Magnesium in PDB 7cek: Crystal Structure of T2R-Ttl-Bml-284 Complex

Protein crystallography data

The structure of Crystal Structure of T2R-Ttl-Bml-284 Complex, PDB code: 7cek was solved by L.J.Chen, Q.Chen, Y.Yu, J.H.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.26 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.571, 158.078, 181.292, 90, 90, 90
R / Rfree (%) 22.8 / 27.1

Other elements in 7cek:

The structure of Crystal Structure of T2R-Ttl-Bml-284 Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Bml-284 Complex (pdb code 7cek). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of T2R-Ttl-Bml-284 Complex, PDB code: 7cek:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7cek

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Magnesium binding site 1 out of 5 in the Crystal Structure of T2R-Ttl-Bml-284 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of T2R-Ttl-Bml-284 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:53.6
occ:1.00
O A:HOH628 1.9 51.0 1.0
O A:HOH607 1.9 54.6 1.0
O A:HOH620 2.0 48.8 1.0
O2G A:GTP501 2.1 47.1 1.0
O A:HOH612 2.1 58.7 1.0
O1B A:GTP501 2.3 50.0 1.0
HZ1 B:LYS252 3.1 68.0 1.0
PG A:GTP501 3.3 47.2 1.0
PB A:GTP501 3.5 50.4 1.0
OE2 A:GLU71 3.5 61.5 1.0
HB2 A:GLN11 3.6 67.8 1.0
HG2 A:GLU71 3.6 72.7 1.0
O3B A:GTP501 3.7 56.8 1.0
HG3 A:GLU71 3.7 72.7 1.0
HB2 A:ASP98 3.8 64.8 1.0
O1G A:GTP501 3.8 47.6 1.0
H A:GLN11 3.8 65.5 1.0
NZ B:LYS252 3.9 56.1 1.0
O3A A:GTP501 4.0 49.3 1.0
OD1 A:ASP69 4.0 56.0 1.0
CG A:GLU71 4.0 60.1 1.0
HB3 A:ASP98 4.1 64.8 1.0
HZ2 B:LYS252 4.1 68.0 1.0
HB3 A:GLN11 4.2 67.8 1.0
CD A:GLU71 4.2 60.4 1.0
HZ3 B:LYS252 4.2 68.0 1.0
OD2 A:ASP69 4.3 57.9 1.0
CB A:ASP98 4.3 53.5 1.0
CB A:GLN11 4.3 56.0 1.0
OD1 B:ASN247 4.3 70.6 1.0
HE21 A:GLN11 4.4 72.0 1.0
OD2 A:ASP98 4.5 55.5 1.0
HG1 A:THR145 4.5 60.9 1.0
O1A A:GTP501 4.5 54.7 1.0
N A:GLN11 4.5 54.1 1.0
O3G A:GTP501 4.6 49.1 1.0
CG A:ASP69 4.6 57.7 1.0
CG A:ASP98 4.6 52.3 1.0
O2B A:GTP501 4.7 55.3 1.0
HB3 B:ASN247 4.7 93.4 1.0
HB A:THR145 4.8 62.4 1.0
NE2 A:GLN11 4.8 59.5 1.0
HA2 A:GLY10 4.9 65.6 1.0
PA A:GTP501 4.9 49.7 1.0

Magnesium binding site 2 out of 5 in 7cek

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Magnesium binding site 2 out of 5 in the Crystal Structure of T2R-Ttl-Bml-284 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of T2R-Ttl-Bml-284 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:55.8
occ:1.00
O B:HOH606 2.0 56.4 1.0
O C:HOH630 2.2 57.4 1.0
O B:HOH611 2.2 52.1 1.0
O1A B:GDP501 2.3 61.2 1.0
OE1 B:GLN11 2.5 57.5 1.0
O B:HOH623 2.7 56.6 1.0
O B:HOH621 2.7 61.5 1.0
CD B:GLN11 3.5 59.5 1.0
PA B:GDP501 3.7 46.2 1.0
HB3 B:GLN11 3.8 69.2 1.0
OD2 B:ASP177 3.8 57.6 1.0
HB2 B:GLN11 4.0 69.2 1.0
HE22 B:GLN11 4.0 75.5 1.0
NE2 B:GLN11 4.2 62.4 1.0
O3B B:GDP501 4.2 54.8 1.0
OD1 B:ASN99 4.2 54.1 1.0
CB B:GLN11 4.2 57.1 1.0
HD21 B:ASN99 4.3 63.7 1.0
H8 B:GDP501 4.3 66.5 1.0
C5' B:GDP501 4.4 56.0 1.0
O5' B:GDP501 4.4 47.6 1.0
O3A B:GDP501 4.4 50.6 1.0
CG B:GLN11 4.5 59.5 1.0
OE1 C:GLU254 4.5 60.0 1.0
O2A B:GDP501 4.7 51.2 1.0
PB B:GDP501 4.7 49.1 1.0
O1B B:GDP501 4.8 52.2 1.0
ND2 B:ASN99 4.9 52.5 1.0
HE21 B:GLN11 4.9 75.5 1.0
CG B:ASP177 4.9 58.2 1.0
HG3 B:GLN11 4.9 72.0 1.0

Magnesium binding site 3 out of 5 in 7cek

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Magnesium binding site 3 out of 5 in the Crystal Structure of T2R-Ttl-Bml-284 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of T2R-Ttl-Bml-284 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:44.3
occ:1.00
O C:HOH601 1.8 44.3 1.0
O C:HOH623 1.9 46.7 1.0
O1B C:GTP501 2.0 46.2 1.0
O C:HOH633 2.1 53.2 1.0
O1G C:GTP501 2.1 44.1 1.0
O C:HOH619 2.2 47.2 1.0
HZ1 D:LYS252 3.2 63.4 1.0
PB C:GTP501 3.3 38.5 1.0
PG C:GTP501 3.3 39.4 1.0
HZ3 D:LYS252 3.5 63.4 1.0
HB2 C:GLN11 3.5 56.7 1.0
OE2 C:GLU71 3.6 54.7 1.0
O3B C:GTP501 3.7 47.1 1.0
HG2 C:GLU71 3.7 61.3 1.0
HG3 C:GLU71 3.7 61.3 1.0
NZ D:LYS252 3.7 52.3 1.0
O2G C:GTP501 3.8 44.7 1.0
HB2 C:ASP98 3.8 59.3 1.0
O3A C:GTP501 3.8 47.0 1.0
H C:GLN11 3.9 50.6 1.0
OD2 C:ASP69 3.9 44.2 1.0
OD1 C:ASP69 3.9 44.9 1.0
HE21 C:GLN11 3.9 64.6 1.0
CG C:GLU71 4.1 50.6 1.0
HZ2 D:LYS252 4.1 63.4 1.0
CD C:GLU71 4.3 51.2 1.0
HB3 C:GLN11 4.3 56.7 1.0
CG C:ASP69 4.4 43.7 1.0
CB C:GLN11 4.4 46.7 1.0
HB3 C:ASP98 4.4 59.3 1.0
O2B C:GTP501 4.5 46.8 1.0
HG1 C:THR145 4.5 55.7 1.0
CB C:ASP98 4.5 48.9 1.0
NE2 C:GLN11 4.6 53.3 1.0
O3G C:GTP501 4.6 48.4 1.0
N C:GLN11 4.6 41.6 1.0
OD2 C:ASP98 4.6 53.4 1.0
O1A C:GTP501 4.6 48.1 1.0
HG21 C:VAL74 4.7 60.4 1.0
HB C:THR145 4.8 56.4 1.0
HE22 C:GLN11 4.8 64.6 1.0
HA2 C:GLY10 4.8 53.1 1.0
PA C:GTP501 4.9 42.7 1.0
OD1 D:ASN247 4.9 59.5 1.0
HD21 D:ASN247 4.9 71.1 1.0
CG D:ASN247 4.9 59.0 1.0
ND2 D:ASN247 5.0 58.7 1.0
HG23 C:VAL74 5.0 60.4 1.0
CE D:LYS252 5.0 52.4 1.0

