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Magnesium in PDB 4qv8: Ycp BETA5-C52F Mutant

Enzymatic activity of Ycp BETA5-C52F Mutant

All present enzymatic activity of Ycp BETA5-C52F Mutant:
3.4.25.1;

Protein crystallography data

The structure of Ycp BETA5-C52F Mutant, PDB code: 4qv8 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 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.180, 300.700, 144.400, 90.00, 112.95, 90.00
R / Rfree (%) 19.2 / 22.1

Other elements in 4qv8:

The structure of Ycp BETA5-C52F Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ycp BETA5-C52F Mutant (pdb code 4qv8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Ycp BETA5-C52F Mutant, PDB code: 4qv8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4qv8

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Magnesium binding site 1 out of 9 in the Ycp BETA5-C52F 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-C52F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:48.4
occ:1.00
 O G:MET125 2.2 53.9 1.0
OG1 G:THR8 2.8 44.1 1.0
O G:ARG122 2.8 44.5 1.0
O G:TYR119 3.0 39.5 1.0
O G:ALA123 3.2 51.7 1.0
CG2 G:THR8 3.3 44.8 1.0
C G:MET125 3.3 52.5 1.0
CB G:THR8 3.6 44.8 1.0
C G:ALA123 3.6 50.9 1.0
CA G:ALA123 3.7 47.9 1.0
C G:ARG122 3.9 45.9 1.0
CA G:ARG126 4.0 45.4 1.0
N G:ARG126 4.0 47.9 1.0
N G:THR8 4.1 49.0 1.0
N G:MET125 4.2 55.5 1.0
C G:TYR119 4.2 38.2 1.0
N G:ALA123 4.3 46.4 1.0
CA G:MET125 4.3 55.1 1.0
CD G:PRO127 4.5 40.9 1.0
CA G:THR8 4.5 46.5 1.0
N G:TYR124 4.5 52.3 1.0
C G:ARG126 4.7 45.0 1.0
C G:TYR124 4.8 53.8 1.0
O F:HOH310 4.8 54.6 1.0
N G:PRO127 4.9 41.6 1.0
CA G:TYR119 5.0 36.1 1.0

Magnesium binding site 2 out of 9 in 4qv8

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Magnesium binding site 2 out of 9 in the Ycp BETA5-C52F 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-C52F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:52.6
occ:1.00
 OD1 N:ASP51 2.8 29.9 1.0
NE2 H:GLN91 3.4 64.3 1.0
OD2 N:ASP51 3.5 37.6 1.0
CG N:ASP51 3.6 28.5 1.0
O N:ASN92 3.7 47.2 1.0
CD H:GLN91 4.5 60.4 1.0
CE1 H:PHE88 4.7 31.6 1.0
C N:ASN92 4.9 45.4 1.0
OG N:SER48 4.9 38.4 1.0
CG H:GLN91 4.9 49.7 1.0

Magnesium binding site 3 out of 9 in 4qv8

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Magnesium binding site 3 out of 9 in the Ycp BETA5-C52F 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-C52F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:40.1
occ:1.00
 O I:ASP177 2.6 38.7 1.0
O I:SER180 2.9 42.0 1.0
O I:HOH401 3.0 36.8 1.0
OXT I:ASP204 3.3 48.9 1.0
O I:ALA174 3.5 43.6 1.0
C I:ASP177 3.6 40.7 1.0
O I:ALA178 3.6 42.7 1.0
NH1 Y:ARG19 3.7 57.1 1.0
O I:ASP204 3.8 53.4 1.0
CA I:ALA178 3.9 41.5 1.0
C I:ALA178 3.9 42.6 1.0
C I:ASP204 4.0 50.9 1.0
C I:SER180 4.1 42.5 1.0
N I:ALA178 4.2 39.8 1.0
NH2 Y:ARG19 4.3 54.6 1.0
CZ Y:ARG19 4.4 54.6 1.0
N I:SER180 4.6 42.0 1.0
C I:ALA174 4.7 43.4 1.0
N I:ASP177 4.8 40.9 1.0
CA I:ASP177 4.8 41.1 1.0
O I:ASP175 4.8 48.9 1.0
N I:LEU179 4.8 42.4 1.0
CA I:ASP175 4.9 43.7 1.0
CA I:SER180 5.0 41.5 1.0
C I:ASP175 5.0 44.0 1.0

Magnesium binding site 4 out of 9 in 4qv8

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Magnesium binding site 4 out of 9 in the Ycp BETA5-C52F 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-C52F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:40.7
occ:1.00
 O K:ASP168 2.4 39.5 1.0
O K:ALA165 2.4 46.2 1.0
O W:ASP204 2.5 54.0 1.0
O K:SER171 3.1 46.1 1.0
C W:ASP204 3.1 53.0 1.0
C K:ASP168 3.2 39.7 1.0
O K:HIS166 3.5 46.3 1.0
CA W:ASP204 3.5 53.2 1.0
C K:ALA165 3.5 42.7 1.0
CA K:ALA169 3.6 40.4 1.0
N K:ALA169 3.8 40.4 1.0
CB W:ASP204 3.9 53.1 1.0
C K:HIS166 4.0 44.7 1.0
C K:ALA169 4.0 41.9 1.0
OXT W:ASP204 4.0 53.9 1.0
NH1 K:ARG19 4.0 55.8 1.0
O K:ALA169 4.0 43.9 1.0
C K:SER171 4.3 42.8 1.0
N K:ASP168 4.3 41.1 1.0
CA K:ASP168 4.4 39.7 1.0
N K:HIS166 4.4 42.0 1.0
CA K:HIS166 4.4 43.5 1.0
C K:ARG167 4.4 42.1 1.0
CA K:ALA165 4.5 42.3 1.0
O K:ARG167 4.6 41.9 1.0
O K:ALA164 4.6 41.8 1.0
N K:SER171 4.6 39.0 1.0
N K:ARG167 4.7 44.3 1.0
CZ K:ARG19 4.8 52.9 1.0
N K:TYR170 4.8 42.4 1.0
N W:ASP204 4.9 53.0 1.0
CB K:ALA169 4.9 38.8 1.0

Magnesium binding site 5 out of 9 in 4qv8

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Magnesium binding site 5 out of 9 in the Ycp BETA5-C52F 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-C52F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:47.8
occ:1.00
 O K:ILE82 3.0 37.0 1.0
CB K:ASN85 3.5 35.2 1.0
CA K:ILE82 3.8 36.9 1.0
C K:ILE82 3.8 36.5 1.0
N K:LEU86 3.9 34.0 1.0
CG2 K:ILE82 4.1 36.2 1.0
C K:ASN85 4.2 33.8 1.0
CB K:ILE82 4.4 36.5 1.0
CA K:ASN85 4.4 34.3 1.0
CA K:LEU86 4.4 32.8 1.0
CB K:LEU86 4.5 32.8 1.0
O K:LYS81 4.5 34.1 1.0
OD1 K:ASN85 4.6 38.7 1.0
CG K:ASN85 4.6 35.4 1.0
CH2 K:TRP58 4.7 35.4 1.0
CG1 K:ILE82 4.7 37.3 1.0
N K:ILE82 4.9 37.4 1.0
O K:ASN85 4.9 33.9 1.0
N K:ASN85 4.9 33.2 1.0

Magnesium binding site 6 out of 9 in 4qv8

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Magnesium binding site 6 out of 9 in the Ycp BETA5-C52F 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-C52F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:34.1
occ:1.00
 O N:SER169 2.9 36.1 1.0
O N:ILE163 2.9 39.2 1.0
O N:ASP166 3.3 41.2 1.0
NH1 N:ARG19 3.5 36.8 1.0
CD1 a:LEU34 3.5 46.0 1.0
C N:ILE163 4.0 39.5 1.0
C N:SER169 4.0 36.2 1.0
CG2 N:ILE163 4.0 37.7 1.0
CZ N:ARG19 4.1 35.7 1.0
C N:ASP166 4.2 39.1 1.0
NH2 N:ARG19 4.2 36.2 1.0
CA N:GLY167 4.2 37.8 1.0
CA N:GLY170 4.4 36.8 1.0
O N:GLY167 4.4 35.8 1.0
C N:GLY167 4.6 36.7 1.0
N N:GLY167 4.6 38.0 1.0
CA N:ILE163 4.6 38.7 1.0
N N:GLY170 4.7 36.0 1.0
CG a:LEU34 4.8 45.6 1.0
CB N:ILE163 5.0 37.8 1.0
N N:LYS164 5.0 42.2 1.0
NE N:ARG19 5.0 35.6 1.0

Magnesium binding site 7 out of 9 in 4qv8

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Magnesium binding site 7 out of 9 in the Ycp BETA5-C52F 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-C52F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:59.8
occ:1.00
 OXT L:ASP222 1.9 65.2 1.0
O V:ILE163 2.2 41.6 1.0
O V:ASP166 2.2 41.4 1.0
O V:SER169 2.4 39.6 1.0
C L:ASP222 3.0 60.7 1.0
C V:ASP166 3.2 40.5 1.0
C V:ILE163 3.3 45.1 1.0
C V:SER169 3.6 40.2 1.0
CA V:LEU167 3.7 40.1 1.0
CA L:ASP222 3.8 60.0 1.0
N V:LEU167 3.8 40.7 1.0
NH1 V:ARG19 3.9 54.8 1.0
O V:TRP164 3.9 40.5 1.0
O L:ASP222 4.0 63.1 1.0
O V:GLY162 4.0 47.5 1.0
C V:TRP164 4.1 44.1 1.0
C V:LEU167 4.1 39.5 1.0
N V:ASP166 4.2 37.4 1.0
CA V:ILE163 4.2 44.6 1.0
N V:TRP164 4.2 45.5 1.0
O V:LEU167 4.2 38.5 1.0
CA V:ASP166 4.3 38.2 1.0
CB L:ASP222 4.3 61.3 1.0
N V:SER169 4.4 39.4 1.0
CA V:TRP164 4.4 45.0 1.0
CZ V:ARG19 4.5 52.4 1.0
CA V:GLY170 4.5 43.4 1.0
N V:GLY170 4.5 40.7 1.0
CA V:SER169 4.5 39.2 1.0
NH2 V:ARG19 4.7 53.3 1.0
N V:ASN165 4.7 42.1 1.0
C V:ASN165 4.8 39.0 1.0
C V:GLY162 4.9 44.3 1.0
N V:GLY168 4.9 39.9 1.0
CB V:SER169 5.0 39.3 1.0
CD2 V:LEU167 5.0 37.3 1.0

Magnesium binding site 8 out of 9 in 4qv8

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Magnesium binding site 8 out of 9 in the Ycp BETA5-C52F 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-C52F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:37.5
occ:1.00
 O Y:ASP168 2.3 40.9 1.0
O I:ASP204 2.5 53.4 1.0
O Y:ALA165 2.6 41.7 1.0
O Y:SER171 3.0 41.5 1.0
C I:ASP204 3.2 50.9 1.0
C Y:ASP168 3.2 39.0 1.0
CA Y:ALA169 3.5 40.5 1.0
CA I:ASP204 3.6 51.4 1.0
N Y:ALA169 3.7 40.2 1.0
O Y:HIS166 3.7 40.4 1.0
C Y:ALA165 3.7 40.4 1.0
O Y:ALA169 3.7 39.9 1.0
C Y:ALA169 3.8 40.0 1.0
NH1 Y:ARG19 3.8 57.1 1.0
CB I:ASP204 4.0 51.8 1.0
OXT I:ASP204 4.1 48.9 1.0
C Y:SER171 4.2 40.1 1.0
C Y:HIS166 4.2 40.5 1.0
N Y:ASP168 4.4 38.5 1.0
CA Y:ASP168 4.4 37.8 1.0
N Y:SER171 4.5 38.6 1.0
C Y:ARG167 4.6 39.1 1.0
CZ Y:ARG19 4.6 54.6 1.0
CA Y:ALA165 4.6 39.2 1.0
N Y:HIS166 4.6 41.0 1.0
N Y:TYR170 4.6 39.2 1.0
CA Y:HIS166 4.7 40.4 1.0
O Y:ARG167 4.7 37.7 1.0
O Y:ALA164 4.8 40.6 1.0
CB Y:ALA169 4.8 40.2 1.0
N Y:ARG167 4.9 39.9 1.0
CA Y:SER171 4.9 38.1 1.0
NH2 Y:ARG19 4.9 54.6 1.0

Magnesium binding site 9 out of 9 in 4qv8

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Magnesium binding site 9 out of 9 in the Ycp BETA5-C52F 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-C52F Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:44.8
occ:1.00
 O Z:VAL198 2.6 44.8 1.0
O Z:THR192 2.8 55.1 1.0
O Z:HIS195 3.0 39.5 1.0
O Z:ASP222 3.4 56.8 1.0
O Z:ILE196 3.6 45.5 1.0
NH2 Z:ARG28 3.7 53.3 1.0
C Z:VAL198 3.8 45.3 1.0
C Z:THR192 3.9 54.6 1.0
CA Z:ILE196 3.9 45.5 1.0
CG2 Z:THR192 3.9 54.1 1.0
C Z:ILE196 3.9 45.4 1.0
C Z:HIS195 3.9 43.6 1.0
NH2 H:ARG19 4.1 59.6 1.0
CA Z:THR192 4.2 54.7 1.0
N Z:ILE196 4.3 44.6 1.0
OD1 Z:ASP222 4.3 63.4 1.0
N Z:VAL198 4.4 42.8 1.0
C Z:ASP222 4.5 69.8 1.0
CA Z:VAL198 4.6 44.0 1.0
CZ Z:ARG28 4.7 49.5 1.0
NH1 H:ARG19 4.7 60.1 1.0
CB Z:THR192 4.7 54.1 1.0
N Z:GLY199 4.7 45.5 1.0
CA Z:GLY199 4.8 46.6 1.0
CZ H:ARG19 4.8 58.2 1.0
NH1 Z:ARG28 4.8 47.7 1.0
N Z:GLN197 4.9 45.0 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 19:25:26 2020

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