52, 90.00
R / Rfree (%) 20.1 / 23.1

Other elements in 4qv6:

The structure of Ycp BETA5-A49V Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-A49V Mutant (pdb code 4qv6). 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-A49V Mutant, PDB code: 4qv6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 4qv6

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Magnesium binding site 1 out of 10 in the Ycp BETA5-A49V 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-A49V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:47.0
occ:1.00
O G:MET125 2.2 53.0 1.0
OG1 G:THR8 2.9 48.0 1.0
O G:ARG122 3.0 51.3 1.0
O G:ALA123 3.0 49.4 1.0
O G:TYR119 3.1 42.2 1.0
CG2 G:THR8 3.3 48.1 1.0
C G:MET125 3.3 50.5 1.0
C G:ALA123 3.6 48.2 1.0
CB G:THR8 3.6 46.9 1.0
CA G:ALA123 3.7 47.5 1.0
CA G:ARG126 4.0 45.3 1.0
C G:ARG122 4.0 48.5 1.0
N G:THR8 4.0 47.0 1.0
N G:ARG126 4.0 46.9 1.0
N G:MET125 4.2 50.6 1.0
C G:TYR119 4.2 42.2 1.0
CA G:MET125 4.4 54.1 1.0
N G:ALA123 4.4 48.3 1.0
CD G:PRO127 4.4 42.9 1.0
CA G:THR8 4.5 46.0 1.0
N G:TYR124 4.6 51.4 1.0
C G:ARG126 4.7 45.9 1.0
C G:TYR124 4.8 48.9 1.0
N G:PRO127 4.9 43.1 1.0
CA G:TYR119 5.0 39.9 1.0

Magnesium binding site 2 out of 10 in 4qv6

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Magnesium binding site 2 out of 10 in the Ycp BETA5-A49V 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-A49V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:49.2
occ:1.00
OD1 N:ASP51 3.3 37.3 1.0
NE2 H:GLN91 3.5 70.5 1.0
OD2 N:ASP51 3.7 45.9 1.0
O N:ASN92 3.9 49.3 1.0
CG N:ASP51 3.9 34.9 1.0
CD H:GLN91 4.6 67.3 1.0
CD2 H:HIS116 4.7 42.8 1.0
C N:ASN92 5.0 49.0 1.0
CG H:GLN91 5.0 56.3 1.0
OG N:SER48 5.0 40.2 1.0
CB H:GLN91 5.0 50.1 1.0

Magnesium binding site 3 out of 10 in 4qv6

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Magnesium binding site 3 out of 10 in the Ycp BETA5-A49V 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-A49V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:66.3
occ:1.00
O I:ASP177 2.4 54.3 1.0
O I:SER180 2.6 47.6 1.0
O I:ALA174 2.9 55.7 1.0
C I:ASP177 3.6 50.0 1.0
OXT I:ASP204 3.6 68.6 1.0
C I:SER180 3.8 49.1 1.0
O I:ALA178 4.0 51.9 1.0
C I:ALA174 4.0 54.2 1.0
CA I:ALA178 4.2 49.6 1.0
C I:ALA178 4.2 50.0 1.0
NH1 Y:ARG19 4.2 67.1 1.0
N I:ALA178 4.3 47.8 1.0
CA I:ASP175 4.4 54.0 1.0
O I:ASP204 4.4 63.4 1.0
C I:ASP204 4.5 65.3 1.0
N I:SER180 4.5 46.7 1.0
NH2 Y:ARG19 4.5 69.7 1.0
N I:ASP177 4.5 50.4 1.0
N I:ASP175 4.6 52.9 1.0
CA I:ASP177 4.6 50.5 1.0
C I:ASP175 4.6 54.0 1.0
CZ Y:ARG19 4.7 67.1 1.0
CA I:SER180 4.7 48.5 1.0
N I:GLY181 4.7 49.0 1.0
CA I:GLY181 4.8 51.4 1.0
O I:ASP175 4.8 56.9 1.0
N I:LEU179 5.0 49.2 1.0

Magnesium binding site 4 out of 10 in 4qv6

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Magnesium binding site 4 out of 10 in the Ycp BETA5-A49V 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-A49V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:66.0
occ:1.00
OE1 J:GLN118 3.1 47.8 1.0
O J:THR124 3.1 42.0 1.0
O J:GLN118 3.5 37.7 1.0
CG J:GLN118 3.7 41.6 1.0
CD J:GLN118 3.8 42.8 1.0
N J:ASP120 3.8 38.5 1.0
C J:GLN118 4.0 38.3 1.0
CB J:ASP120 4.1 41.4 1.0
C J:THR124 4.2 40.8 1.0
CG J:ASP120 4.2 43.4 1.0
CE1 J:HIS133 4.2 40.9 1.0
OD2 J:ASP120 4.3 44.3 1.0
CA J:ILE119 4.3 36.8 1.0
C J:ILE119 4.3 38.7 1.0
CB J:THR124 4.3 42.8 1.0
N J:ILE119 4.3 37.6 1.0
CB J:GLN118 4.4 40.1 1.0
CG2 J:THR124 4.5 42.4 1.0
CA J:ASP120 4.6 39.4 1.0
CG1 I:VAL35 4.6 49.9 1.0
OD1 J:ASP120 4.8 48.6 1.0
CA J:GLN118 4.8 38.8 1.0
CG2 J:VAL126 4.9 49.9 1.0
CA J:THR124 4.9 41.5 1.0

Magnesium binding site 5 out of 10 in 4qv6

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Magnesium binding site 5 out of 10 in the Ycp BETA5-A49V 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-A49V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:54.5
occ:1.00
O K:ASP168 2.2 48.4 1.0
O K:ALA165 2.5 41.7 1.0
O W:ASP204 2.5 52.7 1.0
C K:ASP168 3.1 46.8 1.0
O K:SER171 3.1 48.9 1.0
C W:ASP204 3.1 52.8 1.0
O K:HIS166 3.4 52.0 1.0
CA K:ALA169 3.5 49.0 1.0
CA W:ASP204 3.6 57.1 1.0
N K:ALA169 3.6 48.8 1.0
C K:ALA165 3.6 44.2 1.0
C K:ALA169 3.9 48.0 1.0
O K:ALA169 3.9 49.1 1.0
C K:HIS166 3.9 47.3 1.0
CB W:ASP204 4.0 55.4 1.0
NH1 K:ARG19 4.0 63.0 1.0
OXT W:ASP204 4.0 59.4 1.0
N K:ASP168 4.1 44.7 1.0
CA K:ASP168 4.2 42.8 1.0
C K:SER171 4.3 47.2 1.0
C K:ARG167 4.3 45.6 1.0
O K:ARG167 4.5 47.1 1.0
CA K:HIS166 4.5 46.8 1.0
N K:HIS166 4.5 45.5 1.0
CA K:ALA165 4.6 44.5 1.0
N K:ARG167 4.6 44.9 1.0
N K:SER171 4.6 44.8 1.0
O K:ALA164 4.6 49.1 1.0
N K:TYR170 4.7 47.6 1.0
CB K:ALA169 4.8 47.5 1.0
CZ K:ARG19 4.8 59.9 1.0
N W:ASP204 4.9 56.1 1.0
CA K:SER171 5.0 43.3 1.0
CA K:ARG167 5.0 45.2 1.0
NE1 W:TRP182 5.0 52.6 1.0

Magnesium binding site 6 out of 10 in 4qv6

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Magnesium binding site 6 out of 10 in the Ycp BETA5-A49V 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-A49V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:51.8
occ:1.00
O K:ILE82 2.9 38.6 1.0
CB K:ASN85 3.7 37.3 1.0
N K:LEU86 3.8 37.8 1.0
C K:ILE82 3.8 39.7 1.0
CA K:ILE82 3.9 41.6 1.0
CG2 K:ILE82 4.0 43.0 1.0
C K:ASN85 4.2 36.2 1.0
CA K:LEU86 4.2 37.4 1.0
CB K:LEU86 4.2 37.6 1.0
CH2 K:TRP58 4.3 40.8 1.0
CA K:ASN85 4.5 35.5 1.0
CB K:ILE82 4.5 41.9 1.0
O K:LYS81 4.8 35.8 1.0
O K:ASN85 4.9 33.4 1.0
CG K:ASN85 4.9 38.2 1.0
OE1 K:GLN89 4.9 74.0 1.0
OD1 K:ASN85 4.9 40.4 1.0
CG1 K:ILE82 4.9 43.3 1.0

Magnesium binding site 7 out of 10 in 4qv6

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Magnesium binding site 7 out of 10 in the Ycp BETA5-A49V 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-A49V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:42.3
occ:1.00
O N:ILE163 2.6 42.9 1.0
O N:SER169 2.7 43.0 1.0
O N:ASP166 3.1 43.8 1.0
NH1 N:ARG19 3.6 43.5 1.0
CD1 a:LEU34 3.6 48.9 1.0
C N:ILE163 3.7 43.1 1.0
C N:SER169 3.8 41.0 1.0
CG2 N:ILE163 3.8 42.5 1.0
C N:ASP166 4.1 41.7 1.0
CZ N:ARG19 4.1 42.2 1.0
CA N:GLY170 4.3 44.2 1.0
NH2 N:ARG19 4.3 42.6 1.0
CA N:GLY167 4.3 41.1 1.0
CA N:ILE163 4.4 42.7 1.0
N N:GLY170 4.5 41.2 1.0
O N:GLY167 4.6 42.7 1.0
N N:GLY167 4.6 40.5 1.0
C N:GLY167 4.7 41.5 1.0
CB N:ILE163 4.7 41.8 1.0
N N:LYS164 4.7 44.6 1.0
CG a:LEU34 4.9 49.0 1.0
O N:LYS164 4.9 51.4 1.0
CA N:SER169 4.9 39.0 1.0
C N:LYS164 4.9 47.5 1.0
N N:SER169 5.0 40.3 1.0
CA N:LYS164 5.0 46.4 1.0

Magnesium binding site 8 out of 10 in 4qv6

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Magnesium binding site 8 out of 10 in the Ycp BETA5-A49V 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-A49V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:61.8
occ:1.00
OXT L:ASP222 2.0 71.5 1.0
O V:ILE163 2.0 54.1 1.0
O V:ASP166 2.3 43.6 1.0
O V:SER169 2.7 51.2 1.0
C L:ASP222 2.9 66.0 1.0
C V:ILE163 3.1 53.5 1.0
C V:ASP166 3.2 44.9 1.0
CA L:ASP222 3.6 64.0 1.0
O V:TRP164 3.7 61.5 1.0
O V:GLY162 3.8 53.7 1.0
C V:TRP164 3.8 53.9 1.0
C V:SER169 3.8 47.5 1.0
O L:ASP222 3.9 69.0 1.0
N V:LEU167 3.9 46.2 1.0
CA V:LEU167 3.9 46.7 1.0
N V:ASP166 4.0 41.7 1.0
N V:TRP164 4.0 52.8 1.0
CA V:ILE163 4.1 52.1 1.0
CA V:TRP164 4.1 51.7 1.0
CB L:ASP222 4.2 62.9 1.0
CA V:ASP166 4.2 45.6 1.0
NH1 V:ARG19 4.2 62.4 1.0
N V:ASN165 4.3 50.9 1.0
C V:LEU167 4.5 45.5 1.0
C V:ASN165 4.6 48.3 1.0
CA V:GLY170 4.6 50.3 1.0
N V:SER169 4.6 43.8 1.0
N V:GLY170 4.7 47.5 1.0
O V:LEU167 4.7 47.7 1.0
CA V:SER169 4.7 45.4 1.0
O L:ARG221 4.7 63.2 1.0
C V:GLY162 4.7 51.8 1.0
CZ V:ARG19 4.8 57.9 1.0
N L:ASP222 4.9 62.7 1.0
NH2 V:ARG19 4.9 57.3 1.0
N V:ILE163 4.9 51.0 1.0
CA V:ASN165 5.0 48.8 1.0
CD2 V:LEU167 5.0 42.7 1.0
CB V:ASP166 5.0 44.5 1.0

Magnesium binding site 9 out of 10 in 4qv6

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Magnesium binding site 9 out of 10 in the Ycp BETA5-A49V 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-A49V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:52.8
occ:1.00
O Y:ASP168 2.3 50.0 1.0
O I:ASP204 2.3 63.4 1.0
O Y:ALA165 2.6 53.7 1.0
O Y:SER171 3.0 53.9 1.0
C I:ASP204 3.1 65.3 1.0
C Y:ASP168 3.2 50.0 1.0
CA Y:ALA169 3.5 51.3 1.0
CA I:ASP204 3.5 64.2 1.0
O Y:HIS166 3.6 44.3 1.0
N Y:ALA169 3.7 51.8 1.0
O Y:ALA169 3.7 46.6 1.0
C Y:ALA165 3.7 50.3 1.0
C Y:ALA169 3.8 50.2 1.0
NH1 Y:ARG19 3.8 67.1 1.0
CB I:ASP204 4.0 65.4 1.0
OXT I:ASP204 4.0 68.6 1.0
C Y:HIS166 4.1 49.2 1.0
C Y:SER171 4.1 49.3 1.0
N Y:ASP168 4.4 48.5 1.0
CA Y:ASP168 4.4 47.7 1.0
N Y:SER171 4.5 47.8 1.0
C Y:ARG167 4.5 48.5 1.0
CZ Y:ARG19 4.6 67.1 1.0
N Y:HIS166 4.6 52.5 1.0
CA Y:HIS166 4.6 49.5 1.0
CA Y:ALA165 4.6 47.6 1.0
N Y:TYR170 4.7 51.6 1.0
O Y:ARG167 4.7 48.4 1.0
CB Y:ALA169 4.8 50.2 1.0
O Y:ALA164 4.8 51.2 1.0
N Y:ARG167 4.8 48.3 1.0
N I:ASP204 4.9 63.2 1.0
CA Y:SER171 4.9 47.2 1.0
NH2 Y:ARG19 4.9 69.7 1.0

Magnesium binding site 10 out of 10 in 4qv6

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Magnesium binding site 10 out of 10 in the Ycp BETA5-A49V 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-A49V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:51.0
occ:1.00
O Z:VAL198 2.6 57.0 1.0
O Z:THR192 3.0 60.6 1.0
O Z:HIS195 3.2 41.4 1.0
O Z:ASP222 3.3 67.5 1.0
NH2 Z:ARG28 3.5 66.7 1.0
O Z:ILE196 3.7 50.8 1.0
C Z:VAL198 3.8 56.3 1.0
CG2 Z:THR192 3.8 62.8 1.0
C Z:THR192 4.0 61.8 1.0
CA Z:ILE196 4.1 50.5 1.0
C Z:ILE196 4.1 49.6 1.0
OD1 Z:ASP222 4.1 75.3 1.0
NH2 H:ARG19 4.1 66.6 1.0
C Z:HIS195 4.2 48.5 1.0
C Z:ASP222 4.3 75.0 1.0
CA Z:THR192 4.4 63.3 1.0
CZ Z:ARG28 4.4 62.0 1.0
NH1 Z:ARG28 4.5 58.8 1.0
N Z:VAL198 4.6 51.4 1.0
CA Z:GLY199 4.6 56.6 1.0
N Z:ILE196 4.6 51.0 1.0
N Z:GLY199 4.6 55.4 1.0
CB Z:THR192 4.7 60.6 1.0
CA Z:VAL198 4.7 53.3 1.0
NH1 H:ARG19 4.8 67.0 1.0
O Z:LYS220 4.8 68.3 1.0
OXT Z:ASP222 4.8 76.5 1.0
CZ H:ARG19 4.8 65.8 1.0
CG Z:ASP222 5.0 74.6 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: Mon Dec 14 19:25:13 2020

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