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Magnesium in PDB 8jk3: Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form

Enzymatic activity of Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form

All present enzymatic activity of Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form, PDB code: 8jk3 was solved by K.Dhankhar, S.Hazra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.13 / 1.50
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 121.192, 121.192, 72.128, 90, 90, 120
R / Rfree (%) 15 / 20.9

Other elements in 8jk3:

The structure of Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form (pdb code 8jk3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form, PDB code: 8jk3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8jk3

Go back to Magnesium Binding Sites List in 8jk3
Magnesium binding site 1 out of 4 in the Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form


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 Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:47.2
occ:1.00
 HD2 B:ARG216 2.3 26.9 1.0
O B:HOH655 2.5 35.5 1.0
HH11 B:ARG216 2.6 28.4 1.0
HH12 B:ARG216 2.6 28.5 1.0
NH1 B:ARG216 2.7 27.7 1.0
HG2 B:ARG216 2.8 23.3 1.0
O B:HOH567 2.8 30.2 1.0
HB2 B:ALA247 2.8 22.4 1.0
HG21 B:THR193 2.9 17.0 1.0
HA B:ALA247 3.0 20.8 1.0
CD B:ARG216 3.0 27.1 1.0
HG3 B:ARG216 3.0 23.4 1.0
HG23 B:THR193 3.1 17.0 1.0
CG B:ARG216 3.1 23.0 1.0
CG2 B:THR193 3.3 17.7 1.0
HG22 B:THR193 3.4 17.1 1.0
CB B:ALA247 3.4 22.9 1.0
HB1 B:ALA247 3.4 22.3 1.0
CA B:ALA247 3.5 20.5 1.0
CZ B:ARG216 3.6 34.4 1.0
NE B:ARG216 3.7 30.1 1.0
HD3 B:ARG216 3.8 26.6 1.0
HD12 B:ILE250 3.8 18.4 1.0
N B:ALA247 3.9 19.4 1.0
O B:HOH636 3.9 25.3 1.0
H B:ALA247 4.1 20.1 1.0
O B:HOH514 4.1 25.1 1.0
O B:HOH627 4.3 36.0 1.0
HB3 B:ALA247 4.3 22.2 1.0
HD13 B:ILE250 4.5 18.5 1.0
C B:ARG246 4.5 22.3 1.0
HB2 B:ARG246 4.5 25.2 1.0
HE B:ARG216 4.5 29.8 1.0
CD1 B:ILE250 4.6 18.9 1.0
CB B:ARG216 4.6 21.8 1.0
O B:ARG246 4.7 19.9 1.0
CB B:THR193 4.8 15.0 1.0
HB3 B:ARG246 4.8 25.1 1.0
O B:HOH575 4.8 46.5 1.0
O B:GLY243 4.8 32.5 1.0
NH2 B:ARG216 4.9 32.3 1.0
HG21 B:THR208 5.0 16.6 1.0
C B:ALA247 5.0 20.4 1.0
HB2 B:ARG216 5.0 21.1 1.0
HB B:THR193 5.0 15.3 1.0

Magnesium binding site 2 out of 4 in 8jk3

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Magnesium binding site 2 out of 4 in the Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form


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 Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:44.9
occ:1.00
 CL B:CL305 2.1 48.7 1.0
HG1 B:THR93 2.5 30.0 0.0
HB3 B:PRO63 2.9 24.7 1.0
HD12 B:ILE96 3.2 18.0 1.0
OG1 B:THR93 3.4 25.4 1.0
HG22 B:THR93 3.5 25.2 1.0
HD23 B:LEU53 3.5 18.3 1.0
HA B:THR93 3.5 17.4 1.0
HB2 B:PRO63 3.6 24.8 1.0
CB B:PRO63 3.7 25.4 1.0
HD11 B:ILE56 3.8 21.7 1.0
HD21 B:LEU53 3.8 18.3 1.0
OE1 B:GLN179 3.9 28.4 1.0
HD12 B:ILE56 3.9 21.7 1.0
CD1 B:ILE96 4.0 19.1 1.0
HD11 B:ILE96 4.1 18.1 1.0
CD2 B:LEU53 4.1 18.8 1.0
HA B:PRO63 4.1 23.3 1.0
CB B:THR93 4.1 23.1 1.0
CD1 B:ILE56 4.2 21.6 1.0
CG2 B:THR93 4.2 25.7 1.0
HD13 B:ILE56 4.2 21.5 1.0
HD13 B:ILE96 4.2 17.9 1.0
CA B:THR93 4.2 17.0 1.0
HG12 B:VAL92 4.3 18.1 1.0
O B:HOH589 4.3 38.2 1.0
O B:HOH532 4.4 30.4 1.0
CA B:PRO63 4.5 23.6 1.0
HG21 B:THR93 4.5 25.1 1.0
HD22 B:LEU53 4.5 18.5 1.0
O B:HOH695 4.6 39.2 1.0
HB B:ILE96 4.7 14.5 1.0
CD B:GLN179 4.8 23.3 1.0
N B:THR93 4.8 17.7 1.0
HG3 B:PRO63 4.8 23.4 1.0
HG23 B:ILE96 4.8 15.1 1.0
CG B:PRO63 4.9 23.5 1.0
HE22 B:GLN179 4.9 26.9 1.0
HB3 B:GLN179 4.9 18.0 1.0
HG23 B:THR93 5.0 24.9 1.0

Magnesium binding site 3 out of 4 in 8jk3

Go back to Magnesium Binding Sites List in 8jk3
Magnesium binding site 3 out of 4 in the Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form


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 Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:55.1
occ:1.00
 O B:HOH667 2.0 49.9 1.0
CL B:CL306 2.0 57.3 1.0
O B:HOH688 3.0 35.0 1.0
OH B:TYR77 4.1 15.9 1.0
CZ B:TYR77 4.1 16.8 1.0
HH B:TYR77 4.2 30.0 0.0
HG21 B:THR189 4.3 14.6 1.0
CE1 B:TYR77 4.4 17.6 1.0
HE1 B:TYR77 4.5 17.3 1.0
CL B:CL307 4.6 27.5 1.0
CE2 B:TYR77 4.6 15.1 1.0
O B:HOH672 4.6 38.0 1.0
MG B:MG304 4.7 38.0 1.0
HB3 B:SER103 4.7 14.9 1.0
HG23 B:THR189 4.8 14.7 1.0
O B:HOH685 4.8 39.2 1.0
HE2 B:TYR77 4.8 15.4 1.0
O B:HOH575 4.9 46.5 1.0
HB B:THR189 4.9 14.8 1.0
CG2 B:THR189 5.0 14.5 1.0

Magnesium binding site 4 out of 4 in 8jk3

Go back to Magnesium Binding Sites List in 8jk3
Magnesium binding site 4 out of 4 in the Crystal Structure of Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form


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 Bel-1 Extended Spectrum Beta-Lactamase in Hexagonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:38.0
occ:1.00
 CL B:CL307 1.7 27.5 1.0
HG B:SER42 2.8 30.0 0.0
OG B:SER103 2.8 17.3 1.0
HB2 B:SER42 3.0 18.0 1.0
O B:HOH619 3.0 35.4 1.0
CL B:CL306 3.0 57.3 1.0
O B:HOH465 3.1 25.4 1.0
HG B:SER103 3.1 30.0 0.0
OG B:SER42 3.2 20.0 1.0
HB3 B:SER103 3.2 14.9 1.0
CB B:SER103 3.4 14.8 1.0
CB B:SER42 3.5 17.2 1.0
HA2 B:GLY209 3.5 15.6 1.0
HB2 B:SER103 3.6 14.9 1.0
HZ3 B:LYS207 3.6 14.6 1.0
H B:SER210 3.7 19.3 1.0
HB3 B:SER42 3.8 17.7 1.0
HB3 B:SER210 3.8 25.6 1.0
O B:HOH685 3.9 39.2 1.0
HB2 B:SER210 4.0 25.2 1.0
HZ2 B:LYS45 4.1 18.2 1.0
N B:SER210 4.3 19.7 1.0
CB B:SER210 4.3 24.9 1.0
NZ B:LYS207 4.3 14.8 1.0
HZ2 B:LYS207 4.4 14.6 1.0
CA B:GLY209 4.4 15.3 1.0
O B:THR208 4.5 15.1 1.0
O B:HOH576 4.5 28.9 1.0
HZ1 B:LYS207 4.5 14.7 1.0
H B:SER42 4.6 18.5 1.0
MG B:MG303 4.7 55.1 1.0
C B:GLY209 4.7 17.1 1.0
O B:HOH414 4.8 27.6 1.0
O B:HOH636 4.8 25.3 1.0
CA B:SER103 4.8 14.3 1.0
OG1 B:THR208 4.8 14.8 1.0
O B:SER103 4.9 16.8 1.0
CA B:SER42 4.9 17.5 1.0
NZ B:LYS45 4.9 18.3 1.0
C B:THR208 4.9 16.1 1.0
CA B:SER210 5.0 22.5 1.0
N B:GLY209 5.0 15.7 1.0

Reference:

K.Dhankhar, S.Hazra. Crystal Structure of Bel-1 Esbl in Hexagonal Form To Be Published.
Page generated: Fri Oct 4 13:11:06 2024

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