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Magnesium in PDB 4qwl: Ycp BETA5-A50V Mutant in Complex with Carfilzomib

Protein crystallography data

The structure of Ycp BETA5-A50V Mutant in Complex with Carfilzomib, PDB code: 4qwl 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 (°) 134.480, 300.280, 143.960, 90.00, 112.71, 90.00
R / Rfree (%) 19.3 / 21.9

Other elements in 4qwl:

The structure of Ycp BETA5-A50V Mutant in Complex with Carfilzomib also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 4qwl

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Magnesium binding site 1 out of 8 in the Ycp BETA5-A50V Mutant in Complex with Carfilzomib


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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:43.2
occ:1.00
 O G:MET125 2.2 47.0 1.0
O G:HOH406 2.2 29.8 1.0
O G:ARG122 2.4 48.4 1.0
OG1 G:THR8 2.6 41.2 1.0
O G:TYR119 2.7 39.6 1.0
O G:ALA123 3.3 46.5 1.0
C G:MET125 3.3 46.3 1.0
CG2 G:THR8 3.4 44.5 1.0
C G:ARG122 3.5 47.3 1.0
C G:ALA123 3.6 47.2 1.0
CB G:THR8 3.6 44.2 1.0
CA G:ALA123 3.6 46.4 1.0
C G:TYR119 3.9 40.1 1.0
N G:ALA123 4.0 45.9 1.0
N G:MET125 4.1 48.5 1.0
N G:ARG126 4.2 42.6 1.0
CA G:ARG126 4.2 41.5 1.0
N G:THR8 4.3 48.2 1.0
CA G:MET125 4.3 49.8 1.0
N G:TYR124 4.5 49.3 1.0
CA G:THR8 4.6 46.8 1.0
CA G:TYR119 4.6 39.2 1.0
CD G:PRO127 4.7 39.5 1.0
CA G:ARG122 4.8 49.1 1.0
C G:ARG126 4.8 41.3 1.0
N G:ARG122 4.9 46.0 1.0
CB G:MET125 4.9 54.6 1.0
C G:TYR124 4.9 48.6 1.0
N G:THR120 4.9 39.8 1.0
CB G:ALA123 4.9 45.1 1.0

Magnesium binding site 2 out of 8 in 4qwl

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Magnesium binding site 2 out of 8 in the Ycp BETA5-A50V Mutant in Complex with Carfilzomib


Mono view


Stereo pair view

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

b:69.2
occ:1.00
 O I:ASP177 2.5 40.6 1.0
O I:SER180 2.6 45.9 1.0
O I:ALA174 2.6 45.8 1.0
C I:ALA174 3.6 47.5 1.0
C I:ASP177 3.6 41.7 1.0
C I:SER180 3.8 44.9 1.0
OXT I:ASP204 3.8 56.5 1.0
O I:HOH414 3.9 35.4 1.0
CA I:ASP175 3.9 48.6 1.0
N I:ASP175 4.2 48.2 1.0
C I:ASP175 4.3 47.3 1.0
N I:ASP177 4.4 40.5 1.0
O I:ALA178 4.5 46.4 1.0
N I:ALA178 4.5 41.4 1.0
O I:ASP175 4.5 51.0 1.0
CA I:ALA178 4.5 42.4 1.0
CA I:ASP177 4.6 42.0 1.0
CA I:GLY181 4.6 44.6 1.0
C I:ALA178 4.6 43.7 1.0
OD1 I:ASP175 4.6 49.6 1.0
N I:GLY181 4.6 43.9 1.0
N I:SER180 4.6 41.7 1.0
CA I:ALA174 4.7 46.6 1.0
CA I:SER180 4.8 43.3 1.0
C I:ASP204 4.8 55.0 1.0
NH1 Y:ARG19 4.9 51.3 1.0
O I:ASP204 4.9 54.2 1.0
N I:ARG176 5.0 43.2 1.0
CB I:ALA174 5.0 46.8 1.0

Magnesium binding site 3 out of 8 in 4qwl

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Magnesium binding site 3 out of 8 in the Ycp BETA5-A50V Mutant in Complex with Carfilzomib


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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:49.5
occ:1.00
 O W:ASP204 2.1 53.2 1.0
O K:ASP168 2.3 39.0 1.0
O K:SER171 2.4 43.9 1.0
O K:ALA165 2.5 40.5 1.0
C W:ASP204 3.0 53.2 1.0
C K:ASP168 3.3 40.1 1.0
CA W:ASP204 3.6 52.2 1.0
C K:SER171 3.6 42.1 1.0
C K:ALA165 3.6 42.3 1.0
CA K:ALA169 3.6 41.7 1.0
NH1 K:ARG19 3.7 51.0 1.0
O K:ALA169 3.7 43.1 1.0
C K:ALA169 3.8 41.8 1.0
N K:ALA169 3.9 40.8 1.0
OXT W:ASP204 3.9 54.1 1.0
CB W:ASP204 4.0 51.9 1.0
O K:HIS166 4.1 45.3 1.0
N K:SER171 4.1 40.2 1.0
CZ K:ARG19 4.3 48.7 1.0
CA K:ALA165 4.4 43.0 1.0
CA K:SER171 4.4 39.8 1.0
C K:HIS166 4.5 42.8 1.0
NH2 K:ARG19 4.5 51.9 1.0
N K:TYR170 4.5 40.0 1.0
CA K:ASP168 4.5 39.9 1.0
N K:GLY172 4.6 42.5 1.0
N K:HIS166 4.6 42.1 1.0
N K:ASP168 4.6 41.0 1.0
O K:ALA164 4.7 40.8 1.0
CA K:GLY172 4.7 42.7 1.0
CA K:HIS166 4.8 42.4 1.0
CB K:SER171 5.0 38.9 1.0
N W:ASP204 5.0 51.0 1.0
CG W:ASP204 5.0 51.0 1.0

Magnesium binding site 4 out of 8 in 4qwl

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Magnesium binding site 4 out of 8 in the Ycp BETA5-A50V Mutant in Complex with Carfilzomib


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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:45.5
occ:1.00
 O N:SER169 2.6 38.6 1.0
O N:ILE163 2.6 37.9 1.0
O N:ASP166 3.0 40.3 1.0
NH1 N:ARG19 3.6 42.9 1.0
CD1 a:LEU34 3.6 42.6 1.0
C N:ILE163 3.7 40.9 1.0
C N:SER169 3.8 37.7 1.0
CG2 N:ILE163 3.9 39.9 1.0
C N:ASP166 4.0 39.4 1.0
CZ N:ARG19 4.3 42.3 1.0
CA N:GLY167 4.3 38.8 1.0
CA N:ILE163 4.4 41.0 1.0
CA N:GLY170 4.4 39.9 1.0
NH2 N:ARG19 4.5 43.6 1.0
O N:GLY167 4.5 37.9 1.0
N N:GLY170 4.6 38.3 1.0
N N:GLY167 4.6 38.4 1.0
C N:GLY167 4.6 37.7 1.0
N N:LYS164 4.7 41.8 1.0
CB N:ILE163 4.8 40.3 1.0
N N:SER169 4.8 36.7 1.0
CA N:SER169 4.8 35.5 1.0
O N:LYS164 4.9 44.9 1.0
CG a:LEU34 4.9 43.5 1.0
C N:LYS164 4.9 43.4 1.0
CA N:LYS164 4.9 43.6 1.0

Magnesium binding site 5 out of 8 in 4qwl

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Magnesium binding site 5 out of 8 in the Ycp BETA5-A50V Mutant in Complex with Carfilzomib


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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg203

b:42.5
occ:1.00
 O H:HOH418 2.2 57.2 1.0
OD1 N:ASP51 2.7 28.1 1.0
OE1 H:GLN91 2.7 52.1 1.0
O N:ASN92 3.0 44.9 1.0
NE2 H:GLN91 3.4 53.5 1.0
CG N:ASP51 3.4 26.0 1.0
CD H:GLN91 3.4 54.8 1.0
OD2 N:ASP51 3.4 31.6 1.0
O H:HOH401 3.6 39.5 1.0
C N:ASN92 4.2 45.7 1.0
CZ H:PHE88 4.4 38.1 1.0
CE1 H:PHE88 4.4 37.8 1.0
CB N:ASP51 4.8 27.7 1.0
O N:HOH303 4.9 36.7 1.0
CD2 N:LEU93 4.9 41.9 1.0
CG H:GLN91 4.9 52.7 1.0
C18 N:3BV201 5.0 79.0 1.0

Magnesium binding site 6 out of 8 in 4qwl

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Magnesium binding site 6 out of 8 in the Ycp BETA5-A50V Mutant in Complex with Carfilzomib


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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:55.1
occ:1.00
 O V:ASP166 2.0 41.5 1.0
O V:ILE163 2.1 52.6 1.0
OXT L:ASP222 2.3 67.0 1.0
O V:HOH404 2.4 44.3 1.0
O V:SER169 2.4 44.9 1.0
C V:ASP166 3.1 45.2 1.0
C V:ILE163 3.2 53.5 1.0
C L:ASP222 3.2 67.4 1.0
O V:GLY162 3.6 48.0 1.0
C V:SER169 3.6 45.4 1.0
N V:LEU167 3.8 45.9 1.0
CA L:ASP222 3.9 66.8 1.0
CA V:LEU167 3.9 46.5 1.0
N V:ASP166 3.9 45.8 1.0
CA V:ILE163 4.0 52.5 1.0
C V:TRP164 4.1 51.4 1.0
N V:TRP164 4.1 52.5 1.0
CA V:ASP166 4.1 45.4 1.0
O L:ASP222 4.1 68.5 1.0
O V:TRP164 4.1 51.8 1.0
NH1 V:ARG19 4.1 49.8 1.0
CA V:TRP164 4.3 52.3 1.0
C V:LEU167 4.3 46.0 1.0
N V:SER169 4.3 43.4 1.0
CB L:ASP222 4.4 67.5 1.0
N V:ASN165 4.4 49.2 1.0
CA V:SER169 4.5 44.6 1.0
N V:GLY170 4.5 46.9 1.0
CA V:GLY170 4.6 48.8 1.0
C V:GLY162 4.6 49.1 1.0
C V:ASN165 4.6 45.8 1.0
O V:LEU167 4.6 49.8 1.0
CZ V:ARG19 4.7 50.6 1.0
N V:ILE163 4.8 49.9 1.0
CB V:ASP166 4.8 44.7 1.0
CB V:SER169 4.8 45.1 1.0
NH2 V:ARG19 4.9 51.0 1.0
N V:GLY168 4.9 44.5 1.0

Magnesium binding site 7 out of 8 in 4qwl

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Magnesium binding site 7 out of 8 in the Ycp BETA5-A50V Mutant in Complex with Carfilzomib


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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:44.6
occ:1.00
 O Y:ASP168 2.1 41.0 1.0
O I:ASP204 2.3 54.2 1.0
O Y:SER171 2.5 45.4 1.0
O Y:ALA165 2.5 41.5 1.0
O Y:HOH414 2.6 46.5 1.0
C I:ASP204 3.2 55.0 1.0
C Y:ASP168 3.2 39.9 1.0
CA Y:ALA169 3.5 40.8 1.0
C Y:ALA165 3.6 42.2 1.0
C Y:SER171 3.6 43.0 1.0
CA I:ASP204 3.7 55.9 1.0
C Y:ALA169 3.7 40.7 1.0
O Y:ALA169 3.7 43.2 1.0
N Y:ALA169 3.8 40.6 1.0
NH1 Y:ARG19 3.8 51.3 1.0
O Y:HIS166 4.0 39.6 1.0
N Y:SER171 4.1 39.7 1.0
CB I:ASP204 4.1 55.2 1.0
OXT I:ASP204 4.1 56.5 1.0
CA Y:ASP168 4.4 39.5 1.0
CZ Y:ARG19 4.4 50.5 1.0
C Y:HIS166 4.4 41.2 1.0
CA Y:SER171 4.4 40.2 1.0
CA Y:ALA165 4.4 42.3 1.0
N Y:TYR170 4.5 40.2 1.0
N Y:ASP168 4.5 40.4 1.0
N Y:HIS166 4.6 42.6 1.0
O Y:ALA164 4.6 39.2 1.0
N Y:GLY172 4.7 45.1 1.0
NH2 Y:ARG19 4.7 52.0 1.0
CA Y:HIS166 4.7 41.5 1.0
CA Y:GLY172 4.8 46.2 1.0
C Y:ARG167 4.9 40.4 1.0
CB Y:SER171 4.9 40.0 1.0
CB Y:ALA169 4.9 39.4 1.0

Magnesium binding site 8 out of 8 in 4qwl

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Magnesium binding site 8 out of 8 in the Ycp BETA5-A50V Mutant in Complex with Carfilzomib


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 in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:63.0
occ:1.00
 O Z:THR192 2.7 57.0 1.0
O Z:VAL198 2.7 52.0 1.0
O Z:HIS195 2.9 44.1 1.0
O Z:ASP222 3.6 70.2 1.0
NH2 Z:ARG28 3.6 60.8 1.0
C Z:THR192 3.7 55.9 1.0
CG2 Z:THR192 3.8 55.9 1.0
C Z:VAL198 3.9 51.0 1.0
C Z:HIS195 3.9 45.6 1.0
O Z:ILE196 3.9 50.4 1.0
CA Z:ILE196 4.0 46.4 1.0
CA Z:THR192 4.1 56.1 1.0
C Z:ILE196 4.1 47.0 1.0
NH2 H:ARG19 4.3 54.9 1.0
OD1 Z:ASP222 4.3 66.2 1.0
N Z:ILE196 4.4 45.8 1.0
C Z:ASP222 4.5 68.5 1.0
N Z:VAL198 4.6 46.7 1.0
CB Z:THR192 4.6 54.7 1.0
CZ Z:ARG28 4.7 59.3 1.0
CA Z:VAL198 4.8 48.5 1.0
N Z:GLY199 4.8 52.1 1.0
CA Z:GLY199 4.8 53.8 1.0
N Z:GLU193 4.9 56.5 1.0
NH1 H:ARG19 4.9 54.3 1.0
NH1 Z:ARG28 4.9 59.5 1.0
OXT Z:ASP222 4.9 69.3 1.0
CZ H:ARG19 5.0 53.1 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 02:29:52 2024

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