Magnesium binding site 4 out of 5 in 7cek

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Magnesium binding site 4 out of 5 in the Crystal Structure of T2R-Ttl-Bml-284 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of T2R-Ttl-Bml-284 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:79.4
occ:1.00
O D:HOH613 1.9 71.2 1.0
O3G D:GTP504 2.5 76.6 1.0
O D:HOH605 2.5 69.6 1.0
O2G D:GTP504 3.0 74.6 1.0
O2B D:GTP504 3.1 73.1 1.0
HB3 D:GLU69 3.3 101.3 1.0
PG D:GTP504 3.3 83.2 1.0
HB2 D:GLN11 3.4 91.2 1.0
HB2 D:GLU69 3.5 101.3 1.0
CB D:GLU69 3.8 83.9 1.0
OD2 D:ASP67 3.8 74.7 1.0
H D:GLN11 3.9 86.5 1.0
HG2 D:GLU69 3.9 108.6 1.0
OD1 D:ASP67 3.9 72.3 1.0
O3B D:GTP504 4.2 77.5 1.0
PB D:GTP504 4.2 74.6 1.0
OE1 D:GLU69 4.2 89.8 1.0
HG1 D:THR143 4.2 92.1 1.0
CG D:ASP67 4.3 74.4 1.0
CG D:GLU69 4.3 90.0 1.0
HG23 D:THR72 4.3 100.7 1.0
CB D:GLN11 4.3 75.5 1.0
HG21 D:THR72 4.4 100.7 1.0
N D:GLN11 4.5 71.5 1.0
O1G D:GTP504 4.5 75.3 1.0
O2A D:GTP504 4.6 78.1 1.0
HB3 D:GLN11 4.6 91.2 1.0
CD D:GLU69 4.6 94.2 1.0
HA2 D:GLY10 4.7 81.0 1.0
HE21 D:GLN11 4.7 88.4 1.0
CG2 D:THR72 4.8 83.3 1.0
OG1 D:THR143 4.8 76.2 1.0
CA D:GLN11 4.9 72.0 1.0
O D:HOH604 4.9 69.4 1.0
HG22 D:THR72 4.9 100.7 1.0
H D:GLU69 5.0 100.6 1.0
HA D:GLN11 5.0 87.1 1.0

Magnesium binding site 5 out of 5 in 7cek

Go back to Magnesium Binding Sites List in 7cek
Magnesium binding site 5 out of 5 in the Crystal Structure of T2R-Ttl-Bml-284 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of T2R-Ttl-Bml-284 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:106.2
occ:1.00
O2B F:ACP402 2.6 107.8 1.0
HZ1 F:LYS74 2.9 127.0 1.0
O1G F:ACP402 3.3 105.1 1.0
HZ3 F:LYS74 3.4 127.0 1.0
OG F:SER152 3.5 109.1 1.0
OE1 F:GLU331 3.5 98.0 1.0
NZ F:LYS74 3.5 105.3 1.0
HD21 F:ASN333 3.6 114.0 1.0
O1B F:ACP402 3.7 113.2 1.0
HG F:SER152 3.7 131.6 1.0
PB F:ACP402 3.7 114.8 1.0
HA F:SER152 3.8 144.5 1.0
OE2 F:GLU331 3.9 99.9 1.0
ND2 F:ASN333 4.0 94.5 1.0
HZ2 F:LYS74 4.1 127.0 1.0
HD22 F:ASN333 4.1 114.0 1.0
CD F:GLU331 4.1 94.9 1.0
HE2 F:LYS74 4.3 129.9 1.0
PG F:ACP402 4.5 115.4 1.0
CB F:SER152 4.5 114.6 1.0
CE F:LYS74 4.6 107.8 1.0
CA F:SER152 4.6 119.9 1.0
O F:SER152 4.7 123.9 1.0
HB2 F:ASN333 4.7 99.8 1.0
C3B F:ACP402 4.8 111.0 1.0
HB2 F:SER152 4.8 138.2 1.0
O3G F:ACP402 4.9 103.8 1.0
CG F:ASN333 5.0 86.2 1.0
HE3 F:LYS74 5.0 129.9 1.0

Reference:

L.J.Chen, Q.Chen, J.H.Yang, Y.Yu. Small Molecular Promote Selective Destabilization and Degradation of Tubular Heterodimers By Specific Charging of GLU198 of Beta-Tubulin Through A Low Barrier Hydrogen Bond To Be Published.
Page generated: Sun Jul 11 16:08:29 2021

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