Atomistry » Magnesium » PDB 5a2q-5ac0 » 5a6b
Atomistry »
  Magnesium »
    PDB 5a2q-5ac0 »
      5a6b »

Magnesium in PDB 5a6b: GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac

Protein crystallography data

The structure of GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac, PDB code: 5a6b was solved by M.Cid, C.S.Robb, M.A.Higgins, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.69 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.699, 136.937, 201.446, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac (pdb code 5a6b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac, PDB code: 5a6b:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5a6b

Go back to Magnesium Binding Sites List in 5a6b
Magnesium binding site 1 out of 3 in the GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1628

b:27.7
occ:1.00
O A:HOH2046 3.1 31.3 1.0
OG A:SER38 3.2 25.6 1.0
NE2 A:GLN57 3.3 24.0 1.0
NH1 A:ARG53 3.5 40.4 1.0
CD A:ARG53 3.6 36.7 1.0
CE A:LYS54 3.7 40.7 1.0
CB A:SER38 3.9 22.8 1.0
OE1 A:GLN57 4.0 27.0 1.0
CD A:GLN57 4.1 25.6 1.0
CD A:LYS54 4.3 35.2 1.0
CZ A:ARG53 4.3 40.3 1.0
CA A:SER38 4.3 24.8 1.0
NE A:ARG53 4.3 38.8 1.0
CB A:ALA81 4.4 26.7 1.0
NZ A:LYS54 4.4 43.3 1.0
CG A:ARG53 4.5 30.3 1.0
CB A:ARG53 4.5 30.5 1.0
CG A:LYS54 4.5 32.5 1.0
N A:ALA81 4.9 26.0 1.0
N A:SER38 5.0 27.4 1.0

Magnesium binding site 2 out of 3 in 5a6b

Go back to Magnesium Binding Sites List in 5a6b
Magnesium binding site 2 out of 3 in the GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1628

b:22.5
occ:1.00
OG B:SER574 3.0 24.4 1.0
O B:HOH2461 3.2 27.5 1.0
NH1 B:ARG571 3.2 18.0 1.0
CD B:ARG575 3.6 21.4 1.0
CB B:SER574 3.7 23.6 1.0
N B:ARG575 3.8 22.3 1.0
C B:SER574 3.8 22.8 1.0
CG B:ARG575 3.9 21.4 1.0
CD B:ARG571 3.9 17.0 1.0
O B:SER574 4.1 21.3 1.0
CA B:ARG575 4.1 22.0 1.0
CA B:SER574 4.4 20.7 1.0
CZ B:ARG571 4.4 16.1 1.0
CG2 B:VAL578 4.4 29.1 1.0
O A:HOH2357 4.6 34.3 1.0
CB B:ARG575 4.6 19.9 1.0
NE B:ARG571 4.6 17.6 1.0
O B:HOH2459 4.8 22.7 1.0
O B:ARG571 4.8 18.2 1.0
CD1 A:LEU547 4.9 20.4 1.0
NE B:ARG575 4.9 22.5 1.0

Magnesium binding site 3 out of 3 in 5a6b

Go back to Magnesium Binding Sites List in 5a6b
Magnesium binding site 3 out of 3 in the GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of GH20C, Beta-Hexosaminidase From Streptococcus Pneumoniae in Complex with Pugnac within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1628

b:21.2
occ:1.00
O C:HOH2051 3.0 23.0 1.0
OG C:SER38 3.1 20.0 1.0
NH1 C:ARG53 3.3 30.6 1.0
NE2 C:GLN57 3.3 21.0 1.0
CD C:ARG53 3.8 25.9 1.0
CE C:LYS54 3.9 28.0 1.0
CB C:SER38 4.0 19.9 1.0
OE1 C:GLN57 4.1 21.4 1.0
CD C:GLN57 4.1 18.3 1.0
CZ C:ARG53 4.2 30.4 1.0
NZ C:LYS54 4.3 29.6 1.0
CA C:SER38 4.3 21.6 1.0
CD C:LYS54 4.3 26.9 1.0
NE C:ARG53 4.4 28.8 1.0
CB C:ARG53 4.5 23.7 1.0
CB C:ALA81 4.5 22.8 1.0
O C:HOH2045 4.5 38.9 1.0
CG C:ARG53 4.5 26.1 1.0
CG C:LYS54 4.6 25.6 1.0
N C:SER38 5.0 21.3 1.0
N C:ALA81 5.0 22.6 1.0

Reference:

M.Robb, C.S.Robb, M.A.Higgins, J.K.Hobbs, J.C.Paton, A.B.Boraston. A Second Beta-Hexosaminidase Encoded in the Streptococcus Pneumoniae Genome Provides An Expanded Biochemical Ability to Degrade Host Glycans. J. Biol. Chem. V. 290 30888 2015.
ISSN: ESSN 1083-351X
PubMed: 26491009
DOI: 10.1074/JBC.M115.688630
Page generated: Sun Sep 29 00:19:15 2024

Last articles

Ca in 2Q16
Ca in 2Q0R
Ca in 2PYH
Ca in 2Q0U
Ca in 2PY2
Ca in 2PZ0
Ca in 2PYZ
Ca in 2PYG
Ca in 2PWF
Ca in 2PWH
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy