Atomistry » Magnesium » PDB 4qq8-4qwi » 4qv1
Atomistry »
  Magnesium »
    PDB 4qq8-4qwi »
      4qv1 »

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

Go back to Magnesium Binding Sites List in 4qv1
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

Go back to Magnesium Binding Sites List in 4qv1
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

Go back to Magnesium Binding Sites List in 4qv1
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

Go back to Magnesium Binding Sites List in 4qv1
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

Go back to Magnesium Binding Sites List in 4qv1
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

Go back to Magnesium Binding Sites List in 4qv1
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

Go back to Magnesium Binding Sites List in 4qv1
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

Go back to Magnesium Binding Sites List in 4qv1
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

Go back to Magnesium Binding Sites List in 4qv1
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

Go back to Magnesium Binding Sites List in 4qv1
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy